diff --git a/.github/workflows/ci-dev.yml b/.github/workflows/ci-dev.yml
new file mode 100644
index 000000000..9e666f776
--- /dev/null
+++ b/.github/workflows/ci-dev.yml
@@ -0,0 +1,51 @@
+name: CI
+
+on:
+ pull_request:
+ branches:
+ - develop
+
+jobs:
+
+ test-full:
+ name: Full Test Suite
+ runs-on: ${{ matrix.os }}
+
+ strategy:
+ fail-fast: false
+ matrix:
+ os: [ubuntu-latest, macos-latest]
+ python-version: [3.8]
+
+ steps:
+ - uses: actions/checkout@v2
+
+ - name: Install Linux dependencies
+ if: runner.os == 'Linux'
+ run: sudo apt-get install libopenblas-dev
+
+ - name: Install macOS Dependencies
+ shell: bash -l {0}
+ if: runner.os == 'macOS'
+ run: |
+ brew tap sfarrens/sf
+ brew install bigmac libomp
+
+ - name: Set up conda
+ uses: conda-incubator/setup-miniconda@v2
+ with:
+ auto-update-conda: true
+ python-version: ${{ matrix.python-version }}
+ auto-activate-base: true
+
+ - name: Install package
+ shell: bash -l {0}
+ run: |
+ ./install_shapepipe --env-dev --develop
+
+ - name: Run tests
+ shell: bash -l {0}
+ run: |
+ conda activate shapepipe-dev
+ python setup.py test
+ shapepipe_run -c example/config.ini
diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-release.yml
similarity index 98%
rename from .github/workflows/ci-tests.yml
rename to .github/workflows/ci-release.yml
index cc4ae4e93..ef1f6a013 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-release.yml
@@ -5,7 +5,6 @@ on:
branches:
- main
- master
- - develop
jobs:
diff --git a/.github/workflows/deploy-image.yml b/.github/workflows/deploy-image.yml
new file mode 100644
index 000000000..81c31c7ad
--- /dev/null
+++ b/.github/workflows/deploy-image.yml
@@ -0,0 +1,41 @@
+name: Create and publish a Docker image
+
+on:
+ push:
+ branches: ['master']
+
+env:
+ REGISTRY: ghcr.io
+ IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+ build-and-push-image:
+ runs-on: ubuntu-latest
+ permissions:
+ contents: read
+ packages: write
+
+ steps:
+ - name: Checkout repository
+ uses: actions/checkout@v3
+
+ - name: Log in to the Container registry
+ uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+ with:
+ registry: ${{ env.REGISTRY }}
+ username: ${{ github.actor }}
+ password: ${{ secrets.GITHUB_TOKEN }}
+
+ - name: Extract metadata (tags, labels) for Docker
+ id: meta
+ uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+ with:
+ images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+ - name: Build and push Docker image
+ uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+ with:
+ context: .
+ push: true
+ tags: ${{ steps.meta.outputs.tags }}
+ labels: ${{ steps.meta.outputs.labels }}
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 000000000..7d2785ab2
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,57 @@
+FROM continuumio/miniconda3
+
+LABEL Description="ShapePipe Docker Image"
+ENV SHELL /bin/bash
+
+ARG CC=gcc-9
+ARG CXX=g++-9
+
+# gcc < 10 is required to compile ww
+ENV CC=gcc-9
+ENV CXX=g++-9
+
+RUN apt-get update --allow-releaseinfo-change && \
+ apt-get update && \
+ apt-get upgrade -y && \
+ apt-get install apt-utils -y && \
+ apt-get install make -y && \
+ apt-get install automake -y && \
+ apt-get install autoconf -y && \
+ apt-get install gcc-9 g++-9 -y && \
+ apt-get install gfortran -y && \
+ apt-get install locales -y && \
+ apt-get install libgl1-mesa-glx -y && \
+ apt-get install xterm -y && \
+ apt-get install cmake protobuf-compiler -y && \
+ apt-get install libtool libtool-bin libtool-doc -y && \
+ apt-get install libfftw3-bin libfftw3-dev -y && \
+ apt-get install libatlas-base-dev liblapack-dev libblas-dev -y && \
+ apt-get install vim -y && \
+ apt-get install locate -y && \
+ apt-get install curl -y && \
+ apt-get install acl -y && \
+ apt-get install sssd -y && \
+ apt-get clean
+
+ADD nsswitch.conf /etc/
+
+RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && \
+ locale-gen
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8
+
+SHELL ["/bin/bash", "--login", "-c"]
+
+COPY ./environment.yml ./
+COPY install_shapepipe README.rst setup.py setup.cfg ./
+RUN touch ./README.md
+
+RUN conda update -n base -c defaults conda -c defaults
+RUN conda env create --file environment.yml
+
+COPY shapepipe ./shapepipe
+COPY scripts ./scripts
+
+RUN source activate shapepipe
+#RUN pip install jupyter
diff --git a/auxdir/CFIS/tiles_202402/tiles_COSMOS.txt b/auxdir/CFIS/tiles_202402/tiles_COSMOS.txt
new file mode 100644
index 000000000..ff9d7e4cf
--- /dev/null
+++ b/auxdir/CFIS/tiles_202402/tiles_COSMOS.txt
@@ -0,0 +1,9 @@
+299.183
+300.183
+301.183
+299.184
+300.184
+301.184
+299.185
+300.185
+301.185
diff --git a/auxdir/CFIS/tiles_202402/tiles_all.txt b/auxdir/CFIS/tiles_202402/tiles_all.txt
new file mode 100644
index 000000000..97dce4eb3
--- /dev/null
+++ b/auxdir/CFIS/tiles_202402/tiles_all.txt
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diff --git a/auxdir/CFIS/tiles_cuts.txt b/auxdir/CFIS/tiles_cuts.txt
deleted file mode 100644
index b1c181630..000000000
--- a/auxdir/CFIS/tiles_cuts.txt
+++ /dev/null
@@ -1,12055 +0,0 @@
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diff --git a/docs/source/canfar.md b/docs/source/canfar.md
new file mode 100644
index 000000000..1f490c504
--- /dev/null
+++ b/docs/source/canfar.md
@@ -0,0 +1,94 @@
+# Running `shapepipe` on the canfar science portal
+
+## Introduction
+
+## Steps from testing to parallel running
+
+Before starting a batch remote session job on a large number of images (step 5.),
+it is recommended to perform some or all of the testing steps (1. - 4.).
+
+
+1. Run the basic `shapepipe` runner script to test (one or several) modules in question, specified by a given config file, on one image.
+ This step has to be run in the image run directory. The command is
+ ```bash
+ shapepipe_run -c config.ini
+ ```
+
+2. Run the job script to test the job management, on one image.
+ This step has to be run in the image run directory. The command is
+ ```bash
+ job_sp_canfar -j JOB [OPTIONS]
+ ```
+
+3. Run the pipeline script to test the processing step(s), on one image.
+ This step has to be run in the patch base directory.
+
+ 1. First, run in dry mode:
+ ```bash
+ init_run_exclusive_canfar.sh -j JOB -e ID -p [psfex|mccd] -k [tile|exp] -n
+ ```
+ 2. Next, perform a real run with
+ ```bash
+ init_run_exclusive_canfar.sh -j JOB -e ID -p [psfex|mccd] -k [tile|exp] -n
+ ```
+
+4. Run remote session script to test job submission using docker images, on one image.
+ This step has to be run in the patch base directory.
+ 1. First, run in dry mode=2, to display curl command, with
+ ```bash
+ curl_canfar_local.sh -j JOB -e ID -p [psfex|mccd] -k [tile|exp] -n 2
+ ```
+
+ 2. Next, run in dry mode=1, to use curl command without processing:
+ ```bash
+ curl_canfar_local.sh -j JOB -e ID -p [psfex|mccd] -k [tile|exp] -n 1
+ ```
+ 3. Then, perform a real run, to use curl with processing:
+ ```bash
+ curl_canfar_local.sh -j JOB -e ID -p [psfex|mccd] -k [tile|exp]
+ ```
+
+5. Full run: Call remote session script and docker image with collection of images
+ ```bash
+ curl_canfar_local.sh -j JOB -f path_IDs -p [psfex|mccd] -k [tile|exp]
+ ```
+ with `path_IDs` being a text file with one image ID per line.
+
+## Monitoring
+
+
+### Status and output of submitted job
+
+Monitoring of the currently active remote session can be performed using the session IDs `session_IDs.txt` written by the
+remote session script `curl_canfar_local.sh`. In the patch main directory, run
+```bash
+curl_canfar_monitor.sh events
+```
+to display the remotely started docker image status, and
+```bash
+curl_canfar_monitor.sh logs
+```
+to print `stdout` of the remotely run pipeline script.
+
+### Number of submitted running jobs
+
+The script
+```bash
+stats_headless_canfar.py
+```
+returns the number of actively running headless jobs.
+
+
+## Post-hoc summary
+
+In the patch main directory, run
+```bash
+summary_run PATCH
+```
+to print a summary with missing image IDs per job and module.
+
+## Deleting jobs
+
+```bash
+ for id in `cat session_IDs.txt`; do echo $id; curl -X DELETE -E /arc/home/kilbinger/.ssl/cadcproxy.pem https://ws-uv.canfar.net/skaha/v0/session/$id; done
+ ```
diff --git a/docs/source/conf.py b/docs/source/conf.py
index a191341a1..ab410f0db 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -14,18 +14,19 @@
#
import os
import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
# -- Project information -----------------------------------------------------
-project = 'ShapePipe'
-copyright = '2022, CosmoStat'
-author = 'CosmoStat'
+project = "ShapePipe"
+copyright = "2022, CosmoStat"
+author = "CosmoStat"
# The short X.Y version
-version = '1.0'
+version = "1.0"
# The full version, including alpha/beta/rc tags
-release = '1.0.1'
+release = "1.0.1"
# -- General configuration ---------------------------------------------------
@@ -38,34 +39,34 @@
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
- 'sphinx.ext.autodoc',
- 'sphinx.ext.autosummary',
- 'sphinx.ext.coverage',
- 'sphinx.ext.doctest',
- 'sphinx.ext.ifconfig',
- 'sphinx.ext.intersphinx',
- 'sphinx.ext.mathjax',
- 'sphinx.ext.napoleon',
- 'sphinx.ext.todo',
- 'sphinx.ext.viewcode',
- 'sphinxcontrib.bibtex',
- 'myst_parser',
- 'numpydoc',
+ "sphinx.ext.autodoc",
+ "sphinx.ext.autosummary",
+ "sphinx.ext.coverage",
+ "sphinx.ext.doctest",
+ "sphinx.ext.ifconfig",
+ "sphinx.ext.intersphinx",
+ "sphinx.ext.mathjax",
+ "sphinx.ext.napoleon",
+ "sphinx.ext.todo",
+ "sphinx.ext.viewcode",
+ "sphinxcontrib.bibtex",
+ "myst_parser",
+ "numpydoc",
]
# Include module names for objects
add_module_names = False
# Include init in class documentation.
-autoclass_content = 'class'
+autoclass_content = "class"
# Audodoc options
autodoc_default_options = {
- 'member-order': 'bysource',
- 'private-members': True,
- 'special-members': '__call__',
- 'show-inheritance': True,
- 'exclude-members': 'urand,randint'
+ "member-order": "bysource",
+ "private-members": True,
+ "special-members": "__call__",
+ "show-inheritance": True,
+ "exclude-members": "urand,randint",
}
# Generate summaries
@@ -77,56 +78,56 @@
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
# The master toctree document.
-master_doc = 'index'
+master_doc = "index"
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
show_authors = True
# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'default'
+pygments_style = "default"
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True
# -- Options for Markdown files ----------------------------------------------
-myst_enable_extensions = ['html_image']
+myst_enable_extensions = ["html_image"]
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
-html_theme = 'sphinx_book_theme'
+html_theme = "sphinx_book_theme"
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#
html_theme_options = {
- 'repository_url': 'https://github.com/CosmoStat/shapepipe',
- 'use_repository_button': True,
- 'use_issues_button': True,
- 'use_download_button': False,
- 'use_fullscreen_button': False,
- 'use_edit_page_button': True,
- 'path_to_docs': 'docs/source',
- 'extra_navbar': "",
+ "repository_url": "https://github.com/CosmoStat/shapepipe",
+ "use_repository_button": True,
+ "use_issues_button": True,
+ "use_download_button": False,
+ "use_fullscreen_button": False,
+ "use_edit_page_button": True,
+ "path_to_docs": "docs/source",
+ "extra_navbar": "",
}
html_collapsible_definitions = True
html_awesome_headerlinks = True
# The name for this set of Sphinx documents. If None, it defaults to
# " v documentation".
-html_title = '{0} v{1}'.format(project, version)
+html_title = "{0} v{1}".format(project, version)
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
-html_last_updated_fmt = '%d %b, %Y'
+html_last_updated_fmt = "%d %b, %Y"
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
@@ -142,21 +143,21 @@
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
-htmlhelp_basename = 'ShapePipedoc'
+htmlhelp_basename = "ShapePipedoc"
# -- Intersphinx Mapping ----------------------------------------------
# Refer to the package libraries for type definitions
intersphinx_mapping = {
- 'python': ('http://docs.python.org/3', None),
- 'numpy': ('https://numpy.org/doc/stable/', None),
- 'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
- 'matplotlib': ('https://matplotlib.org', None),
- 'astropy': ('http://docs.astropy.org/en/latest/', None),
+ "python": ("http://docs.python.org/3", None),
+ "numpy": ("https://numpy.org/doc/stable/", None),
+ "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+ "matplotlib": ("https://matplotlib.org", None),
+ "astropy": ("http://docs.astropy.org/en/latest/", None),
}
# -- BibTeX Setting ----------------------------------------------
-bibtex_bibfiles = ['refs.bib']
-bibtex_default_style = 'unsrt'
-bibtex_reference_style = 'author_year'
+bibtex_bibfiles = ["refs.bib"]
+bibtex_default_style = "unsrt"
+bibtex_reference_style = "author_year"
diff --git a/docs/source/pipeline_canfar.md b/docs/source/pipeline_canfar.md
new file mode 100644
index 000000000..9f867b85e
--- /dev/null
+++ b/docs/source/pipeline_canfar.md
@@ -0,0 +1,154 @@
+patch="P7"
+psf="psfex"
+
+# Terminal title
+echo -ne "\033]0;$patch\007"
+
+# Run directory
+dir=~/cosmostat/v2/pre_v2/$psf/$patch
+cd $dir
+
+# Get tile number list
+ln -s ~/shapepipe/auxdir/CFIS/tiles_202106/tiles_$patch.txt tile_numbers.txt
+
+
+# Get images
+
+## Download and link separately
+
+### Download
+### Create and link to central image storage directory
+mkdir -p ~/cosmostat/v2/data_tiles/$patch
+ln -s ~/cosmostat/v2/data_tiles/$patch data_tiles
+mkdir -p ~/cosmostat/v2/data_exp/$patch
+ln -s ~/cosmostat/v2/data_tiles/$patch data_exp
+
+### Download and move tiles
+ln -s ~/shapepipe/example/cfis
+mkdir -p output
+export SP_RUN=`pwd`
+
+shapepipe_run -c cfis/config_Git_vos.ini
+ls -l data_tiles/ | wc; mv -i output/run_sp_Git_*/get_images_runner/output/CFIS.???.???.*fits* data_tiles; ls -l data_tiles/ | wc
+rm -rf output/run_sp_Git_*; update_runs_log_file.py
+# repeat the above block
+
+### Find exposures; this run can be stopped after Fe
+shapepipe_run -c cfis/config_GitFe_symlink.ini
+# You can also run Fe alone
+
+### Download and move exposures
+
+shapepipe_run -c cfis/config_Gie_vos.ini
+mv -i output/run_sp_Gie_*/get_images_runner/output/*.fits*fz data_exp
+rm -rf output/run_sp_Gie_*
+update_runs_log_file.py
+# repeat the above; or:
+while true; do shapepipe_run -c cfis/config_Gie_vos.ini; ls -l data_exp/ | wc; mv -i output/run_sp_Gie_*/get_images_runner/output/*.fits*fz data_exp; ls -l data_exp/ | wc; rm -rf output/run_sp_Gie_*; update_runs_log_file.py; done
+# Make sure that after all images are downloaded there is no Gie run. This would
+# mess up later modules since last:get_image_runner could point to this run.
+
+### Create links (and re-run Fe, not necessary)
+job_sp_canfar.bash -p $psf `cat tile_numbers.txt` -j 1 -r symlink
+
+# Get single-HDU single-exposure IDs file (from missing 32 job)
+~/shapepipe/scripts/python/summary_run.py P$patch [32]
+
+# Mask tiles
+
+## Run repeatedly if necessary
+job_sp_canfar.bash -p $psf -n $OMP_NUM_THREADS -j 4
+
+## Combine all runs
+combine_runs.bash -c flag_tile
+
+# Tile detection
+curl_canfar_local.sh -j 16 -f tile_numbers.txt -p $psf -N $OMP_NUM_THREADS
+
+# Option 0, global split and exp masks: sp_local=0
+# Todo: split Uz and SpMh
+
+# For sp_local=- both mh_local (0, 1) are ok
+export mh_local=0
+#export mh_local=1
+
+## Uncompress weights, split exposures into single HDUs
+job_sp_canfar.bash -p $psf -n $OMP_NUM_THREADS -j 2
+
+# Mask exposures
+
+## Run repeatedly if necessary
+job_sp_canfar.bash -p $psf -n $OMP_NUM_THREADS -j 8
+
+# Combine all runs
+combine_runs.bash -c flag_exp
+
+# Option 1: sp_local=1, local split and mask exp
+export mh_local=1
+
+# Split exposures
+curl_canfar_local.sh -j 2 -f all.txt -p $psf -N $OMP_NUM_THREADS
+
+# Mask exposures
+curl_canfar_local.sh -j 8 -f all.txt -p $psf -N $OMP_NUM_THREADS
+
+# Exposure detection
+
+cp summary/missing_job_32_sextractor.txt all.txt
+curl_canfar_local.sh -j 32 -m $mh_local -f all.txt -p $psf -N $OMP_NUM_THREADS
+
+# Tile preparation
+curl_canfar_local.sh -j 64 -f tile_numbers.txt -p $psf -N $OMP_NUM_THREADS
+
+# Tile shape measurement
+curl_canfar_local.sh -j 128 -f tile_numbers.txt -p $psf -N 8
+
+# Merge subcatalogues
+curl_canfar_local.sh -j 256 -f tile_numbers.txt -p $psf -N 8
+
+# Create final cat
+curl_canfar_local.sh -j 512 -f tile_numbers.txt -p $psf -N $OMP_NUM_THREADS
+# Run in parallel
+cat mc.txt | xargs -I {} -P 16 bash -c 'init_run_exclusive_canfar.sh -p psfex -j 512 -e {} --n_smp 1'
+
+# Combine all final cats in common output dir as links
+combine_runs.bash -c final -p psfex
+
+# Merge all final cats
+# (W3: 140GB RAM)
+merge_final_cat -i output/run_sp_combined_final/make_catalog_runner/output -p cfis/final_cat.param -v
+
+
+# Star catalogue
+combine_runs.bash -p $psf -c psf
+shapepipe_run -c $SP_CONFIG/config_Ms_$psf.ini
+shapepipe_run -c $SP_CONFIG/config_Pl_$psf.ini
+
+# Convert star cat to WCS
+## Convert all input validation psf files and create directories par patch
+## psf_conv_all/P?
+cd ../star_cat
+ ~/shapepipe/scripts/python/convert_psf_pix2world.py -i ../ -P $patch -v
+
+# Combine previously created files within one SP run dir
+cd P$patch
+combine_runs.bash -p psfex -c psf_conv
+
+# Merge all converted star catalogues and create final-starcat.fits
+export SP_RUN=`pwd`
+shapepipe_run -c ~/shapepipe/example/cfis/config_Ms_psfex_conv.ini
+
+
+# Extra stuff
+
+## Delete jobs
+SSL=~/.ssl/cadcproxy.pem
+SESSION=https://ws-uv.canfar.net/skaha/v0/session
+for ID in `cat session_IDs.txt`; do echo $ID; curl -X DELETE -E $SSL $SESSION/$ID; done
+
+## Run in terminal in parallel (-e needs to be last arg)
+cat all.txt | xargs -P 16 -n 1 init_run_exclusive_canfar.sh -j 64 -p psfex -n -e
+
+## Get missing jobs that are not currently running
+stats_jobs_canfar.sh
+grep -F -v -f jobs_running.txt summary/missing_job_128_ngmix_runner_3.txt > all3.txt
diff --git a/docs/source/post_processing.md b/docs/source/post_processing.md
index ebd123889..8d9922dbb 100644
--- a/docs/source/post_processing.md
+++ b/docs/source/post_processing.md
@@ -3,63 +3,14 @@
This page shows all required steps of post-processing the results from one or
more `ShapePipe` runs. Post-processing combines various individual `ShapePipe`
output files, and creates joint results, for example combining individual tile
-catalogues in a large sky area. The output of post-processing is a joint _shape
+catalogues into a large sky area. The output of post-processing is a joint _shape
catalogue_, containing all required information to create a calibrated shear
catalogue via _metacalibration_), a joint star catalogue, and PSF diagnostic plots.
-Some of the following steps pertain specifically to runs carried out on [canfar](https://www.canfar.net/en),
-but most are general.
+If main ShapePipe processing happened at the old canfar VM system (e.g. CFIS v0 and v1), go
+[here](vos_retrieve.md) for details how to retrieve the ShapePipe output files.
-1. Retrieve `ShapePipe` result files
-
- For a local run on the same machine as for post-processing, nothing needs to be done.
- In some cases, the run was carried out on a remote machine or cluster, and the resulting `ShapePipe`
- output files need to be retrieved.
-
- In the specific case of canfar_avail_results.py, this is done as follows.
-
- A. Check availability of results
-
- A `canfar` job can submit a large number of tiles, whose processing time can vary a lot.
- We assume that the submitted tile ID list is available locally via the ascii file `tile_numbers.txt`.
- To check which tiles have finished running, and whose results have been uploaded, use
- ```bash
- canfar_avail_results -i tile_numbers.txt -v -p PSF --input_path INPUT_PATH
- ```
- where PSF is one in [`psfex`|`mccd`], and INPUT_PATH the input path on vos, default `vos:cfis/cosmostat/kilbinger/results`.
- See `-h` for all options.
-
- B. Download results
-
- All results files will be downloaded with
- ```bash
- canfar_download_results -i tile_numbers.txt -v -p PSF --input_vos INPUT_VOS
- ```
- Use the same options as for same as for `canfar_avail_results`.
-
- This command can be run in the same directory at subsequent times, to complete an ongoing run: Only newer files will be downloaded
- from the `vos` directory. This also assures that partially downloaded or corrupt files will be replaced.
-
- Checking the `vos` directorty can be slow for large patches.
- To only download files that are not yet present locally (in `.`), first write the missing ones to an ascii file, using again the
- script `canfar_avail_results`, but this time with `.` as input path:
- ```bash
- canfar_avail_results -i tile_numbers.txt --input_path . -p PSF -v -o missing.txt
- '''
- Then, download only the missing files with
- ```bash
- canfar_download_results -i missing.txt --input_vos cosmostat/kilbinger/results_mccd_oc2 -p mccd -v
- ```
-
- C. Un-tar results
- ```bash
- untar_results -p PSF
- ```
- On success, `ShapePipe` output `fits` and `log` files will be now in various subdirs of the `output` directory.
-
-At this step all required `ShapePipe` resulting output files are available in the current working directory.
-
-2. Optional: Split output in sub-samples
+1. Optional: Split output into sub-samples
An optional intermediate step is to create directories for sub-samples, for example one directory
for each patch on the sky. This will create symbolic links to the results `.tgz` files downloaded in
@@ -70,33 +21,34 @@ At this step all required `ShapePipe` resulting output files are available in th
```
The following steps will then be done in the directory `tiles_W3`.
-3. Run PSF diagnostics, create merged catalogue
+2. Run PSF diagnostics, create merged catalogue
Type
```bash
post_proc_sp -p PSF
```
- to automatically perform a number of post-processing steps. Chose the PSF model with the option
+ to automatically perform a number of post-processing steps. Choose the PSF model with the option
`-p psfex|mccd`. In detail, these are (and can also be done individually
by hand):
- A. Analyse psf validation files
+ 1. Analyse psf validation files
```bash
- prepare_star_cat -p PSF
+ combine_runs -t psf -p PSF
```
with options as for `post_proc_sp`.
- This script identifies all psf validation files (from all processed tiles downloaded to `pwd`), creates symbolic links,
- merges the catalogues, and creates plots of PSF ellipticity, size, and residuals over the focal plane.
+ This script creates a new combined psf run in the ShapePipe `output` directory, by identifying all psf validation files
+ and creating symbolic links. The run log file is updated.
- B. Create plots of the PSF and their residuals in the focal plane, as a diagnostic of the overall PSF model.
- As a scale-dependend test, which propagates directly to the shear correlation function, the rho statistics are computed,
- see {cite:p}`rowe:10` and {cite:p}`jarvis:16`,
+ 3. Merge individual psf validation files into one catalogue. Create plots of the PSF and their residuals in the focal plane,
+ as a diagnostic of the overall PSF model.
+ As a scale-dependend test, which propagates directly to the shear correlation function, the rho statistics are computed,
+ see {cite:p}`rowe:10` and {cite:p}`jarvis:16`,
```bash
shapepipe_run -c /path/to/shapepipe/example/cfis/config_MsPl_PSF.ini
```
- C. Prepare output directory
+ 4. Prepare output directory
Create links to all 'final_cat' result files with
```bash
@@ -105,7 +57,7 @@ At this step all required `ShapePipe` resulting output files are available in th
The corresponding output directory that is created is `output/run_sp_combined/make_catalog_runner/output`.
On success, it contains links to all `final_cat` output catalogues
- D. Merge final output files
+ 5. Merge final output files
Create a single main shape catalog:
```bash
diff --git a/docs/source/vos_retrieve.md b/docs/source/vos_retrieve.md
new file mode 100644
index 000000000..3606752c8
--- /dev/null
+++ b/docs/source/vos_retrieve.md
@@ -0,0 +1,51 @@
+## Retrieve files from VOspace
+
+This page describes how ShapePipe output files can be retrieved via the Virtual Observatory Space
+on canfar. This system was used for the CFIS v0 and v1 runs, and is now obsolete.
+
+1. Retrieve ShapePipe result files
+
+ For a local run on the same machine as for post-processing, nothing needs to be done. In some cases, the run was carried out on a remote machine or cluster, and the resulting ShapePipe output files
+ need to be retrieved.
+
+ In the specific case of canfar_avail_results.py, this is done as follows.
+
+ 1. Check availability of results
+
+ A canfar job can submit a large number of tiles, whose processing time can vary a lot. We assume that the submitted tile ID list is available locally via the ascii file tile_numbers.txt. To check
+ which tiles have finished running, and whose results have been uploaded, use
+ ```bash
+ canfar_avail_results -i tile_numbers.txt -v -p PSF --input_path INPUT_PATH
+ ```
+ where PSF is one in [`psfex`|`mccd`], and INPUT_PATH the input path on vos, default `vos:cfis/cosmostat/kilbinger/results`.
+ See `-h` for all options.
+
+ 2. Download results
+
+ All results files will be downloaded with
+ ```bash
+ canfar_download_results -i tile_numbers.txt -v -p PSF --input_vos INPUT_VOS
+ ```
+ Use the same options as for same as for `canfar_avail_results`.
+
+ This command can be run in the same directory at subsequent times, to complete an ongoing run: Only newer files will be downloaded
+ from the `vos` directory. This also assures that partially downloaded or corrupt files will be replaced.
+
+ Checking the `vos` directorty can be slow for large patches.
+ To only download files that are not yet present locally (in `.`), first write the missing ones to an ascii file, using again the
+ script `canfar_avail_results`, but this time with `.` as input path:
+ ```bash
+ canfar_avail_results -i tile_numbers.txt --input_path . -p PSF -v -o missing.txt
+ ```
+ Then, download only the missing files with
+ ```bash
+ canfar_download_results -i missing.txt --input_vos cosmostat/kilbinger/results_mccd_oc2 -p mccd -v
+ ```
+
+ 3. Un-tar results
+ ```bash
+ untar_results -p PSF
+ ```
+ On success, `ShapePipe` output `fits` and `log` files will be now in various subdirs of the `output` directory.
+
+At this step all required `ShapePipe` resulting output files are available in the current working directory.
diff --git a/environment-dev.yml b/environment-dev.yml
new file mode 100644
index 000000000..703c19172
--- /dev/null
+++ b/environment-dev.yml
@@ -0,0 +1,38 @@
+# ShapePipe Development Environment
+# ---------------------------------
+# This environment should only be used for development and testing of
+# ShapePipe (i.e. nothing that could be published). Packages need only
+# specify the minimum compatible versions. This environment can updated
+# as needed.
+name: shapepipe-dev
+channels:
+ - conda-forge
+dependencies:
+ - python>=3.9.18
+ - pip>=23.3.1
+ - astropy>=5.1.1
+ - autoconf>=2.71
+ - automake>=1.16.5
+ - cmake>=3.27.7
+ - galsim>=2.5.1
+ - joblib>=1.3.2
+ - libtool>=2.4
+ - matplotlib>=3.8.1
+ - numba>=0.58.1
+ - pandas>=2.1
+ - pyqt5-sip>=12.13
+ - pyqtgraph>=0.13.3
+ - reproject>=0.12
+ - sqlitedict>=2.1
+ - termcolor>=2.3
+ - tqdm>=4.66.1
+ - treecorr>=4.3.3
+ - pip:
+ - cs_util==0.0.5
+ - mccd==1.2.4
+ - modopt==1.6.1
+ - sip_tpv==1.1
+ - sf_tools==2.0.4
+ - git+https://github.com/CEA-COSMIC/pysap@develop
+ - git+https://github.com/aguinot/ngmix@stable_version
+ - git+https://github.com/tobias-liaudat/Stile@v0.1
diff --git a/environment.yml b/environment.yml
index 9279402ef..de62b5a37 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,33 +1,42 @@
-name: shapepipe
+name: shapepipe_v1.4
+# ShapePipe Production Environment
+# --------------------------------
+# This environment should be used for any production runs of ShapePipe
+# (i.e. anything that could be published). All packages are pinned to
+# specific versions to maximise the reproducibility of the results.
+# This environment should be updated for each release of ShapePipe.
channels:
- conda-forge
dependencies:
- python=3.9
- pip>=21.2.4
- - numpy==1.21.6
- - astropy==5.0
- - automake==1.16.2
- - autoconf==2.69
- - cmake==3.19.6
- - galsim==2.2.5
- - joblib==1.1.0
- - libtool==2.4.6
- - matplotlib==3.5.1
- - numba==0.54.1
- - pandas==1.4.1
+ - astromatic-psfex==3.21.1
+ - astromatic-source-extractor==2.25.0
+ - astropy==5.2
+ - automake
+ - autoconf
+ - cmake
+ - galsim
+ - joblib
+ - libtool
+ - matplotlib==3.8.4
+ - numba==0.58.1
+ - numpy==1.26.4
- pip:
- - cs_util==0.0.5
- - mccd==1.2.3
- - modopt==1.6.0
- - PyQt5==5.15.6
- - pyqtgraph==0.12.4
- - python-pysap==0.0.6
- - reproject==0.8
- - sip_tpv==1.1
- - sf_tools==2.0.4
- - sqlitedict==2.0.0
- - termcolor==1.1.0
- - tqdm==4.63.0
- - treecorr==4.2.6
+ - cs_util==0.1
+ - modopt
+ - PyQt5
+ - pyqtgraph
+ - python-pysap==0.2.1
+ - reproject
+ - shear_psf_leakage
+ - skaha
+ - sip_tpv
+ - sf_tools
+ - sqlitedict
+ - termcolor
+ - tqdm
+ - treecorr
+ - vos
- git+https://github.com/aguinot/ngmix@stable_version
- git+https://github.com/tobias-liaudat/Stile@v0.1
diff --git a/example/cfis/config_Fe.ini b/example/cfis/config_Fe.ini
new file mode 100644
index 000000000..240c3a747
--- /dev/null
+++ b/example/cfis/config_Fe.ini
@@ -0,0 +1,72 @@
+# ShapePipe configuration file for: find exposures
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = False
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_Fe
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = True
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = find_exposures_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 1
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+# Get tiles
+[FIND_EXPOSURES_RUNNER]
+
+INPUT_DIR = run_sp_Git:get_images_runner_run_1
+
+FILE_PATTERN = CFIS_image
+
+FILE_EXT = .fits
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+# Column number of exposure name in FITS header
+COLNUM = 3
+
+# Prefix to remove from exposure name
+EXP_PREFIX = p
+
diff --git a/example/cfis/config_Gie_symlink.ini b/example/cfis/config_Gie_symlink.ini
new file mode 100644
index 000000000..e6fa49f4c
--- /dev/null
+++ b/example/cfis/config_Gie_symlink.ini
@@ -0,0 +1,97 @@
+# ShapePipe configuration file for: get images
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = False
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_Gie
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = True
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = get_images_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 1
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+# Get exposures
+[GET_IMAGES_RUNNER]
+
+INPUT_DIR = last:find_exposures_runner
+
+FILE_PATTERN = exp_numbers
+
+FILE_EXT = .txt
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+
+# Paths
+
+# Output path (optional, default is [FILE]:OUTPUT_DIR
+# OUTPUT_PATH = input_images
+
+# Input path where original images are stored. Can be local path or vos url.
+# Single string or list of strings
+INPUT_PATH = $SP_RUN/data_exp, $SP_RUN/data_exp, $SP_RUN/data_exp
+
+# Input file pattern including tile number as dummy template
+INPUT_FILE_PATTERN = 000000, 000000.weight, 000000.flag
+
+# Input file extensions
+INPUT_FILE_EXT = .fits.fz, .fits.fz, .fits.fz
+
+# Input numbering scheme, python regexp
+INPUT_NUMBERING = \d{6}
+
+# Output file pattern without number
+OUTPUT_FILE_PATTERN = image-, weight-, flag-
+
+# Method to retrieve images, one in 'vos', 'symlink'
+RETRIEVE = symlink
+
+# If RETRIEVE=vos, number of attempts to download
+# Optional, default=3
+N_TRY = 3
+
+# Retrieve command options, optional
+RETRIEVE_OPTIONS = --certfile=$HOME/.ssl/cadcproxy.pem
diff --git a/example/cfis/config_Gie_vos.ini b/example/cfis/config_Gie_vos.ini
new file mode 100644
index 000000000..ee4b92f30
--- /dev/null
+++ b/example/cfis/config_Gie_vos.ini
@@ -0,0 +1,103 @@
+# ShapePipe configuration file for: get images
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = False
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_Gie
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = True
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = get_images_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 1
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+# Get exposures
+[GET_IMAGES_RUNNER]
+
+INPUT_DIR = last:find_exposures_runner
+
+FILE_PATTERN = exp_numbers
+
+FILE_EXT = .txt
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+
+# Paths
+
+# Output path (optional, default is [FILE]:OUTPUT_DIR
+# OUTPUT_PATH = input_images
+
+# Input path where original images are stored. Can be local path or vos url.
+# Single string or list of strings
+INPUT_PATH = vos:cfis/pitcairn, vos:cfis/weights, vos:cfis/flags
+# LSB images:
+#INPUT_PATH = vos:cfis/lsb_individual, vos:cfis/weights, vos:cfis/flags
+
+# Input file pattern including tile number as dummy template
+INPUT_FILE_PATTERN = 000000, 000000.weight, 000000.flag
+# LSB images
+#INPUT_FILE_PATTERN = 000000s, 000000p.weight, 000000p.flag
+
+# Input file extensions
+INPUT_FILE_EXT = .fits.fz, .fits.fz, .fits.fz
+
+# Input numbering scheme, python regexp
+INPUT_NUMBERING = \d{6}
+
+# Output file pattern without number
+OUTPUT_FILE_PATTERN = image-, weight-, flag-
+
+# Method to retrieve images, one in 'vos', 'symlink'
+RETRIEVE = vos
+
+# If RETRIEVE=vos, number of attempts to download
+# Optional, default=3
+N_TRY = 3
+
+# Retrieve command options, optional
+RETRIEVE_OPTIONS = --certfile=$HOME/.ssl/cadcproxy.pem
+
+CHECK_EXISTING_DIR = $SP_RUN/data_exp
diff --git a/example/cfis/config_GitFeGie_symlink.ini b/example/cfis/config_GitFeGie_symlink.ini
index 22e834533..6f84d1482 100644
--- a/example/cfis/config_GitFeGie_symlink.ini
+++ b/example/cfis/config_GitFeGie_symlink.ini
@@ -80,6 +80,8 @@ INPUT_NUMBERING = \d{3}\.\d{3}
# Output file pattern without number
OUTPUT_FILE_PATTERN = CFIS_image-, CFIS_weight-
+#CHECK_EXISTING_DIR = $SP_RUN/output/run_sp_Git/get_images_runner_run_1/output
+
# Copy/download method, one in 'vos', 'symlink'
RETRIEVE = symlink
@@ -98,8 +100,12 @@ FILE_EXT = .fits
# NUMBERING_SCHEME (optional) string with numbering pattern for input files
NUMBERING_SCHEME = -000-000
+# Column number of exposure name in FITS header
COLNUM = 3
+# Prefix to remove from exposure name
+EXP_PREFIX = p
+
# Get exposures
[GET_IMAGES_RUNNER_RUN_2]
diff --git a/example/cfis/config_GitFeGie_vos.ini b/example/cfis/config_GitFeGie_vos.ini
index fd3207bb3..75044bf44 100644
--- a/example/cfis/config_GitFeGie_vos.ini
+++ b/example/cfis/config_GitFeGie_vos.ini
@@ -66,7 +66,7 @@ NUMBERING_SCHEME =
# Input path where original images are stored. Can be local path or vos url.
# Single string or list of strings
-INPUT_PATH = vos:cfis/tiles_DR3, vos:cfis/tiles_DR3
+INPUT_PATH = vos:cfis/tiles_DR5, vos:cfis/tiles_DR5
# Input file pattern including tile number as dummy template
INPUT_FILE_PATTERN = CFIS.000.000.r, CFIS.000.000.r.weight
@@ -84,8 +84,9 @@ OUTPUT_FILE_PATTERN = CFIS_image-, CFIS_weight-
RETRIEVE = vos
# Copy command options, optional
-RETRIEVE_OPTIONS = --certfile=$VM_HOME/.ssl/cadcproxy.pem
+RETRIEVE_OPTIONS = --certfile=$HOME/.ssl/cadcproxy.pem
+CHECK_EXISTING_DIR = $SP_RUN/output/run_sp_Git/get_images_runner_run_1/output
[FIND_EXPOSURES_RUNNER]
@@ -98,6 +99,12 @@ FILE_EXT = .fits
# NUMBERING_SCHEME (optional) string with numbering pattern for input files
NUMBERING_SCHEME = -000-000
+# Column number of exposure name in FITS header
+COLNUM = 3
+
+# Prefix to remove from exposure name
+EXP_PREFIX = p
+
# Get exposures
[GET_IMAGES_RUNNER_RUN_2]
@@ -145,4 +152,4 @@ RETRIEVE = vos
N_TRY = 3
# Retrieve command options, optional
-RETRIEVE_OPTIONS = --certfile=$VM_HOME/.ssl/cadcproxy.pem
+RETRIEVE_OPTIONS = --certfile=$HOME/.ssl/cadcproxy.pem
diff --git a/example/cfis/config_GitFe_symlink.ini b/example/cfis/config_GitFe_symlink.ini
new file mode 100644
index 000000000..4e7ce75cb
--- /dev/null
+++ b/example/cfis/config_GitFe_symlink.ini
@@ -0,0 +1,105 @@
+# ShapePipe configuration file for: get images and find exposures
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = False
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_GitFe
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = True
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = get_images_runner, find_exposures_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 1
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+# Get tiles
+[GET_IMAGES_RUNNER]
+
+FILE_PATTERN = tile_numbers
+
+FILE_EXT = .txt
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME =
+
+# Paths
+
+# Input path where original images are stored. Can be local path or vos url.
+# Single string or list of strings
+INPUT_PATH = $SP_RUN/data_tiles, $SP_RUN/data_tiles
+
+# Input file pattern including tile number as dummy template
+INPUT_FILE_PATTERN = CFIS.000.000.r, CFIS.000.000.r.weight
+
+# Input file extensions
+INPUT_FILE_EXT = .fits, .fits.fz
+
+# Input numbering scheme, python regexp
+INPUT_NUMBERING = \d{3}\.\d{3}
+
+# Output file pattern without number
+OUTPUT_FILE_PATTERN = CFIS_image-, CFIS_weight-
+
+# Copy/download method, one in 'vos', 'symlink'
+RETRIEVE = symlink
+
+# Copy command options, optional
+RETRIEVE_OPTIONS = -L
+
+
+[FIND_EXPOSURES_RUNNER]
+
+INPUT_MODULE = get_images_runner
+
+FILE_PATTERN = CFIS_image
+
+FILE_EXT = .fits
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+# Column number of exposure name in FITS header
+COLNUM = 3
+
+# Prefix to remove from exposure name
+EXP_PREFIX = p
diff --git a/example/cfis/config_Git_vos.ini b/example/cfis/config_Git_vos.ini
new file mode 100644
index 000000000..26edf3efc
--- /dev/null
+++ b/example/cfis/config_Git_vos.ini
@@ -0,0 +1,93 @@
+# ShapePipe configuration file for: get images
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = False
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_Git
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = True
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = get_images_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 1
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+# Get tiles
+[GET_IMAGES_RUNNER]
+
+FILE_PATTERN = tile_numbers
+
+FILE_EXT = .txt
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME =
+
+# Paths
+
+# Input path where original images are stored. Can be local path or vos url.
+# Single string or list of strings
+INPUT_PATH = vos:cfis/tiles_DR5, vos:cfis/tiles_DR5
+
+# Input file pattern including tile number as dummy template
+INPUT_FILE_PATTERN = CFIS.000.000.r, CFIS.000.000.r.weight
+
+# Input file extensions
+INPUT_FILE_EXT = .fits, .fits.fz
+
+# Input numbering scheme, python regexp
+INPUT_NUMBERING = \d{3}\.\d{3}
+
+# Output file pattern without number
+OUTPUT_FILE_PATTERN = CFIS_image-, CFIS_weight-
+
+# Copy/download method, one in 'vos', 'symlink'
+RETRIEVE = vos
+
+# If RETRIEVE=vos, number of attempts to download
+# Optional, default=3
+N_TRY = 3
+
+# Copy command options, optional
+RETRIEVE_OPTIONS = --certfile=$HOME/.ssl/cadcproxy.pem
+
+CHECK_EXISTING_DIR = $SP_RUN/data_tiles
diff --git a/example/cfis/config_MaMa_onthefly.ini b/example/cfis/config_MaMa_onthefly.ini
index bde813940..84f117e65 100644
--- a/example/cfis/config_MaMa_onthefly.ini
+++ b/example/cfis/config_MaMa_onthefly.ini
@@ -44,7 +44,7 @@ OUTPUT_DIR = $SP_RUN/output
[JOB]
# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
-SMP_BATCH_SIZE = 8
+SMP_BATCH_SIZE = 16
# Timeout value (optional), default is None, i.e. no timeout limit applied
TIMEOUT = 96:00:00
diff --git a/example/cfis/config_MsPl_psfex.ini b/example/cfis/config_MsPl_psfex.ini
index 7fcb3ba20..d21fdd126 100644
--- a/example/cfis/config_MsPl_psfex.ini
+++ b/example/cfis/config_MsPl_psfex.ini
@@ -35,7 +35,7 @@ LOG_NAME = log_sp
RUN_LOG_NAME = log_run_sp
# Input directory, containing input files, single string or list of names
-INPUT_DIR = $SP_RUN/psf_validation_ind
+INPUT_DIR = $SP_RUN/output
# Output directory
OUTPUT_DIR = $SP_RUN/output
@@ -54,7 +54,7 @@ TIMEOUT = 96:00:00
## Module options
[MERGE_STARCAT_RUNNER]
-INPUT_DIR = psf_validation_ind
+INPUT_DIR = last:psfex_interp_runner
PSF_MODEL = psfex
diff --git a/example/cfis/config_Ms_psfex.ini b/example/cfis/config_Ms_psfex.ini
new file mode 100644
index 000000000..5698ee6dd
--- /dev/null
+++ b/example/cfis/config_Ms_psfex.ini
@@ -0,0 +1,70 @@
+# ShapePipe configuration file for post-processing.
+# merge star cat.
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_Ms
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = merge_starcat_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN/output
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 4
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+[MERGE_STARCAT_RUNNER]
+
+INPUT_DIR = last:psfex_interp_runner
+
+PSF_MODEL = psfex
+
+NUMBERING_SCHEME = -0000000-0
+
+# Input file pattern(s), list of strings with length matching number of expected input file types
+# Cannot contain wild cards
+FILE_PATTERN = validation_psf
+
+# FILE_EXT (optional) list of string extensions to identify input files
+FILE_EXT = .fits
+
+HDU = 2
diff --git a/example/cfis/config_Ms_psfex_conv.ini b/example/cfis/config_Ms_psfex_conv.ini
new file mode 100644
index 000000000..9c8b763e5
--- /dev/null
+++ b/example/cfis/config_Ms_psfex_conv.ini
@@ -0,0 +1,68 @@
+# ShapePipe configuration file for post-processing.
+# merge star cat (converted to WCS)
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_Ms
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = merge_starcat_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN/output
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 4
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+[MERGE_STARCAT_RUNNER]
+
+INPUT_DIR = last:psfex_interp_runner
+
+PSF_MODEL = psfex
+
+NUMBERING_SCHEME = -0-0
+
+# Input file pattern(s), list of strings with length matching number of expected input file types
+# Cannot contain wild cards
+FILE_PATTERN = validation_psf_conv
+
+# FILE_EXT (optional) list of string extensions to identify input files
+FILE_EXT = .fits
diff --git a/example/cfis/config_Pl_mccd.ini b/example/cfis/config_Pl_mccd.ini
index a666d09dd..844246019 100644
--- a/example/cfis/config_Pl_mccd.ini
+++ b/example/cfis/config_Pl_mccd.ini
@@ -35,7 +35,7 @@ LOG_NAME = log_sp
RUN_LOG_NAME = log_run_sp
# Input directory, containing input files, single string or list of names
-INPUT_DIR = .
+INPUT_DIR = $SP_RUN/output
# Output directory
OUTPUT_DIR = $SP_RUN/output
diff --git a/example/cfis/config_Pl_psfex.ini b/example/cfis/config_Pl_psfex.ini
index c561f15a5..f1c8904cf 100644
--- a/example/cfis/config_Pl_psfex.ini
+++ b/example/cfis/config_Pl_psfex.ini
@@ -12,7 +12,7 @@ VERBOSE = True
RUN_NAME = run_sp_Pl
# Add date and time to RUN_NAME, optional, default: False
-RUN_DATETIME = True
+RUN_DATETIME = False
## ShapePipe execution options
@@ -35,7 +35,7 @@ LOG_NAME = log_sp
RUN_LOG_NAME = log_run_sp
# Input directory, containing input files, single string or list of names
-INPUT_DIR = .
+INPUT_DIR = $SP_RUN/output
# Output directory
OUTPUT_DIR = $SP_RUN/output
@@ -57,11 +57,16 @@ TIMEOUT = 96:00:00
# NUMBERING_SCHEME (optional) string with numbering pattern for input files
NUMBERING_SCHEME = -0000000
+#FILE_PATTERN = test
FILE_PATTERN = full_starcat
FILE_EXT = .fits
+HDU = 1
+
PSF = psfex
-PLOT_MEANSHAPES = True
+
+# was True
+PLOT_MEANSHAPES = False
X_GRID = 5
Y_GRID = 10
@@ -72,7 +77,8 @@ MIN_R2 = 4.5
MAX_R2 = 7
MAX_DR2 = 0.03
-PLOT_HISTOGRAMS = True
+# was True
+PLOT_HISTOGRAMS = False
REMOVE_OUTLIERS = False
# X_GRID, Y_GRID: correspond to the number of bins in each direction of each
@@ -82,7 +88,7 @@ REMOVE_OUTLIERS = False
# before drawing the plots.
PLOT_RHO_STATS = True
-RHO_STATS_STYLE = HSC
+RHO_STATS_STYLE = UNIONS
RHO_STATS_YLIM_L = 1e-10, 4e-5
RHO_STATS_YLIM_R = 1e-8, 4e-5
diff --git a/example/cfis/config_Pl_psfex_conv.ini b/example/cfis/config_Pl_psfex_conv.ini
new file mode 100644
index 000000000..de2c0679d
--- /dev/null
+++ b/example/cfis/config_Pl_psfex_conv.ini
@@ -0,0 +1,93 @@
+# ShapePipe configuration file for post-processing.
+# merge star cat and PSF plots.
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_Pl
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = mccd_plots_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN/output
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 4
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+[MCCD_PLOTS_RUNNER]
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -0000000
+
+FILE_PATTERN = full_starcat
+FILE_EXT = .fits
+
+HDU = 1
+
+PSF = psfex
+
+# was True
+PLOT_MEANSHAPES = False
+X_GRID = 5
+Y_GRID = 10
+
+# Optional: max values for elliptity and residual ellipticities
+MAX_E = 0.1
+MAX_DE = 0.01
+MIN_R2 = 4.5
+MAX_R2 = 7
+MAX_DR2 = 0.03
+
+# was True
+PLOT_HISTOGRAMS = False
+REMOVE_OUTLIERS = False
+
+# X_GRID, Y_GRID: correspond to the number of bins in each direction of each
+# CCD from the focal plane. Ex: each CCD will be binned in 5x10 regular grids.
+#
+# REMOVE_OUTLIERS: Remove validated stars that are outliers in terms of shape
+# before drawing the plots.
+
+PLOT_RHO_STATS = True
+RHO_STATS_STYLE = UNIONS
+
+RHO_STATS_YLIM_L = 1e-10, 4e-5
+RHO_STATS_YLIM_R = 1e-8, 4e-5
diff --git a/example/cfis/config_exp_Ma_onthefly.ini b/example/cfis/config_exp_Ma_onthefly.ini
new file mode 100644
index 000000000..a2ff95fe6
--- /dev/null
+++ b/example/cfis/config_exp_Ma_onthefly.ini
@@ -0,0 +1,79 @@
+# ShapePipe configuration file for masking of exposures
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_exp_Ma
+
+# Add date and time to RUN_NAME, optional, default: False
+; RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = mask_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = .
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 16
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+### Mask exposures
+[MASK_RUNNER]
+
+# Parent module
+INPUT_DIR = last:split_exp_runner
+
+# Update numbering convention, accounting for HDU number of
+# single-exposure single-HDU files
+NUMBERING_SCHEME = -0000000-0
+
+# Path of mask config file
+MASK_CONFIG_PATH = $SP_CONFIG/config_onthefly.mask
+
+# External mask file flag, use if True, otherwise ignore
+USE_EXT_FLAG = True
+
+# External star catalogue flag, use external cat if True,
+# obtain from online catalogue if False
+USE_EXT_STAR = False
+
+# File name suffix for the output flag files (optional)
+PREFIX = pipeline
+
+# Path to check for existing output mask files
+CHECK_EXISTING_DIR = $SP_RUN/output/run_sp_Ma_exp/mask_runner/output
diff --git a/example/cfis/config_exp_Mh.ini b/example/cfis/config_exp_Mh.ini
new file mode 100644
index 000000000..2ad16ef0d
--- /dev/null
+++ b/example/cfis/config_exp_Mh.ini
@@ -0,0 +1,67 @@
+# ShapePipe configuration file for single-exposures,
+# merge headers
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_exp_Mh
+
+# Add date and time to RUN_NAME, optional, default: True
+; RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = merge_headers_runner
+
+# Run mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names with length matching FILE_PATTERN
+INPUT_DIR = .
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 16
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+[MERGE_HEADERS_RUNNER]
+
+INPUT_DIR = last:split_exp_runner
+
+FILE_PATTERN = headers
+
+FILE_EXT = .npy
+
+# Single-exposure numbering scheme
+NUMBERING_SCHEME = -0000000
+
+OUTPUT_PATH = $SP_RUN/output
diff --git a/example/cfis/config_exp_Pi.ini b/example/cfis/config_exp_Pi.ini
new file mode 100644
index 000000000..12056341b
--- /dev/null
+++ b/example/cfis/config_exp_Pi.ini
@@ -0,0 +1,82 @@
+# ShapePipe configuration file for single-HDU single exposure images..
+# PSFex PSF model; interpolation for validation.
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_exp_Pi
+
+# Add date and time to RUN_NAME, optional, default: True
+; RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = psfex_interp_runner
+
+
+# Run mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names with length matching FILE_PATTERN
+INPUT_DIR = .
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 1
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+[PSFEX_INTERP_RUNNER]
+
+# Use 20% sample for PSF validation
+FILE_PATTERN = star_split_ratio_80, star_split_ratio_20, psfex_cat
+
+FILE_EXT = .psf, .fits, .cat
+
+NUMBERING_SCHEME = -0000000-0
+
+# Run mode for psfex interpolation:
+# CLASSIC: 'classical' run, interpolate to object positions
+# MULTI-EPOCH: interpolate for multi-epoch images
+# VALIDATION: validation for single-epoch images
+MODE = VALIDATION
+
+# Column names of position parameters
+POSITION_PARAMS = XWIN_IMAGE,YWIN_IMAGE
+
+# If True, measure and store ellipticity of the PSF (using moments)
+GET_SHAPES = True
+
+# Minimum number of stars per CCD for PSF model to be computed
+STAR_THRESH = 22
+
+# Maximum chi^2 for PSF model to be computed on CCD
+CHI2_THRESH = 2
diff --git a/example/cfis/config_exp_Sp.ini b/example/cfis/config_exp_Sp.ini
new file mode 100644
index 000000000..2ee1676b8
--- /dev/null
+++ b/example/cfis/config_exp_Sp.ini
@@ -0,0 +1,74 @@
+# ShapePipe configuration file for single-exposures,
+# split images, merge headers
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_exp_Sp
+
+# Add date and time to RUN_NAME, optional, default: True
+RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = split_exp_runner
+
+# Run mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names with length matching FILE_PATTERN
+INPUT_DIR = .
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 16
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+[SPLIT_EXP_RUNNER]
+
+INPUT_DIR = last:get_images_runner_run_2
+
+FILE_PATTERN = image, weight, flag
+
+# Matches compressed single-exposure files
+FILE_EXT = .fitsfz, .fitsfz, .fitsfz
+
+NUMBERING_SCHEME = -0000000
+
+# OUTPUT_SUFFIX, actually file name prefixes.
+# Expected keyword "flag" will lead to a behavior where the data are saved as int.
+# The code also expects the image data to use the "image" suffix
+# (default value in the pipeline).
+OUTPUT_SUFFIX = image, weight, flag
+
+# Number of HDUs/CCDs of mosaic
+N_HDU = 40
diff --git a/example/cfis/config_exp_SpMh.ini b/example/cfis/config_exp_SpMh.ini
index 76f87ddd7..b05b8f0c2 100644
--- a/example/cfis/config_exp_SpMh.ini
+++ b/example/cfis/config_exp_SpMh.ini
@@ -12,7 +12,7 @@ VERBOSE = True
RUN_NAME = run_sp_exp_SpMh
# Add date and time to RUN_NAME, optional, default: True
-; RUN_DATETIME = False
+RUN_DATETIME = False
## ShapePipe execution options
@@ -57,13 +57,15 @@ TIMEOUT = 96:00:00
INPUT_DIR = last:get_images_runner_run_2
+FILE_PATTERN = image, weight, flag
+
# Matches compressed single-exposure files
FILE_EXT = .fitsfz, .fitsfz, .fitsfz
NUMBERING_SCHEME = -0000000
# OUTPUT_SUFFIX, actually file name prefixes.
-# Expected keyword "flag" will lead to a behavior where the data are save as int.
+# Expected keyword "flag" will lead to a behavior where the data are saved as int.
# The code also expects the image data to use the "image" suffix
# (default value in the pipeline).
OUTPUT_SUFFIX = image, weight, flag
diff --git a/example/cfis/config_exp_mccd.ini b/example/cfis/config_exp_mccd.ini
new file mode 100644
index 000000000..e838f1733
--- /dev/null
+++ b/example/cfis/config_exp_mccd.ini
@@ -0,0 +1,244 @@
+# ShapePipe configuration file for single-exposures, MCCD PSF model.
+# Process exposures after masking, from star detection to PSF model.
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_exp_SxSePsf
+
+# Add date and time to RUN_NAME, optional, default: True
+; RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = sextractor_runner, setools_runner,
+ mccd_preprocessing_runner, mccd_fit_val_runner,
+ merge_starcat_runner, mccd_plots_runner
+
+# Run mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names with length matching FILE_PATTERN
+INPUT_DIR = .
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 1
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+[SEXTRACTOR_RUNNER]
+
+# Somehow this works but not
+# - omitting
+# - $SP_RUN/output
+#INPUT_DIR = .
+
+# Input from two modules
+INPUT_MODULE = split_exp_runner, mask_runner
+
+# Read pipeline flag files created by mask module
+FILE_PATTERN = image, weight, pipeline_flag
+
+NUMBERING_SCHEME = -0000000-0
+
+# SExtractor executable path
+EXEC_PATH = sex
+
+# SExtractor configuration files
+DOT_SEX_FILE = $SP_CONFIG/default_exp.sex
+DOT_PARAM_FILE = $SP_CONFIG//default.param
+DOT_CONV_FILE = $SP_CONFIG/default.conv
+
+# Use input weight image if True
+WEIGHT_IMAGE = True
+
+# Use input flag image if True
+FLAG_IMAGE = True
+
+# Use input PSF file if True
+PSF_FILE = False
+
+# Use distinct image for detection (SExtractor in
+# dual-image mode) if True.
+DETECTION_IMAGE = False
+
+# Distinct weight image for detection (SExtractor
+# in dual-image mode)
+DETECTION_WEIGHT = False
+
+# True if photometry zero-point is to be read from exposure image header
+ZP_FROM_HEADER = True
+
+# If ZP_FROM_HEADER is True, zero-point key name
+ZP_KEY = PHOTZP
+
+# Background information from image header.
+# If BKG_FROM_HEADER is True, background value will be read from header.
+# In that case, the value of BACK_TYPE will be set atomatically to MANUAL.
+# This is used e.g. for the LSB images.
+BKG_FROM_HEADER = False
+# LSB images:
+# BKG_FROM_HEADER = True
+
+# If BKG_FROM_HEADER is True, background value key name
+# LSB images:
+#BKG_KEY = IMMODE
+
+# Type of image check (optional), default not used, can be a list of
+# BACKGROUND, BACKGROUND_RMS, INIBACKGROUND, MINIBACK_RMS, -BACKGROUND,
+# FILTERED, OBJECTS, -OBJECTS, SEGMENTATION, APERTURES
+CHECKIMAGE = BACKGROUND
+
+# File name suffix for the output sextractor files (optional) SUFFIX = tile
+SUFFIX = sexcat
+
+## Post-processing
+
+# Not required for single exposures
+MAKE_POST_PROCESS = FALSE
+
+
+[SETOOLS_RUNNER]
+
+INPUT_MODULE = last:sextractor_runner
+
+# Note: Make sure this doe not match the SExtractor background images
+# (sexcat_background*)
+FILE_PATTERN = sexcat_sexcat
+
+NUMBERING_SCHEME = -0000000-0
+
+# SETools config file
+SETOOLS_CONFIG_PATH = $SP_CONFIG/star_selection.setools
+
+
+[MCCD_PREPROCESSING_RUNNER]
+
+# Path to MCCD config file
+CONFIG_PATH = $SP_CONFIG/config_MCCD.ini
+
+MODE = FIT_VALIDATION
+
+VERBOSE = False
+
+INPUT_DIR = last:setools_runner
+
+# Input are individual CCDs, thus single-exposure single-HDU images
+NUMBERING_SCHEME = -0000000-0
+
+FILE_PATTERN = star_split_ratio_80, star_split_ratio_20
+
+FILE_EXT = .fits, .fits
+
+
+[MCCD_FIT_VAL_RUNNER]
+
+# Path to MCCD config file
+CONFIG_PATH = $SP_CONFIG/config_MCCD.ini
+
+MODE = FIT_VALIDATION
+
+VERBOSE = False
+
+NUMBERING_SCHEME = -0000000
+
+
+[MCCD_MERGE_STARCAT_RUNNER]
+
+# Path to MCCD config file
+CONFIG_PATH = $SP_CONFIG/config_MCCD.ini
+
+MODE = FIT_VALIDATION
+
+VERBOSE = False
+
+NUMBERING_SCHEME = -0000000
+
+
+[MCCD_PLOTS_RUNNER]
+
+# Path to MCCD config file
+CONFIG_PATH = $SP_CONFIG/config_MCCD.ini
+
+MODE = FIT_VALIDATION
+
+VERBOSE = False
+
+# Now MCCD has created a focal-plane PSF model, including all CCDS per images,
+# thus single-exposure files
+NUMBERING_SCHEME = -0000000
+
+PLOT_MEANSHAPES = True
+
+# X_GRID, Y_GRID: correspond to the number of bins in each direction of each
+# CCD from the focal plane. Ex: each CCD will be binned in 5x10 regular grids.
+X_GRID = 5
+Y_GRID = 10
+
+PLOT_HISTOGRAMS = True
+
+# REMOVE_OUTLIERS: Remove validated stars that are outliers in terms of shape
+# before drawing the plots.
+REMOVE_OUTLIERS = False
+
+PLOT_RHO_STATS = True
+
+# RHO_STATS_STYLE: can be 'HSC' or 'DES'
+RHO_STATS_STYLE = HSC
+
+
+[MCCD_INTERP_RUNNER]
+
+# MODE: Define the way the MCCD interpolation will run.
+# CLASSIC for classical run.
+# MULTI-EPOCH for multi epoch.
+MODE = CLASSIC
+
+# Position parameter names
+# for multi-epoch XWIN_WORLD,YWIN_WORLD
+# For classical XWIN_IMAGE,YWIN_IMAGE:
+POSITION_PARAMS = XWIN_IMAGE,YWIN_IMAGE
+
+# Get PSF shapes calculated and saved on the output dict
+GET_SHAPES = True
+
+# Directory with PSF models
+PSF_MODEL_DIR = /Users/tliaudat/Documents/PhD/codes/venv_p3/MCCD_pipeline_integration/test_val_data/fitted_model/
+
+# PSF model patterns
+PSF_MODEL_PATTERN = fitted_model
+
+# PSF model separator
+PSF_MODEL_SEPARATOR = -
+
+# For multi-epoch purposes
+ME_LOG_WCS = $SP_RUN/output/log_exp_headers.sqlite
diff --git a/example/cfis/config_exp_psfex.ini b/example/cfis/config_exp_psfex.ini
new file mode 100644
index 000000000..22bc877f4
--- /dev/null
+++ b/example/cfis/config_exp_psfex.ini
@@ -0,0 +1,178 @@
+# ShapePipe configuration file for single-exposures. PSFex PSF model.
+# Process exposures after masking, from star detection to PSF model.
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_exp_SxSePsfPi
+#RUN_NAME = run_sp_exp_SxSePsf
+
+# Add date and time to RUN_NAME, optional, default: True
+; RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = sextractor_runner, setools_runner, psfex_runner, psfex_interp_runner
+
+
+# Run mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names with length matching FILE_PATTERN
+INPUT_DIR = $SP_RUN/output
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 16
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+[SEXTRACTOR_RUNNER]
+
+# Input from two modules
+#INPUT_DIR = last:split_exp_runner, run_sp_Ma_exp:mask_runner
+INPUT_DIR = last:split_exp_runner, last:mask_runner
+
+# Read pipeline flag files created by mask module
+FILE_PATTERN = image, weight, pipeline_flag
+
+NUMBERING_SCHEME = -0000000-0
+
+# SExtractor executable path
+EXEC_PATH = sex
+
+# SExtractor configuration files
+DOT_SEX_FILE = $SP_CONFIG/default_exp.sex
+DOT_PARAM_FILE = $SP_CONFIG//default.param
+DOT_CONV_FILE = $SP_CONFIG/default.conv
+
+# Use input weight image if True
+WEIGHT_IMAGE = True
+
+# Use input flag image if True
+FLAG_IMAGE = True
+
+# Use input PSF file if True
+PSF_FILE = False
+
+# Use distinct image for detection (SExtractor in
+# dual-image mode) if True.
+DETECTION_IMAGE = False
+
+# Distinct weight image for detection (SExtractor
+# in dual-image mode)
+DETECTION_WEIGHT = False
+
+# True if photometry zero-point is to be read from exposure image header
+ZP_FROM_HEADER = True
+
+# If ZP_FROM_HEADER is True, zero-point key name
+ZP_KEY = PHOTZP
+
+# Background information from image header.
+# If BKG_FROM_HEADER is True, background value will be read from header.
+# In that case, the value of BACK_TYPE will be set atomatically to MANUAL.
+# This is used e.g. for the LSB images.
+BKG_FROM_HEADER = False
+# LSB images:
+# BKG_FROM_HEADER = True
+
+# If BKG_FROM_HEADER is True, background value key name
+# LSB images:
+#BKG_KEY = IMMODE
+
+# Type of image check (optional), default not used, can be a list of
+# BACKGROUND, BACKGROUND_RMS, INIBACKGROUND, MINIBACK_RMS, -BACKGROUND,
+# FILTERED, OBJECTS, -OBJECTS, SEGMENTATION, APERTURES
+CHECKIMAGE = BACKGROUND
+
+# File name suffix for the output sextractor files (optional) SUFFIX = tile
+SUFFIX = sexcat
+
+## Post-processing
+
+# Not required for single exposures
+MAKE_POST_PROCESS = FALSE
+
+
+[SETOOLS_RUNNER]
+
+INPUT_DIR = last:sextractor_runner
+
+# Note: Make sure this doe not match the SExtractor background images
+# (sexcat_background*)
+FILE_PATTERN = sexcat
+
+NUMBERING_SCHEME = -0000000-0
+
+# SETools config file
+SETOOLS_CONFIG_PATH = $SP_CONFIG/star_selection.setools
+
+
+[PSFEX_RUNNER]
+
+# Use 80% sample for PSF model
+FILE_PATTERN = star_split_ratio_80
+
+NUMBERING_SCHEME = -0000000-0
+
+# Path to executable for the PSF model (optional)
+EXEC_PATH = psfex
+
+# Default psfex configuration file
+DOT_PSFEX_FILE = $SP_CONFIG/default.psfex
+
+[PSFEX_INTERP_RUNNER]
+
+# Use 20% sample for PSF validation
+FILE_PATTERN = star_split_ratio_80, star_split_ratio_20, psfex_cat
+
+FILE_EXT = .psf, .fits, .cat
+
+NUMBERING_SCHEME = -0000000-0
+
+# Run mode for psfex interpolation:
+# CLASSIC: 'classical' run, interpolate to object positions
+# MULTI-EPOCH: interpolate for multi-epoch images
+# VALIDATION: validation for single-epoch images
+MODE = VALIDATION
+
+# Column names of position parameters
+POSITION_PARAMS = XWIN_IMAGE,YWIN_IMAGE
+
+# If True, measure and store ellipticity of the PSF (using moments)
+GET_SHAPES = True
+
+# Minimum number of stars per CCD for PSF model to be computed
+STAR_THRESH = 22
+
+# Maximum chi^2 for PSF model to be computed on CCD
+CHI2_THRESH = 2
diff --git a/example/cfis/config_get_tiles_vos_headers.ini b/example/cfis/config_get_tiles_vos_headers.ini
index e28347ebf..4b79a2493 100644
--- a/example/cfis/config_get_tiles_vos_headers.ini
+++ b/example/cfis/config_get_tiles_vos_headers.ini
@@ -69,7 +69,7 @@ NUMBERING_SCHEME =
# Input path where original images are stored. Can be local path or vos url.
# Single string or list of strings
-INPUT_PATH = vos:cfis/tiles_DR3
+INPUT_PATH = vos:cfis/tiles_DR5
# Input file pattern including tile number as dummy template
INPUT_FILE_PATTERN = CFIS.000.000.r
diff --git a/example/cfis/config_make_cat_psfex.ini b/example/cfis/config_make_cat_psfex.ini
index fdf5414b5..a7407d990 100644
--- a/example/cfis/config_make_cat_psfex.ini
+++ b/example/cfis/config_make_cat_psfex.ini
@@ -55,7 +55,7 @@ TIMEOUT = 96:00:00
[MAKE_CAT_RUNNER]
# Input directory, containing input files, single string or list of names with length matching FILE_PATTERN
-INPUT_DIR = last:sextractor_runner_run_1, last:spread_model_runner, last:psfex_interp_runner, last:merge_sep_cats_runner
+INPUT_DIR = run_sp_tile_Sx:sextractor_runner, last:spread_model_runner, last:psfex_interp_runner, last:merge_sep_cats_runner
# Input file pattern(s), list of strings with length matching number of expected input file types
# Cannot contain wild cards
diff --git a/example/cfis/config_merge_sep_cats_template.ini b/example/cfis/config_merge_sep_cats_template.ini
index e14e5fe74..36b99e8da 100644
--- a/example/cfis/config_merge_sep_cats_template.ini
+++ b/example/cfis/config_merge_sep_cats_template.ini
@@ -35,7 +35,6 @@ RUN_LOG_NAME = log_run_sp
# Input directory, containing input files, single string or list of names with length matching FILE_PATTERN
INPUT_DIR = ./output/run_sp_tile_ngmix_Ng1u/ngmix_runner/output
-#, ./output/run_sp_tile_ngmix_Ng1u/galsim_shapes_v2_runner/output
# Output directory
OUTPUT_DIR = ./output
@@ -58,11 +57,9 @@ TIMEOUT = 96:00:00
# Input file pattern(s), list of strings with length matching number of expected input file types
# Cannot contain wild cards
FILE_PATTERN = ngmix
-#, galsim
# FILE_EXT (optional) list of string extensions to identify input files
FILE_EXT = .fits
-#, .fits
# Numbering convention, string that exemplifies a numbering pattern.
NUMBERING_SCHEME = -000-000
diff --git a/example/cfis/config_tile_Ma_onthefly.ini b/example/cfis/config_tile_Ma_onthefly.ini
new file mode 100644
index 000000000..1b1fbbbea
--- /dev/null
+++ b/example/cfis/config_tile_Ma_onthefly.ini
@@ -0,0 +1,82 @@
+# ShapePipe configuration file for masking of tiles
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_tile_Ma
+
+# Add date and time to RUN_NAME, optional, default: False
+; RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = mask_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = $SP_RUN/output
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 8
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+### Mask tiles
+[MASK_RUNNER]
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = last:get_images_runner_run_1, last:uncompress_fits_runner
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+# Input file pattern(s), list of strings with length matching number of expected input file types
+# Cannot contain wild cards
+FILE_PATTERN = CFIS_image, CFIS_weight
+
+# FILE_EXT (optional) list of string extensions to identify input files
+FILE_EXT = .fits, .fits
+
+# Path of mask config file
+MASK_CONFIG_PATH = $SP_CONFIG/config_tile_onthefly.mask
+
+# External mask file flag, use if True, otherwise ignore
+USE_EXT_FLAG = False
+
+# External star catalogue flag, use external cat if True,
+# obtain from online catalogue if False
+USE_EXT_STAR = False
+
+# File name suffix for the output flag files (optional)
+PREFIX = pipeline
diff --git a/example/cfis/config_tile_MiViSmVi.ini b/example/cfis/config_tile_MiViSmVi.ini
index 6198c324c..7dcbe6c50 100644
--- a/example/cfis/config_tile_MiViSmVi.ini
+++ b/example/cfis/config_tile_MiViSmVi.ini
@@ -47,7 +47,7 @@ OUTPUT_DIR = $SP_RUN/output
[JOB]
# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
-SMP_BATCH_SIZE = 12
+SMP_BATCH_SIZE = 1
# Timeout value (optional), default is None, i.e. no timeout limit applied
TIMEOUT = 96:00:00
diff --git a/example/cfis/config_tile_Ng_template.ini b/example/cfis/config_tile_Ng_template.ini
index f9d733d71..cf988f2b5 100644
--- a/example/cfis/config_tile_Ng_template.ini
+++ b/example/cfis/config_tile_Ng_template.ini
@@ -21,7 +21,7 @@ RUN_DATETIME = False
MODULE = ngmix_runner
# Parallel processing mode, SMP or MPI
-MODE = SMP
+MODE = MPI
## ShapePipe file handling options
@@ -44,10 +44,10 @@ OUTPUT_DIR = $SP_RUN/output
[JOB]
# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
-SMP_BATCH_SIZE = 1
+SMP_BATCH_SIZE = 8
# Timeout value (optional), default is None, i.e. no timeout limit applied
-TIMEOUT = 96:00:00
+TIMEOUT = 48:00:00
## Module options
@@ -55,13 +55,14 @@ TIMEOUT = 96:00:00
# Model-fitting shapes with ngmix
[NGMIX_RUNNER]
-INPUT_DIR = last:sextractor_runner_run_1,last:X_interp_runner,last:vignetmaker_runner_run_2
+INPUT_DIR = run_sp_tile_Sx:sextractor_runner,last:X_interp_runner,last:vignetmaker_runner_run_2
FILE_PATTERN = sexcat, image_vignet, background_vignet, galaxy_psf, weight_vignet, flag_vignet
FILE_EXT = .fits, .sqlite, .sqlite, .sqlite, .sqlite, .sqlite
# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+#NUMBERING_SCHEME = \d{0}-\d{3}-\d{2}9
NUMBERING_SCHEME = -000-000
# Multi-epoch mode: Path to file with single-exposure WCS header information
@@ -75,25 +76,3 @@ PIXEL_SCALE = 0.186
ID_OBJ_MIN = X
ID_OBJ_MAX = X
-
-
-# Moment-based (KSB) shapes with galsim
-[GALSIM_SHAPES_V2_RUNNER]
-
-INPUT_DIR = last:sextractor_runner_run_2, last:vignetmaker_runner_run_1, last:X_interp_runner,last:vignetmaker_runner_run_2
-
-FILE_PATTERN = sexcat, weight_vignet, image_vignet, background_vignet, galaxy_psf, weight_vignet, flag_vignet
-
-FILE_EXT = .fits, .fits, .sqlite, .sqlite, .sqlite, .sqlite, .sqlite
-
-# NUMBERING_SCHEME (optional) string with numbering pattern for input files
-NUMBERING_SCHEME = -000-000
-
-# Multi-epoch mode: Path to file with single-exposure WCS header information
-LOG_WCS = $SP_RUN/output/log_exp_headers.sqlite
-
-# Magnitude zero-point
-MAG_ZP = 30.0
-
-ID_OBJ_MIN = X
-ID_OBJ_MAX = X
diff --git a/example/cfis/config_tile_PiViSmVi_canfar.ini b/example/cfis/config_tile_PiViSmVi_canfar.ini
new file mode 100644
index 000000000..0ce5fe056
--- /dev/null
+++ b/example/cfis/config_tile_PiViSmVi_canfar.ini
@@ -0,0 +1,188 @@
+# ShapePipe configuration file for tile, from detection up to shape measurement.
+# PSFEx PSF model.
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_tile_PsViSmVi
+
+# Add date and time to RUN_NAME, optional, default: False
+; RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+#MODULE = psfex_interp_runner,
+
+MODULE = psfex_interp_runner, vignetmaker_runner, spread_model_runner,
+ vignetmaker_runner
+
+# Parallel processing mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names
+INPUT_DIR = .
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 16
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+[PSFEX_INTERP_RUNNER]
+
+INPUT_DIR = run_sp_tile_Sx:sextractor_runner
+
+FILE_PATTERN = sexcat
+
+FILE_EXT = .fits
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+# Run mode for psfex interpolation:
+# CLASSIC: 'classical' run, interpolate to object positions
+# MULTI-EPOCH: interpolate for multi-epoch images
+# VALIDATION: validation for single-epoch images
+MODE = MULTI-EPOCH
+
+# Column names of position parameters
+POSITION_PARAMS = XWIN_WORLD,YWIN_WORLD
+
+# If True, measure and store ellipticity of the PSF
+GET_SHAPES = True
+
+# Number of stars threshold
+STAR_THRESH = 20
+
+# chi^2 threshold
+CHI2_THRESH = 2
+
+# Multi-epoch mode parameters
+
+ME_DOT_PSF_DIR = all:psfex_runner
+
+# Input psf file pattern
+ME_DOT_PSF_PATTERN = star_split_ratio_80
+
+# Multi-epoch mode: Path to file with single-exposure WCS header information
+ME_LOG_WCS = $SP_RUN/output/log_exp_headers.sqlite
+
+
+# Create vignets for tiles weights
+[VIGNETMAKER_RUNNER_RUN_1]
+
+INPUT_DIR = run_sp_tile_Sx:sextractor_runner, last:uncompress_fits_runner
+
+FILE_PATTERN = sexcat, CFIS_weight
+
+FILE_EXT = .fits, .fits
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+MASKING = False
+MASK_VALUE = 0
+
+# Run mode for psfex interpolation:
+# CLASSIC: 'classical' run, interpolate to object positions
+# MULTI-EPOCH: interpolate for multi-epoch images
+# VALIDATION: validation for single-epoch images
+MODE = CLASSIC
+
+# Coordinate frame type, one in PIX (pixel frame), SPHE (spherical coordinates)
+COORD = PIX
+POSITION_PARAMS = XWIN_IMAGE,YWIN_IMAGE
+
+# Vignet size in pixels
+STAMP_SIZE = 51
+
+# Output file name prefix, file name is _vignet.fits
+PREFIX = weight
+
+
+[SPREAD_MODEL_RUNNER]
+
+INPUT_DIR = run_sp_tile_Sx:sextractor_runner, last:psfex_interp_runner, last:vignetmaker_runner_run_1
+
+FILE_PATTERN = sexcat, galaxy_psf, weight_vignet
+
+FILE_EXT = .fits, .sqlite, .fits
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+# Pixel scale in arcsec
+PIXEL_SCALE = 0.186
+
+# Output mode:
+# new: create a new catalog with: [number, mag, sm, sm_err]
+# add: create a copy of the input SExtractor with the column sm and sm_err
+OUTPUT_MODE = new
+
+
+[VIGNETMAKER_RUNNER_RUN_2]
+
+# Create multi-epoch vignets for tiles corresponding to
+# positions on single-exposures
+
+INPUT_DIR = run_sp_tile_Sx:sextractor_runner
+
+FILE_PATTERN = sexcat
+
+FILE_EXT = .fits
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+MASKING = False
+MASK_VALUE = 0
+
+# Run mode for psfex interpolation:
+# CLASSIC: 'classical' run, interpolate to object positions
+# MULTI-EPOCH: interpolate for multi-epoch images
+# VALIDATION: validation for single-epoch images
+MODE = MULTI-EPOCH
+
+# Coordinate frame type, one in PIX (pixel frame), SPHE (spherical coordinates)
+COORD = SPHE
+POSITION_PARAMS = XWIN_WORLD,YWIN_WORLD
+
+# Vignet size in pixels
+STAMP_SIZE = 51
+
+# Output file name prefix, file name is vignet.fits
+PREFIX =
+
+# Additional parameters for path and file pattern corresponding to single-exposure
+# run outputs
+ME_IMAGE_DIR = all:split_exp_runner, all:split_exp_runner, all:split_exp_runner, all:sextractor_runner
+ME_IMAGE_PATTERN = flag, image, weight, background
+ME_LOG_WCS = $SP_RUN/output/log_exp_headers.sqlite
diff --git a/example/cfis/config_tile_Sx.ini b/example/cfis/config_tile_Sx.ini
new file mode 100644
index 000000000..42b3a09a9
--- /dev/null
+++ b/example/cfis/config_tile_Sx.ini
@@ -0,0 +1,117 @@
+# ShapePipe configuration file for tile detection
+
+
+## Default ShapePipe options
+[DEFAULT]
+
+# verbose mode (optional), default: True, print messages on terminal
+VERBOSE = True
+
+# Name of run (optional) default: shapepipe_run
+RUN_NAME = run_sp_tile_Sx
+
+# Add date and time to RUN_NAME, optional, default: True
+; RUN_DATETIME = False
+
+
+## ShapePipe execution options
+[EXECUTION]
+
+# Module name, single string or comma-separated list of valid module runner names
+MODULE = sextractor_runner
+
+
+# Run mode, SMP or MPI
+MODE = SMP
+
+
+## ShapePipe file handling options
+[FILE]
+
+# Log file master name, optional, default: shapepipe
+LOG_NAME = log_sp
+
+# Runner log file name, optional, default: shapepipe_runs
+RUN_LOG_NAME = log_run_sp
+
+# Input directory, containing input files, single string or list of names with length matching FILE_PATTERN
+INPUT_DIR = $SP_RUN/output
+
+# Output directory
+OUTPUT_DIR = $SP_RUN/output
+
+
+## ShapePipe job handling options
+[JOB]
+
+# Batch size of parallel processing (optional), default is 1, i.e. run all jobs in serial
+SMP_BATCH_SIZE = 16
+
+# Timeout value (optional), default is None, i.e. no timeout limit applied
+TIMEOUT = 96:00:00
+
+
+## Module options
+
+[SEXTRACTOR_RUNNER]
+
+INPUT_DIR = last:get_images_runner_run_1, last:uncompress_fits_runner, run_sp_Ma_tile:mask_runner
+
+FILE_PATTERN = CFIS_image, CFIS_weight, pipeline_flag
+
+FILE_EXT = .fits, .fits, .fits
+
+# NUMBERING_SCHEME (optional) string with numbering pattern for input files
+NUMBERING_SCHEME = -000-000
+
+# SExtractor executable path
+EXEC_PATH = sex
+
+# SExtractor configuration files
+DOT_SEX_FILE = $SP_CONFIG/default_tile.sex
+DOT_PARAM_FILE = $SP_CONFIG/default.param
+DOT_CONV_FILE = $SP_CONFIG/default.conv
+
+# Use input weight image if True
+WEIGHT_IMAGE = True
+
+# Use input flag image if True
+FLAG_IMAGE = True
+
+# Use input PSF file if True
+PSF_FILE = False
+
+# Use distinct image for detection (SExtractor in
+# dual-image mode) if True
+DETECTION_IMAGE = False
+
+# Distinct weight image for detection (SExtractor
+# in dual-image mode)
+DETECTION_WEIGHT = False
+
+ZP_FROM_HEADER = False
+
+BKG_FROM_HEADER = False
+
+# Type of image check (optional), default not used, can be a list of
+# BACKGROUND, BACKGROUND_RMS, INIBACKGROUND,
+# MINIBACK_RMS, -BACKGROUND, #FILTERED,
+# OBJECTS, -OBJECTS, SEGMENTATION, APERTURES
+CHECKIMAGE = BACKGROUND
+
+# File name suffix for the output sextractor files (optional)
+SUFFIX = sexcat
+
+## Post-processing
+
+# Necessary for tiles, to enable multi-exposure processing
+MAKE_POST_PROCESS = True
+
+# Multi-epoch mode: Path to file with single-exposure WCS header information
+LOG_WCS = $SP_RUN/output/log_exp_headers.sqlite
+
+# World coordinate keywords, SExtractor output. Format: KEY_X,KEY_Y
+WORLD_POSITION = XWIN_WORLD,YWIN_WORLD
+
+# Number of pixels in x,y of a CCD. Format: Nx,Ny
+CCD_SIZE = 33,2080,1,4612
diff --git a/example/cfis/default.param b/example/cfis/default.param
index 6521a94d5..09ad8405e 100644
--- a/example/cfis/default.param
+++ b/example/cfis/default.param
@@ -51,7 +51,7 @@ MU_MAX #Peak surface brightness above background
FLAGS #Extraction flags
FLAGS_WIN #Flags for WINdowed parameters
-#!!! REQUIRE FLAG_IMAGE !!!
+# The following flag requires a flag image
IMAFLAGS_ISO #FLAG-image flags OR'ed over the iso. profile !!! REQUIRE FLAG_IMAGE !!!
FWHM_IMAGE #FWHM assuming a gaussian core [pixel]
@@ -61,9 +61,8 @@ ELLIPTICITY #1 - B_IMAGE/A_IMAGE
VIGNET(51,51) #Pixel data around detection [count]
-#VECTOR_ASSOC #ASSOCiated parameter vector
-#NUMBER_ASSOC #Number of ASSOCiated IDs
+# For GaaP photometry
+A_WORLD
+B_WORLD
+THETA_J2000
-#SPREAD_MODEL
-#SPREADERR_MODEL
-#FWHMPSF_IMAGE
diff --git a/example/cfis/final_cat.param b/example/cfis/final_cat.param
index 6372a13e8..a70de962d 100644
--- a/example/cfis/final_cat.param
+++ b/example/cfis/final_cat.param
@@ -76,12 +76,23 @@ NGMIX_FLUX_ERR_2M
NGMIX_FLUX_ERR_2P
NGMIX_FLUX_ERR_NOSHEAR
-# magnitude, mainly for plots
+# magnitudes
MAG_AUTO
-
-# SNR from SExtractor, used for cuts on GALSIM shapes
+MAGERR_AUTO
+MAG_WIN
+MAGERR_WIN
+FLUX_AUTO
+FLUXERR_AUTO
+FLUX_APER
+FLUXERR_APER
+FLUX_RADIUS
+
+# SNR from SExtractor
SNR_WIN
+FWHM_IMAGE
+FWHM_WORLD
+
# PSF size measured on original image
NGMIX_T_PSFo_NOSHEAR
diff --git a/example/config.ini b/example/config.ini
index 49541f944..51d1479b5 100644
--- a/example/config.ini
+++ b/example/config.ini
@@ -14,7 +14,7 @@
# MODULE (required) must be a valid module runner name (or a comma separated list of names)
MODULE = python_example_runner, serial_example_runner, execute_example_runner, python_example_runner, execute_example_runner
# MODE (optional) options are smp or mpi, default is smp
-; MODE = mpi
+MODE = mpi
## ShapePipe file handling options
[FILE]
diff --git a/example/output/.gitkeep b/example/output/.gitkeep
deleted file mode 100644
index e69de29bb..000000000
diff --git a/example/pbs/candide_mpi.sh b/example/pbs/candide_mpi.sh
index 0abbbb7f4..41f7a5a25 100644
--- a/example/pbs/candide_mpi.sh
+++ b/example/pbs/candide_mpi.sh
@@ -21,20 +21,36 @@
#PBS -l nodes=2:ppn=2
# Full path to environment
-export SPENV="$HOME/.conda/envs/shapepipe"
+export SPENV="$HOME/.conda/envs/shapepipe_mpi"
# Full path to example config file and input data
export SPDIR="$HOME/shapepipe"
# Load modules
-module load intelpython/3
-module load openmpi/4.0.5
+module load gcc/9.3.0
+module load intelpython/3-2023.1.0
+module load openmpi/5.0.0
# Activate conda environment
source activate $SPENV
-# Run ShapePipe using full paths to executables
-$SPENV/bin/mpiexec --map-by node $SPENV/bin/shapepipe_run -c $SPDIR/example/config_mpi.ini
+# Other options to test
+# -map-by
+
+if [ -f "$PBS_NODEFILE" ]; then
+ NSLOTS=`cat $PBS_NODEFILE | wc -l`
+ echo "Using $NSLOTS CPUs from PBS_NODEFILE $PBS_NODEFILE"
+else
+ NSLOTS=4
+ echo "Using $NSLOTS CPUs set by hand"
+fi
+
+# Creates #node output dirs
+MPI_CMD=/softs/openmpi/5.0.0-torque-CentOS7/bin/mpirun
+MPI_ARGS="-np $NSLOTS"
+
+${MPI_CMD} ${MPI_ARGS} hostname
+${MPI_CMD} ${MPI_ARGS} $SPENV/bin/shapepipe_run -c $SPDIR/example/pbs/config_mpi.ini
# Return exit code
exit 0
diff --git a/example/pbs/config_mpi.ini b/example/pbs/config_mpi.ini
index bb2b8f95d..559fe1151 100644
--- a/example/pbs/config_mpi.ini
+++ b/example/pbs/config_mpi.ini
@@ -1,8 +1,14 @@
# ShapePipe Configuration File Example for MPI
+## Default ShapePipe options
+[DEFAULT]
+
+# Add date and time to RUN_NAME, optional, default: False
+RUN_DATETIME = True
+
## ShapePipe execution options
[EXECUTION]
-MODULE = python_example, serial_example, execute_example
+MODULE = python_example_runner, serial_example_runner, execute_example_runner
MODE = mpi
## ShapePipe file handling options
@@ -15,8 +21,8 @@ OUTPUT_DIR = $SPDIR/example/output
TIMEOUT = 00:01:35
## Module options
-[PYTHON_EXAMPLE]
+[PYTHON_EXAMPLE_RUNNER]
MESSAGE = The obtained value is:
-[SERIAL_EXAMPLE]
+[SERIAL_EXAMPLE_RUNNER]
ADD_INPUT_DIR = $SPDIR/example/data/numbers, $SPDIR/example/data/letters
diff --git a/install_shapepipe b/install_shapepipe
index c370d91d0..584540d6b 100755
--- a/install_shapepipe
+++ b/install_shapepipe
@@ -22,23 +22,9 @@ last_update="08/03/22"
# Conda package versions
fftw_ver="3.3.10"
libpng_ver="1.6.37"
-mpi4py_ver="3.1.3"
+mpi4py_ver="3.1.5"
openblas_ver="0.3.18"
-# SExtractor Package
-sex_url="https://github.com/astromatic/sextractor/archive/2.25.0.tar.gz"
-sex_tar="2.25.0.tar.gz"
-sex_dir="sextractor-2.25.0"
-sex_bin="sex"
-sex_version=TRUE
-
-# PSFEx Package
-psfex_url="https://github.com/astromatic/psfex/archive/3.21.1.tar.gz"
-psfex_tar="3.21.1.tar.gz"
-psfex_dir="psfex-3.21.1"
-psfex_bin="psfex"
-psfex_version=TRUE
-
# WeightWatcher Package
ww_url="http://snapshot.debian.org/archive/debian/20171211T160522Z/pool/main/w/weightwatcher/weightwatcher_1.12.orig.tar.gz"
ww_tar="weightwatcher_1.12.orig.tar.gz"
@@ -81,11 +67,11 @@ NC='\033[0m'
PIPE_DIR=$PWD
BUILD_DIR=$PIPE_DIR/build
ENV_NAME='shapepipe'
+ENV_DEV=FALSE
+USE_CONDA_SOURCE=FALSE
BUILD_ENV=TRUE
DEVELOP=FALSE
VOS=FALSE
-INSTALL_SEX=TRUE
-INSTALL_PSFEX=TRUE
INSTALL_WW=TRUE
INSTALL_CDSCLIENT=TRUE
ATLAS_SEARCH=FALSE
@@ -105,66 +91,6 @@ download_package() {
rm $2
}
-# Function to build SExtractor with OpenBLAS
-build_sex_blas() {
- astromatic_setup
- cd $BUILD_DIR/$1
- ./autogen.sh
- ./configure --prefix=$CONDA_PREFIX --enable-openblas --with-fftw-libdir=$FFTW_LIB \
- --with-fftw-incdir=$FFTW_INC --with-openblas-libdir=$BLAS_LIB \
- --with-openblas-incdir=$BLAS_INC --quiet
- make -j --quiet
- make install
-}
-
-# Function to build SExtractor with ATLAS
-build_sex_atlas() {
- astromatic_setup
- cd $BUILD_DIR/$1
- ./autogen.sh
- if [ "$ATLAS_SEARCH" == TRUE ]
- then
- ./configure --prefix=$CONDA_PREFIX --with-fftw-libdir=$FFTW_LIB \
- --with-fftw-incdir=$FFTW_INC --quiet
- else
- ./configure --prefix=$CONDA_PREFIX --with-fftw-libdir=$FFTW_LIB \
- --with-fftw-incdir=$FFTW_INC --with-atlas-libdir=$ATLAS_LIB \
- --with-atlas-incdir=$ATLAS_INC --quiet
- fi
- make -j --quiet
- make install
-}
-
-# Function to build PSFEx with OpenBLAS
-build_psfex_blas() {
- astromatic_setup
- cd $BUILD_DIR/$1
- ./autogen.sh
- ./configure --prefix=$CONDA_PREFIX --enable-openblas --enable-plplot=no \
- --with-fftw-libdir=$FFTW_LIB --with-fftw-incdir=$FFTW_INC \
- --with-openblas-libdir=$BLAS_LIB --with-openblas-incdir=$BLAS_INC --quiet
- make -j --quiet
- make install
-}
-
-# Function to build PSFEx with ATLAS
-build_psfex_atlas() {
- astromatic_setup
- cd $BUILD_DIR/$1
- ./autogen.sh
- if [ "$ATLAS_SEARCH" == TRUE ]
- then
- ./configure --prefix=$CONDA_PREFIX --enable-plplot=no \
- --with-fftw-libdir=$FFTW_LIB --with-fftw-incdir=$FFTW_INC --quiet
- else
- ./configure --prefix=$CONDA_PREFIX --enable-plplot=no \
- --with-fftw-libdir=$FFTW_LIB --with-fftw-incdir=$FFTW_INC \
- --with-atlas-libdir=$ATLAS_LIB --with-atlas-incdir=$ATLAS_INC --quiet
- fi
- make -j --quiet
- make install
-}
-
# Function to build a standard package
build_standard() {
cd $BUILD_DIR/$1
@@ -200,26 +126,28 @@ check_conda() {
echo -ne "${RED}ERROR: Found Conda version $CONDA_VERSION but require 4.0.0 or greater.${NC}\n"
exit 1
fi
- # Check Conda minor version
- if [ "$CONDA_VERSION_MINOR" -gt 4 ]
+ # Look for conda.sh file
+ if [ -f "/opt/conda/$CONDA_SH" ]
then
- if [ -f "$CONDA_PREFIX_1$CONDA_SH" ]
- then
- source "$CONDA_PREFIX_1$CONDA_SH"
- elif [ -f "$CONDA_PREFIX$CONDA_SH" ]
- then
- source "$CONDA_PREFIX$CONDA_SH"
- else
- echo -ne "${RED}ERROR: Could not find $CONDA_SH in \$CONDA_PREFIX.${NC}\n"
- echo -ne "${RED}Activate the base/root Conda environment and try again.${NC}\n"
- exit 1
- fi
- CONDA_ACTIVATE="conda activate"
- CONDA_DEACTIVATE="conda deactivate"
+ source "/opt/conda/$CONDA_SH"
+ elif [ -f "$CONDA_PREFIX$CONDA_SH" ]
+ then
+ source "$CONDA_PREFIX$CONDA_SH"
else
+ echo -ne "${RED}ERROR: Could not find $CONDA_SH in /opt/conda or \$CONDA_PREFIX.${NC}\n"
+ echo -ne "${RED}Activate the base/root Conda environment and try again.${NC}\n"
+ exit 1
+ fi
+ # Set environment activation command
+ if [ "$USE_CONDA_SOURCE" == TRUE ]
+ then
CONDA_ACTIVATE="source activate"
CONDA_DEACTIVATE="source deactivate"
+ else
+ CONDA_ACTIVATE="conda activate"
+ CONDA_DEACTIVATE="conda deactivate"
fi
+
}
# Check if a binary executable is already installed in the conda environment
@@ -256,6 +184,14 @@ check_binary2() {
echo ""
}
+# Check the environment name
+check_env_name() {
+if [ "$ENV_DEV" == TRUE ]
+then
+ ENV_NAME='shapepipe-dev'
+fi
+}
+
# Check if a python site-package is installed correctly in the conda environment
check_site_pkg() {
if compgen -G "$CONDA_PREFIX/lib/python3.*/site-packages/$1*" > /dev/null
@@ -290,8 +226,6 @@ start() {
# Function to report package versions
packages() {
- check_binary2 $sex_bin "SExtractor" $sex_version $INSTALL_SEX
- check_binary2 $psfex_bin "PSFEx" $psfex_version $INSTALL_PSFEX
check_binary2 $ww_bin "WeightWatcher" $ww_version $INSTALL_WW
check_binary2 $cdsclient_bin "CDSclient" $cdsclient_version $INSTALL_CDSCLIENT
check_binary2 $mpi_bin "MPI" $mpi_version $USE_MPI $MPI_ROOT
@@ -332,8 +266,6 @@ package_report() {
then
activate_shapepipe
fi
- INSTALL_SEX=FALSE
- INSTALL_PSFEX=FALSE
INSTALL_WW=FALSE
INSTALL_CDSCLIENT=FALSE
USE_MPI=FALSE
@@ -341,7 +273,9 @@ package_report() {
echo 'Package Report'
echo ''
packages
- python -m piplist
+ echo 'Python Package Check List:'
+ echo ''
+ site-packages
echo ''
exit_code
}
@@ -381,8 +315,6 @@ setup() {
check_status 'Operating System:' $SYSOS
check_status 'Conda Version:' $CONDA_VERSION
check_status 'Build Conda Environment:' $BUILD_ENV $ENV_NAME
- check_status 'Install SExtractor:' $INSTALL_SEX
- check_status 'Install PSFEx:' $INSTALL_PSFEX
check_status 'Install WeightWatcher:' $INSTALL_WW
check_status 'Install CDSclient:' $INSTALL_CDSCLIENT
check_status 'Use MPI:' $USE_MPI $MPI_ROOT
@@ -408,6 +340,7 @@ astromatic_setup() {
# Function to uninstall ShapePipe and dependencies
uninstall() {
+ check_env_name
read -p "Uninstall $ENV_NAME environment [y/N]: " response
response=${response:-n}
if [ $response == "y" ]
@@ -463,12 +396,12 @@ Options:\n
\t--uninstall\t uninstall ShapePipe\n
\t--pipe-dir\t set the path to the ShapePipe base directory (default is \$PWD)\n
\t--build-dir\t set the path to the ShapePipe build (default is \$PWD/build)\n
-\t--env-name\t set the name of the conda environment (default is shapepipe)\n
+\t--env-name\t set the name of the Conda environment (default is shapepipe)\n
+\t--env-dev\t use the developers Conda environment instead of the standard production environment\n
+\t--use-conda-source\t use 'conda source' instead of the default 'conda activate' to activate the shapepipe environment\n
\t--develop\t option to install additional development packages\n
\t--vos\t\t option to install virtual observatory software\n
\t--no-env\t do not build Conda environment\n
-\t--no-sex\t do not build SExtractor\n
-\t--no-psfex\t do not build PSFEx\n
\t--no-ww\t\t do not build WeightWatcher\n
\t--no-cds\t do not build CDSclient\n
\t--no-exe\t do not build any system executables\n\n
@@ -525,6 +458,14 @@ case $i in
ENV_NAME="${i#*=}"
shift
;;
+ --env-dev)
+ ENV_DEV=TRUE
+ shift
+ ;;
+ --use-conda-source)
+ USE_CONDA_SOURCE=TRUE
+ shift
+ ;;
--develop)
DEVELOP=TRUE
shift
@@ -537,14 +478,6 @@ case $i in
BUILD_ENV=FALSE
shift
;;
- --no-sex)
- INSTALL_SEX=FALSE
- shift
- ;;
- --no-psfex)
- INSTALL_PSFEX=FALSE
- shift
- ;;
--no-ww)
INSTALL_WW=FALSE
shift
@@ -590,8 +523,6 @@ case $i in
shift
;;
--no-exe)
- INSTALL_SEX=FALSE
- INSTALL_PSFEX=FALSE
INSTALL_WW=FALSE
INSTALL_CDSCLIENT=FALSE
shift
@@ -613,6 +544,9 @@ start
# Check if conda is installed
check_conda
+# Check the Conda environment name
+check_env_name
+
# Find the operating system
case "$OSTYPE" in
darwin*)
@@ -645,7 +579,12 @@ setup
if [ "$BUILD_ENV" == TRUE ]
then
report_progress 'ShapePipe Environment'
- conda env create -f environment.yml -n $ENV_NAME
+ if [ "$ENV_DEV" == TRUE ]
+ then
+ conda env create -f environment-dev.yml -n $ENV_NAME
+ else
+ conda env create -f environment.yml -n $ENV_NAME
+ fi
fi
# Activate conda environment
@@ -716,37 +655,6 @@ fi
# BUILD EXTERNAL EXECUTABLES
##############################################################################
-# Build SExtractor
-if [ "$INSTALL_SEX" == TRUE ] && check_binary $sex_bin
-then
- report_progress 'SExtractor'
- conda install -n $ENV_NAME -c conda-forge "fftw==${fftw_ver}" -y
- download_package $sex_url $sex_tar
- if [ "$use_atlas" == TRUE ]
- then
- build_sex_atlas $sex_dir
- else
- conda install -n $ENV_NAME -c conda-forge "openblas==${openblas_ver}" -y
- build_sex_blas $sex_dir
- fi
-fi
-
-# Build PSFEx
-if [ "$INSTALL_PSFEX" == TRUE ] && check_binary $psfex_bin
-then
- report_progress 'PSFEx'
- conda install "libpng==${libpng_ver}" -y
- conda install -n $ENV_NAME -c conda-forge "fftw==${fftw_ver}" -y
- download_package $psfex_url $psfex_tar
- if [ "$use_atlas" == TRUE ]
- then
- build_psfex_atlas $psfex_dir
- else
- conda install -n $ENV_NAME -c conda-forge "openblas==${openblas_ver}" -y
- build_psfex_blas $psfex_dir
- fi
-fi
-
# Build WeightWatcher
if [ "$INSTALL_WW" == TRUE ] && check_binary $ww_bin
then
diff --git a/nsswitch.conf b/nsswitch.conf
new file mode 100644
index 000000000..22d8d9949
--- /dev/null
+++ b/nsswitch.conf
@@ -0,0 +1,62 @@
+#
+# /etc/nsswitch.conf
+#
+# An example Name Service Switch config file. This file should be
+# sorted with the most-used services at the beginning.
+#
+# The entry '[NOTFOUND=return]' means that the search for an
+# entry should stop if the search in the previous entry turned
+# up nothing. Note that if the search failed due to some other reason
+# (like no NIS server responding) then the search continues with the
+# next entry.
+#
+# Valid entries include:
+#
+# nisplus Use NIS+ (NIS version 3)
+# nis Use NIS (NIS version 2), also called YP
+# dns Use DNS (Domain Name Service)
+# files Use the local files
+# db Use the local database (.db) files
+# compat Use NIS on compat mode
+# hesiod Use Hesiod for user lookups
+# [NOTFOUND=return] Stop searching if not found so far
+#
+
+# To use db, put the "db" in front of "files" for entries you want to be
+# looked up first in the databases
+#
+# Example:
+#passwd: db files nisplus nis
+#shadow: db files nisplus nis
+#group: db files nisplus nis
+
+passwd: sss files
+shadow: files sss
+group: sss files
+
+#hosts: db files nisplus nis dns
+hosts: files dns
+
+# Example - obey only what nisplus tells us...
+#services: nisplus [NOTFOUND=return] files
+#networks: nisplus [NOTFOUND=return] files
+#protocols: nisplus [NOTFOUND=return] files
+#rpc: nisplus [NOTFOUND=return] files
+#ethers: nisplus [NOTFOUND=return] files
+#netmasks: nisplus [NOTFOUND=return] files
+
+bootparams: nisplus [NOTFOUND=return] files
+
+ethers: files
+netmasks: files
+networks: files
+protocols: files
+rpc: files
+services: files
+
+netgroup: nisplus
+
+publickey: nisplus
+
+automount: files nisplus
+aliases: files nisplus
diff --git a/scripts/jupyter/summary_run.ipynb b/scripts/jupyter/summary_run.ipynb
new file mode 100644
index 000000000..44f2f2545
--- /dev/null
+++ b/scripts/jupyter/summary_run.ipynb
@@ -0,0 +1,399 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "130112a4-f2ca-4d26-b884-d8b054676f9c",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "%load_ext autoreload\n",
+ "%autoreload 3\n",
+ "%reload_ext autoreload"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "id": "196beca5-10a1-4cf5-9462-be145167cc70",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [
+ {
+ "ename": "ModuleNotFoundError",
+ "evalue": "No module named 'shapepipe'",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
+ "Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mshapepipe\u001b[39;00m\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mshapepipe\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mutilities\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01msummary\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;241m*\u001b[39m\n",
+ "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'shapepipe'"
+ ]
+ }
+ ],
+ "source": [
+ "import shapepipe\n",
+ "from shapepipe.utilities.summary import *"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "id": "ca63c72d-212c-463e-a792-71efbac0b908",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Setting\n",
+ "patch = \"P7\"\n",
+ "\n",
+ "verbose = False"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "id": "dcb5604c-d61f-4705-8295-63875455cadb",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Load parameters\n",
+ "%run ~/shapepipe/scripts/python/summary_params_pre_v2"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "id": "e69b7dab-1fea-4fcc-a8d9-0720e1d628c3",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "Checking main directory = /arc/home/kilbinger/cosmostat/v2/pre_v2/psfex/P7\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Set job info for patch P7\n"
+ ]
+ }
+ ],
+ "source": [
+ "jobs, list_tile_IDs = set_jobs_v2_pre_v2(patch, verbose)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "id": "2c3a9dde-cf88-493f-926e-7ae7e8e10916",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Initialize runtime dicionary.\n",
+ "par_runtime = init_par_runtime(list_tile_IDs)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "id": "1e9c1487-3cec-4394-9fcf-c12e92a0f984",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# No effect in notebook\n",
+ "#print_par_runtime(par_runtime, verbose=verbose)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "id": "b7c63a22-ead1-4d6a-b081-a74ade515439",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "module expected found miss_expl missing uniq_miss fr_found\n",
+ "====================================================================================================\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Start program\n",
+ "job_data.print_stats_header()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "id": "4720ae18-0633-4646-b392-b1b24e0294c3",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ " (Job 1)\n",
+ "get_images_runner_run_1 462 462 0 0 0.0 100.0%\n",
+ "find_exposures_runner 231 231 0 0 0.0 100.0%\n",
+ "get_images_runner_run_2 537 0 0 537 179.0 0.0%\n"
+ ]
+ }
+ ],
+ "source": [
+ "for key in \"1\":\n",
+ " jobs[key].print_intro()\n",
+ " jobs[key].check_numbers(par_runtime=par_runtime, indices=[0, 1])\n",
+ "\n",
+ " all_exposures = get_all_exposures(jobs[key]._paths_in_dir[1], verbose=verbose)\n",
+ " par_runtime[\"n_exposures\"] = len(all_exposures)\n",
+ " par_runtime[\"list_exposures\"] = all_exposures\n",
+ "\n",
+ " jobs[key].check_numbers(par_runtime, indices=[2])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "id": "f149f404-64e7-4d92-8f54-f300ed620130",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Update runtime dictionary with numbers of exposures\n",
+ "par_runtime = update_par_runtime_after_find_exp(par_runtime, all_exposures)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "id": "78a9065f-8983-41cf-a34c-21892fc52dd2",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Get all keys after \"1\"\n",
+ "keys = sorted(jobs.keys(), key=int)\n",
+ "_ = keys.pop(0)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "id": "79e39954-1155-4ca3-b0b2-64bc5670db53",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ " (Job 2)\n",
+ "uncompress_fits_runner 1268 1268 0 0 0.0 100.0%\n",
+ "merge_headers_runner 0 0 0 0 0.0 100.0%\n",
+ "split_exp_runner 137940 137940 0 0 0.0 100.0%\n",
+ " (Job 4)\n",
+ "mask_runner 1268 1268 0 0 0.0 100.0%\n",
+ " (Job 8)\n",
+ "mask_runner 45600 45600 0 0 0.0 100.0%\n",
+ " (Job 16)\n",
+ "sextractor_runner 2536 2536 0 0 0.0 100.0%\n",
+ " (Job 32)\n",
+ "sextractor_runner 91200 91200 0 0 0.0 100.0%\n",
+ "setools_runner 91200 91032 0 168 84.0 99.8%\n",
+ "psfex_runner 91200 91032 0 168 84.0 99.8%\n",
+ " (Job 64)\n",
+ "psfex_interp_runner 1268 1268 0 0 0.0 100.0%\n",
+ "vignetmaker_runner_run_1 1268 1268 0 0 0.0 100.0%\n",
+ "spread_model_runner 1268 1268 0 0 0.0 100.0%\n",
+ "vignetmaker_runner_run_2 5072 5072 0 0 0.0 100.0%\n",
+ " (Job 128)\n",
+ "ngmix_runner 1268 1225 0 43 43.0 96.6%\n",
+ "ngmix_runner 1268 1216 0 52 52.0 95.9%\n",
+ "ngmix_runner 1268 1216 0 52 52.0 95.9%\n",
+ "ngmix_runner 1268 1217 0 51 51.0 96.0%\n",
+ "ngmix_runner 1268 1228 0 40 40.0 96.8%\n",
+ "ngmix_runner 1268 1216 0 52 52.0 95.9%\n",
+ "ngmix_runner 1268 1216 0 52 52.0 95.9%\n",
+ "ngmix_runner 1268 1216 0 52 52.0 95.9%\n",
+ " (Job 256)\n",
+ "merge_sep_cats_runner 1268 0 0 1268 1268.0 0.0%\n",
+ "make_cat_runner 1268 0 0 1268 1268.0 0.0%\n",
+ " (Job 1024)\n",
+ "psfex_interp_runner 45600 41132 0 4468 4468.0 90.2%\n"
+ ]
+ }
+ ],
+ "source": [
+ "for key in keys:\n",
+ " jobs[key].print_intro()\n",
+ " jobs[key].check_numbers(par_runtime=par_runtime)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 65,
+ "id": "b3d51a05-ecca-420b-b8b3-1fb2b1ec9fe3",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ " (Job 128)\n",
+ "ngmix_runner 1268 1267 0 1 1.0 99.9%\n",
+ "ngmix_runner 1268 1265 0 3 3.0 99.8%\n",
+ "ngmix_runner 1268 1267 0 1 1.0 99.9%\n",
+ "ngmix_runner 1268 1267 0 1 1.0 99.9%\n",
+ "ngmix_runner 1268 1267 0 1 1.0 99.9%\n",
+ "ngmix_runner 1268 1266 0 2 2.0 99.8%\n",
+ "ngmix_runner 1268 1268 0 0 0.0 100.0%\n",
+ "ngmix_runner 1268 1266 0 2 2.0 99.8%\n"
+ ]
+ }
+ ],
+ "source": [
+ "## Update some runs\n",
+ "for key in [\"128\"]:\n",
+ " jobs[key].print_intro()\n",
+ " jobs[key].check_numbers(par_runtime=par_runtime)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 64,
+ "id": "67b50a61-e3cc-4559-941d-f39c6a200294",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ " (Job 128)\n",
+ "ngmix_runner 1268 1267 0 1 1.0 99.9%\n",
+ "ngmix_runner 1268 1265 0 3 3.0 99.8%\n",
+ "ngmix_runner 1268 1267 0 1 1.0 99.9%\n",
+ "ngmix_runner 1268 1267 0 1 1.0 99.9%\n",
+ "ngmix_runner 1268 1267 0 1 1.0 99.9%\n",
+ "ngmix_runner 1268 1266 0 2 2.0 99.8%\n",
+ "ngmix_runner 1268 1268 0 0 0.0 100.0%\n",
+ "ngmix_runner 1268 1266 0 2 2.0 99.8%\n"
+ ]
+ }
+ ],
+ "source": [
+ "for key in [\"128\"]:\n",
+ " jobs[key].print_intro()\n",
+ " \n",
+ " \n",
+ " jobs[key].check_numbers(par_runtime=par_runtime)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "id": "affa8293-daf9-4d2b-9215-fe19f8e2c1e2",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "session = Session()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 36,
+ "id": "269496d1-cd89-4d13-a5e4-41b897669e22",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "ids = [session[\"id\"] for session in session.fetch(kind=\"headless\")]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 38,
+ "id": "80af8dff-98c7-4db4-8bcc-06936e1875cf",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [
+ {
+ "ename": "RuntimeError",
+ "evalue": "This event loop is already running",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m/tmp/ipykernel_69/559116804.py\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0msession\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdestroy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mids\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+ "\u001b[0;32m~/.local/lib/python3.7/site-packages/skaha/session.py\u001b[0m in \u001b[0;36mdestroy\u001b[0;34m(self, id)\u001b[0m\n\u001b[1;32m 264\u001b[0m \u001b[0marguments\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0;34m\"url\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mserver\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\"/\"\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 265\u001b[0m \u001b[0mloop\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mget_event_loop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 266\u001b[0;31m \u001b[0mresults\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mloop\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_until_complete\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mscale\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msession\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdelete\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0marguments\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 267\u001b[0m \u001b[0mresponses\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mDict\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbool\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 268\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mindex\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0midentity\u001b[0m \u001b[0;32min\u001b[0m \u001b[0menumerate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mid\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/opt/conda/lib/python3.7/asyncio/base_events.py\u001b[0m in \u001b[0;36mrun_until_complete\u001b[0;34m(self, future)\u001b[0m\n\u001b[1;32m 561\u001b[0m \"\"\"\n\u001b[1;32m 562\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_check_closed\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 563\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_check_runnung\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 564\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 565\u001b[0m \u001b[0mnew_task\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mfutures\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0misfuture\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfuture\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/opt/conda/lib/python3.7/asyncio/base_events.py\u001b[0m in \u001b[0;36m_check_runnung\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 521\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_check_runnung\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 522\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_running\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 523\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mRuntimeError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'This event loop is already running'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 524\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mevents\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_running_loop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 525\u001b[0m raise RuntimeError(\n",
+ "\u001b[0;31mRuntimeError\u001b[0m: This event loop is already running"
+ ]
+ }
+ ],
+ "source": [
+ "session.destroy(ids[0])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "66a3ed14-8aaf-4028-b933-10ecb7376d68",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.11.9"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/scripts/python/canfar_avail_results.py b/scripts/python/canfar_avail_results.py
index c44c90e31..62fbf0564 100755
--- a/scripts/python/canfar_avail_results.py
+++ b/scripts/python/canfar_avail_results.py
@@ -38,10 +38,10 @@ def params_default():
"""
p_def = cfis.param(
- input_IDs = '.',
- input_path = 'vos:cfis/cosmostat/kilbinger/results',
- psf = 'mccd',
- extension = 'tgz',
+ input_IDs=".",
+ input_path="vos:cfis/cosmostat/kilbinger/results",
+ psf="mccd",
+ extension="tgz",
)
return p_def
@@ -63,25 +63,78 @@ def parse_options(p_def):
Command line string
"""
- usage = "%prog [OPTIONS]"
+ usage = "%prog [OPTIONS]"
parser = OptionParser(usage=usage)
# I/O
- parser.add_option('-i', '--input_IDs', dest='input_IDs', type='string', default=p_def.input_IDs,
- help='input tile ID file(s) or directory path, default=\'{}\''.format(p_def.input_IDs))
- parser.add_option('', '--input_path', dest='input_path', type='string', default=p_def.input_path,
- help='input path, local or vos url, default=\'{}\''.format(p_def.input_path))
- parser.add_option('-o', '--output_not_avail', dest='output_not_avail', type='string',
- help='output file for not-available IDs, default no output')
-
- parser.add_option('-p', '--psf', dest='psf', type='string', default=p_def.psf,
- help='PSF model, one in [\'psfex\'|\'mccd\'], default=\'{}\''.format(p_def.psf))
-
- parser.add_option('-f', '--final_only', dest='final_only', action='store_true', help='only check final catalogues')
- parser.add_option('-m', '--mask_only', dest='mask_only', action='store_true', help='only check mask files (pipeline_flag)')
- parser.add_option('-x', '--extension', dest='extension', type='string', default=p_def.extension,
- help=f'file extension, default=\'{p_def.extension}\'')
- parser.add_option('-v', '--verbose', dest='verbose', action='store_true', help='verbose output')
+ parser.add_option(
+ "-i",
+ "--input_IDs",
+ dest="input_IDs",
+ type="string",
+ default=p_def.input_IDs,
+ help="input tile ID file(s) or directory path, default='{}'".format(
+ p_def.input_IDs
+ ),
+ )
+ parser.add_option(
+ "",
+ "--input_path",
+ dest="input_path",
+ type="string",
+ default=p_def.input_path,
+ help="input path, local or vos url, default='{}'".format(
+ p_def.input_path
+ ),
+ )
+ parser.add_option(
+ "-o",
+ "--output_not_avail",
+ dest="output_not_avail",
+ type="string",
+ help="output file for not-available IDs, default no output",
+ )
+
+ parser.add_option(
+ "-p",
+ "--psf",
+ dest="psf",
+ type="string",
+ default=p_def.psf,
+ help="PSF model, one in ['psfex'|'mccd'], default='{}'".format(
+ p_def.psf
+ ),
+ )
+
+ parser.add_option(
+ "-f",
+ "--final_only",
+ dest="final_only",
+ action="store_true",
+ help="only check final catalogues",
+ )
+ parser.add_option(
+ "-m",
+ "--mask_only",
+ dest="mask_only",
+ action="store_true",
+ help="only check mask files (pipeline_flag)",
+ )
+ parser.add_option(
+ "-x",
+ "--extension",
+ dest="extension",
+ type="string",
+ default=p_def.extension,
+ help=f"file extension, default='{p_def.extension}'",
+ )
+ parser.add_option(
+ "-v",
+ "--verbose",
+ dest="verbose",
+ action="store_true",
+ help="verbose output",
+ )
options, args = parser.parse_args()
@@ -102,12 +155,12 @@ def check_options(options):
Result of option check. False if invalid option value.
"""
- if options.psf not in ['psfex', 'mccd']:
- print('Invalid PSF model \'{}\''.format(options.psf))
+ if options.psf not in ["psfex", "mccd"]:
+ print("Invalid PSF model '{}'".format(options.psf))
return False
if options.final_only and options.mask_only:
- print('One one of the options \'-f\' or \'-m\' can be given')
+ print("One one of the options '-f' or '-m' can be given")
return False
return True
@@ -163,25 +216,32 @@ def read_input_files(input_path, verbose=False):
"""
if os.path.isdir(input_path):
- input_files = glob.glob('{}/*'.format(input_path))
+ input_files = glob.glob("{}/*".format(input_path))
else:
- input_files = cfis.my_string_split(input_path, stop=True, sep=' ')
+ input_files = cfis.my_string_split(input_path, stop=True, sep=" ")
ID_files = []
for f in input_files:
if os.path.isdir(f):
if verbose:
- print('Skipping directory \'{}\''.format(f))
+ print("Skipping directory '{}'".format(f))
else:
ID_files.append(f)
if verbose:
- print('{} input files found'.format(len(ID_files)))
+ print("{} input files found".format(len(ID_files)))
return ID_files
-def check_results(ID_files, input_path, result_base_names, n_complete, extension, verbose=False):
+def check_results(
+ ID_files,
+ input_path,
+ result_base_names,
+ n_complete,
+ extension,
+ verbose=False,
+):
"""Count the number of result files uploaded to vos for each input ID file.
Parameters
@@ -207,11 +267,11 @@ def check_results(ID_files, input_path, result_base_names, n_complete, extension
IDs that are not available on vos
"""
- m = re.match('vos:', input_path)
+ m = re.match("vos:", input_path)
if m:
ls_tmp = dir_list(input_path)
else:
- ls_tmp = glob.glob(f'{input_path}/*')
+ ls_tmp = glob.glob(f"{input_path}/*")
ls_out = [os.path.basename(path) for path in ls_tmp]
n_found = {}
@@ -222,7 +282,7 @@ def check_results(ID_files, input_path, result_base_names, n_complete, extension
for ID_list in ID_files:
with open(ID_list) as f:
if verbose:
- print('Checking ID list file {}...'.format(ID_list))
+ print("Checking ID list file {}...".format(ID_list))
n_found[ID_list] = {}
n_IDs[ID_list] = 0
@@ -231,14 +291,14 @@ def check_results(ID_files, input_path, result_base_names, n_complete, extension
ID = line.rstrip()
n_found[ID_list][ID] = 0
- if extension == 'fits':
- ID_fname = ID.replace('.', '-')
- ID_fname = f'-{ID_fname}'
+ if extension == "fits":
+ ID_fname = ID.replace(".", "-")
+ ID_fname = f"-{ID_fname}"
else:
- ID_fname = f'_{ID}'
+ ID_fname = f"_{ID}"
# Count how many result files are available
for base in result_base_names:
- name = '{}{}.{}'.format(base, ID_fname, extension)
+ name = "{}{}.{}".format(base, ID_fname, extension)
if name in ls_out:
n_found[ID_list][ID] = n_found[ID_list][ID] + 1
n_IDs[ID_list] = n_IDs[ID_list] + 1
@@ -265,7 +325,14 @@ def output_summary(n_found, n_IDs, n_complete):
for ID_list in n_found.keys():
nf = sum(value == n_complete for value in n_found[ID_list].values())
- print('{}: {}/{} ({:.1f}%) complete'.format(os.path.basename(ID_list), nf, n_IDs[ID_list], nf/n_IDs[ID_list]*100))
+ print(
+ "{}: {}/{} ({:.1f}%) complete".format(
+ os.path.basename(ID_list),
+ nf,
+ n_IDs[ID_list],
+ nf / n_IDs[ID_list] * 100,
+ )
+ )
def output_IDs(ID_list, output):
@@ -279,7 +346,7 @@ def output_IDs(ID_list, output):
output file name
"""
- f = open(output, 'w')
+ f = open(output, "w")
for ID in ID_list:
print(ID, file=f)
f.close()
@@ -301,52 +368,57 @@ def main(argv=None):
# Save calling command
cfis.log_command(argv)
if param.verbose:
- cfis.log_command(argv, name='sys.stdout')
-
+ cfis.log_command(argv, name="sys.stdout")
### Start main program ###
if param.verbose:
- print('Start of program {}'.format(os.path.basename(argv[0])))
+ print("Start of program {}".format(os.path.basename(argv[0])))
ID_files = read_input_files(param.input_IDs, verbose=param.verbose)
if param.final_only:
- result_base_names = ['final_cat']
+ result_base_names = ["final_cat"]
elif param.mask_only:
- result_base_names = ['pipeline_flag']
+ result_base_names = ["pipeline_flag"]
else:
result_base_names = []
types = [
- 'final_cat',
- 'pipeline_flag',
- 'logs',
- 'setools_mask',
- 'setools_stat',
- 'setools_plot',
+ "final_cat",
+ "pipeline_flag",
+ "logs",
+ "setools_mask",
+ "setools_stat",
+ "setools_plot",
]
for t in types:
result_base_names.append(t)
- if param.psf == 'psfex':
- result_base_names.append('psfex_interp_exp')
- elif param.psf == 'mccd':
- result_base_names.append('mccd_fit_val_runner')
+ if param.psf == "psfex":
+ result_base_names.append("psfex_interp_exp")
+ elif param.psf == "mccd":
+ result_base_names.append("mccd_fit_val_runner")
n_complete = len(result_base_names)
- n_found, n_IDs, IDs_not_avail = check_results(ID_files, param.input_path, result_base_names, n_complete, param.extension, verbose=param.verbose)
+ n_found, n_IDs, IDs_not_avail = check_results(
+ ID_files,
+ param.input_path,
+ result_base_names,
+ n_complete,
+ param.extension,
+ verbose=param.verbose,
+ )
output_summary(n_found, n_IDs, n_complete)
if param.output_not_avail:
output_IDs(IDs_not_avail, param.output_not_avail)
-
### End main program
if param.verbose:
- print('End of program {}'.format(os.path.basename(argv[0])))
+ print("End of program {}".format(os.path.basename(argv[0])))
return 0
diff --git a/scripts/python/canfar_run_analyse.py b/scripts/python/canfar_run_analyse.py
index f43ef69bc..72da60474 100755
--- a/scripts/python/canfar_run_analyse.py
+++ b/scripts/python/canfar_run_analyse.py
@@ -19,8 +19,7 @@
class param:
- """General class to store (default) variables
- """
+ """General class to store (default) variables"""
def __init__(self, **kwds):
self.__dict__.update(kwds)
@@ -46,7 +45,7 @@ def params_default():
"""
p_def = param(
- input_job = 'job_tile.sh',
+ input_job="job_tile.sh",
)
return p_def
@@ -68,16 +67,33 @@ def parse_options(p_def):
Command line string
"""
- usage = "%prog [OPTIONS]"
+ usage = "%prog [OPTIONS]"
parser = OptionParser(usage=usage)
# I/O
- parser.add_option('-i', '--input_job', dest='input_job', type='string', default=p_def.input_job,
- help='input job file, default=\'{}\''.format(p_def.input_job))
- parser.add_option('-o', '--output_fail', dest='output_fail', type='string',
- help='output file for failed jobs, none if not given')
+ parser.add_option(
+ "-i",
+ "--input_job",
+ dest="input_job",
+ type="string",
+ default=p_def.input_job,
+ help="input job file, default='{}'".format(p_def.input_job),
+ )
+ parser.add_option(
+ "-o",
+ "--output_fail",
+ dest="output_fail",
+ type="string",
+ help="output file for failed jobs, none if not given",
+ )
- parser.add_option('-v', '--verbose', dest='verbose', action='store_true', help='verbose output')
+ parser.add_option(
+ "-v",
+ "--verbose",
+ dest="verbose",
+ action="store_true",
+ help="verbose output",
+ )
options, args = parser.parse_args()
@@ -159,61 +175,83 @@ def update_param(p_def, options):
def get_status(tile_num):
- base_name = 'log_canfar_sp_'
- #base_name = 'log_sp_tile_'
+ base_name = "log_canfar_sp_"
+ # base_name = 'log_sp_tile_'
- log_name = '{}{}.log'.format(base_name, tile_num)
- out_name = '{}{}.out'.format(base_name, tile_num)
- err_name = '{}{}.err'.format(base_name, tile_num)
+ log_name = "{}{}.log".format(base_name, tile_num)
+ out_name = "{}{}.out".format(base_name, tile_num)
+ err_name = "{}{}.err".format(base_name, tile_num)
- status = res_unk, 'unknown status'
+ status = res_unk, "unknown status"
if not os.path.exists(log_name):
- status = res_wait, 'waiting for submission'
+ status = res_wait, "waiting for submission"
else:
if os.path.exists(out_name):
final_cat_found = False
with open(out_name) as out_file:
for line in out_file:
- m = re.match('Upload.*final_cat_*', line)
+ m = re.match("Upload.*final_cat_*", line)
if m:
final_cat_found = True
- status = res_ok, 'successful upload of final_cat'
+ status = res_ok, "successful upload of final_cat"
# TODO: check next line for upload success
if final_cat_found == False:
- status = res_unk, 'Failed before final_cat'
+ status = res_unk, "Failed before final_cat"
# Look for known errors in error log file
with open(err_name) as err_file:
for line_err in err_file:
- mm = re.search('NodeNotFound', line_err)
+ mm = re.search("NodeNotFound", line_err)
if mm:
- status = status + (fail_vos_not_found, 'vos file not found')
+ status = status + (
+ fail_vos_not_found,
+ "vos file not found",
+ )
break
- mm = re.search('Empty or corrupt FITS file', line_err)
+ mm = re.search("Empty or corrupt FITS file", line_err)
if mm:
- status = status + (fail_corrupt_fits, 'corrupt input FITS file')
+ status = status + (
+ fail_corrupt_fits,
+ "corrupt input FITS file",
+ )
break
- mm = re.search('ERROR:: HTTPSConnectionPool.*Max retries', line_err)
+ mm = re.search(
+ "ERROR:: HTTPSConnectionPool.*Max retries", line_err
+ )
if mm:
- status = status + (fail_time_out, 'vos time out')
+ status = status + (fail_time_out, "vos time out")
break
- mm = re.search('ERROR:: __str__ returned non-string', line_err)
+ mm = re.search(
+ "ERROR:: __str__ returned non-string", line_err
+ )
if mm:
- status = status + (fail_connection, 'Connection/HTTP error')
+ status = status + (
+ fail_connection,
+ "Connection/HTTP error",
+ )
break
- mm = re.search('ERROR:: 503 Server Error', line_err)
+ mm = re.search("ERROR:: 503 Server Error", line_err)
if mm:
- status = status + (fail_server, 'server connection error')
+ status = status + (
+ fail_server,
+ "server connection error",
+ )
break
- mm = re.search('ERROR:: \[Errno 14\] vos', line_err)
+ mm = re.search("ERROR:: \[Errno 14\] vos", line_err)
if mm:
- status = status + (fail_transient, 'TransientException')
+ status = status + (
+ fail_transient,
+ "TransientException",
+ )
break
- mm = re.search('Connection aborted', line_err)
+ mm = re.search("Connection aborted", line_err)
if mm:
- status = status + (fail_vos_no_resp, 'vos no response')
+ status = status + (
+ fail_vos_no_resp,
+ "vos no response",
+ )
break
if len(status) == 2:
@@ -222,53 +260,59 @@ def get_status(tile_num):
module_last = None
with open(out_name) as out_file:
for line in out_file:
- mmm = re.search('\- Module: (.*)', line)
+ mmm = re.search("\- Module: (.*)", line)
if mmm:
module_last = mmm[1]
- mmm = re.search('A total of (\d+) errors were recorded.', line)
+ mmm = re.search(
+ "A total of (\d+) errors were recorded.", line
+ )
if mmm and int(mmm[1]) != 0:
- status = status + (fail_res_err_mod, '{} errors recorded, last module was {}'.format(mmm[1], module_last))
+ status = status + (
+ fail_res_err_mod,
+ "{} errors recorded, last module was {}".format(
+ mmm[1], module_last
+ ),
+ )
break
if len(status) == 2:
- status = status + (fail_unknown, 'unknown error')
-
+ status = status + (fail_unknown, "unknown error")
else:
log_file = open(log_name)
lines = log_file.readlines()
log_file.close()
for line in lines:
- if re.match('.*aborted', line):
- status = res_abort, 'job aborted by user'
+ if re.match(".*aborted", line):
+ status = res_abort, "job aborted by user"
return status
for line in lines:
- if re.match('.*executing', line):
- status = res_wait, 'job running'
+ if re.match(".*executing", line):
+ status = res_wait, "job running"
return status
- status = res_subm, 'job submitted, not started yet'
+ status = res_subm, "job submitted, not started yet"
return status
def output(status):
- print('## Issues')
+ print("## Issues")
n_issue = 0
for tile_num in sorted(status.keys()):
if status[tile_num][0] == res_noout or status[tile_num][0] == res_unk:
- print(' ', tile_num, status[tile_num])
+ print(" ", tile_num, status[tile_num])
n_issue = n_issue + 1
if n_issue == 0:
- print(' none')
+ print(" none")
hist = Counter(status.values())
- print('## Summary')
- print('# Nb: status (code)')
+ print("## Summary")
+ print("# Nb: status (code)")
for s in hist:
- print('{:6d}: {} ({})'.format(hist[s], s[1], int(s[0])), end='')
+ print("{:6d}: {} ({})".format(hist[s], s[1], int(s[0])), end="")
if len(s) == 4:
- print('; {} ({})'.format(s[3], int(s[2])), end='')
+ print("; {} ({})".format(s[3], int(s[2])), end="")
print()
@@ -276,11 +320,14 @@ def output_failed(output_fail, status):
if output_fail:
- with open(output_fail, 'w') as f_out:
+ with open(output_fail, "w") as f_out:
for tile_num in status.keys():
- if status[tile_num][0] == res_noout or status[tile_num][0] == res_unk:
+ if (
+ status[tile_num][0] == res_noout
+ or status[tile_num][0] == res_unk
+ ):
print(tile_num, file=f_out)
-
+
def main(argv=None):
@@ -295,7 +342,6 @@ def main(argv=None):
param = update_param(p_def, options)
-
### Start main program ###
job_tile_path = param.input_job
@@ -303,7 +349,7 @@ def main(argv=None):
status = {}
with open(job_tile_path) as job_file:
for line in job_file:
- m = re.match('(\d{3}\.\d{3})', line)
+ m = re.match("(\d{3}\.\d{3})", line)
if m:
tile_num = m[0]
diff --git a/scripts/python/cfis_field_select.py b/scripts/python/cfis_field_select.py
index efe961ca7..08f79d804 100755
--- a/scripts/python/cfis_field_select.py
+++ b/scripts/python/cfis_field_select.py
@@ -51,17 +51,23 @@ def get_images_used_in_tiles(images, band, image_type):
try:
hdu = fits.open(img.name)
- hist = hdu[0].header['HISTORY']
+ hist = hdu[0].header["HISTORY"]
except:
- raise cfis.CfisError('Error while reading tile FITS file {}'.format(img.name))
+ raise cfis.CfisError(
+ "Error while reading tile FITS file {}".format(img.name)
+ )
for h in hist:
- temp = h.split(' ')
+ temp = h.split(" ")
- pattern = r'(.*)p\.{1}.*'
+ pattern = r"(.*)p\.{1}.*"
m = re.search(pattern, temp[3])
if not m:
- raise cfis.CfisError('re match \'{}\' failed for filename \'{}\''.format(pattern, temp[3]))
+ raise cfis.CfisError(
+ "re match '{}' failed for filename '{}'".format(
+ pattern, temp[3]
+ )
+ )
exp_name = m.group(1)
exp_list.append(exp_name)
@@ -71,7 +77,9 @@ def get_images_used_in_tiles(images, band, image_type):
return exp_list_uniq
-def get_coord_at_image(number, band, image_type, images, no_cuts=False, verbose=False):
+def get_coord_at_image(
+ number, band, image_type, images, no_cuts=False, verbose=False
+):
"""Return coordinate of image with given number.
Parameters
@@ -97,18 +105,22 @@ def get_coord_at_image(number, band, image_type, images, no_cuts=False, verbose=
img_found = None
- if image_type == 'tile':
+ if image_type == "tile":
nix, niy = cfis.my_string_split(number, num=2, stop=True)
tile_name = cfis.get_tile_name(nix, niy, band)
if verbose == True:
- print('Looking for coordinates for tile with numbers ({},{})'.format(nix, niy))
+ print(
+ "Looking for coordinates for tile with numbers ({},{})".format(
+ nix, niy
+ )
+ )
- ra, dec = cfis.get_tile_coord_from_nixy(nix, niy)
+ ra, dec = cfis.get_tile_coord_from_nixy(nix, niy)
img_found = cfis.image(tile_name, ra, dec)
- elif image_type == 'exposure':
- ra = []
+ elif image_type == "exposure":
+ ra = []
dec = []
for img in images:
m = re.findall(number, img.name)
@@ -117,18 +129,19 @@ def get_coord_at_image(number, band, image_type, images, no_cuts=False, verbose=
img_found = img
else:
- raise cfis.CfisError('Image type \'{}\' not implemented yet'.format(image_type))
+ raise cfis.CfisError(
+ "Image type '{}' not implemented yet".format(image_type)
+ )
return img_found
-
def test_tile_number():
- #ra = Angle(180, unit=units.deg)
- #dec = Angle(35, unit=units.deg)
- ra = Angle('10:44:00.0 hours')
- dec = Angle('30:00:00 degrees')
+ # ra = Angle(180, unit=units.deg)
+ # dec = Angle(35, unit=units.deg)
+ ra = Angle("10:44:00.0 hours")
+ dec = Angle("30:00:00 degrees")
print(ra, dec)
print(ra.deg, dec.deg)
@@ -153,11 +166,11 @@ def params_default():
"""
p_def = cfis.param(
- input = '.',
- input_format = 'full',
- mode = 'c',
- band = 'r',
- image_type = 'tile',
+ input=".",
+ input_format="full",
+ mode="c",
+ band="r",
+ image_type="tile",
)
return p_def
@@ -179,53 +192,147 @@ def parse_options(p_def):
Command line string
"""
- usage = "%prog [OPTIONS]"
+ usage = "%prog [OPTIONS]"
parser = OptionParser(usage=usage)
# I/O
- parser.add_option('-i', '--input', dest='input', type='string', default=p_def.input,
- help='input image list, can be ascii file or directory path')
- parser.add_option('-c', '--column', dest='col', type='string', default=None,
- help='column name if input is file, default=file has only one column)')
- parser.add_option('', '--input_format', dest='input_format', type='string',
- default=p_def.input_format,
- help='input format, one of \'full\', \'ID_only\', default=\'{}\''.format(p_def.input_format))
- parser.add_option('-o', '--outbase', dest='outbase', type='string', default=None,
- help='output file name base (\'.txt\' is added), default=stdout')
- parser.add_option('', '--plot', dest='plot', action='store_true',
- help='create plots')
- parser.add_option('', '--out_base_name', dest='out_base_name', action='store_true',
- help='output base names, not entire path if input is directory')
- parser.add_option('', '--out_name_only', dest='out_name_only', action='store_true',
- help='output only file names, not coordinates and metainfo')
- parser.add_option('', '--out_ID_only', dest='out_ID_only', action='store_true',
- help='output only file IDs, not full file names')
- parser.add_option('', '--interactive', dest='interactive', action='store_true',
- help='interactive mode (showing plots, recommended for call from jupyer notebook)')
- parser.add_option('-s', '--short', dest='short', action='store_true', help='short output')
+ parser.add_option(
+ "-i",
+ "--input",
+ dest="input",
+ type="string",
+ default=p_def.input,
+ help="input image list, can be ascii file or directory path",
+ )
+ parser.add_option(
+ "-c",
+ "--column",
+ dest="col",
+ type="string",
+ default=None,
+ help="column name if input is file, default=file has only one column)",
+ )
+ parser.add_option(
+ "",
+ "--input_format",
+ dest="input_format",
+ type="string",
+ default=p_def.input_format,
+ help="input format, one of 'full', 'ID_only', default='{}'".format(
+ p_def.input_format
+ ),
+ )
+ parser.add_option(
+ "-o",
+ "--outbase",
+ dest="outbase",
+ type="string",
+ default=None,
+ help="output file name base ('.txt' is added), default=stdout",
+ )
+ parser.add_option(
+ "", "--plot", dest="plot", action="store_true", help="create plots"
+ )
+ parser.add_option(
+ "",
+ "--out_base_name",
+ dest="out_base_name",
+ action="store_true",
+ help="output base names, not entire path if input is directory",
+ )
+ parser.add_option(
+ "",
+ "--out_name_only",
+ dest="out_name_only",
+ action="store_true",
+ help="output only file names, not coordinates and metainfo",
+ )
+ parser.add_option(
+ "",
+ "--out_ID_only",
+ dest="out_ID_only",
+ action="store_true",
+ help="output only file IDs, not full file names",
+ )
+ parser.add_option(
+ "",
+ "--interactive",
+ dest="interactive",
+ action="store_true",
+ help="interactive mode (showing plots, recommended for call from jupyer notebook)",
+ )
+ parser.add_option(
+ "-s", "--short", dest="short", action="store_true", help="short output"
+ )
# Job control
- parser.add_option('', '--no_cuts', dest='no_cuts', action='store_true',
- help='output all exposures, no cuts (default: cut short and invalid exposures)')
+ parser.add_option(
+ "",
+ "--no_cuts",
+ dest="no_cuts",
+ action="store_true",
+ help="output all exposures, no cuts (default: cut short and invalid exposures)",
+ )
# Field and image options
- parser.add_option('-b', '--band', dest='band', type='string', default=p_def.band,
- help='band, one of \'r\' (default)|\'u\'')
- parser.add_option('-t', '--type', dest='image_type', type='string', default=p_def.image_type,
- help='image type, one of \'tile\' (default)|\'weight\'|\'weight.fz\'|\'exposure\'|\'exposure_weight\''
- '|\'exposure_weight.fz\'|\'exposure_flag\'|\'exposure_flag.fz\'|\'cat\'')
-
- parser.add_option('', '--coord', dest='coord', type='string', default=None,
- help='(white-space or \'_\' separated) string of input coordinates, as astropy.coordinates.Angle')
- parser.add_option('', '--number', dest='number', type='string', default=None,
- help='input image number')
- parser.add_option('', '--area', dest='area', type='string', default=None,
- help='area corner coordinates ra0_dec0_ra1_dec1')
- parser.add_option('', '--tile', dest='tile', action='store_true',
- help='return exposures used in input tile(s)')
+ parser.add_option(
+ "-b",
+ "--band",
+ dest="band",
+ type="string",
+ default=p_def.band,
+ help="band, one of 'r' (default)|'u'",
+ )
+ parser.add_option(
+ "-t",
+ "--type",
+ dest="image_type",
+ type="string",
+ default=p_def.image_type,
+ help="image type, one of 'tile' (default)|'weight'|'weight.fz'|'exposure'|'exposure_weight'"
+ "|'exposure_weight.fz'|'exposure_flag'|'exposure_flag.fz'|'cat'",
+ )
+
+ parser.add_option(
+ "",
+ "--coord",
+ dest="coord",
+ type="string",
+ default=None,
+ help="(white-space or '_' separated) string of input coordinates, as astropy.coordinates.Angle",
+ )
+ parser.add_option(
+ "",
+ "--number",
+ dest="number",
+ type="string",
+ default=None,
+ help="input image number",
+ )
+ parser.add_option(
+ "",
+ "--area",
+ dest="area",
+ type="string",
+ default=None,
+ help="area corner coordinates ra0_dec0_ra1_dec1",
+ )
+ parser.add_option(
+ "",
+ "--tile",
+ dest="tile",
+ action="store_true",
+ help="return exposures used in input tile(s)",
+ )
# Monitoring
- parser.add_option('-v', '--verbose', dest='verbose', action='store_true', help='verbose output')
+ parser.add_option(
+ "-v",
+ "--verbose",
+ dest="verbose",
+ action="store_true",
+ help="verbose output",
+ )
options, args = parser.parse_args()
@@ -246,34 +353,51 @@ def check_options(options):
Result of option check. False if invalid option value.
"""
- if int(options.number != None) + int(options.coord != None) \
- + int(options.area != None) + int(options.tile != None) > 1:
- raise cfis.CfisError('Only one option out of \'--number\', \'--coord\', \'--area\', \'--tile\' can be given')
-
- if options.image_type != 'exposure' and options.no_cuts == True:
- raise cfis.CfisError('option \'--no_cuts\' only possible for image_type=exposure')
-
- if options.input in ['{}.txt'.format(options.outbase), '{}.pdf',format(options.outbase)]:
- raise cfis.CfisError('Output base same as input, latter will be overwritten!')
-
- if options.input_format not in ['full', 'ID_only']:
- raise cfis.CfisError('input_format needs to be one of \'fulll\', \'ID_only\'')
-
- see_help = 'See option \'-h\' for help.'
+ if (
+ int(options.number != None)
+ + int(options.coord != None)
+ + int(options.area != None)
+ + int(options.tile != None)
+ > 1
+ ):
+ raise cfis.CfisError(
+ "Only one option out of '--number', '--coord', '--area', '--tile' can be given"
+ )
+
+ if options.image_type != "exposure" and options.no_cuts == True:
+ raise cfis.CfisError(
+ "option '--no_cuts' only possible for image_type=exposure"
+ )
+
+ if options.input in [
+ "{}.txt".format(options.outbase),
+ "{}.pdf",
+ format(options.outbase),
+ ]:
+ raise cfis.CfisError(
+ "Output base same as input, latter will be overwritten!"
+ )
+
+ if options.input_format not in ["full", "ID_only"]:
+ raise cfis.CfisError(
+ "input_format needs to be one of 'fulll', 'ID_only'"
+ )
+
+ see_help = "See option '-h' for help."
return True
def update_param(p_def, options):
"""Return default parameter, updated and complemented according to options.
-
+
Parameters
----------
p_def: class param
parameter values
optiosn: tuple
command line options
-
+
Returns
-------
param: class param
@@ -294,7 +418,7 @@ def update_param(p_def, options):
# Do extra stuff if necessary
if param.outbase is not None:
- param.fout = open('{}.txt'.format(param.outbase), 'w')
+ param.fout = open("{}.txt".format(param.outbase), "w")
else:
param.fout = sys.stdout
@@ -323,70 +447,117 @@ def run_mode(images, param):
if param.coord:
# Image number search: Return name of image(s) covering input coordinate
- images_found = cfis.find_image_at_coord(images, param.coord, param.band, param.image_type,
- no_cuts=param.no_cuts, input_format=param.input_format,
- verbose=param.verbose)
+ images_found = cfis.find_image_at_coord(
+ images,
+ param.coord,
+ param.band,
+ param.image_type,
+ no_cuts=param.no_cuts,
+ input_format=param.input_format,
+ verbose=param.verbose,
+ )
if len(images_found) > 0:
if not param.short:
images_found[0].print_header(file=param.fout)
for img in images_found:
- img.print(file=param.fout, base_name=param.out_base_name, name_only=param.out_name_only, ID_only=param.out_ID_only)
+ img.print(
+ file=param.fout,
+ base_name=param.out_base_name,
+ name_only=param.out_name_only,
+ ID_only=param.out_ID_only,
+ )
ex = 0
elif param.number:
# Coordinate search: Return coordinate covered by image with input number/file name
- img_found = get_coord_at_image(param.number, param.band, param.image_type, images, no_cuts=param.no_cuts, verbose=param.verbose)
+ img_found = get_coord_at_image(
+ param.number,
+ param.band,
+ param.image_type,
+ images,
+ no_cuts=param.no_cuts,
+ verbose=param.verbose,
+ )
if img_found != None:
if not param.short:
img_found.print_header(file=param.fout)
- img_found.print(file=param.fout, base_name=param.out_base_name, name_only=param.out_name_only, ID_only=param.out_ID_only)
+ img_found.print(
+ file=param.fout,
+ base_name=param.out_base_name,
+ name_only=param.out_name_only,
+ ID_only=param.out_ID_only,
+ )
ex = 0
else:
if param.verbose:
- print('No image found, try with --no_cuts', file=sys.stderr)
+ print("No image found, try with --no_cuts", file=sys.stderr)
elif param.area:
# Area search: Return images within input area
angles = cfis.get_Angle_arr(param.area, num=4, verbose=param.verbose)
- images_found = cfis.find_images_in_area(images, angles, param.band, param.image_type, no_cuts=param.no_cuts, verbose=param.verbose)
+ images_found = cfis.find_images_in_area(
+ images,
+ angles,
+ param.band,
+ param.image_type,
+ no_cuts=param.no_cuts,
+ verbose=param.verbose,
+ )
if len(images_found) > 0:
if not param.short:
images_found[0].print_header(file=param.fout)
for img in images_found:
- img.print(file=param.fout, base_name=param.out_base_name, name_only=param.out_name_only, ID_only=param.out_ID_only)
+ img.print(
+ file=param.fout,
+ base_name=param.out_base_name,
+ name_only=param.out_name_only,
+ ID_only=param.out_ID_only,
+ )
if param.plot == True:
if param.verbose == True:
- print('Creating plots')
- ra_c, dec_c, radius = cfis.plot_area(images_found, angles, param.image_type, param.outbase, param.interactive, show_numbers=True)
+ print("Creating plots")
+ ra_c, dec_c, radius = cfis.plot_area(
+ images_found,
+ angles,
+ param.image_type,
+ param.outbase,
+ param.interactive,
+ show_numbers=True,
+ )
if param.verbose:
- print('RA_c[deg] DEC_c[deg] radius[argmin] = {:.2f} {:.2f} {:.2f}'.format(ra_c.deg, dec_c.deg, radius*60))
+ print(
+ "RA_c[deg] DEC_c[deg] radius[argmin] = {:.2f} {:.2f} {:.2f}".format(
+ ra_c.deg, dec_c.deg, radius * 60
+ )
+ )
ex = 0
elif param.tile:
# Search exposures used in input tile(s)
- images_found = get_images_used_in_tiles(images, param.band, param.image_type)
+ images_found = get_images_used_in_tiles(
+ images, param.band, param.image_type
+ )
if len(images_found) > 0:
for img in images_found:
print(img, file=param.fout)
ex = 0
-
else:
- raise cfis.CfisError('One of \'--coord\', \'--number\', '
- '\'--area\', \'--tile\' needs to be specified')
+ raise cfis.CfisError(
+ "One of '--coord', '--number', "
+ "'--area', '--tile' needs to be specified"
+ )
return ex
def main(argv=None):
- """Main program.
- """
+ """Main program."""
-
# Set default parameters
p_def = params_default()
@@ -399,54 +570,57 @@ def main(argv=None):
param = update_param(p_def, options)
-
# Save calling command
cfis.log_command(argv)
if param.verbose:
- cfis.log_command(argv, name='sys.stdout')
-
+ cfis.log_command(argv, name="sys.stdout")
if param.verbose and not param.short:
- print('Start of program {}'.format(os.path.basename(argv[0])))
-
+ print("Start of program {}".format(os.path.basename(argv[0])))
### Start main program ###
if param.tile:
# For search of exposures in tiles, image list from directory needs to be tiles
- image_type = 'tile'
+ image_type = "tile"
else:
image_type = param.image_type
- images = cfis.get_image_list(param.input, param.band, image_type, col=param.col,
- input_format=param.input_format, verbose=param.verbose)
-
+ images = cfis.get_image_list(
+ param.input,
+ param.band,
+ image_type,
+ col=param.col,
+ input_format=param.input_format,
+ verbose=param.verbose,
+ )
# Check wether images have been found, if necessary
if param.number:
if images is None:
- raise cfis.CfisError('Input list file \'{}\' not found, neither '
- 'existing file nor directory'.format(param.input))
+ raise cfis.CfisError(
+ "Input list file '{}' not found, neither "
+ "existing file nor directory".format(param.input)
+ )
if len(images) == 0:
- raise cfis.CfisError('No corresponding image files found in input \'{}\''.format(param.input))
-
+ raise cfis.CfisError(
+ "No corresponding image files found in input '{}'".format(
+ param.input
+ )
+ )
# Run
ex = run_mode(images, param)
-
if param.outbase is not None:
param.fout.close()
-
### End main program
if param.verbose and not param.short:
- print('End of program {}'.format(os.path.basename(argv[0])))
+ print("End of program {}".format(os.path.basename(argv[0])))
return ex
-
if __name__ == "__main__":
sys.exit(main(sys.argv))
-
diff --git a/scripts/python/convert_psf_pix2world.py b/scripts/python/convert_psf_pix2world.py
new file mode 100755
index 000000000..dea99656b
--- /dev/null
+++ b/scripts/python/convert_psf_pix2world.py
@@ -0,0 +1,826 @@
+#! /usr/bin/env python3
+
+import sys
+import os
+import re
+import glob
+from tqdm import tqdm
+from joblib import Parallel, delayed
+import gc
+
+import numpy as np
+from astropy.io import fits
+import galsim
+
+from cs_util import args as cs_args
+from cs_util import logging
+
+
+def transform_shape(mom_list, jac):
+ """Transform Shape.
+
+ Transform shape (ellipticity and size) using a Jacobian.
+
+ Parameters
+ ----------
+ mom_list : list
+ input moment measurements; each list element contains
+ first and second ellipticity component and size
+ jac : galsim.JacobianWCS
+ Jacobian transformation matrix information
+
+ Returns
+ -------
+ list
+ transformed shape parameters, which are
+ first and second ellipticity component and size
+
+ """
+ scale, shear, theta, flip = jac.getDecomposition()
+
+ sig_tmp = mom_list[2] * scale
+ shape = galsim.Shear(g1=mom_list[0], g2=mom_list[1])
+ if flip:
+ # The following output is not observed
+ print("FLIP!")
+ shape = galsim.Shear(g1=-shape.g1, g2=shape.g2)
+ shape = galsim.Shear(g=shape.g, beta=shape.beta + theta)
+ shape = shear + shape
+
+ return shape.g1, shape.g2, sig_tmp
+
+
+class Loc2Glob(object):
+ r"""Change from local to global coordinates.
+
+ Class to pass from local coordinates to global coordinates under
+ CFIS (CFHT) MegaCam instrument. The geometrical informcation of the
+ instrument is encoded in this function.
+
+ Parameters
+ ----------
+ x_gap : int
+ Gap between the CCDs along the horizontal direction;
+ default is ``70`` (MegaCam value)
+ y_gap : int
+ Gap between the CCDs along the vertical direction;
+ Default is ``425`` (MegaCam value)
+ x_npix : int
+ Number of pixels per CCD along the horizontal direction;
+ default is ``2048`` (MegaCam value)
+ y_npix : int
+ Number of pixels per CCD along the vertical direction;
+ default to ``4612`` (MegaCam value)
+ ccd_tot : int
+ Total number of CCDs;
+ default to ``40`` (MegaCam value)
+
+ Notes
+ -----
+ This is the geometry of MegaCam. Watch out with the conventions ba,ab that means where
+ is the local coordinate system origin for each CCD.
+ For more info check out MegaCam's instrument webpage.
+
+ Examples
+ --------
+ 'COMMENT (North on top, East to the left)',
+ 'COMMENT --------------------------',
+ 'COMMENT ba ba ba ba ba ba ba ba ba',
+ 'COMMENT 00 01 02 03 04 05 06 07 08',
+ 'COMMENT --------------------------------',
+ 'COMMENT ba ba ba ba ba ba ba ba ba ba ba',
+ 'COMMENT 36 09 10 11 12 13 14 15 16 17 37',
+ 'COMMENT --------------*-----------------',
+ 'COMMENT 38 18 19 20 21 22 23 24 25 26 39',
+ 'COMMENT ab ab ab ab ab ab ab ab ab ab ab',
+ 'COMMENT --------------------------------',
+ 'COMMENT 27 28 29 30 31 32 33 34 35',
+ 'COMMENT ab ab ab ab ab ab ab ab ab',
+ 'COMMENT __________________________'
+ """
+
+ def __init__(
+ self, x_gap=70, y_gap=425, x_npix=2048, y_npix=4612, ccd_tot=40
+ ):
+ r"""Initialize with instrument geometry."""
+ self.x_gap = x_gap
+ self.y_gap = y_gap
+ self.x_npix = x_npix
+ self.y_npix = y_npix
+ self.ccd_tot = ccd_tot
+
+ def loc2glob_img_coord(self, ccd_n, x_coor, y_coor):
+ """loc2glob Img Coord.
+
+ Go from the local to the global img (pixel) coordinate system.
+
+ Global system with (0,0) in the intersection of ccds [12,13,21,22].
+
+ Parameters
+ ----------
+ ccd_n: int
+ CCD number of the considered positions
+ x_coor: float
+ Local coordinate system hotizontal value
+ y_coor: float
+ Local coordinate system vertical value
+
+ Returns
+ -------
+ glob_x_coor: float
+ Horizontal position in global coordinate system
+ glob_y_coor: float
+ Vertical position in global coordinate system
+
+ """
+ # Flip axes
+ x_coor, y_coor = self.flip_coord(ccd_n, x_coor, y_coor)
+
+ # Calculate the shift
+ x_shift, y_shift = self.shift_coord(ccd_n)
+
+ # Return new coordinates
+ return x_coor + x_shift, y_coor + y_shift
+
+ def flip_coord(self, ccd_n, x_coor, y_coor):
+ r"""Change of coordinate convention.
+
+ So that all of them are coherent on the global coordinate system.
+ So that the origin is on the south-west corner.
+ Positive: South to North ; West to East.
+ """
+ if ccd_n < 18 or ccd_n in [36, 37]:
+ x_coor = self.x_npix - x_coor + 1
+ y_coor = self.y_npix - y_coor + 1
+ else:
+ pass
+
+ return x_coor, y_coor
+
+ def x_coord_range(self):
+ r"""Return range of the x coordinate."""
+ max_x = self.x_npix * 6 + self.x_gap * 5
+ min_x = self.x_npix * (-5) + self.x_gap * (-5)
+ return min_x, max_x
+
+ def y_coord_range(self):
+ r"""Return range of the y coordinate."""
+ max_y = self.y_npix * 2 + self.y_gap * 1
+ min_y = self.y_npix * (-2) + self.y_gap * (-2)
+ return min_y, max_y
+
+ def shift_coord(self, ccd_n):
+ r"""Provide the shifting.
+
+ It is needed to go from the local coordinate
+ system origin to the global coordinate system origin.
+ """
+ if ccd_n < 9:
+ # first row
+ x_shift = (ccd_n - 4) * (self.x_gap + self.x_npix)
+ y_shift = self.y_gap + self.y_npix
+ return x_shift, y_shift
+
+ elif ccd_n < 18:
+ # second row, non-ears
+ x_shift = (ccd_n - 13) * (self.x_gap + self.x_npix)
+ y_shift = 0.0
+ return x_shift, y_shift
+
+ elif ccd_n < 27:
+ # third row non-ears
+ x_shift = (ccd_n - 22) * (self.x_gap + self.x_npix)
+ y_shift = -1.0 * (self.y_gap + self.y_npix)
+ return x_shift, y_shift
+
+ elif ccd_n < 36:
+ # fourth row
+ x_shift = (ccd_n - 31) * (self.x_gap + self.x_npix)
+ y_shift = -2.0 * (self.y_gap + self.y_npix)
+ return x_shift, y_shift
+
+ elif ccd_n < 37:
+ # ccd= 36 ears, second row
+ x_shift = (-5.0) * (self.x_gap + self.x_npix)
+ y_shift = 0.0
+ return x_shift, y_shift
+
+ elif ccd_n < 38:
+ # ccd= 37 ears, second row
+ x_shift = 5.0 * (self.x_gap + self.x_npix)
+ y_shift = 0.0
+ return x_shift, y_shift
+
+ elif ccd_n < 39:
+ # ccd= 38 ears, third row
+ x_shift = (-5.0) * (self.x_gap + self.x_npix)
+ y_shift = -1.0 * (self.y_gap + self.y_npix)
+ return x_shift, y_shift
+
+ elif ccd_n < 40:
+ # ccd= 39 ears, third row
+ x_shift = 5.0 * (self.x_gap + self.x_npix)
+ y_shift = -1.0 * (self.y_gap + self.y_npix)
+ return x_shift, y_shift
+
+
+class Glob2CCD(object):
+ r"""Get the CCD ID number from the global coordinate position.
+
+ The Loc2Glob() object as input is the one that defines the instrument's
+ geometry.
+
+ Parameters
+ ----------
+ loc2glob: Loc2Glob object
+ Object with the desired focal plane geometry.
+ with_gaps: bool
+ If add the gaps to the CCD area.
+ """
+
+ def __init__(self, loc2glob, with_gaps=True):
+ # Save loc2glob object
+ self.loc2glob = loc2glob
+ self.with_gaps = with_gaps
+ self.ccd_list = np.arange(self.loc2glob.ccd_tot)
+ # Init edges defininf the CCDs
+ self.edge_x_list, self.edge_y_list = self.build_all_edges()
+
+ def build_all_edges(self):
+ """Build the edges for all the CCDs in the focal plane."""
+ edge_xy_list = []
+ for idx in (0, 1):
+ edge_list = np.array(
+ [self.build_edge(ccd_n)[idx] for ccd_n in self.ccd_list]
+ )
+ edge_xy_list.append(edge_list)
+
+ return edge_xy_list
+
+ def build_edge(self, ccd_n):
+ """Build the edges of the `ccd_n` in global coordinates."""
+ if self.with_gaps:
+ corners = np.array(
+ [
+ [-self.loc2glob.x_gap / 2, -self.loc2glob.y_gap / 2],
+ [
+ self.loc2glob.x_npix + self.loc2glob.x_gap / 2,
+ -self.loc2glob.y_gap / 2,
+ ],
+ [
+ -self.loc2glob.x_gap / 2,
+ self.loc2glob.y_npix + self.loc2glob.y_gap / 2,
+ ],
+ [
+ self.loc2glob.x_npix + self.loc2glob.x_gap / 2,
+ self.loc2glob.y_npix + self.loc2glob.y_gap / 2,
+ ],
+ ]
+ )
+ else:
+ corners = np.array(
+ [
+ [0, 0],
+ [self.loc2glob.x_npix, 0],
+ [0, self.loc2glob.y_npix],
+ [self.loc2glob.x_npix, self.loc2glob.y_npix],
+ ]
+ )
+
+ glob_corners = np.array(
+ [
+ self.loc2glob.loc2glob_img_coord(ccd_n, pos[0], pos[1])
+ for pos in corners
+ ]
+ )
+
+ edge_xy = []
+ for idx in (0, 1):
+ edge = np.array(
+ [np.min(glob_corners[:, idx]), np.max(glob_corners[:, idx])]
+ )
+ edge_xy.append(edge)
+
+ return edge_xy
+
+ def is_inside(self, x, y, edge_x, edge_y):
+ """Is the position inside the edges.
+
+ Return True if the position is within the rectangle
+ defined by the edges.
+
+ Parameters
+ ----------
+ x: float
+ Horizontal position in global coordinate system.
+ y: float
+ Vertical position in global coordinate system.
+ edge_x: np.ndarray
+ Edge defined as `np.array([min_x, max_x])`.
+ edge_y: np.ndarray
+ Edge defined as `np.array([min_y, max_y])`.
+ """
+ if (
+ (x > edge_x[0])
+ and (x < edge_x[1])
+ and (y > edge_y[0])
+ and (y < edge_y[1])
+ ):
+ return True
+ else:
+ return False
+
+ def get_ccd_n(self, x, y):
+ """Returns the CCD number from the position `(x, y)`.
+
+ Returns `None` if the position is not found.
+ """
+ bool_list = np.array(
+ [
+ self.is_inside(x, y, edge_x, edge_y)
+ for edge_x, edge_y in zip(self.edge_x_list, self.edge_y_list)
+ ]
+ )
+
+ try:
+ return self.ccd_list[bool_list][0]
+ except Exception:
+ return None
+
+
+class Convert(object):
+
+ def __init__(self):
+
+ self.params_default()
+
+ def set_params_from_command_line(self, args):
+ """Set Params From Command line.
+
+ Only use when calling using python from command line.
+ Does not work from ipython or jupyter.
+
+ """
+ # Read command line options
+ options = cs_args.parse_options(
+ self._params,
+ self._short_options,
+ self._types,
+ self._help_strings,
+ )
+ self._params = options
+
+ # Save calling command
+ logging.log_command(args)
+
+ def params_default(self):
+
+ self._params = {
+ "input_base_dir": ".",
+ "output_base_dir": ".",
+ "mode": "merge",
+ "patches": "",
+ "psf": "psfex",
+ "file_pattern_psfint": "validation_psf",
+ }
+
+ self._short_options = {
+ "input_base_dir": "-i",
+ "mode": "-m",
+ "psf": "-p",
+ "patches": "-P",
+ }
+
+ self._types = {}
+
+ self._help_strings = {
+ "input_base_dir": (
+ "input base dir, runs are expected in"
+ + " /P/output;"
+ " default is {}"
+ ),
+ "mode": (
+ "run mode, allowed are 'merge', 'test'; default is" + " '{}'"
+ ),
+ "psf": "PSF model, allowed are 'psfex' and 'mccd'; default is {}",
+ "patches": "(list of) input patches",
+ }
+
+ # Output column names with types
+ self._dt = [
+ ("X", float),
+ ("Y", float),
+ ("RA", float),
+ ("DEC", float),
+ ("E1_PSF_HSM", float),
+ ("E2_PSF_HSM", float),
+ ("SIGMA_PSF_HSM", float),
+ ("FLAG_PSF_HSM", float),
+ ("E1_STAR_HSM", float),
+ ("E2_STAR_HSM", float),
+ ("SIGMA_STAR_HSM", float),
+ ("FLAG_STAR_HSM", float),
+ ("CCD_NB", int),
+ ]
+
+ # Extra columns for MCCD:737
+ self._dt_mccd = self._dt.copy()
+ self._dt_mccd.append(("GLOB_X", float))
+ self._dt_mccd.append(("GLOB_Y", float))
+
+ def update_params(self):
+ """Update Params.
+
+ Update parameters.
+
+ """
+ if self._params["psf"] == "psfex":
+ #self._params["sub_dir_pattern"] = "run_sp_exp_202"
+ self._params["sub_dir_pattern"] = "run_sp_combined_psf"
+ self._params["sub_dir_psfint"] = "psfex_interp_runner"
+ elif self._params["psf"] == "mccd":
+ self._params["sub_dir_pattern"] = "run_sp_exp_SxSePsf_202"
+ self._params["sub_dir_psfint"] = "mccd_fit_val_runner"
+ self._params["sub_dir_setools"] = "setools_runner/output/mask"
+ else:
+ raise ValueError(f"Invalid PSF model {self._params['psf']}")
+ self._params["sub_dir_psfint"] = (
+ f"{self._params['sub_dir_psfint']}/output"
+ )
+
+ def run(self):
+ """Run.
+
+ Main processing function.
+
+ """
+ if self._params["mode"] == "test":
+ patch_nums = ["3", "4"]
+ else:
+ patch_nums = cs_args.my_string_split(self._params["patches"])
+
+ do_parallel = True
+
+ # Loop over patches
+ for patch in patch_nums:
+
+ output_dir = f"{self._params['output_base_dir']}/P{patch}"
+ if not os.path.isdir(output_dir):
+ os.makedirs(output_dir, exist_ok=False)
+
+ print("Running patch:", patch)
+
+ patch_dir = f"{self._params['input_base_dir']}/P{patch}/output/"
+ subdirs = f"{patch_dir}/{self._params['sub_dir_pattern']}*"
+ exp_run_dirs = glob.glob(subdirs)
+ n_exp_runs = len(exp_run_dirs)
+ print(
+ f"Found {n_exp_runs} input single-exposure run(s) for patch"
+ + f" {patch_dir} ({subdirs})"
+ )
+
+ if self._params["mode"] == "test":
+ exp_run_dirs = exp_run_dirs[:2]
+ n_exp_runs = len(exp_run_dirs)
+ print(
+ f"test mode: only using {n_exp_runs} input single-exposure"
+ + f" runs"
+ )
+
+ # Loop over exposure runs
+ if not do_parallel:
+ for idx_exp, exp_run_dir in tqdm(
+ enumerate(exp_run_dirs),
+ total=n_exp_runs,
+ disable=self._params["verbose"],
+ ):
+ self.transform_exposures(
+ output_dir, patch, idx_exp, exp_run_dir
+ )
+ else:
+ res = Parallel(n_jobs=-1, backend="loky")(
+ delayed(self.transform_exposures)(
+ output_dir, patch, idx_exp, exp_run_dir
+ )
+ for idx_exp, exp_run_dir in tqdm(
+ enumerate(exp_run_dirs),
+ total=n_exp_runs,
+ disable=self._params["verbose"],
+ )
+ )
+
+ def transform_exposures(self, output_dir, patch, idx, exp_run_dir):
+ """Transform exposures.
+
+ Transform shapes for exposure for a given run (input exp run dir).
+
+ """
+ output_path = (
+ f"{output_dir}/{self._params['file_pattern_psfint']}_conv"
+ + f"-{patch}-{idx}.fits"
+ )
+ if os.path.exists(output_path):
+ print(f"Skipping transform_exposures, file {output_path} exists")
+ return
+
+ psf_dir = f"{exp_run_dir}/{self._params['sub_dir_psfint']}"
+ try:
+ all_files = os.listdir(psf_dir)
+ if self._params["verbose"]:
+ print(f"Found {len(all_files)} file(s) in {psf_dir}")
+ except Exception:
+ if self._params["verbose"]:
+ print(f"Found zero PSFEx files in {psf_dir}, skipping")
+ return
+
+ cat_list = []
+ for file_name in all_files:
+ if self._params["file_pattern_psfint"] not in file_name:
+ continue
+
+ tmp = re.findall(r"\d+", file_name)
+
+ if self._params["psf"] == "psfex":
+ exp_name, ccd_id = int(tmp[0]), int(tmp[1])
+ elif self._params["psf"] == "mccd":
+ exp_name = int(tmp[0])
+ ccd_id = -1
+
+ if self._params["verbose"]:
+ print("Match found ", exp_name, ccd_id)
+
+ psf_file_path = f"{psf_dir}/{file_name}"
+
+ try:
+ if self._params["psf"] == "psfex":
+ psf_file_hdus = fits.open(psf_file_path, memmap=False)
+ psf_file = psf_file_hdus[2].data
+ header_file = psf_file_hdus[1].data
+ psf_file_hdus.close()
+ mod = "RA"
+ else:
+ psf_file = fits.getdata(psf_file_path, 1, memmap=True)
+ mod = "RA_LIST"
+ except Exception:
+ continue
+
+ new_e1_psf = np.zeros_like(psf_file[mod])
+ new_e2_psf = np.zeros_like(psf_file[mod])
+ new_sig_psf = np.zeros_like(psf_file[mod])
+ new_e1_star = np.zeros_like(psf_file[mod])
+ new_e2_star = np.zeros_like(psf_file[mod])
+ new_sig_star = np.zeros_like(psf_file[mod])
+
+ if self._params["psf"] == "psfex":
+ header = fits.Header.fromstring(
+ "\n".join(header_file[0][0]), sep="\n"
+ )
+ wcs = galsim.AstropyWCS(header=header)
+
+ k = 0
+ for ind, obj in enumerate(psf_file):
+ try:
+ # jac = wcs.jacobian(world_pos=galsim.CelestialCoord(
+ # ra=obj["RA"]*galsim.degrees,
+ # dec=obj["DEC"]*galsim.degrees
+ # ))
+ jac = wcs.jacobian(
+ image_pos=galsim.PositionD(
+ obj["X"],
+ obj["Y"],
+ )
+ )
+ except Exception:
+ continue
+ g1_psf_tmp, g2_psf_tmp, sig_psf_tmp = transform_shape(
+ [
+ obj["E1_PSF_HSM"],
+ obj["E2_PSF_HSM"],
+ obj["SIGMA_PSF_HSM"],
+ ],
+ jac,
+ )
+
+ new_e1_psf[ind] = g1_psf_tmp
+ new_e2_psf[ind] = g2_psf_tmp
+ new_sig_psf[ind] = sig_psf_tmp
+
+ g1_star_tmp, g2_star_tmp, sig_star_tmp = transform_shape(
+ [
+ obj["E1_STAR_HSM"],
+ obj["E2_STAR_HSM"],
+ obj["SIGMA_STAR_HSM"],
+ ],
+ jac,
+ )
+ new_e1_star[ind] = g1_star_tmp
+ new_e2_star[ind] = g2_star_tmp
+ new_sig_star[ind] = sig_star_tmp
+ k += 1
+
+ exp_cat = np.array(
+ list(
+ map(
+ tuple,
+ np.array(
+ [
+ psf_file["X"],
+ psf_file["Y"],
+ psf_file["RA"],
+ psf_file["DEC"],
+ new_e1_psf,
+ new_e2_psf,
+ new_sig_psf,
+ psf_file["FLAG_PSF_HSM"],
+ new_e1_star,
+ new_e2_star,
+ new_sig_star,
+ psf_file["FLAG_STAR_HSM"],
+ np.ones_like(psf_file["RA"], dtype=int)
+ * ccd_id,
+ ]
+ ).T.tolist(),
+ )
+ ),
+ dtype=self._dt,
+ )
+ cat_list.append(exp_cat)
+
+ else:
+ l2g = Loc2Glob()
+ g2c = Glob2CCD(l2g)
+ new_ccd_id = np.array(
+ [
+ int(
+ g2c.get_ccd_n(
+ psf_file["GLOB_POSITION_IMG_LIST"][ii, 0],
+ psf_file["GLOB_POSITION_IMG_LIST"][ii, 1],
+ )
+ )
+ for ii in range(len(psf_file))
+ ]
+ )
+
+ new_x = np.zeros_like(psf_file[mod])
+ new_y = np.zeros_like(psf_file[mod])
+ new_flag_psf = np.zeros_like(psf_file[mod])
+ new_flag_star = np.zeros_like(psf_file[mod])
+ for ccd_id in range(40):
+ m_ccd_id = new_ccd_id == ccd_id
+ if sum(m_ccd_id) == 0:
+ continue
+
+ x_shift, y_shift = l2g.shift_coord(ccd_id)
+
+ new_x[m_ccd_id] = (
+ psf_file["GLOB_POSITION_IMG_LIST"][:, 0][m_ccd_id]
+ - x_shift
+ )
+ new_y[m_ccd_id] = (
+ psf_file["GLOB_POSITION_IMG_LIST"][:, 1][m_ccd_id]
+ - y_shift
+ )
+
+ header_file_path = (
+ self._params["sub_dir_setools"]
+ + self._params["file_pattern_psfint"]
+ + f"{exp_name}-{ccd_id}.fits"
+ )
+ try:
+ header_file = fits.getdata(header_file_path, 1)
+ except Exception:
+ continue
+ header = fits.Header.fromstring(
+ "\n".join(header_file[0][0]), sep="\n"
+ )
+ wcs = galsim.AstropyWCS(header=header)
+
+ g1_psf_tmp_l = []
+ g2_psf_tmp_l = []
+ sig_psf_tmp_l = []
+ g1_star_tmp_l = []
+ g2_star_tmp_l = []
+ sig_star_tmp_l = []
+ flag_psf_tmp_l = []
+ flag_star_tmp_l = []
+
+ for obj in psf_file[m_ccd_id]:
+ try:
+ jac = wcs.jacobian(
+ world_pos=galsim.CelestialCoord(
+ ra=obj["RA_LIST"] * galsim.degrees,
+ dec=obj["DEC_LIST"] * galsim.degrees,
+ )
+ )
+ except Exception:
+ flag_star_tmp_l.append(16)
+ flag_psf_tmp_l.append(16)
+ g1_psf_tmp_l.append(0)
+ g2_psf_tmp_l.append(0)
+ sig_psf_tmp_l.append(0)
+ g1_star_tmp_l.append(0)
+ g2_star_tmp_l.append(0)
+ sig_star_tmp_l.append(0)
+ continue
+ g1_psf_tmp, g2_psf_tmp, sig_psf_tmp = transform_shape(
+ obj["PSF_MOM_LIST"], jac
+ )
+
+ g1_psf_tmp_l.append(g1_psf_tmp)
+ g2_psf_tmp_l.append(g2_psf_tmp)
+ sig_psf_tmp_l.append(sig_psf_tmp)
+ flag_psf_tmp_l.append(obj["PSF_MOM_LIST"][3])
+
+ g1_star_tmp, g2_star_tmp, sig_star_tmp = (
+ transform_shape(obj["STAR_MOM_LIST"], jac)
+ )
+ g1_star_tmp_l.append(g1_star_tmp)
+ g2_star_tmp_l.append(g2_star_tmp)
+ sig_star_tmp_l.append(sig_star_tmp)
+ flag_star_tmp_l.append(obj["STAR_MOM_LIST"][3])
+
+ new_e1_psf[m_ccd_id] = g1_psf_tmp_l
+ new_e2_psf[m_ccd_id] = g2_psf_tmp_l
+ new_sig_psf[m_ccd_id] = sig_psf_tmp_l
+ new_flag_psf[m_ccd_id] = flag_psf_tmp_l
+ new_e1_star[m_ccd_id] = g1_star_tmp_l
+ new_e2_star[m_ccd_id] = g2_star_tmp_l
+ new_sig_star[m_ccd_id] = sig_star_tmp_l
+ new_flag_star[m_ccd_id] = flag_star_tmp_l
+
+ exp_cat = np.array(
+ list(
+ map(
+ tuple,
+ np.array(
+ [
+ new_x,
+ new_y,
+ psf_file["RA_LIST"],
+ psf_file["DEC_LIST"],
+ new_e1_psf,
+ new_e2_psf,
+ new_sig_psf,
+ psf_file["PSF_MOM_LIST"][:, 3],
+ new_e1_star,
+ new_e2_star,
+ new_sig_star,
+ psf_file["STAR_MOM_LIST"][:, 3],
+ new_ccd_id,
+ psf_file["GLOB_POSITION_IMG_LIST"][:, 0],
+ psf_file["GLOB_POSITION_IMG_LIST"][:, 1],
+ ]
+ ).T.tolist(),
+ )
+ ),
+ dtype=self._dt_mccd,
+ )
+ cat_list.append(exp_cat)
+
+ del psf_file
+
+ if len(cat_list) == 0:
+ return
+
+ # Finalize catalogue
+ patch_cat = np.concatenate(cat_list)
+ hdul = fits.HDUList()
+ hdul.append(fits.PrimaryHDU())
+ hdul.append(fits.BinTableHDU(patch_cat))
+
+ # Write catalogue
+ hdul.writeto(
+ output_path,
+ overwrite=True,
+ )
+
+ del cat_list
+ del hdul
+ gc.collect()
+
+
+def run_convert(*args):
+
+ # Create instance
+ obj = Convert()
+
+ obj.set_params_from_command_line(args)
+ obj.update_params()
+
+ obj.run()
+
+
+def main(argv=None):
+ """Main
+
+ Main program
+ """
+ if argv is None:
+ argv = sys.argv[1:]
+ run_convert(*argv)
+
+ return 0
+
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv))
diff --git a/scripts/python/create_sample_results.py b/scripts/python/create_sample_results.py
index 25e00ec39..0e0223ffe 100755
--- a/scripts/python/create_sample_results.py
+++ b/scripts/python/create_sample_results.py
@@ -34,9 +34,7 @@ def params_default():
parameter values
"""
- p_def = cfis.param(
- psf = 'mccd'
- )
+ p_def = cfis.param(psf="mccd")
return p_def
@@ -57,49 +55,49 @@ def parse_options(p_def):
Command line string
"""
- usage = "%prog [OPTIONS]"
+ usage = "%prog [OPTIONS]"
parser = OptionParser(usage=usage)
# I/O
parser.add_option(
- '',
- '--input_IDs',
- dest='input_IDs',
- type='string',
- help='input tile ID file specifying sample'
+ "",
+ "--input_IDs",
+ dest="input_IDs",
+ type="string",
+ help="input tile ID file specifying sample",
)
parser.add_option(
- '-i',
- '--input_dir',
- dest='input_dir',
- type='string',
- help='input directory name'
+ "-i",
+ "--input_dir",
+ dest="input_dir",
+ type="string",
+ help="input directory name",
)
parser.add_option(
- '-o',
- '--output_dir',
- dest='output_dir',
- type='string',
- help='output directory name'
+ "-o",
+ "--output_dir",
+ dest="output_dir",
+ type="string",
+ help="output directory name",
)
# Misc
parser.add_option(
- '-p',
- '--psf',
- dest='psf',
- type='string',
+ "-p",
+ "--psf",
+ dest="psf",
+ type="string",
default=p_def.psf,
- help=f'PSF model, one in [\'psfex\'|\'mccd\'], default=\'{p_def.psf}\''
+ help=f"PSF model, one in ['psfex'|'mccd'], default='{p_def.psf}'",
)
# Control
parser.add_option(
- '-v',
- '--verbose',
- dest='verbose',
- action='store_true',
- help='verbose output'
+ "-v",
+ "--verbose",
+ dest="verbose",
+ action="store_true",
+ help="verbose output",
)
options, args = parser.parse_args()
@@ -122,13 +120,13 @@ def check_options(options):
"""
if options.input_IDs is None:
- print('No input ID file list given (option \'--input_IDs\')')
+ print("No input ID file list given (option '--input_IDs')")
return False
if options.input_dir is None:
- print('No input directory name given (option \'--input_dir\')')
+ print("No input directory name given (option '--input_dir')")
return False
if options.output_dir is None:
- print('No output directory name given (option \'--output_dir\')')
+ print("No output directory name given (option '--output_dir')")
return False
return True
@@ -184,7 +182,7 @@ def read_ID_list(input_ID_path, verbose=False):
"""
if verbose:
- print('Reading input ID list...')
+ print("Reading input ID list...")
input_IDs = []
with open(input_ID_path) as f:
@@ -192,12 +190,14 @@ def read_ID_list(input_ID_path, verbose=False):
input_IDs.append(line.rstrip())
if verbose:
- print('{} IDs found in input file'.format(len(input_IDs)))
+ print("{} IDs found in input file".format(len(input_IDs)))
return input_IDs
-def create_links(input_dir, output_dir, input_IDs, result_base_names, verbose=False):
+def create_links(
+ input_dir, output_dir, input_IDs, result_base_names, verbose=False
+):
"""Create symbolic links to result files corresponding to (sub-)sample.
Parameters
@@ -215,7 +215,7 @@ def create_links(input_dir, output_dir, input_IDs, result_base_names, verbose=Fa
"""
if verbose:
- print('Creating links...')
+ print("Creating links...")
n_total = {}
n_created = 0
@@ -223,16 +223,16 @@ def create_links(input_dir, output_dir, input_IDs, result_base_names, verbose=Fa
for ID in input_IDs:
n_total[ID] = 0
for base in result_base_names:
- name = '{}_{}.tgz'.format(base, ID)
- src = '{}/{}'.format(os.path.abspath(input_dir), name)
- link_name = '{}/{}'.format(output_dir, name)
+ name = "{}_{}.tgz".format(base, ID)
+ src = "{}/{}".format(os.path.abspath(input_dir), name)
+ link_name = "{}/{}".format(output_dir, name)
- #if verbose:
- #print('Creating link {} <- {}'.format(src, link_name))
+ # if verbose:
+ # print('Creating link {} <- {}'.format(src, link_name))
if not os.path.exists(src):
- #raise IOError('Source file \'{}\' does not exist'.format(src))
- print('Source file \'{}\' does not exist, skipping'.format(src))
+ # raise IOError('Source file \'{}\' does not exist'.format(src))
+ print("Source file '{}' does not exist, skipping".format(src))
elif not os.path.exists(link_name):
os.symlink(src, link_name)
n_created = n_created + 1
@@ -243,11 +243,15 @@ def create_links(input_dir, output_dir, input_IDs, result_base_names, verbose=Fa
n_expected = len(input_IDs) * len(result_base_names)
if verbose:
- print('{:5d} links created'.format(n_created))
- print('{:5d} links existed already'.format(n_existed))
- print('{:5d}/{} links available now'.format(n_created + n_existed, n_expected))
+ print("{:5d} links created".format(n_created))
+ print("{:5d} links existed already".format(n_existed))
+ print(
+ "{:5d}/{} links available now".format(
+ n_created + n_existed, n_expected
+ )
+ )
n_tot = sum(n_total.values())
- print('{:5d} as cross-check'.format(n_tot))
+ print("{:5d} as cross-check".format(n_tot))
def main(argv=None):
@@ -267,42 +271,50 @@ def main(argv=None):
# Save calling command
cfis.log_command(argv)
if param.verbose:
- cfis.log_command(argv, name='sys.stdout')
-
+ cfis.log_command(argv, name="sys.stdout")
### Start main program ###
if param.verbose:
- print('Start of program {}'.format(os.path.basename(argv[0])))
+ print("Start of program {}".format(os.path.basename(argv[0])))
input_IDs = read_ID_list(param.input_IDs, verbose=param.verbose)
result_base_names = [
- 'final_cat',
- 'logs',
- 'setools_mask',
- 'setools_stat',
- 'setools_plot',
- 'pipeline_flag',
+ "final_cat",
+ "logs",
+ "setools_mask",
+ "setools_stat",
+ "setools_plot",
+ "pipeline_flag",
]
- if param.psf == 'psfex':
- result_base_names.append('psfex_interp_exp')
- elif param.psf == 'mccd':
- result_base_names.append('mccd_fit_val_runner')
+ if param.psf == "psfex":
+ result_base_names.append("psfex_interp_exp")
+ elif param.psf == "mccd":
+ result_base_names.append("mccd_fit_val_runner")
if os.path.isdir(param.output_dir):
if param.verbose:
- print('Directory {} already exists, continuing...'.format(param.output_dir))
+ print(
+ "Directory {} already exists, continuing...".format(
+ param.output_dir
+ )
+ )
else:
mkdir(param.output_dir)
- create_links(param.input_dir, param.output_dir, input_IDs, result_base_names, verbose=param.verbose)
-
+ create_links(
+ param.input_dir,
+ param.output_dir,
+ input_IDs,
+ result_base_names,
+ verbose=param.verbose,
+ )
### End main program
if param.verbose:
- print('End of program {}'.format(os.path.basename(argv[0])))
+ print("End of program {}".format(os.path.basename(argv[0])))
return 0
diff --git a/scripts/python/create_star_cat.py b/scripts/python/create_star_cat.py
index 2c87d3f8d..f990942f7 100755
--- a/scripts/python/create_star_cat.py
+++ b/scripts/python/create_star_cat.py
@@ -45,16 +45,16 @@ def _get_wcs(header):
"""
final_wcs = WCS(naxis=2)
- final_wcs.wcs.ctype = [header['CTYPE1'], header['CTYPE2']]
+ final_wcs.wcs.ctype = [header["CTYPE1"], header["CTYPE2"]]
try:
- final_wcs.wcs.cunit = [header['CUNIT1'], header['CUNIT2']]
+ final_wcs.wcs.cunit = [header["CUNIT1"], header["CUNIT2"]]
except:
- final_wcs.wcs.cunit = ['deg', 'deg']
- final_wcs.wcs.crpix = [header['CRPIX1'], header['CRPIX2']]
- final_wcs.wcs.crval = [header['CRVAL1'], header['CRVAL2']]
+ final_wcs.wcs.cunit = ["deg", "deg"]
+ final_wcs.wcs.crpix = [header["CRPIX1"], header["CRPIX2"]]
+ final_wcs.wcs.crval = [header["CRVAL1"], header["CRVAL2"]]
final_wcs.wcs.cd = [
- [header['CD1_1'], header['CD1_2']],
- [header['CD2_1'], header['CD2_2']]
+ [header["CD1_1"], header["CD1_2"]],
+ [header["CD2_1"], header["CD2_2"]],
]
return final_wcs
@@ -79,17 +79,17 @@ def _get_image_radius(center, wcs):
"""
if center is None:
- raise ValueError('center cannot be None')
+ raise ValueError("center cannot be None")
else:
if type(center) is np.ndarray:
return SphereDist(center, np.zeros(2), wcs) / 60.0
else:
- raise TypeError('center has to be a numpy.ndarray')
+ raise TypeError("center has to be a numpy.ndarray")
def SphereDist(position1, position2, wcs):
"""Sphere Dist.
-
+
Compute distance between two points on the sphere.
Parameters
@@ -105,11 +105,10 @@ def SphereDist(position1, position2, wcs):
distance (in degrees)
"""
- if (
- (type(position1) is not np.ndarray)
- & (type(position2) is not np.ndarray)
+ if (type(position1) is not np.ndarray) & (
+ type(position2) is not np.ndarray
):
- raise ValueError('Positions need to be of type numpy.ndarray')
+ raise ValueError("Positions need to be of type numpy.ndarray")
rad2deg = np.pi / 180.0
p1 = rad2deg * np.hstack(wcs.all_pix2world(position1[0], position1[1], 1))
@@ -120,10 +119,13 @@ def SphereDist(position1, position2, wcs):
dLat = dTheta[1]
dist = 2 * np.arcsin(
- np.sqrt(np.sin(dLat/2.0)**2 + np.cos(p1[1])*np.cos(p2[1])*np.sin(dLong/2.0)**2)
+ np.sqrt(
+ np.sin(dLat / 2.0) ** 2
+ + np.cos(p1[1]) * np.cos(p2[1]) * np.sin(dLong / 2.0) ** 2
+ )
)
- return dist*(180./np.pi)*3600.
+ return dist * (180.0 / np.pi) * 3600.0
def find_stars(position, output_name, radius=None):
@@ -145,16 +147,16 @@ def find_stars(position, output_name, radius=None):
# check ra dec types
- if dec > 0.:
- sign = '+'
+ if dec > 0.0:
+ sign = "+"
else:
- sign = ''
+ sign = ""
- cmd_line = f'findgsc2.2 {ra} {sign}{dec} -r {radius} -n 1000000'
+ cmd_line = f"findgsc2.2 {ra} {sign}{dec} -r {radius} -n 1000000"
CDS_stdout, CDS_stderr = execute(cmd_line)
- output_file = open(output_name, 'w')
+ output_file = open(output_name, "w")
output_file.write(CDS_stdout)
output_file.close()
@@ -164,38 +166,36 @@ def main(input_dir, output_dir, kind):
file_list = os.listdir(input_dir)
for f in file_list:
- if 'image' not in f:
+ if "image" not in f:
continue
- if kind == 'exp':
+ if kind == "exp":
list_ind = range(1, 41)
else:
list_ind = [0]
for ind in list_ind:
- if kind == 'exp':
- exp_suff = '-{}'.format(ind-1)
+ if kind == "exp":
+ exp_suff = "-{}".format(ind - 1)
else:
- exp_suff = ''
+ exp_suff = ""
- img_number = re.split('image', os.path.splitext(f)[0])[1]
- output_name = f'{output_dir}/star_cat{img_number}{exp_suff}.cat'
+ img_number = re.split("image", os.path.splitext(f)[0])[1]
+ output_name = f"{output_dir}/star_cat{img_number}{exp_suff}.cat"
if os.path.isfile(output_name):
continue
- h = fits.getheader(input_dir + '/' + f, ind)
+ h = fits.getheader(input_dir + "/" + f, ind)
w = _get_wcs(h)
- img_shape = (h['NAXIS2'], h['NAXIS1'])
- img_center = np.array([img_shape[1]/2., img_shape[0]/2.])
+ img_shape = (h["NAXIS2"], h["NAXIS1"])
+ img_center = np.array([img_shape[1] / 2.0, img_shape[0] / 2.0])
wcs_center = w.all_pix2world([img_center], 1)[0]
astropy_center = SkyCoord(
- ra=wcs_center[0],
- dec=wcs_center[1],
- unit='deg'
+ ra=wcs_center[0], dec=wcs_center[1], unit="deg"
)
rad = _get_image_radius(img_center, w)
@@ -203,29 +203,29 @@ def main(input_dir, output_dir, kind):
find_stars(
np.array([astropy_center.ra.value, astropy_center.dec.value]),
output_name,
- rad
+ rad,
)
return 0
-if __name__ == '__main__':
+if __name__ == "__main__":
argv = sys.argv
try:
input_path = argv[1]
except:
- input_path = '.'
+ input_path = "."
try:
output_path = argv[2]
except:
- output_path = '.'
+ output_path = "."
try:
kind = argv[3]
except:
- kind = ''
+ kind = ""
main(input_path, output_path, kind)
diff --git a/scripts/python/get_number_objects.py b/scripts/python/get_number_objects.py
index 67cdb294d..e2b6c9a15 100755
--- a/scripts/python/get_number_objects.py
+++ b/scripts/python/get_number_objects.py
@@ -14,15 +14,16 @@
import copy
import glob
-from optparse import OptionParser
+from optparse import OptionParser
from astropy.io import fits
-from shapepipe.pipeline.run_log import get_last_dir
-from shapepipe.utilities import cfis
+from shapepipe.pipeline.run_log import get_last_dir, get_all_dirs
+from shapepipe.utilities import cfis
class param:
"""General class to store (default) variables"""
+
def __init__(self, **kwds):
self.__dict__.update(kwds)
@@ -43,8 +44,8 @@ class param
"""
p_def = param(
- input_path='.',
- input_name_base='final_cat',
+ input_path=".",
+ input_name_base="final_cat",
hdu_num=1,
)
@@ -66,60 +67,60 @@ def parse_options(p_def):
command line str
"""
- usage = "%prog [OPTIONS]"
+ usage = "%prog [OPTIONS]"
parser = OptionParser(usage=usage)
# IO
parser.add_option(
- '-i',
- '--input_path',
- dest='input_path',
- type='string',
+ "-i",
+ "--input_path",
+ dest="input_path",
+ type="string",
default=p_def.input_path,
- help=f'input path, default=\'{p_def.input_path}\''
+ help=f"input path, default='{p_def.input_path}'",
)
parser.add_option(
- '-n',
- '--input_name_base',
- dest='input_name_base',
- type='string',
+ "-n",
+ "--input_name_base",
+ dest="input_name_base",
+ type="string",
default=p_def.input_name_base,
- help=f'input name base, default=\'{p_def.input_name_base}\''
+ help=f"input name base, default='{p_def.input_name_base}'",
)
parser.add_option(
- '-l',
- '--list_tile_ID_path',
- dest='tile_ID_list_path',
- type='string',
+ "-l",
+ "--list_tile_ID_path",
+ dest="tile_ID_list_path",
+ type="string",
default=None,
- help=f'tile ID list, default: Use all data in input files'
+ help=f"tile ID list, default: Use all data in input files",
)
# Control
parser.add_option(
- '-p',
- '--param_path',
- dest='param_path',
- type='string',
+ "-p",
+ "--param_path",
+ dest="param_path",
+ type="string",
default=None,
- help='parameter file path, default=None'
+ help="parameter file path, default=None",
)
parser.add_option(
- '',
- '--hdu_num',
- dest='hdu_num',
- type='int',
+ "",
+ "--hdu_num",
+ dest="hdu_num",
+ type="int",
default=p_def.hdu_num,
- help=f'input HDU number, default=\'{p_def.hdu_num}\''
+ help=f"input HDU number, default='{p_def.hdu_num}'",
)
parser.add_option(
- '-v',
- '--verbose',
- dest='verbose',
- action='store_true',
- help='verbose output'
+ "-v",
+ "--verbose",
+ dest="verbose",
+ action="store_true",
+ help="verbose output",
)
options, args = parser.parse_args()
@@ -177,94 +178,6 @@ class param
return param
-def read_param_file(path, verbose=False):
- """Return parameter list read from file
-
- Parameters
- ----------
- path: str
- input file name
- verbose: bool, optional, default=False
- verbose output if True
-
- Returns
- -------
- list of str
- parameter names
-
- """
- param_list = []
-
- if path:
-
- with open(path) as f:
- for line in f:
- if line.startswith('#'):
- continue
- entry = line.rstrip()
- if not entry or entry == '':
- continue
- param_list.append(entry)
-
- if verbose:
- if len(param_list) > 0:
- print(f'Copying {len(param_list)} columns', end='')
- else:
- print('Copying all columns', end='')
- print(' into merged catalogue')
-
- # Check for multiples
- multiples = []
- for param in param_list:
- if param_list.count(param) > 1:
- multiples.append(param)
-
- if len(multiples) > 0:
- print('The following parameters are more than one times '
- 'in the parameter file: ', end='')
- for m in multiples:
- print(m, end=' ')
- print()
- raise ValueError('Multiple identical keys found')
-
- return param_list
-
-
-def get_data(path, hdu_num, param_list):
- """Return data of selected columns from FITS file.
-
- Parameters
- ----------
- path: str
- input file name
- hdu_num: int
- HDU number
- param_list: list of str
- parameters to be extracted. If none, copy
- all columns
-
- Returns
- -------
- numpy array
- data columns
-
- """
- hdu_list = fits.open(path)
- hdu = hdu_list[hdu_num]
-
- if param_list:
- cols = []
- for p in param_list:
- cols.append(hdu.columns[p])
- coldefs = fits.ColDefs(cols)
- hdu_new = fits.BinTableHDU.from_columns(coldefs)
- d = hdu_new.data
- else:
- d = hdu.data
-
- return d
-
-
def main(argv=None):
# Set default parameters
@@ -281,22 +194,46 @@ def main(argv=None):
# Save command line arguments to log file
f_log = cfis.log_command(argv, close_no_return=False)
- module = 'sextractor_runner_run_1'
- pattern = 'sexcat'
- run_log_file = 'output/log_run_sp.txt'
- last_dir = get_last_dir(run_log_file, module)
+ pattern = "sexcat"
+ run_log_file = "output/log_run_sp.txt"
+
+ # For v1
+ # module = 'sextractor_runner_run_1'
+
+ # For v2
+ module = "sextractor_runner"
+
+ # Get all sextractor output directories
+ all_dir = get_all_dirs(run_log_file, module)
+ paths = []
+
+ # Find tile runs
+ for path in all_dir:
+ if "run_sp_tile_Sx" in path:
+ paths.append(path)
+ paths = sorted(paths)
+
+ # Get latest run
+ last_dir = paths[-1]
+<<<<<<< HEAD
+ # Get all output SExtractor catalogues
file_list = glob.glob(f'{last_dir}/{pattern}*.fits')
+=======
+ file_list = glob.glob(f"{last_dir}/{pattern}*.fits")
+>>>>>>> origin/v1.4
if len(file_list) == 0:
- raise ValueError(f'No files {last_dir}/{pattern}*.fits found')
+ raise ValueError(f"No files {last_dir}/{pattern}*.fits found")
+ # Add up number of objects over all catalogues
n_obj = 0
hdu_no = -1
for fpath in file_list:
hdu_list = fits.open(fpath)
header = hdu_list[-1].header
- n_obj += int(header['NAXIS2'])
+ n_obj += int(header["NAXIS2"])
+ # Compute average
n_obj = int(n_obj / len(file_list))
print(n_obj)
diff --git a/scripts/python/link_to_exp_for_tile.py b/scripts/python/link_to_exp_for_tile.py
new file mode 100755
index 000000000..069121740
--- /dev/null
+++ b/scripts/python/link_to_exp_for_tile.py
@@ -0,0 +1,340 @@
+#!/usr/bin/env python
+
+# -*- coding: utf-8 -*-
+
+"""Script link_to_exp_for_tile.py
+
+:Description: Link to exposure and PSF catalogue
+ for a given tile.
+
+:Author: Martin Kilbinger
+
+"""
+
+import os
+import sys
+import re
+import copy
+
+from optparse import OptionParser
+
+
+class param:
+ """General class to store (default) variables"""
+
+ def __init__(self, **kwds):
+ self.__dict__.update(kwds)
+
+ def print(self, **kwds):
+ print(self.__dict__)
+
+ def var_list(self, **kwds):
+ return vars(self)
+
+
+def params_default():
+ """Params Default.
+
+ Set default parameter values.
+
+ Returns
+ -------
+ class param
+ parameter values
+
+ """
+ p_def = param(
+ tile_base_dir=".",
+ exp_base_dir=".",
+ )
+
+ return p_def
+
+
+def parse_options(p_def):
+ """Parse Options.
+
+ Parse command line options.
+
+ Parameters
+ ----------
+ p_def: class param
+ parameter values
+
+ Returns
+ -------
+ list
+ command line options
+ command line str
+
+ """
+ usage = "%prog [OPTIONS]"
+ parser = OptionParser(usage=usage)
+
+ # IO
+ parser.add_option(
+ "-i",
+ "--input_tile_dir",
+ dest="tile_base_dir",
+ type="string",
+ default=p_def.tile_base_dir,
+ help=f"input tile base directory, default='{p_def.tile_base_dir}'",
+ )
+ parser.add_option(
+ "-t",
+ "--tile_ID",
+ dest="tile_ID",
+ type="string",
+ help=f"input tile ID",
+ )
+ parser.add_option(
+ "-I",
+ "--input_exp_dir",
+ dest="exp_base_dir",
+ type="string",
+ default=p_def.exp_base_dir,
+ help=f"input exposure base directory, default='{p_def.exp_base_dir}'",
+ )
+ parser.add_option(
+ "-v",
+ "--verbose",
+ dest="verbose",
+ action="store_true",
+ help="verbose output",
+ )
+
+ options, args = parser.parse_args()
+
+ return options, args
+
+
+def check_options(options):
+ """Check Options.
+
+ Check command line options.
+
+ Parameters
+ ----------
+ options: tuple
+ Command line options
+
+ Returns
+ -------
+ bool
+ Result of option check. False if invalid option value.
+
+ """
+ return True
+
+
+def update_param(p_def, options):
+ """Update Param.
+
+ Return default parameter, updated and complemented according to options.
+
+ Parameters
+ ----------
+ p_def: class param
+ parameter values
+ optiosn: tuple
+ command line options
+
+ Returns
+ -------
+ class param
+ updated paramter values
+
+ """
+ param = copy.copy(p_def)
+
+ # Update keys in param according to options values
+ for key in vars(param):
+ if key in vars(options):
+ setattr(param, key, getattr(options, key))
+
+ # Add remaining keys from options to param
+ for key in vars(options):
+ if not key in vars(param):
+ setattr(param, key, getattr(options, key))
+
+ # Do extra stuff if necessary
+
+ return param
+
+
+# TODO: move to cs_util
+def matching_subdirs(base_dir, pattern):
+
+ # Find all matching subdirectories
+ subdirs = []
+ if os.path.exists(base_dir):
+ for entry in os.listdir(base_dir):
+ full_path = os.path.join(base_dir, entry)
+ if os.path.isdir(full_path) and entry.startswith(pattern):
+ subdirs.append(full_path)
+ else:
+ print(f"Warning: {base_dir} does not exist, continuing...")
+
+ # Sort according to creation date
+ subdirs.sort(key=os.path.getctime)
+
+ return subdirs
+
+
+def get_tile_out_dir(tile_base_dir, tile_ID):
+
+ tile_out_dir = f"{tile_base_dir}/{tile_ID}/output"
+
+ return tile_out_dir
+
+
+def get_exp_IDs(tile_base_dir, tile_ID, verbose=False):
+
+ tile_out_dir = get_tile_out_dir(tile_base_dir, tile_ID)
+
+ pattern = "run_sp_GitFeGie"
+ subdirs = matching_subdirs(tile_out_dir, pattern)
+
+ if len(subdirs) == 0:
+ raise IOError(
+ f"No matching directory '{pattern}' in {tile_out_dir} found"
+ )
+ if len(subdirs) != 1:
+ raise IOError(
+ f"Exactly one directory natching {pattern} in {tile_out_dir} "
+ + f"expected, not {len(subdirs)}"
+ )
+
+ # Replace dot with dash in tile ID
+ tile_ID_sp = re.sub(r"\.", "-", tile_ID)
+ exp_ID_file = (
+ f"{subdirs[0]}/find_exposures_runner/output/"
+ + f"exp_numbers-{tile_ID_sp}.txt"
+ )
+
+ exp_IDs = []
+ with open(exp_ID_file) as f_in:
+ for line in f_in:
+ name = line.strip()
+ # Remove any letter
+ ID = re.sub("[a-zA-Z]", "", name)
+ exp_IDs.append(ID)
+
+ if verbose:
+ print("Exposures: ", exp_IDs)
+ return exp_IDs
+
+
+def get_exp_single_HDU_IDs(exp_IDs, n_CPU):
+
+ exp_shdu_IDs = []
+ for exp_ID in exp_IDs:
+ for idx in range(n_CPU):
+ ID = f"{exp_ID}-{idx}"
+ exp_shdu_IDs.append(ID)
+
+ return exp_shdu_IDs
+
+
+def get_paths(exp_base_dir, exp_shdu_IDs, pattern):
+
+ number = {}
+ paths = []
+ for exp_shdu_ID in exp_shdu_IDs:
+
+ name = f"{exp_base_dir}/{exp_shdu_ID}/output"
+ path = os.path.abspath(name)
+ subdirs = matching_subdirs(path, pattern)
+ n_subdirs = len(subdirs)
+
+ if n_subdirs not in number:
+ number[n_subdirs] = 1
+ else:
+ number[n_subdirs] += 1
+
+ if n_subdirs != 1:
+ msg = (
+ f"Exactly one directory matching {pattern} in {path} expected,"
+ + f" not {n_subdirs}"
+ )
+ print(msg)
+ # More than one match: sort according to name = creation time
+ subdirs = sorted(subdirs)
+ if n_subdirs == 0:
+ continue
+
+ # Append matching subdir; if more than one append newest
+ paths.append(f"{subdirs[-1]}")
+
+ return paths, number
+
+
+def create_links_paths(tile_base_dir, tile_ID, paths, verbose=False):
+
+ tile_out_dir = get_tile_out_dir(tile_base_dir, tile_ID)
+
+ for path in paths:
+
+ head, tail = os.path.split(path)
+ src = path
+ dst = f"{tile_out_dir}/{tail}"
+ if os.path.exists(dst):
+ src_existing = os.readlink(dst)
+ if src_existing == src:
+ if verbose:
+ # print("link {src} <- {dst}")
+ f"Warning: {src} <- {dst} already exists, no link created"
+ # )
+ continue
+ else:
+ idx = 1
+ dst_orig = dst
+ while True:
+ dst = f"{dst_orig}_{idx}"
+ if os.path.exists(dst):
+ idx += 1
+ else:
+ if verbose:
+ print(f"link {src} <- {dst}")
+ os.symlink(src, dst)
+ break
+ else:
+ if verbose:
+ print(f"link {src} <- {dst}")
+ os.symlink(src, dst)
+
+
+def main(argv=None):
+
+ # Set default parameters
+ p_def = params_default()
+
+ # Command line options
+ options, args = parse_options(p_def)
+
+ if check_options(options) is False:
+ return 1
+
+ param = update_param(p_def, options)
+
+ tile_base_dir = param.tile_base_dir
+ exp_base_dir = param.exp_base_dir
+ tile_ID = param.tile_ID
+ n_CPU = 40
+ verbose = param.verbose
+
+ exp_IDs = get_exp_IDs(tile_base_dir, tile_ID, verbose=verbose)
+ exp_shdu_IDs = get_exp_single_HDU_IDs(exp_IDs, n_CPU)
+
+ # Note: psfex P3 is mostly run_sp_exp_SxSePsf
+ patterns = ["run_sp_exp_SxSePsfPi"] # , "run_sp_exp_Pi"]
+ for pattern in patterns:
+ paths, number = get_paths(exp_base_dir, exp_shdu_IDs, pattern)
+
+ create_links_paths(tile_base_dir, tile_ID, paths, verbose=verbose)
+
+ return 0
+
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv))
diff --git a/scripts/python/merge_final_cat.py b/scripts/python/merge_final_cat.py
index 1a160c449..ed0b962e8 100755
--- a/scripts/python/merge_final_cat.py
+++ b/scripts/python/merge_final_cat.py
@@ -20,15 +20,12 @@
from optparse import OptionParser
-from tqdm import tqdm
-
from shapepipe.utilities import cfis
class param:
- """General class to store (default) variables
+ """General class to store (default) variables"""
- """
def __init__(self, **kwds):
self.__dict__.update(kwds)
@@ -41,7 +38,7 @@ def var_list(self, **kwds):
def params_default():
"""Params Default.
-
+
Set default parameter values.
Returns
@@ -51,9 +48,9 @@ class param
"""
p_def = param(
- input_path = '.',
- input_name_base = 'final_cat',
- hdu_num = 1,
+ input_path=".",
+ input_name_base="final_cat",
+ hdu_num=1,
)
return p_def
@@ -61,7 +58,7 @@ class param
def parse_options(p_def):
"""Parse Options.
-
+
Parse command line options.
Parameters
@@ -76,60 +73,60 @@ def parse_options(p_def):
command line str
"""
- usage = "%prog [OPTIONS]"
+ usage = "%prog [OPTIONS]"
parser = OptionParser(usage=usage)
# IO
parser.add_option(
- '-i',
- '--input_path',
- dest='input_path',
- type='string',
+ "-i",
+ "--input_path",
+ dest="input_path",
+ type="string",
default=p_def.input_path,
- help=f'input path, default=\'{p_def.input_path}\''
+ help=f"input path, default='{p_def.input_path}'",
)
parser.add_option(
- '-n',
- '--input_name_base',
- dest='input_name_base',
- type='string',
+ "-n",
+ "--input_name_base",
+ dest="input_name_base",
+ type="string",
default=p_def.input_name_base,
- help=f'input name base, default=\'{p_def.input_name_base}\''
+ help=f"input name base, default='{p_def.input_name_base}'",
)
parser.add_option(
- '-l',
- '--list_tile_ID_path',
- dest='tile_ID_list_path',
- type='string',
+ "-l",
+ "--list_tile_ID_path",
+ dest="tile_ID_list_path",
+ type="string",
default=None,
- help=f'tile ID list, default: Use all data in input files'
+ help=f"tile ID list, default: Use all data in input files",
)
# Control
parser.add_option(
- '-p',
- '--param_path',
- dest='param_path',
- type='string',
+ "-p",
+ "--param_path",
+ dest="param_path",
+ type="string",
default=None,
- help='parameter file path, default=None'
+ help="parameter file path, default=None",
)
parser.add_option(
- '',
- '--hdu_num',
- dest='hdu_num',
- type='int',
+ "",
+ "--hdu_num",
+ dest="hdu_num",
+ type="int",
default=p_def.hdu_num,
- help=f'input HDU number, default=\'{p_def.hdu_num}\''
+ help=f"input HDU number, default='{p_def.hdu_num}'",
)
parser.add_option(
- '-v',
- '--verbose',
- dest='verbose',
- action='store_true',
- help='verbose output'
+ "-v",
+ "--verbose",
+ dest="verbose",
+ action="store_true",
+ help="verbose output",
)
options, args = parser.parse_args()
@@ -139,7 +136,7 @@ def parse_options(p_def):
def check_options(options):
"""Check Options.
-
+
Check command line options.
Parameters
@@ -158,7 +155,7 @@ def check_options(options):
def update_param(p_def, options):
"""Update Param.
-
+
Return default parameter, updated and complemented according to options.
Parameters
@@ -193,7 +190,7 @@ class param
def read_param_file(path, verbose=False):
"""Read Param File.
-
+
Return parameter list read from file.
Parameters
@@ -215,19 +212,19 @@ def read_param_file(path, verbose=False):
with open(path) as f:
for line in f:
- if line.startswith('#'):
- continue
+ if line.startswith("#"):
+ continue
entry = line.rstrip()
- if not entry or entry == '':
+ if not entry or entry == "":
continue
param_list.append(entry)
if verbose:
- if len(param_list) > 0:
- print(f'Copying {len(param_list)} columns', end='')
+ if len(param_list) > 0:
+ print(f"Copying {len(param_list)} columns", end="")
else:
- print('Copying all columns', end='')
- print(' into merged catalogue')
+ print("Copying all columns", end="")
+ print(" into merged catalogue")
# Check for multiples
multiples = []
@@ -236,19 +233,22 @@ def read_param_file(path, verbose=False):
multiples.append(param)
if len(multiples) > 0:
- print('The following parameters are more than one times '
- 'in the parameter file: ', end='')
+ print(
+ "The following parameters are more than one times "
+ "in the parameter file: ",
+ end="",
+ )
for m in multiples:
- print(m, end=' ')
+ print(m, end=" ")
print()
- raise ValueError('Multiple identical keys found')
+ raise ValueError("Multiple identical keys found")
return param_list
-
+
def get_data(path, hdu_num, param_list):
"""Get Data.
-
+
Return data of selected columns from FITS file.
Parameters
@@ -273,7 +273,7 @@ def get_data(path, hdu_num, param_list):
if param_list:
cols = []
for p in param_list:
- cols.append(hdu.columns[p])
+ cols.append(hdu.columns[p])
coldefs = fits.ColDefs(cols)
hdu_new = fits.BinTableHDU.from_columns(coldefs)
d = hdu_new.data
@@ -285,6 +285,7 @@ def get_data(path, hdu_num, param_list):
def main(argv=None):
+
# Set default parameters
p_def = params_default()
@@ -296,20 +297,28 @@ def main(argv=None):
param = update_param(p_def, options)
+ if param.verbose:
+ print("Start")
+
# Save command line arguments to log file
f_log = cfis.log_command(argv, close_no_return=False)
path = param.input_path
+ if param.verbose:
+ print("Read parameter file")
param.param_list = read_param_file(param.param_path, verbose=param.verbose)
# read (optional) input tile ID file
if param.tile_ID_list_path:
+ if param.verbose:
+ print("Read tile ID list")
tile_ID_list = cfis.read_list(param.tile_ID_list_path)
- # find input catalogue FITS files
+ if param.verbose:
+ print("Find input catalogue FITS files")
l = os.listdir(path=path)
- ext = 'fits'
+ ext = "fits"
lpath = []
for this_l in l:
@@ -318,22 +327,22 @@ def main(argv=None):
# mark to add if correct extension, matches input pattern,
if (
this_l.endswith(ext)
- and (f'{param.input_name_base}' in this_l)
- and ('.npy' not in this_l)
+ and (f"{param.input_name_base}" in this_l)
+ and (".npy" not in this_l)
):
add_this_l = True
# unmark to add if no in (optional) input tile ID file
- if param.tile_ID_list_path:
+ if param.tile_ID_list_path:
nix, niy = cfis.get_tile_number(this_l)
- tile_ID = f'{nix}.{niy}'
+ tile_ID = f"{nix}.{niy}"
if tile_ID not in tile_ID_list:
add_this_l = False
if add_this_l:
lpath.append(os.path.join(path, this_l))
if param.verbose:
- print(f'{len(lpath)} files files to merge found')
+ print(f"{len(lpath)} files files to merge found")
count = 0
@@ -344,7 +353,7 @@ def main(argv=None):
d[key] = d_tmp[key]
count = count + 1
if param.verbose:
- print(f'File \'{lpath[0]}\' copied ({count}/{len(lpath)})')
+ print(f"File '{lpath[0]}' copied ({count}/{len(lpath)})")
# merge remaining catalogue files
for fname in lpath[1:]:
@@ -358,21 +367,21 @@ def main(argv=None):
count = count + 1
if param.verbose:
- print(f'File \'{fname}\' copied ({count}/{len(lpath)})')
+ print(f"File '{fname}' copied ({count}/{len(lpath)})")
d = np.concatenate((d, dd))
except:
print(
- f'Error while adding file \'{fname}\', {len(dd)} objects'
- ' not in final cat'
+ f"Error while adding file '{fname}', {len(dd)} objects"
+ " not in final cat"
)
# Save merged catalogue as numpy binary file
if param.verbose:
- print('Saving merged catalogue')
- np.save(f'{param.input_name_base}.npy', d)
+ print("Saving merged catalogue")
+ np.save(f"{param.input_name_base}.npy", d)
- msg = f'{count} catalog files merged with success'
+ msg = f"{count} catalog files merged with success"
if param.verbose:
print(msg)
print(msg, file=f_log)
diff --git a/scripts/python/shapepipe_run.py b/scripts/python/shapepipe_run.py
index 18d7de774..a60f1eaed 100755
--- a/scripts/python/shapepipe_run.py
+++ b/scripts/python/shapepipe_run.py
@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#!/arc/home/kilbinger/.conda/envs/shapepipe/bin/python
"""SHAPEPIPE RUN SCRIPT
diff --git a/scripts/python/stats_global.py b/scripts/python/stats_global.py
index 950abba78..b3a6964b7 100755
--- a/scripts/python/stats_global.py
+++ b/scripts/python/stats_global.py
@@ -40,9 +40,9 @@ def params_default():
"""
p_def = cfis.param(
- input_dir = '.',
- output_dir = '.',
- pattern = 'star_stat-',
+ input_dir=".",
+ output_dir=".",
+ pattern="star_stat-",
)
return p_def
@@ -64,23 +64,49 @@ def parse_options(p_def):
Command line string
"""
- usage = "%prog [OPTIONS]"
+ usage = "%prog [OPTIONS]"
parser = OptionParser(usage=usage)
# I/O
- parser.add_option('-i', '--input_dir', dest='input_dir', type='string', \
- default=p_def.input_dir, \
- help='input directory, default=\'{}\''.format(p_def.input_dir))
- parser.add_option('-o', '--output_dir', dest='output_dir', type='string', \
- default=p_def.output_dir, \
- help='output directory, default=\'{}\''.format(p_def.output_dir))
- parser.add_option('-c', '--config', dest='config', type='string', \
- help='configuration file, default=none')
- parser.add_option('-p', '--pattern', dest='pattern', type='string', \
- default=p_def.pattern, \
- help='input file pattern, default=\'{}\''.format(p_def.pattern))
-
- parser.add_option('-v', '--verbose', dest='verbose', action='store_true', help='verbose output')
+ parser.add_option(
+ "-i",
+ "--input_dir",
+ dest="input_dir",
+ type="string",
+ default=p_def.input_dir,
+ help="input directory, default='{}'".format(p_def.input_dir),
+ )
+ parser.add_option(
+ "-o",
+ "--output_dir",
+ dest="output_dir",
+ type="string",
+ default=p_def.output_dir,
+ help="output directory, default='{}'".format(p_def.output_dir),
+ )
+ parser.add_option(
+ "-c",
+ "--config",
+ dest="config",
+ type="string",
+ help="configuration file, default=none",
+ )
+ parser.add_option(
+ "-p",
+ "--pattern",
+ dest="pattern",
+ type="string",
+ default=p_def.pattern,
+ help="input file pattern, default='{}'".format(p_def.pattern),
+ )
+
+ parser.add_option(
+ "-v",
+ "--verbose",
+ dest="verbose",
+ action="store_true",
+ help="verbose output",
+ )
options, args = parser.parse_args()
@@ -106,14 +132,14 @@ def check_options(options):
def update_param(p_def, options):
"""Return default parameter, updated and complemented according to options.
-
+
Parameters
----------
p_def: class param
parameter values
options: tuple
command line options
-
+
Returns
-------
param: class param
@@ -152,8 +178,11 @@ def get_stats_file_list(param):
"""
# Full paths
- paths = glob.glob('{}/output/*/setools_runner/output/stat/{}*'.
- format(param.input_dir, param.pattern))
+ paths = glob.glob(
+ "{}/output/*/setools_runner/output/stat/{}*".format(
+ param.input_dir, param.pattern
+ )
+ )
# File names w/o directories
names = []
@@ -170,8 +199,11 @@ def get_stats_file_list(param):
paths_unq.append(paths[i])
if param.verbose:
- print('{} files in total, {} unique files found'.
- format(len(paths), len(paths_unq)))
+ print(
+ "{} files in total, {} unique files found".format(
+ len(paths), len(paths_unq)
+ )
+ )
return paths_unq
@@ -196,11 +228,11 @@ def gather_values(paths, verbose=False):
for path in paths:
with open(path) as f:
lines = f.readlines()
- for line in lines:
+ for line in lines:
m = re.search("#", line)
if m:
continue
- m = re.search('(.*) = (\S*)', line)
+ m = re.search("(.*) = (\S*)", line)
if m:
key = m[1]
val = float(m[2])
@@ -210,13 +242,14 @@ def gather_values(paths, verbose=False):
values[key].append(val)
else:
if verbose:
- print('NaN found in file \'{}\', key \'{}\''
- .format(path, key))
+ print(
+ "NaN found in file '{}', key '{}'".format(path, key)
+ )
if verbose:
- print('{} keys created'.format(len(values)))
+ print("{} keys created".format(len(values)))
for key in values:
- print('#{{values[{}]}} = {}'.format(key, len(values[key])))
+ print("#{{values[{}]}} = {}".format(key, len(values[key])))
return values
@@ -239,12 +272,12 @@ def compute_histograms(values, config=None, verbose=False):
histograms for all keys
"""
- if config and config.has_option('ALL', 'nbins'):
- nbins_global = config.getint('ALL', 'nbins')
+ if config and config.has_option("ALL", "nbins"):
+ nbins_global = config.getint("ALL", "nbins")
else:
nbins_global = 50
- print('nbins_global = {}'.format(nbins_global))
+ print("nbins_global = {}".format(nbins_global))
hists = {}
i = 0
@@ -252,22 +285,22 @@ def compute_histograms(values, config=None, verbose=False):
si = str(i)
- if config and config.has_option(si, 'nbins'):
- nbins = config.getint(si, 'nbins')
+ if config and config.has_option(si, "nbins"):
+ nbins = config.getint(si, "nbins")
else:
nbins = nbins_global
try:
hists[key] = np.histogram(values[key], bins=nbins)
except ValueError as err:
- print('Skipping histogram #{}: {}'.format(i, err))
+ print("Skipping histogram #{}: {}".format(i, err))
i = i + 1
return hists
-def plot_histograms(hists, config=None, output_dir='.', verbose=False):
+def plot_histograms(hists, config=None, output_dir=".", verbose=False):
"""Create histogram plots.
Parameters
@@ -285,9 +318,9 @@ def plot_histograms(hists, config=None, output_dir='.', verbose=False):
fig, (ax) = plt.subplots()
plt.tight_layout()
- if config and config.has_option('ALL', 'fontsize'):
- fontsize = config.getint('ALL', 'fontsize')
- plt.rcParams.update({'font.size': fontsize})
+ if config and config.has_option("ALL", "fontsize"):
+ fontsize = config.getint("ALL", "fontsize")
+ plt.rcParams.update({"font.size": fontsize})
xlim_fac = 0.05
@@ -296,11 +329,13 @@ def plot_histograms(hists, config=None, output_dir='.', verbose=False):
si = str(i)
- if config and \
- config.has_option(si, 'plot') and \
- config.getboolean(si, 'plot') == False:
+ if (
+ config
+ and config.has_option(si, "plot")
+ and config.getboolean(si, "plot") == False
+ ):
if verbose:
- print('Skipping histogram #{} {}'.format(i, key))
+ print("Skipping histogram #{} {}".format(i, key))
else:
@@ -314,12 +349,12 @@ def plot_histograms(hists, config=None, output_dir='.', verbose=False):
# Overwrite limits if found in config file.
# If not stretch bin boundaries
- if config and config.has_option(si, 'xmin'):
- xmin = config.getfloat(si, 'xmin')
+ if config and config.has_option(si, "xmin"):
+ xmin = config.getfloat(si, "xmin")
else:
xmin = min(bins)
- if config and config.has_option(si, 'xmax'):
- xmax = config.getfloat(si, 'xmax')
+ if config and config.has_option(si, "xmax"):
+ xmax = config.getfloat(si, "xmax")
else:
xmax = max(bins)
@@ -327,19 +362,19 @@ def plot_histograms(hists, config=None, output_dir='.', verbose=False):
# If limits from bin boundaries: extend by small
# amount
- if config and config.has_option(si, 'xmin'):
+ if config and config.has_option(si, "xmin"):
xxmin = xmin
else:
xxmin = xmin - dx * xlim_fac
- if config and config.has_option(si, 'xmax'):
+ if config and config.has_option(si, "xmax"):
xxmax = xmax
else:
xxmax = xmax + dx * xlim_fac
plt.xlim(xxmin, xxmax)
- if config and config.has_option(si, 'xlabel'):
- xlabel = config.get(si, 'xlabel')
+ if config and config.has_option(si, "xlabel"):
+ xlabel = config.get(si, "xlabel")
else:
xlabel = key
plt.xlabel(xlabel)
@@ -347,28 +382,33 @@ def plot_histograms(hists, config=None, output_dir='.', verbose=False):
ymin = min(freq)
ymax = max(freq)
plt.ylim(ymin, ymax)
- ylabel = 'frequency'
+ ylabel = "frequency"
plt.ylabel(ylabel)
- if config and config.has_option(si, 'title'):
- plt.title(config.get(si, 'title'))
+ if config and config.has_option(si, "title"):
+ plt.title(config.get(si, "title"))
- if config and config.has_option(si, 'fname'):
- file_base = config.getexpanded(si, 'fname')
+ if config and config.has_option(si, "fname"):
+ file_base = config.getexpanded(si, "fname")
else:
- file_base = 'hist_{}'.format(i)
+ file_base = "hist_{}".format(i)
if verbose:
- print('Creating files \'{}.*\''.format(file_base))
-
- plt.savefig('{}/{}.png'.format(output_dir, file_base), bbox_inches='tight')
- np.savetxt('{}/{}.txt'.format(output_dir, file_base), np.transpose([bins, freq]),
- fmt='%10g', header='[{}] [{}]'.format(xlabel, ylabel)),
+ print("Creating files '{}.*'".format(file_base))
+
+ plt.savefig(
+ "{}/{}.png".format(output_dir, file_base), bbox_inches="tight"
+ )
+ np.savetxt(
+ "{}/{}.txt".format(output_dir, file_base),
+ np.transpose([bins, freq]),
+ fmt="%10g",
+ header="[{}] [{}]".format(xlabel, ylabel),
+ ),
i = i + 1
-
def get_config(config_path, verbose=False):
"""Return configuration file values.
@@ -391,10 +431,12 @@ def get_config(config_path, verbose=False):
from shapepipe.pipeline.config import CustomParser
if verbose:
- print('Reading configuration file \'{}\''.format(config_path))
+ print("Reading configuration file '{}'".format(config_path))
if not os.path.exists(config_path):
- raise OSError('Configuration file \'{}\' does not exist'.format(config_path))
+ raise OSError(
+ "Configuration file '{}' does not exist".format(config_path)
+ )
conf = CustomParser()
conf.read(config_path)
@@ -419,13 +461,12 @@ def main(argv=None):
# Save calling command
cfis.log_command(argv)
if param.verbose:
- cfis.log_command(argv, name='sys.stdout')
-
+ cfis.log_command(argv, name="sys.stdout")
### Start main program ###
if param.verbose:
- print('Start of program {}'.format(os.path.basename(argv[0])))
+ print("Start of program {}".format(os.path.basename(argv[0])))
files = get_stats_file_list(param)
@@ -436,22 +477,23 @@ def main(argv=None):
hists = compute_histograms(values, config=config, verbose=param.verbose)
if os.path.isfile(param.output_dir):
- raise OSError('Output path \'{}\' is a regular file'
- ''.format(param.output_dir))
+ raise OSError(
+ "Output path '{}' is a regular file" "".format(param.output_dir)
+ )
if not os.path.isdir(param.output_dir):
os.mkdir(param.output_dir)
- plot_histograms(hists, config=config, output_dir=param.output_dir,
- verbose=param.verbose)
+ plot_histograms(
+ hists, config=config, output_dir=param.output_dir, verbose=param.verbose
+ )
### End main program
if param.verbose:
- print('End of program {}'.format(os.path.basename(argv[0])))
+ print("End of program {}".format(os.path.basename(argv[0])))
return 0
if __name__ == "__main__":
sys.exit(main(sys.argv))
-
diff --git a/scripts/python/stats_headless_canfar.py b/scripts/python/stats_headless_canfar.py
new file mode 100755
index 000000000..1f728949d
--- /dev/null
+++ b/scripts/python/stats_headless_canfar.py
@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+
+# Name: stats_headless_canfar.py
+
+# Caution: Does not show all running or pending
+# headless jobs, for some reason.
+
+import sys
+from skaha.session import Session
+
+
+def main(argv=None):
+
+ print(
+ "# Depreciated, does not show pending jobs; use stats_jobs_canfar.sh",
+ file=sys.stderr,
+ )
+
+ session = Session()
+
+ n_headless = session.stats()["instances"]["headless"]
+
+ print(n_headless)
+
+ return 0
+
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv))
diff --git a/scripts/python/summary_params_pre_v2.py b/scripts/python/summary_params_pre_v2.py
new file mode 100644
index 000000000..70eda073c
--- /dev/null
+++ b/scripts/python/summary_params_pre_v2.py
@@ -0,0 +1,240 @@
+# Parameters for summary run
+
+import os
+from shapepipe.utilities.summary import *
+
+
+def set_jobs_v2_pre_v2(patch, verbose):
+ """Return information about shapepipe jobs"""
+ print(f"Set job info for patch {patch}")
+
+ # Main input and output directory
+ path_main = f"{os.environ['HOME']}/cosmostat/v2/pre_v2/psfex/{patch}"
+
+ # Logging
+ path = f"{path_main}/summary"
+ if not os.path.isdir(path):
+ os.mkdir(path)
+ log_file_name = f"{path}/summary_log.txt"
+ handlers = [
+ logging.FileHandler(log_file_name, mode="w"),
+ logging.StreamHandler(),
+ ]
+ logging.basicConfig(
+ level=logging.INFO, format="%(message)s", handlers=handlers
+ )
+
+ logging.info(f"Checking main directory = {path_main}")
+
+ # Tile IDs
+ tile_ID_path = f"{path_main}/tile_numbers.txt"
+
+ ## Tile IDs with dots
+ list_tile_IDs_dot = get_IDs_from_file(tile_ID_path)
+
+ jobs = {}
+
+ # Set the first job (retrieve images)
+
+ # With "CFIS_" only the linked images are counted. The original
+ # ones do not match the IDdash pattern.
+ # If images were downloaded in several runs:
+ # - Only copy original images, then (re-)set links in SP numbering format
+ # - get_images_runner_run_[12] consistent
+ # - remove previous output dirs since only last is searched
+ jobs["1"] = job_data(
+ 1,
+ "run_sp_GitFeGie",
+ [
+ "get_images_runner_run_1",
+ "find_exposures_runner",
+ "get_images_runner_run_2",
+ ],
+ ["tile_IDs", "tile_IDs", "exposures"],
+ pattern=["CFIS_", "", ""],
+ n_mult=[2, 1, 3],
+ path_main=path_main,
+ path_left="output",
+ verbose=verbose,
+ )
+
+ jobs["2"] = job_data(
+ 2,
+ ["run_sp_Uz", "run_sp_exp_SpMh", "run_sp_exp_SpMh"],
+ ["uncompress_fits_runner", "merge_headers_runner", "split_exp_runner"],
+ ["tile_IDs", 0, "exposures"],
+ n_mult=[1, 1, 121],
+ path_main=path_main,
+ path_left="output",
+ verbose=verbose,
+ )
+
+ jobs["4"] = job_data(
+ 4,
+ ["run_sp_Ma_tile"],
+ ["mask_runner"],
+ ["tile_IDs"],
+ path_main=path_main,
+ path_left="output",
+ verbose=verbose,
+ )
+
+ jobs["8"] = job_data(
+ 8,
+ ["run_sp_Ma_exp"],
+ ["mask_runner"],
+ ["shdus"],
+ path_main=path_main,
+ path_left="output",
+ verbose=verbose,
+ )
+
+ jobs["16"] = job_data(
+ 16,
+ "run_sp_tile_Sx",
+ ["sextractor_runner"],
+ ["tile_IDs"],
+ n_mult=2,
+ path_main=path_main,
+ path_left="tile_runs",
+ output_subdirs=[f"{tile_ID}/output" for tile_ID in list_tile_IDs_dot],
+ verbose=verbose,
+ )
+
+ # TODO 1 setools_runner output/rand_split
+ # TODO 2 add back Pi
+ jobs["32"] = job_data(
+ 32,
+ [
+ "run_sp_exp_SxSePsf",
+ "run_sp_exp_SxSePsf",
+ "run_sp_exp_SxSePsf",
+ "run_sp_exp_SxSePsf",
+ "run_sp_exp_SxSePsf",
+ #"run_sp_exp_Pi"
+ ],
+ [
+ "sextractor_runner",
+ "setools_runner",
+ "setools_runner",
+ "setools_runner",
+ "psfex_runner",
+ # "psfex_interp_runner"],
+ ],
+ "shdus",
+ n_mult=[2, 2, 1, 1, 2],
+ path_main=path_main,
+ path_left="exp_runs",
+ output_subdirs="shdus",
+ path_right="output",
+ path_output=[
+ "output",
+ "output/rand_split",
+ "output/stat",
+ "logs",
+ "output",
+ ],
+ special=[False, False, True, True, False],
+ verbose=verbose,
+ )
+
+ # For P3
+ # jobs["33"] = job_data(
+ # 33,
+ # "run_sp_exp_Pi",
+ # ["psfex_interp_runner"],
+ # "shdus",
+ # path_main=path_main,
+ # path_left="exp_runs",
+ # output_subdirs="shdus",
+ # path_right="output",
+ # verbose=verbose,
+ # )
+
+ jobs["64"] = job_data(
+ "64",
+ "run_sp_tile_PsViSmVi",
+ [
+ "psfex_interp_runner",
+ "psfex_interp_runner",
+ "vignetmaker_runner_run_1",
+ "spread_model_runner",
+ "vignetmaker_runner_run_2",
+ ],
+ "tile_IDs",
+ n_mult=[1, 1, 1, 1, 4],
+ path_main=path_main,
+ path_left="tile_runs",
+ output_subdirs=[f"{tile_ID}/output" for tile_ID in list_tile_IDs_dot],
+ path_output=["output", "logs", "output", "output", "output"],
+ special=[False, True, False, False, False],
+ verbose=verbose,
+ )
+
+ if patch in ("P2", "P5"):
+ n_sh = 1
+ else:
+ n_sh = 8
+ run_dirs = [f"run_sp_tile_ngmix_Ng{idx+1}u" for idx in range(n_sh)]
+ output_path_missing_IDs = [
+ f"{path_main}/summary/missing_job_128_ngmix_runner_{idx+1}.txt"
+ for idx in range(n_sh)
+ ]
+ jobs["128"] = job_data(
+ "128",
+ run_dirs,
+ ["ngmix_runner"] * n_sh,
+ "tile_IDs",
+ path_main=path_main,
+ path_left="tile_runs",
+ output_subdirs=[f"{tile_ID}/output" for tile_ID in list_tile_IDs_dot],
+ output_path_missing_IDs=output_path_missing_IDs,
+ verbose=verbose,
+ )
+
+ jobs["256"] = job_data(
+ "256",
+ ["run_sp_Ms"],
+ ["merge_sep_cats_runner"],
+ "tile_IDs",
+ path_main=path_main,
+ path_left="tile_runs",
+ output_subdirs=[f"{tile_ID}/output" for tile_ID in list_tile_IDs_dot],
+ verbose=verbose,
+ )
+
+ jobs["512"] = job_data(
+ "512",
+ ["run_sp_Mc"],
+ ["make_cat_runner"],
+ "tile_IDs",
+ path_main=path_main,
+ path_left="tile_runs",
+ output_subdirs=[f"{tile_ID}/output" for tile_ID in list_tile_IDs_dot],
+ verbose=verbose,
+ )
+
+ # Post-processing
+ jobs["1024"] = job_data(
+ "1024",
+ ["run_sp_combined_final"],
+ ["make_catalog_runner"],
+ "tile_IDs",
+ path_main=path_main,
+ path_left="output",
+ verbose=verbose,
+ )
+
+ jobs["2048"] = job_data(
+ "2048",
+ "run_sp_combined_psf",
+ ["psfex_interp_runner"],
+ "shdus",
+ path_main=path_main,
+ path_left="output",
+ verbose=verbose,
+ )
+
+ return jobs, list_tile_IDs_dot
+
+
diff --git a/scripts/python/summary_run.py b/scripts/python/summary_run.py
new file mode 100755
index 000000000..f24d6574d
--- /dev/null
+++ b/scripts/python/summary_run.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+import sys
+import os
+
+from shapepipe.utilities.summary import *
+
+from summary_params_pre_v2 import *
+
+
+def main(argv=None):
+
+ patch = argv[1]
+
+ if len(argv) == 3:
+ job_exclusive = argv[2]
+ else:
+ job_exclusive = None
+
+ verbose = False
+
+ jobs, list_tile_IDs_dot = set_jobs_v2_pre_v2(patch, verbose)
+
+ list_tile_IDs = job_data.replace_dot_dash(list_tile_IDs_dot)
+
+ # Numbers updated at runtime
+ par_runtime = init_par_runtime(list_tile_IDs)
+
+ job_data.print_stats_header()
+
+ exp_IDs_path = "exp_numbers.txt"
+ if os.path.exists(exp_IDs_path):
+ # Read exposure ID list if file exists
+ all_exposures = get_IDs_from_file(exp_IDs_path)
+ par_runtime = update_par_runtime_after_find_exp(
+ par_runtime, all_exposures
+ )
+
+ if (
+ not os.path.exists(exp_IDs_path)
+ or not job_exclusive
+ or int(job_exclusive) & 1
+ ):
+ # Run job 1 if exposure ID list file does not exist or
+ # job_exclusive is 1 or not set
+ key = "1"
+ jobs[key].print_intro()
+ jobs[key].check_numbers(par_runtime=par_runtime, indices=[0, 1])
+
+ all_exposures = get_all_exposures(
+ jobs[key]._paths_in_dir[1], verbose=True
+ )
+ par_runtime = update_par_runtime_after_find_exp(
+ par_runtime, all_exposures
+ )
+
+ jobs[key].write_IDs_to_file("exp_numbers.txt", all_exposures)
+
+ jobs[key].check_numbers(par_runtime, indices=[2])
+
+ print_par_runtime(par_runtime, verbose=verbose)
+
+ # Get all keys after "1"
+ keys = sorted(jobs.keys(), key=int)
+ _ = keys.pop(0)
+
+ for key in keys:
+ if job_exclusive and not int(key) & int(job_exclusive):
+ continue
+ jobs[key].print_intro()
+ jobs[key].check_numbers(par_runtime=par_runtime)
+
+ return 0
+
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv))
diff --git a/scripts/python/update_runs_log_file.py b/scripts/python/update_runs_log_file.py
new file mode 100644
index 000000000..6cd1fde63
--- /dev/null
+++ b/scripts/python/update_runs_log_file.py
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+
+import re
+import sys
+import os
+
+
+# TODO: move to cs_util
+def matching_subdirs(base_dir, pattern, tail=False):
+
+ # Find all matching subdirectories
+ subdirs = []
+ for entry in os.listdir(base_dir):
+ full_path = os.path.join(base_dir, entry)
+ if os.path.isdir(full_path):
+ found = False
+
+ # Look for pattern at start or end
+ if pattern in entry:
+
+ # Get full path or last part ("tail")
+ if not tail:
+ path = full_path
+ else:
+ head, tail = os.path.split(full_path)
+ path = tail
+
+ # Remove postfix in case of multiple runs of same module
+ path = re.sub("_run_.\d?", "", path)
+
+ # Append to result
+ subdirs.append(path)
+
+ # Sort according to creation date
+ if not tail:
+ subdirs.sort(key=os.path.getctime)
+
+ return subdirs
+
+
+def get_module_runs(subdirs):
+
+ all_runs = {}
+ for subdir in subdirs:
+ runs = matching_subdirs(subdir, "_runner", tail=True)
+ if len(runs) > 0:
+ all_runs[subdir] = runs
+
+ return all_runs
+
+
+def update_log_file(module_runs, log_name):
+
+ with open(log_name, "w") as f_out:
+ for key in module_runs:
+ print(key, file=f_out, end=" ")
+ print(",".join(module_runs[key]), file=f_out)
+
+
+def main(argv=None):
+
+ # Set default parameters
+ # p_def = params_default()
+
+ # Command line options
+ # options, args = parse_options(p_def)
+
+ # if check_options(options) is False:
+ # return 1
+
+ # param = update_param(p_def, options)
+
+ base_dir = "./output"
+ pattern = "run_sp_"
+ log_name = f"{base_dir}/log_run_sp.txt"
+
+ subdirs = matching_subdirs(base_dir, pattern)
+ module_runs = get_module_runs(subdirs)
+ # save_prev(log_name)
+ update_log_file(module_runs, log_name)
+
+ return 0
+
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv))
diff --git a/scripts/python/vignets2image.py b/scripts/python/vignets2image.py
index 7fb444246..60933173c 100755
--- a/scripts/python/vignets2image.py
+++ b/scripts/python/vignets2image.py
@@ -35,48 +35,47 @@ def map_vignet(img_arr, dtype):
ys = img_arr[0].shape[1]
nx = int(np.sqrt(n_obj))
- if nx*nx != n_obj:
+ if nx * nx != n_obj:
nx += 1
ny = nx
- img_map=np.ones((xs*nx,ys*ny), dtype=dtype)
+ img_map = np.ones((xs * nx, ys * ny), dtype=dtype)
- ii=0
- jj=0
+ ii = 0
+ jj = 0
for i in range(n_obj):
- if jj>nx-1:
- jj=0
- ii+=1
- img_map[ii*xs:(ii+1)*xs,jj*ys:(jj+1)*ys]=img_arr[i]
- jj+=1
+ if jj > nx - 1:
+ jj = 0
+ ii += 1
+ img_map[ii * xs : (ii + 1) * xs, jj * ys : (jj + 1) * ys] = img_arr[i]
+ jj += 1
return img_map, nx
-
def main(argv=None):
- path = '.'
- pattern = 'UNIONS_'
- prefix_out = 'img_'
+ path = "."
+ pattern = "UNIONS_"
+ prefix_out = "img_"
- files = glob.glob('{}/{}*.fits'.format(path, pattern))
+ files = glob.glob("{}/{}*.fits".format(path, pattern))
for input_path in files:
- output_path = '{}{}'.format(prefix_out, os.path.basename(input_path))
+ output_path = "{}{}".format(prefix_out, os.path.basename(input_path))
hdu = fits.open(input_path)
- image, nx = map_vignet(hdu[2].data['VIGNET'], 'float32')
- print('file = {}, nx = {}'.format(input_path, nx))
+ image, nx = map_vignet(hdu[2].data["VIGNET"], "float32")
+ print("file = {}, nx = {}".format(input_path, nx))
- fout = io.FITSCatalog(output_path, open_mode=io.BaseCatalog.OpenMode.ReadWrite)
+ fout = io.FITSCatalog(
+ output_path, open_mode=io.BaseCatalog.OpenMode.ReadWrite
+ )
fout.save_as_fits(image, image=True)
return 0
-
if __name__ == "__main__":
sys.exit(main(sys.argv))
-
diff --git a/scripts/sh/combine_runs.bash b/scripts/sh/combine_runs.bash
new file mode 100755
index 000000000..c264f3cbf
--- /dev/null
+++ b/scripts/sh/combine_runs.bash
@@ -0,0 +1,216 @@
+#!/usr/bin/env bash
+
+# Name: combine_runs.bash
+# Description: Create new shapepipe run directory with
+# links to source files from combined existing runs
+# Author: Martin Kilbinger
+
+
+# Command line arguments
+
+## Default values
+cat='final'
+psf="mccd"
+
+## Help string
+usage="Usage: $(basename "$0") [OPTIONS]
+\n\nOptions:\n
+ -h\tthis message\n
+ -p, --psf MODEL\n
+ \tPSF model, allowed are 'psfex', 'mccd', 'setools', default='$psf'\n
+ -c, --cat TYPE\n
+ \tCatalogue type, allowed are 'final', 'flag_tile', 'flag_exp', \n
+ \t'psf', 'psf_conv', 'image', default='$cat'\n
+"
+
+## Parse command line
+while [ $# -gt 0 ]; do
+ case "$1" in
+ -h)
+ echo -ne $usage
+ exit 0
+ ;;
+ -c|--cat)
+ cat="$2"
+ shift
+ ;;
+ -p|--psf)
+ psf="$2"
+ shift
+ ;;
+ *)
+ echo -ne $usage
+ exit 1
+ ;;
+ esac
+ shift
+done
+
+
+## Check options
+if [ "$cat" != "final" ] \
+ && [ "$cat" != "flag_tile" ] \
+ && [ "$cat" != "tile_detection" ] \
+ && [ "$cat" != "flag_exp" ] \
+ && [ "$cat" != "psf" ] \
+ && [ "$cat" != "psf_conv" ] \
+ && [ "$cat" != "image" ]; then
+ echo "cat (option -c) needs to be 'final', 'tile_detection', 'flag_tile', 'flag_exp', 'psf', 'psf_conv' or 'image'"
+ exit 2
+fi
+
+## Check options
+if [ "$psf" != "psfex" ] \
+ && [ "$psf" != "mccd" ] \
+ && [ "$psf" != "setools" ]; then
+ echo "PSF (option -p) needs to be 'psfex' or 'mccd'"
+ exit 2
+fi
+
+
+## Functions
+function link_s () {
+ target=$1
+ link_name=$2
+
+ if [ -L "$link_name" ]; then
+ echo "link with name $link_name already exists, skipping..."
+ let "n_skipped+=1"
+ else
+ echo "create link $target <- $link_name"
+ ln -s $target $link_name
+ let "n_created+=1"
+ fi
+}
+
+
+# Start program
+
+n_skipped=0
+n_created=0
+
+pwd=`pwd`
+out_base="output"
+
+# Set paths:
+## run_out: target output new run directory
+## run_in: source input run base directory
+## module: source input module runner sub-directory
+## pattern: source file pattern
+
+run_out="run_sp_combined_$cat"
+
+if [ "$cat" == "final" ]; then
+
+ # v1
+ #run_in="$pwd/$out_base/run_sp_Mc_*"
+ # v2
+ run_in="$pwd/tile_runs/*/$out_base/run_sp_Mc_*"
+
+ module="make_catalog_runner"
+ pattern="final_cat-*"
+
+elif [ "$cat" == "tile_detection" ]; then
+
+ run_in="$pwd/P?/tile_runs/*/$out_base/run_sp_tile_Sx_*"
+ module="sextractor_runner"
+ pattern="sexcat-*"
+
+elif [ "$cat" == "flag_tile" ]; then
+
+ # v1
+ #run_in="$pwd/$out_base/run_sp_MaMa_*/mask_runner_run_1"
+ # v2
+ run_in="$pwd/$out_base/run_sp_tile_Ma_*"
+ run_out="run_sp_Ma_tile"
+
+ module="mask_runner"
+ pattern="pipeline_flag-*"
+
+elif [ "$cat" == "flag_exp" ]; then
+
+ # v1
+ #run_in="$pwd/$out_base/run_sp_MaMa_*/mask_runner_run_2"
+ # v2
+ run_in="$pwd/$out_base/run_sp_exp_Ma_*"
+ run_out="run_sp_Ma_exp"
+
+ module="mask_runner"
+ pattern="pipeline_flag-*"
+
+elif [ "$cat" == "image" ]; then
+
+ run_in="$pwd/$out_base/run_sp_Git_*"
+ module="get_images_runner"
+ pattern="CFIS_image-*"
+
+elif [ "$cat" == "psf" ]; then
+
+ #MKDEBUG TODO: add option
+ # v1
+ #run_in="$pwf/$out_base/run_sp_exp_Pi_*"
+ # v2
+ #run_in="$pwd/exp_runs/*/$out_base/run_sp_exp_Pi_*"
+ run_in="$pwd/exp_runs/*/$out_base/run_sp_exp_SxSePsfPi_*"
+
+ pattern="validation_psf-*"
+ if [ "$psf" == "psfex" ]; then
+ module="psfex_interp_runner"
+ elif [ "$psf" == "setools" ]; then
+ module="setools_runner"
+ else
+ module="mccd_interp_runner"
+ fi
+
+elif [ "$cat" == "psf_conv" ]; then
+
+ run_in="$pwd/../P?"
+ pattern="validation_psf_conv-*"
+ module="psfex_interp_runner"
+
+else
+
+ echo "Invalid catalogue type $cat"
+ exit 2
+
+fi
+
+
+OUTPUT="$pwd/$out_base/$run_out"
+mkdir -p $OUTPUT
+
+
+# Create links
+
+## target directory
+outdir=$OUTPUT/$module/output
+mkdir -p $outdir
+
+## identify source files
+
+# The following can result in an "Argument list too long" error
+#FILES=(`find $run_in -type f -name "$pattern" -print0 | xargs -0 echo`)
+
+i=0
+for dir in $run_in; do
+ FILES=(`find $dir -type f -name "$pattern" -print0 | xargs -0 echo`)
+
+ echo "$dir $pattern"
+
+ ## Look over source files
+ for file in ${FILES[@]}; do
+
+ target=$file
+ link_name=$outdir/`basename $file`
+ link_s $target $link_name
+ ((i=i+1))
+
+ done
+
+done
+
+#echo " $n_files target files, $i links created/skipped"
+echo " $i total, "$n_skipped skipped, "$n_created links created"
+
+# Update log file
+update_runs_log_file.py
diff --git a/scripts/sh/curl_canfar_local.sh b/scripts/sh/curl_canfar_local.sh
new file mode 100755
index 000000000..13e087936
--- /dev/null
+++ b/scripts/sh/curl_canfar_local.sh
@@ -0,0 +1,296 @@
+#!/usr/bin/env bash
+
+# Global variables
+SSL=~/.ssl/cadcproxy.pem
+SESSION=https://ws-uv.canfar.net/skaha/v0/session
+IMAGE=images.canfar.net/unions/shapepipe
+NAME=shapepipe
+
+
+# Command line arguments
+
+## Default values
+job=-1
+psf="psfex"
+ID=-1
+file_IDs=-1
+N_SMP=1
+version="1.1"
+cmd_remote="$HOME/shapepipe/scripts/sh/init_run_exclusive_canfar.sh"
+batch_max=200
+dry_run=0
+mh_local=0
+debug_out="-1"
+
+pat="- "
+
+## Help string
+usage="Usage: $(basename "$0") -j JOB -[e ID |-f file_IDs] -k KIND [OPTIONS]
+\n\nOptions:\n
+ -h\tthis message\n
+ -j, --job JOB\tRunning JOB, bit-coded\n
+ -e, --exclusive ID
+ \timage ID\n
+ -f, --file_IDs path
+ \tfile containing IDs\n
+ -p, --psf MODEL\n
+ \tPSF model, one in ['psfex'|'mccd'], default='$psf'\n
+ -m, --mh_local MH\n
+ \tmerged header file local (MH=0) or global (MH=1); default is $mh_local\n
+ -N, --N_SMP N_SMOp\n
+ \tnumber of jobs (SMP mode only), default=$N_SMP\n
+ -V, --version\n
+ \tversion of docker image, default='$version'\n
+ -C, --command_remote\n
+ \tremote command to run on canfar, default='$cmd_remote'\n
+ -b, --batch_max\n
+ \tmaximum batch size = number of jobs run simultaneously, default=$batch_max\n
+ --debug_out PATH\n
+ \tdebug output file PATH, default not used\n
+ -n, --dry_run LEVEL\n
+ \tdry run, from LEVEL=2 (no processing) to 0 (full run)\n
+"
+
+## Help if no arguments
+if [ -z $1 ]; then
+ echo -ne $usage
+ exit 1
+fi
+
+## Parse command line
+while [ $# -gt 0 ]; do
+ case "$1" in
+ -h)
+ echo -ne $usage
+ exit 0
+ ;;
+ -j|--job)
+ job="$2"
+ shift
+ ;;
+ -p|--psf)
+ psf="$2"
+ shift
+ ;;
+ -m|--mh_local)
+ mh_local="$2"
+ shift
+ ;;
+ -e|--exclusive)
+ ID="$2"
+ shift
+ ;;
+ -f|--file_IDs)
+ file_IDs="$2"
+ shift
+ ;;
+ -N|--N_SMP)
+ N_SMP="$2"
+ shift
+ ;;
+ -b|--batch_max)
+ batch_max="$2"
+ shift
+ ;;
+ --debug_out)
+ debug_out="$2"
+ shift
+ ;;
+ -n|--dry_run)
+ dry_run="$2"
+ shift
+ ;;
+ esac
+ shift
+done
+
+## Check options
+if [ "$job" == "-1" ]; then
+ echo "No job indicated, use option -j"
+ exit 2
+fi
+
+if [ "$ID" == "-1" ] && [ "$file_IDs" == "-1" ]; then
+ echo "No image ID(s) indicated, use option -e ID or -f file_IDs"
+ exit 3
+fi
+
+if [ "$psf" != "psfex" ] && [ "$psf" != "mccd" ]; then
+ echo "PSF (option -p) needs to be 'psfex' or 'mccd'"
+ exit 4
+fi
+
+if [ "$dry_run" != 0 ] && [ "$dry_run" != 1 ] && [ "$dry_run" != 2 ]; then
+ echo "Invalid dry_run option, allowed are 0, 1, and 2"
+ exit 5
+fi
+
+if [ "$debug_out" != "-1" ]; then
+ echo "${pat}Starting $(basename "$0")" >> $debug_out
+ echo $pat`date`$ >> $debug_out
+fi
+
+. /opt/conda/etc/profile.d/conda.sh
+conda activate shapepipe
+if [ "$debug_out" != "-1" ]; then
+ echo "${pat}conda prefix = ${CONDA_PREFIX}" >> $debug_out
+fi
+
+# command line arguments for remote script:
+# collect into string
+
+if [ "$dry_run" == "1" ]; then
+ arg_dry_run="-n $dry_run"
+else
+ arg_dry_run=""
+fi
+
+RESOURCES="ram=4&cores=$N_SMP"
+dir=`pwd`
+
+
+# Return argument for local script to be called via curl
+function set_arg() {
+ my_arg="-j $job -p $psf -e $ID -N $N_SMP $arg_dry_run -d $dir -m $mh_local --debug_out $debug_out"
+ echo $my_arg
+}
+
+
+function call_curl() {
+ my_name=$1
+ dry_run=$2
+
+ my_arg=$(set_arg)
+
+ if [ "$dry_run" == "0" ]; then
+
+ cp ~/sicher.pem ~/.ssl/cadcproxy.pem
+ my_session=`curl -E $SSL "$SESSION?$RESOURCES" -d "image=$IMAGE:$version" -d "name=${my_name}" -d "cmd=$cmd_remote" --data-urlencode "args=${my_arg[@]}" &> /dev/null`
+ fi
+
+
+ cmd=("curl" "-E" "$SSL" "$SESSION?$RESOURCES" "-d" "image=$IMAGE:$version" "-d" "name=${my_name}" "-d" "cmd=$cmd_remote" "--data-urlencode" "args=\"${my_arg}\"")
+
+ if [ "$debug_out" != "-1" ]; then
+ echo "${pat}call_curl $my_name $my_arg" >> $debug_out
+ echo "${pat}Running ${cmd[@]} (dry_run=$dry_run)" >> $debug_out
+ fi
+ echo "${cmd[@]} (dry_run=$dry_run)"
+ cp ~/sicher.pem ~/.ssl/cadcproxy.pem
+
+
+ # Running $cmd does not work due to unknown problems with passing of args
+
+ update_session_logs
+}
+
+# Add session and image IDs to log files
+function update_session_logs() {
+ echo $my_session >> session_IDs.txt
+ echo "$my_session $ID" >> session_image_IDs.txt
+
+}
+
+function submit_batch() {
+ path=$1
+
+ for ID in `cat $path`; do
+ IDt=`echo $ID | tr "." "-"`
+ my_name="SP-${patch}-J${job}-${IDt}"
+
+ call_curl $my_name $dry_run
+
+ done
+
+}
+
+batch=50
+sleep=75
+
+((n_thresh=batch_max-batch))
+
+
+if [ "$dry_run" == 2 ]; then
+
+ # Do not call curl (dry run = 2)
+ echo "Running command dry run:"
+
+ if [ "$ID" == "-1" ]; then
+
+
+ # Submit file (dry run = 2)
+ for ID in `cat $file_IDs`; do
+ IDt=`echo $ID | tr "." "-"`
+ my_name="SP-${patch}-J${job}-${IDt}"
+ call_curl $my_name $dry_run
+ done
+
+ else
+
+ # Submit image (dry run = 2)
+ IDt=`echo $ID | tr "." "-"`
+ my_name="SP-${patch}-J${job}-${IDt}"
+ call_curl $my_name $dry_run
+
+ fi
+
+else
+
+ # Call curl
+ rm -rf session_IDs.txt session_image_IDs.txt
+
+ if [ "$ID" == "-1" ]; then
+
+ # Submit file
+ n_jobs=`cat $file_IDs | wc -l`
+ if [ "$n_jobs" -gt "$batch_max" ]; then
+
+ # Split into batches
+ prefix="${file_IDs}_split_"
+ split -d -l $batch $file_IDs $prefix
+ n_split=`ls -l $prefix* | wc -l`
+ echo "Split '$file_IDs' into $n_split batches of size $batch"
+
+ count=1
+ n_running=`stats_jobs_canfar.sh`
+ for batch in $prefix*; do
+ echo "Number of running jobs = $n_running"
+ echo "Submitting batch $batch ($count/$n_split)"
+ echo -ne "\033]0;curl patch=$patch job=$job $count/$n_split\007"
+ submit_batch $batch
+ ((count=count+1))
+
+ n_running=`stats_jobs_canfar.sh`
+
+ while [ "$n_running" -gt "$n_thresh" ]; do
+ echo "Wait for #jobs = $n_running jobs to go < $n_thresh ..."
+ sleep $sleep
+ n_running=`stats_jobs_canfar.sh`
+ done
+
+ done
+
+ else
+
+ # Submit entire file (single batch)
+ echo "Submit '$file_IDs' in single batch"
+ submit_batch $file_IDs
+
+ fi
+
+ else
+
+ # Submit image
+ IDt=`echo $ID | tr "." "-"`
+ my_name="SP-${patch}-J${job}-${IDt}"
+ call_curl $my_name $dry_run
+
+ fi
+
+fi
+
+echo "Done $(basename "$0")"
+
+if [ "$debug_out" != "-1" ]; then
+ echo "${pat}End $(basename "$0")" >> $debug_out
+fi
diff --git a/scripts/sh/curl_canfar_monitor_local.sh b/scripts/sh/curl_canfar_monitor_local.sh
new file mode 100755
index 000000000..d2b115c1f
--- /dev/null
+++ b/scripts/sh/curl_canfar_monitor_local.sh
@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+
+# -H "Accept-Encoding: gzip" faster?
+
+SSL=~/.ssl/cadcproxy.pem
+SESSION=https://ws-uv.canfar.net/skaha/v0/session
+
+type=$1
+
+echo "type=$type"
+
+for session_ID in `cat ids.txt`; do
+ cmd="curl -E $SSL $SESSION/$session_ID?view=$type"
+ echo $cmd
+ $cmd
+done
+
+exit 0
+
+while [ 1 ]; do
+ session_ID=`tail -n 1 ids.txt`
+ cmd="curl -E $SSL $SESSION/$session_ID?view=$type"
+ echo $cmd
+ $cmd
+done
diff --git a/scripts/sh/init_run_exclusive_canfar.sh b/scripts/sh/init_run_exclusive_canfar.sh
new file mode 100755
index 000000000..1faedc767
--- /dev/null
+++ b/scripts/sh/init_run_exclusive_canfar.sh
@@ -0,0 +1,453 @@
+#!/bin/bash
+
+# init_run_exclusive_canfar.sh
+
+# Command line arguments
+## Default values
+job=-1
+ID=-1
+N_SMP=1
+dry_run=0
+dir=`pwd`
+debug_out=-1
+
+# mh_local is 0 (1) if merge_header_runner is run on all exposures,
+# which is standard so far (run on exposures of given tile only; new)
+mh_local=0
+
+# sp_local is 0 (1) is split_headers_runner and mask_runner is run
+# on all exposures (locally). Not 100% automatic yet.
+sp_local=1
+VERBOSE=1
+
+pat="-- "
+
+
+## Help string
+usage="Usage: $(basename "$0") -j JOB -e ID -k KIND [OPTIONS]
+\n\nOptions:\n
+ -h\tthis message\n
+ -j, --job JOB\tRUnning JOB, bit-coded\n
+ -e, --exclusive ID
+ \timage ID\n
+ -p, --psf MODEL\n
+ \tPSF model, one in ['psfex'|'mccd'], default='$psf'\n
+ -m, --mh_local MH\n
+ \tmerged header file local (MH=0) or global (MH=1); default is $mh_local\n
+ -N, --N_SMP N_SMOp\n
+ \tnumber of jobs (SMP mode only), default from original config files\n
+ -d, --directory\n
+ \trun directory, default is pwd ($dir)\n
+ -n, --dry_run\n
+ \tdry run, no actuall processing\n
+ --debug_out PATH\n
+ \tdebug output file PATH, default not used\n
+"
+
+## Help if no arguments
+if [ -z $1 ]; then
+ echo -ne $usage
+ exit 1
+fi
+
+## Parse command line
+while [ $# -gt 0 ]; do
+ case "$1" in
+ -h)
+ echo -ne $usage
+ exit 0
+ ;;
+ -j|--job)
+ job="$2"
+ shift
+ ;;
+ -e|--exclusive)
+ ID="$2"
+ shift
+ ;;
+ -p|--psf)
+ psf="$2"
+ shift
+ ;;
+ -m|--mh_local)
+ mh_local="$2"
+ shift
+ ;;
+ -N|--N_SMP)
+ N_SMP="$2"
+ shift
+ ;;
+ -d|--directory)
+ dir="$2"
+ shift
+ ;;
+ -n|--dry_run)
+ dry_run=1
+ ;;
+ --debug_out)
+ debug_out="$2"
+ shift
+ ;;
+ esac
+ shift
+done
+
+## Check options
+if [ "$job" == "-1" ]; then
+ echo "No job indicated, use option -j"
+ exit 2
+fi
+
+if [ "$exclusive" == "-1" ]; then
+ echo "No image ID indicated, use option -e"
+ exit 3
+fi
+
+if [ "$psf" != "psfex" ] && [ "$psf" != "mccd" ]; then
+ echo "PSF (option -p) needs to be 'psfex' or 'mccd'"
+ exit 4
+fi
+
+if [ "$mh_local" != "0" ] && [ "$mh_local" != "1" ]; then
+ echo "mh_local (option -m) needs to be 0 or 1"
+ exit 5
+fi
+
+# Functions
+
+## Print string, executes command, and prints return value.
+function command () {
+ cmd=$1
+ dry_run=$2
+
+ RED='\033[0;31m'
+ GREEN='\033[0;32m'
+ NC='\033[0m' # No Color
+ # Color escape characters show up in log files
+ #RED=''
+ #GREEN=''
+ #NC=''
+
+ msg="running '$cmd' (dry run=$dry_run)"
+ if [ $VERBOSE == 1 ]; then
+ echo $msg
+ fi
+ if [ "$debug_out" != "-1" ]; then
+ echo ${pat}$msg >> $debug_out
+ fi
+
+ if [ "$dry_run" == "0" ]; then
+ $cmd
+ res=$?
+
+ if [ "$debug_out" != "-1" ]; then
+ echo "${pat}exit code = $res" >> $debug_out
+ fi
+
+ if [ $VERBOSE == 1 ]; then
+ if [ $res == 0 ]; then
+ echo -e "${GREEN}success, return value = $res${NC}"
+ else
+ echo -e "${RED}error, return value = $res${NC}"
+ if [ $STOP == 1 ]; then
+ echo "${RED}exiting $(basename "$0")', error in command '$cmd'${NC}"
+ exit $res
+ else
+ echo "${RED}continuing '$(basename "$0")', error in command '$cmd'${NC}"
+ fi
+ fi
+ fi
+ fi
+}
+
+msg="Starting $(basename "$0")"
+echo $msg
+if [ "$debug_out" != "-1" ]; then
+ echo $pat$msg >> $debug_out
+ echo ${pat}`date` >> $debug_out
+fi
+
+# Set kind
+job_to_test=2
+kind="none"
+
+# loop over possible job numbers
+while [ $job_to_test -le 1024 ]; do
+
+ (( do_job = $job & $job_to_test ))
+ if [[ $do_job != 0 ]]; then
+
+ if [ $job_to_test == 32 ]; then
+ if [ "$kind" == "tile" ]; then
+ echo "Error: Invalid job $job. mixing tile and exp kinds"
+ exit 6
+ fi
+
+ # job=32 -> set kind to exp
+ kind="exp"
+ elif [ $job_to_test == 2 ]; then
+ if [ "$kind" == "tile" ]; then
+ echo "Error: Invalid job $job. mixing tile and exp kinds"
+ exit 6
+ fi
+
+ kind="exp"
+ elif [ $job_to_test == 8 ]; then
+ if [ "$kind" == "tile" ]; then
+ echo "Error: Invalid job $job. mixing tile and exp kinds"
+ exit 6
+ fi
+
+ kind="exp"
+ else
+ if [ "$kind" == "exp" ]; then
+ echo "Error: Invalid job $job. mixing tile and exp kinds"
+ exit 6
+ fi
+
+ # job != 32 -> set kind to tile
+ kind="tile"
+ fi
+
+ fi
+
+ # Multiply job number by two to get next biwise number
+ job_to_test=$((job_to_test * 2))
+done
+
+if [ "$kind" == "none" ]; then
+ echo "Error: invalid job $job"
+ exit 5
+fi
+
+
+if [ "$dry_run" == 1 ]; then
+ echo "in dry run mode"
+fi
+
+CONDA_PREFIX=/arc/home/kilbinger/.conda/envs/shapepipe
+PATH=$PATH:$CONDA_PREFIX/bin
+if [ "$debug_out" != "-1" ]; then
+ echo "${pat}conda prefix = ${CONDA_PREFIX}" >> $debug_out
+ echo "${pat}HOME = ${HOME}" >> $debug_out
+ echo "${pat}path = ${PATH}" >> $debug_out
+fi
+
+cd $dir
+echo $pwd
+
+if [ ! -d ${kind}_runs ]; then
+ command "mkdir ${kind}_runs" $dry_run
+fi
+
+
+cd ${kind}_runs
+
+if [ ! -d "$ID" ]; then
+ command "mkdir $ID" $dry_run
+fi
+
+cd $ID
+pwd
+
+
+if [ ! -d "output" ]; then
+ command "mkdir output" $dry_run
+fi
+
+cd output
+
+if [ "$mh_local" == "0" ]; then
+ if [ ! -f log_exp_headers.sqlite ]; then
+ # Global Mh and file does not exist -> symlink to
+ # gllobal mh file
+ command "ln -s $dir/output/log_exp_headers.sqlite" $dry_run
+ fi
+fi
+
+
+# Update links to global run directories (GiFeGie, Uz)
+for my_dir in $dir/output/run_sp_[GU]*; do
+ command "ln -sf $my_dir" $dry_run
+done
+
+# Combined flags
+
+## Tiles
+command "ln -sf $dir/output/run_sp_Ma_tile" $dry_run
+
+if [ "$sp_local" == "0" ]; then
+ # Exposures
+ command "ln -sf $dir/output/run_sp_Ma_exp" $dry_run
+else
+ command "rm -f $dir/output/run_sp_Ma_exp" $dry_run
+fi
+
+# Check for existing exp SpMh dir
+if [[ -d "$dir/output/run_sp_exp_SpMh" ]]; then
+ # create link
+ command "ln -sf $dir/output/run_sp_exp_SpMh" $dry_run
+else
+ echo "No global SpMh directory found"
+fi
+
+(( do_job = $job & 2 ))
+if [ $do_job != 0 ] && [ "$sp_local" == "1" ]; then
+ # run local Sp; works only with mh_local=1; this step needs to be done
+ # before following mh_local=1 steps
+ command "rm -rf run_sp_GitFeGie*" $dry_run
+ command "rm -rf run_sp_Gie*" $dry_run
+ command "rm -rf run_sp_exp_Sp*" $dry_run
+
+ # Create new get_image dir
+ new_dir="run_sp_Gie/get_images_runner_run_2/output"
+ command "rm -rf $new_dir" $dry_run
+ command "mkdir -p $new_dir" $dry_run
+
+ # Link to image, weight, and flag file of current exposure
+
+ # Remove HDU extension
+ command "cd $new_dir" $dry_run
+ exp_ID=$(echo "$ID" | sed 's/-[0-9]\{1,2\}//')
+ for file in $dir/output//run_sp_GitFeGie_20*/get_images_runner_run_2/output/*${exp_ID}* ; do
+ echo $file
+ command "ln -s $file" $dry_run
+ done
+ command "cd ../../.." $dry_run
+
+ # Run Sp
+ cd ..
+ command "update_runs_log_file.py" $dry_run
+ export SP_RUN=`pwd`
+ command "shapepipe_run -c cfis/config_exp_Sp.ini -e $exp_ID" $dry_run
+
+ # Only keep CCD of this ID
+ command "mkdir -p output/run_sp_exp_Sp_shdu/split_exp_runner/output" $dry_run
+ command "mv output/run_sp_exp_Sp/split_exp_runner/output/*$ID* output/run_sp_exp_Sp_shdu/split_exp_runner/output" $dry_run
+ command "mv output/run_sp_exp_Sp/split_exp_runner/output/headers* output/run_sp_exp_Sp_shdu/split_exp_runner/output" $dry_run
+ command "rm -rf output/run_sp_exp_Sp" $dry_run
+ command "update_runs_log_file.py" $dry_run
+ cd output
+
+ # Exception: Do not carry out actual job call
+ exit 0
+fi
+
+if [ "$mh_local" == "1" ]; then
+
+ # Remove previous Sx runs
+ command "rm -rf run_sp_tile_Sx_*" $dry_run
+
+ if [ "$ID" == "-1" ]; then
+ echo "ID needs to be given (option -e) for mh_local and job&16"
+ exit 6
+ fi
+
+ if [ -L log_exp_headers.sqlite ]; then
+ # Local Mh and symlink -> remove previous link to
+ # (potentially incomplete) global mh file
+ echo "Removing previous mh sym link"
+ command "rm log_exp_headers.sqlite" $dry_run
+ else
+ echo "no mh link found"
+ fi
+
+ echo "Creating local mh file"
+
+ ## Remove previous (local) split_exp dir
+ #command "rm -rf run_sp_exp_Sp" $dry_run
+
+ ## Create new split exp run dir
+ #new_dir="run_sp_exp_Sp//split_exp_runner/output"
+ #command "mkdir -p $new_dir" $dry_run
+
+ ## Link to all header files of exposures used for the current tile
+ #IDs=`echo $ID | tr "." "-"`
+ #for exp_ID in `cat run_sp_GitFeGie_*/find_exposures_runner/output/exp_numbers-$IDs.txt` ; do
+ #x=`echo $exp_ID | tr -d p `
+ #command "ln -s $dir/output/run_sp_exp_SpMh/split_exp_runner/output/headers-$x.npy $new_dir/headers-$x.npy" $dry_run
+ #done
+
+ # Run merge_headers_runner on local exposure selection
+ cd ..
+ command "update_runs_log_file.py" $dry_run
+ export SP_RUN=`pwd`
+ command "shapepipe_run -c cfis/config_exp_Mh.ini" $dry_run
+ cd output
+
+fi
+
+(( do_job = $job & 8 ))
+if [ $do_job != 0 ] && [ "$sp_local" == "1" ]; then
+ # Remove previous local Ma runs
+ echo "cdsclient = $CDSCLIENT"
+ command "rm -rf run_sp_exp_Ma*" $dry_run
+fi
+
+(( do_job = $job & 16 ))
+if [[ $do_job != 0 ]]; then
+ # Remove previous Sx runs
+ command "rm -rf run_sp_tile_Sx_*" $dry_run
+fi
+
+# Update links to exposure run directories, which were created in job 32
+(( do_job = $job & 64 ))
+if [[ $do_job != 0 ]]; then
+ if [ "$kind" == "tile" ]; then
+ cd ../../..
+ command "link_to_exp_for_tile.py -t $ID -i tile_runs -I exp_runs" $dry_run
+ cd ${kind}_runs/$ID/output
+
+ # Remove duplicate job-16 runs (tile detection)
+ n_16=`ls -rt1d run_sp_tile_Sx_* | wc -l`
+ if [ "$n_16" != "1" ]; then
+ n_remove="$(($n_16-1))"
+ echo "removing $n_remove duplicate old job-16 runs"
+ command "rm -rf `ls -rt1d run_sp_tile_Sx_* | head -$n_remove`" $dry_run
+ fi
+
+ # Remove previous runs of this job
+ rm -rf run_sp_tile_PsViSmVi*
+ fi
+fi
+
+(( do_job = $job & 256 ))
+if [[ $do_job != 0 ]]; then
+
+ # Remove previous runs of this job
+ rm -rf run_sp_Ms_20??_*
+
+fi
+
+(( do_job = $job & 512 ))
+if [[ $do_job != 0 ]]; then
+
+ # Remove previous runs of this job
+ rm -rf run_sp_Mc_20??_*
+
+fi
+
+
+cd ..
+
+# Update log file
+command update_runs_log_file.py $dry_run
+
+echo -n "pwd: "
+pwd
+
+echo -n "environment: "
+echo $CONDA_PREFIX
+
+# To avoid (new?) qt error with setools (-j 32)
+export DISPLAY=:1.0
+
+command "job_sp_canfar.bash -p psfex -j $job -e $ID --n_smp $N_SMP --nsh_jobs $N_SMP --debug_out $debug_out" $dry_run
+
+cd $dir
+
+msg="End $(basename "$0")"
+echo $msg
+if [ "$debug_out" != "-1" ]; then
+ echo $pat$msg >> $debug_out-
+fi
diff --git a/scripts/sh/job_sp.bash b/scripts/sh/job_sp.bash
index 15cb1428a..67aa73444 100755
--- a/scripts/sh/job_sp.bash
+++ b/scripts/sh/job_sp.bash
@@ -8,11 +8,6 @@
# called in interactive mode on a virtual
# machine.
# Author: Martin Kilbinger
-# Date: v1.0 11/2020
-# v1.1 01/2021
-
-# MKDEBUG TODO:
-# Option to change SMP_BATCH_SIZE, not for MPI
# VM home, required for canfar run.
@@ -294,23 +289,6 @@ function upload_logs() {
upload "logs" "$id" "$verbose" "${upl[@]}"
}
-# Print script variables
-function print_env() {
- echo "*** Environment ***"
- echo "Data:"
- echo " TILE_ARR=${TILE_ARR[@]}"
- echo "Paths:"
- echo " VM_HOME=$VM_HOME"
- echo " SP_RUN=$SP_RUN"
- echo " TILE_NUMBERS_PATH=$TILE_NUMBERS_PATH"
- echo " OUTPUT=$OUTPUT"
- echo " SP_CONFIG=$SP_CONFIG"
- echo "Other variables:"
- echo " VCP=$VCP"
- echo " CERTFILE=$CERTFILE"
- echo "***"
-}
-
function set_config_n_smp() {
local config_name=$1
local _n_smp=$2
@@ -420,7 +398,7 @@ if [[ $do_job != 0 ]]; then
### Star detection, selection, PSF model. setools can exit with an error for CCD with insufficient stars,
### the script should continue
STOP=0
- command_sp "shapepipe_run -c $SP_CONFIG/config_tile_Sx_exp_${psf}.ini" "Run shapepipe (tile detection, exp $psf)"
+ command_cfg_shapepipe "config_tile_Sx_exp_${psf}.ini" "Run shapepipe (tile detection, exp $psf)" $n_smp
STOP=1
fi
@@ -432,7 +410,7 @@ if [[ $do_job != 0 ]]; then
### PSF model letter: 'P' (psfex) or 'M' (mccd)
letter=${psf:0:1}
Letter=${letter^}
- command_sp "shapepipe_run -c $SP_CONFIG/config_tile_${Letter}iViSmVi.ini" "Run shapepipe (tile PsfInterp=$Letter}: up to ngmix+galsim)"
+ command_cfg_shapepipe "config_tile_${Letter}iViSmVi.ini" "Run shapepipe (tile PsfInterp=$Letter}: up to ngmix+galsim)" $n_smp
fi
@@ -464,7 +442,7 @@ if [[ $do_job != 0 ]]; then
### Shapes, run $nsh_jobs parallel processes
VERBOSE=0
for k in $(seq 1 $nsh_jobs); do
- command_sp "shapepipe_run -c $SP_CONFIG_MOD/config_tile_Ng${k}u.ini" "Run shapepipe (tile: ngmix+galsim $k)" &
+ command_sp "shapepipe_run -c $SP_CONFIG_MOD/config_tile_Ng${k}u.ini" "Run shapepipe (tile: ngmix $k)" &
done
wait
VERBOSE=1
diff --git a/scripts/sh/job_sp_canfar.bash b/scripts/sh/job_sp_canfar.bash
new file mode 100755
index 000000000..3d31e245c
--- /dev/null
+++ b/scripts/sh/job_sp_canfar.bash
@@ -0,0 +1,568 @@
+#!/bin/bash
+
+# Name: job_sp_canfar.bash
+# Description: General script to process one or more tiles
+# with all contributing exposures.
+# This works as job submission script for
+# the canfar batch system.
+# called in interactive mode on a virtual
+# machine.
+# Author: Martin Kilbinger
+
+
+# Command line arguments
+## Default values
+job=255
+config_dir=$HOME/shapepipe/example/cfis
+psf='mccd'
+retrieve='vos'
+star_cat_for_mask='onthefly'
+exclusive=''
+results='cosmostat/kilbinger/results_v2'
+n_smp=-1
+nsh_jobs=8
+debug_out=-1
+
+pat="--- "
+
+## Help string
+usage="Usage: $(basename "$0") [OPTIONS] [TILE_ID]
+\n\nOptions:\n
+ -h\tthis message\n
+ -j, --job JOB\tRunning JOB, bit-coded\n
+ \t 1: retrieve images (online if method=vos)\n
+ \t 2: prepare images (offline)\n
+ \t 4: mask tiles (online if star_cat_for_mask=onthefly)\n
+ \t 8: mask exposures (online if star_cat_for_mask=onthefly)\n
+ \t 16: detection of galaxies on tiles (offline)\n
+ \t 32: processing of stars on exposures (offline)\n
+ \t 64: galaxy selection on tiles (offline)\n
+ \t 128: shapes and morphology (offline)\n
+ \t 256: paste catalogues (offline)\n
+ -c, --config_dir DIR\n
+ \t config file directory, default='$config_dir'\n
+ -p, --psf MODEL\n
+ \tPSF model, one in ['psfex'|'mccd'], default='$psf'\n
+ -r, --retrieve METHOD\n
+ \tmethod to retrieve images, allowed are 'vos', 'symlink', default='$retrieve'\n
+ -s, --star_cat_for_mask\n
+ \tcatalogue for masking bright stars, allowed are 'onthefly', 'save',\n
+ \tdefault is '${star_cat_for_mask}'\n
+ -e, --exclusive ID\n
+ \texclusive input filer number string ID (default: None)\n
+ -o, --output_dir\n
+ \toutput (upload) directory on vos:cfis, default='$results'\n
+ -n, --n_smp N_SMP\n
+ \tnumber of jobs (SMP mode only), default from original config files\n
+ --nsh_jobs NJOB\n
+ \tnumber of objects per parallel shape module call, \n
+ \tdefault: optimal number is computed\n
+ --debug_out PATH\n
+ \tdebug output file PATH, default not used\n
+ TILE_ID_i\n
+ \ttile ID(s), e.g. 283.247 214.242, only with '-j 1'\n
+"
+
+## Help if no arguments
+if [ -z $1 ]; then
+ echo -ne $usage
+ exit 1
+fi
+
+## Parse command line
+while [ $# -gt 0 ]; do
+ case "$1" in
+ -h)
+ echo -ne $usage
+ exit 0
+ ;;
+ -j|--job)
+ job="$2"
+ shift
+ ;;
+ -c|--config_dir)
+ config_dir="$2"
+ shift
+ ;;
+ -p|--psf)
+ psf="$2"
+ shift
+ ;;
+ -r|--retrieve)
+ retrieve="$2"
+ shift
+ ;;
+ -s|--star_cat_for_mask)
+ star_cat_for_mask="$2"
+ shift
+ ;;
+ -e|--exclusive)
+ exclusive="$2"
+ shift
+ ;;
+ -o|--output_dir)
+ results="$2"
+ shift
+ ;;
+ -n|--n_smp)
+ n_smp="$2"
+ shift
+ ;;
+ --nsh_jobs)
+ nsh_jobs="$2"
+ shift
+ ;;
+ --debug_out)
+ debug_out="$2"
+ shift
+ ;;
+ esac
+ shift
+done
+
+## Check options
+if [ "$psf" != "psfex" ] && [ "$psf" != "mccd" ]; then
+ echo "PSF (option -p) needs to be 'psfex' or 'mccd'"
+ exit 2
+fi
+
+if [ "$star_cat_for_mask" != "onthefly" ] && [ "$star_cat_for_mask" != "save" ]; then
+ echo "Star cat for mask (option -s) needs to be 'onthefly' or 'save'"
+ exit 4
+fi
+
+if [ "$retrieve" != "vos" ] && [ "$retrieve" != "symlink" ]; then
+ echo "method to retrieve images (option -r) needs to be 'vos' or 'symlink'"
+ exit 5
+fi
+
+if [ "$debug_out" != "-1" ]; then
+ echo $pat`date` >> $debug_out
+ echo "${pat}Starting $(basename "$0")" >> $debug_out
+fi
+
+CONDA_PREFIX=/arc/home/kilbinger/.conda/envs/shapepipe
+PATH=$PATH:$CONDA_PREFIX/bin
+
+# For tar archives. TODO: Should be unique to each job
+export ID="test"
+
+## Paths
+
+## Path variables used in shapepipe config files
+
+# Run path and location of input image directories
+export SP_RUN=`pwd`
+
+# Config file path
+export SP_CONFIG=$SP_RUN/cfis
+export SP_CONFIG_MOD=$SP_RUN/cfis_mod
+
+## Other variables
+
+# Output
+OUTPUT=$SP_RUN/output
+
+# For tar archives
+output_rel=`realpath --relative-to=. $OUTPUT`
+
+# Stop on error, default=1
+STOP=1
+
+# Verbose mode (1: verbose, 0: quiet)
+VERBOSE=1
+
+# VCP options
+export CERTFILE=$HOME/.ssl/cadcproxy.pem
+export VCP="vcp --certfile=$CERTFILE"
+
+
+## Functions
+
+# Print string, executes command, and prints return value.
+function command () {
+ cmd=$1
+ str=$2
+
+ RED='\033[0;31m'
+ GREEN='\033[0;32m'
+ NC='\033[0m' # No Color
+ # Color escape characters show up in log files
+ #RED=''
+ #GREEN=''
+ #NC=''
+
+
+ if [ "$debug_out" != "-1" ]; then
+ echo "${pat}pwd = `pwd`" >> $debug_out
+ echo "${pat}SP_RUN = $SP_RUN" >> $debug_out
+ echo "${pat}SP_CONFIG = $SP_CONFIG" >> $debug_out
+ fi
+
+ if [ $# == 2 ]; then
+ if [ $VERBOSE == 1 ]; then
+ echo "$str: running '$cmd'"
+ fi
+ if [ "$debug_out" != "-1" ]; then
+ echo "${pat}Running $cmd" >> $debug_out
+ fi
+
+ $cmd
+
+ else
+ if [ $VERBOSE == 1 ]; then
+ echo "$str: running '$cmd $4 \"$5 $6\"'"
+ fi
+ if [ "$debug_out" != "-1" ]; then
+ echo "${pat}Running $cmd $4 \"$5 $6\"" >> $debug_out
+ fi
+
+ $cmd $4 "$5 $6"
+
+ fi
+
+ res=$?
+
+ if [ "$debug_out" != "-1" ]; then
+ echo "${pat}exit code = $res" >> $debug_out
+ fi
+
+ if [ $VERBOSE == 1 ]; then
+ if [ $res == 0 ]; then
+ echo -e "${GREEN}success, return value = $res${NC}"
+ else
+ echo -e "${RED}error, return value = $res${NC}"
+ if [ $STOP == 1 ]; then
+ echo "${RED}exiting 'canfar_sp.bash', error in command '$cmd'${NC}"
+ exit $res
+ else
+ echo "${RED}continuing 'canfar_sp.bash', error in command '$cmd'${NC}"
+ fi
+ fi
+ fi
+}
+
+# Run shapepipe command. If error occurs, upload sp log files before stopping script.
+function command_sp() {
+ local cmd=$1
+ local str=$2
+
+ command "$1" "$2"
+}
+
+# Set up config file and call shapepipe_run
+function command_cfg_shapepipe() {
+ local config_name=$1
+ local str=$2
+ local _n_smp=$3
+ local _exclusive=$4
+
+ if [ "$exclusive" != "" ]; then
+ exclusive_flag="-e $_exclusive"
+ else
+ exclusive_flag=""
+ fi
+
+ config_upd=$(set_config_n_smp $config_name $_n_smp)
+ #local cmd="/arc/home/kilbinger/.conda/envs/shapepipe/bin/shapepipe_run -c $config_upd $exclusive_flag"
+ local cmd="shapepipe_run -c $config_upd $exclusive_flag"
+ command_sp "$cmd" "$str"
+}
+
+# Tar and upload files to vos
+function upload() {
+ base=$1
+ shift
+ ID=$1
+ shift
+ verbose=$1
+ shift
+ upl=("$@")
+
+ echo "Counting upload files"
+ n_upl=(`ls -l ${upl[@]} | wc`)
+ if [ $n_upl == 0 ]; then
+ if [ $STOP == 1 ]; then
+ echo "Exiting script, no file found for '$base' tar ball"
+ exit 3
+ fi
+ fi
+ tar czf ${base}_${ID}.tgz ${upl[@]}
+ command "$VCP ${base}_${ID}.tgz vos:cfis/$results" "Upload tar ball"
+}
+
+# Upload log files
+function upload_logs() {
+ id=$1
+ verbose=$2
+
+ upl="$output_rel/*/*/logs $output_rel/*/logs"
+ upload "logs" "$id" "$verbose" "${upl[@]}"
+}
+
+function set_config_n_smp() {
+ local config_name=$1
+ local _n_smp=$2
+
+ local config_orig="$SP_CONFIG/$config_name"
+
+ if [[ $_n_smp != -1 ]]; then
+ # Update SMP batch size
+ local config_upd="$SP_CONFIG_MOD/$config_name"
+ update_config $config_orig $config_upd "SMP_BATCH_SIZE" $_n_smp
+ else
+ # Keep original config file
+ local config_upd=$config_orig
+ fi
+
+ # Set "return" value (stdout)
+ echo "$config_upd"
+}
+
+# Update config file
+function update_config() {
+ local config_orig=$1
+ local config_upd=$2
+ local key=$3
+ local val_upd=$4
+
+ cat $config_orig \
+ | perl -ane 's/'$key'\s+=.+/'$key' = '$val_upd'/; print' > $config_upd
+}
+
+### Start ###
+
+echo "Start processing"
+
+# Create input and output directories
+mkdir -p $SP_RUN
+cd $SP_RUN
+mkdir -p $OUTPUT
+mkdir -p $SP_CONFIG_MOD
+
+# Processing
+
+
+### Retrieve config files
+if [[ $config_dir == *"vos:"* ]]; then
+ command_sp "$VCP $config_dir ." "Retrieve shapepipe config files"
+else
+ if [[ ! -L cfis ]]; then
+ command_sp "ln -s $config_dir cfis" "Retrieve shapepipe config files"
+ fi
+fi
+
+
+## Retrieve config files and images (online if retrieve=vos)
+## Retrieve and save star catalogues for masking (if star_cat_for_mask=save)
+(( do_job = $job & 1 ))
+if [[ $do_job != 0 ]]; then
+
+ ### Retrieve files
+ command_cfg_shapepipe \
+ "config_GitFeGie_$retrieve.ini" \
+ "Retrieve images" \
+ -1 \
+ $exclusive
+
+ ### Retrieve and save star catalogues for masking
+ if [ "$star_cat_for_mask" == "save" ]; then
+ #### For tiles
+ mkdir $SP_RUN/star_cat_tiles
+ command_sp \
+ "create_star_cat $SP_RUN/output/run_sp_GitFeGie_*/get_images_runner_run_1/output $SP_RUN/star_cat_tiles" \
+ "Save star cats for masking (tile)"
+
+ #### For single-exposures
+ mkdir $SP_RUN/star_cat_exp
+ command_sp \
+ "create_star_cat $SP_RUN/output/run_sp_GitFeGie_*/get_images_runner_run_2/output $SP_RUN/star_cat_exp exp" \
+ "Save star cats for masking (exp)"
+ fi
+
+fi
+
+## Prepare images (offline)
+(( do_job = $job & 2 ))
+if [[ $do_job != 0 ]]; then
+
+ ### Uncompress tile weights
+ command_cfg_shapepipe "config_tile_Uz.ini" "Run shapepipe (uncompress tile weights)" $n_smp $exclusive
+
+ ### Split images into single-HDU files, merge headers for WCS info
+ command_cfg_shapepipe \
+ "config_exp_SpMh.ini" \
+ "Run shapepipe (split images, merge headers)" \
+ $n_smp \
+ $exclusive
+
+fi
+
+## Mask tiles: add star, halo, and Messier object masks (online if "star_cat_for_mask" is "onthefly")
+(( do_job = $job & 4 ))
+if [[ $do_job != 0 ]]; then
+
+ ### Mask tiles
+ command_cfg_shapepipe \
+ "config_tile_Ma_$star_cat_for_mask.ini" \
+ "Run shapepipe (mask tiles)" \
+ $n_smp \
+ $exclusive
+
+fi
+
+## Mask exposures: add star, halo, and Messier object masks (online if "star_cat_for_mask" is "onthefly")
+(( do_job = $job & 8 ))
+if [[ $do_job != 0 ]]; then
+
+ ### Mask exposures
+ command_cfg_shapepipe \
+ "config_exp_Ma_$star_cat_for_mask.ini" \
+ "Run shapepipe (mask exposures)" \
+ $n_smp \
+ $exclusive
+
+fi
+
+
+## Remaining exposure processing (offline)
+(( do_job = $job & 16 ))
+if [[ $do_job != 0 ]]; then
+
+ ### Object detection on tiles
+ command_cfg_shapepipe \
+ "config_tile_Sx.ini" \
+ "Run shapepipe (tile detection)" \
+ $n_smp \
+ $exclusive
+
+fi
+
+## Exposure processing (offline)
+(( do_job = $job & 32 ))
+if [[ $do_job != 0 ]]; then
+
+ ### Star detection, selection, PSF model. setools can exit with an error for CCD with insufficient stars,
+ ### the script should continue
+ STOP=0
+ command_cfg_shapepipe \
+ "config_exp_${psf}.ini" \
+ "Run shapepipe (exp $psf)" \
+ $n_smp \
+ $exclusive
+ STOP=1
+
+fi
+
+## Process tiles up to shape measurement
+(( do_job = $job & 64 ))
+if [[ $do_job != 0 ]]; then
+
+ ### PSF model letter: 'P' (psfex) or 'M' (mccd)
+ letter=${psf:0:1}
+ Letter=${letter^}
+ command_cfg_shapepipe \
+ "config_tile_${Letter}iViSmVi_canfar.ini" \
+ "Run shapepipe (tile PsfInterp=$Letter}: up to ngmix+galsim)" \
+ $n_smp \
+ $exclusive
+
+fi
+
+## Shape measurement (offline)
+(( do_job = $job & 128 ))
+if [[ $do_job != 0 ]]; then
+
+ ### Prepare config files
+ n_min=0
+ n_obj=`get_number_objects`
+ nsh_step=`echo "$(($n_obj/$nsh_jobs))"`
+
+ n_max=$((nsh_step - 1))
+ for k in $(seq 1 $nsh_jobs); do
+ cat $SP_CONFIG/config_tile_Ng_template.ini | \
+ perl -ane \
+ 's/(ID_OBJ_MIN =) X/$1 '$n_min'/; s/(ID_OBJ_MAX =) X/$1 '$n_max'/; s/NgXu/Ng'$k'u/; s/X_interp/'$psf'_interp/g; print' \
+ > $SP_CONFIG_MOD/config_tile_Ng${k}u.ini
+ n_min=$((n_min + nsh_step))
+ if [ "$k" == $((nsh_jobs - 1)) ]; then
+ n_max=-1
+ else
+ n_max=$((n_min + nsh_step - 1))
+ fi
+ done
+
+ ### Shapes, run $nsh_jobs parallel processes
+ VERBOSE=0
+ for k in $(seq 1 $nsh_jobs); do
+
+ # if output dir for subrun exists but no output: re-run
+ ngmix_run=$OUTPUT/"run_sp_tile_ngmix_Ng${k}u/ngmix_runner"
+ if [ -e "$ngmix_run" ]; then
+ ngmix_out="$ngmix_run/output"
+ n_out=`ls -rlt $ngmix_out | wc -l`
+ if [ "$n_out" -lt 2 ]; then
+ command \
+ "rm -rf $OUTPUT/run_sp_tile_ngmix_Ng${k}u" \
+ "Re-running existing empty ngmix subrun $k"
+ command_sp \
+ "shapepipe_run -c $SP_CONFIG_MOD/config_tile_Ng${k}u.ini" \
+ "Run shapepipe (tile: ngmix $k)" &
+ else
+ echo "Skipping existing non-empty ngmix subrun $k"
+ fi
+ else
+ command_sp \
+ "shapepipe_run -c $SP_CONFIG_MOD/config_tile_Ng${k}u.ini" \
+ "Run shapepipe (tile: ngmix $k)" &
+ fi
+ done
+ wait
+ VERBOSE=1
+
+fi
+
+## Create final catalogues (offline)
+(( do_job = $job & 256 ))
+if [[ $do_job != 0 ]]; then
+
+ cat $SP_CONFIG/config_merge_sep_cats_template.ini | \
+ perl -ane \
+ 's/(N_SPLIT_MAX =) X/$1 '$nsh_jobs'/; print' \
+ > $SP_CONFIG_MOD/config_merge_sep_cats.ini
+
+ ### Merge separated shapes catalogues
+ command_sp \
+ "shapepipe_run -c $SP_CONFIG_MOD/config_merge_sep_cats.ini" \
+ "Run shapepipe (tile: merge sep cats)" \
+ "$VERBOSE" \
+ "$ID"
+fi
+
+(( do_job = $job & 512 ))
+if [[ $do_job != 0 ]]; then
+
+ ### Merge all relevant information into final catalogue
+ command_cfg_shapepipe \
+ "config_make_cat_$psf.ini" \
+ "Run shapepipe (tile: create final cat $psf)" \
+ $n_smp \
+ $exclusive
+
+fi
+
+# MKDEBUG: Putting Mh at the end for now, could be integrated before 16.
+(( do_job = $job & 1024 ))
+if [[ $do_job != 0 ]]; then
+
+ command_cfg_shapepipe \
+ "config_exp_Mh.ini" \
+ "Run shapepipe (merge exp headers)" \
+ $n_smp \
+ $exclusive
+
+fi
+
+if [ "$debug_out" != "-1" ]; then
+ echo "${pat}End $(basename "$0")" >> $debug_out
+fi
diff --git a/scripts/sh/missing_unique.sh b/scripts/sh/missing_unique.sh
new file mode 100644
index 000000000..8820d26f5
--- /dev/null
+++ b/scripts/sh/missing_unique.sh
@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+FILES=("summary/missing_job_128_ngmix_runner_*.txt")
+temp="temp_temp.tmp"
+temp2="temp_temp2.tmp"
+out="missing_job_128_ngmix_runner_cut.txt"
+
+i=0
+for file in ${FILES[@]}; do
+
+ echo $file $i
+
+ if [ "$i" == "0" ]; then
+ cp $file $temp
+ else
+ comm -12 <(sort $file) <(sort $temp) > $temp2
+ cp $temp2 $temp
+ fi
+
+ wc $file $temp
+
+ ((i=i+1))
+
+done
+
+mv $temp $out
+rm $temp2
diff --git a/scripts/sh/post_proc_sp.bash b/scripts/sh/post_proc_sp.bash
index 72c620e68..930d5b79d 100755
--- a/scripts/sh/post_proc_sp.bash
+++ b/scripts/sh/post_proc_sp.bash
@@ -70,7 +70,7 @@ SP_CONFIG=$SP_BASE/example/cfis
# PSF
## Collect all psfinterp results
-prepare_star_cat -p $psf
+combine_runs -p $psf -t psf
## Merge all psfinterp results and compute PSF residuals
shapepipe_run -c $SP_CONFIG/config_MsPl_$psf.ini
@@ -79,7 +79,7 @@ shapepipe_run -c $SP_CONFIG/config_MsPl_$psf.ini
# Galaxies
## Prepare output directory with links to all 'final_cat' result files
-prepare_tiles_for_final
+combine_runs
## Merge final output files to single mother catalog
input_final=output/run_sp_combined/make_catalog_runner/output
diff --git a/scripts/sh/prepare_star_cat.bash b/scripts/sh/prepare_star_cat.bash
deleted file mode 100755
index ff8cb167f..000000000
--- a/scripts/sh/prepare_star_cat.bash
+++ /dev/null
@@ -1,92 +0,0 @@
-#!/usr/bin/env bash
-
-# Name: prepare_star_cat.bash
-# Description: Create directory and links to all PSF or star catalogue files
-# from previous ShapePipe runs.
-# Author: Martin Kilbinger
-
-
-# Command line arguments
-
-## Default values
-psf='mccd'
-
-## Help string
-usage="Usage: $(basename "$0") [OPTIONS]
-\n\nOptions:\n
- -h\tthis message\n
- -p, --psf MODEL\n
- \tPSF model, one in ['psfex'|'mccd'|'setools'], default='$psf'\n
-"
-
-## Parse command line
-while [ $# -gt 0 ]; do
- case "$1" in
- -h)
- echo -ne $usage
- exit 0
- ;;
- -p|--psf)
- psf="$2"
- shift
- ;;
- *)
- echo -ne usage
- exit 1
- ;;
- esac
- shift
-done
-
-
-## Path variables
-if [ "$psf" == "psfex" ] || [ "$psf" == "mccd" ]; then
- psfval_file_base="validation_psf"
- dir_individual="psf_validation_ind"
-else
- psfval_file_base="mask/star_selection"
- dir_individual="star_all_ind"
-fi
-
-pwd=`pwd`
-
-
-## Functions
-function link_s () {
- target=$1
- link_name=$2
-
- if [ -L "$link_name" ]; then
- let "n_skipped+=1"
- else
- ln -s $target $link_name
- let "n_created+=1"
- fi
-
- return $n
-}
-
-
-# Create output dirs
-if [ ! -d "$dir_individual" ]; then
- mkdir -p $dir_individual
-fi
-
-if [ "$psf" == "psfex" ]; then
- runner="psfex_interp_runner"
-elif [ "$psf" == "mccd" ]; then
- runner="mccd_fit_val_runner"
-else
- runner="setools_runner"
-fi
-
-# Find all psf validation files and create links.
-# Assumes untar_results.sh has been run before.
-n_skipped=0
-n_created=0
-FILES=output/*/${runner}/output/${psfval_file_base}*
-for val in ${FILES[@]}; do
- base=`basename $val`
- link_s "$pwd/$val" "$dir_individual/$base"
-done
-echo " Created $n_created links, skipped $n_skipped files"
diff --git a/scripts/sh/prepare_tiles_for_final.bash b/scripts/sh/prepare_tiles_for_final.bash
deleted file mode 100755
index c26f8e8c2..000000000
--- a/scripts/sh/prepare_tiles_for_final.bash
+++ /dev/null
@@ -1,127 +0,0 @@
-#!/usr/bin/env bash
-
-# Name: prepare_tiles_for_final.bash
-# Description: Create shapepipe run directory with
-# links to all `final_cat` fits files
-# Author: Martin Kilbinger
-# Date: 06/2020
-# Version: 0.1
-
-# Command line arguments
-
-## Default values
-cat='final'
-
-## Help string
-usage="Usage: $(basename "$0") [OPTIONS]
-\n\nOptions:\n
- -h\tthis message\n
- -c, --cat TYPE\n
- \tCatalogue type, one in ['final'|'flag'|'image'], default='$cat'\n
-"
-
-## Parse command line
-while [ $# -gt 0 ]; do
- case "$1" in
- -h)
- echo -ne $usage
- exit 0
- ;;
- -c|--cat)
- cat="$2"
- shift
- ;;
- *)
- echo -ne $usage
- exit 1
- ;;
- esac
- shift
-done
-
-
-## Functions
-function link_s () {
- target=$1
- link_name=$2
-
- if [ -e "$link_name" ]; then
- echo "link with name $link_name already exists, skipping..."
- else
- echo "create link $target <- $link_name"
- ln -s $target $link_name
- fi
-}
-
-## Check options
-if [ "$cat" != "final" ] && [ "$cat" != "flag" ] && [ "$cat" != "image" ]; then
- echo "cat (option -c) needs to be 'final', 'flag', or 'image'"
- exit 2
-fi
-
-
-### Start ###
-
-pwd=`pwd`
-out_base="output"
-
-if [ "$cat" == "final" ]; then
- run_dir="run_sp_combined"
- INPUT="$pwd/$out_base/run_sp_Mc_*"
-elif [ "$cat" == "flag" ]; then
- run_dir="run_sp_combined_flag"
- INPUT="$pwd/$out_base/run_sp_tile_Ma_*"
-else
- run_dir="run_sp_combined_image"
- INPUT="$pwd/$out_base/run_sp_Git_*"
-fi
-
-log_path="$pwd/$out_base/log_run_sp.txt"
-OUTPUT="$pwd/$out_base/$run_dir"
-mkdir -p $OUTPUT
-
-# Directories and file patterns to create/link
-if [ "$cat" == "final" ]; then
- DIRS=(
- "make_catalog_runner"
- )
- PATTERNS=(
- "final_cat-*"
- )
-elif [ "$cat" == "flag" ]; then
- DIRS=(
- "mask_runner"
- )
- PATTERNS=(
- "pipeline_flag-*"
- )
-else
- DIRS=(
- "get_images_runner"
- )
- PATTERNS=(
- "CFIS_image-*"
- )
-fi
-
-# Create links
-for n in "${!PATTERNS[@]}"; do
- pattern=${PATTERNS[$n]}
- dir=$OUTPUT/${DIRS[$n]}/output
- echo $n $pattern $dir
- mkdir -p $dir
- FILES=(`find $INPUT -name "$pattern"`)
- n_files=${#FILES[@]}
- i=0
- for file in ${FILES[@]}; do
- target=$file
- link_name=$dir/`basename $file`
- link_s $target $link_name
- ((i=i+1))
- done
- echo " $n_files target files, $i links created/skipped"
-done
-
-# Update log file
-modules=`echo ${DIRS[@]} | tr ' ' ,`
-echo "./$out_base/$run_dir $modules" >> $log_path
diff --git a/scripts/sh/stats_jobs_canfar.sh b/scripts/sh/stats_jobs_canfar.sh
new file mode 100755
index 000000000..3d1ddb156
--- /dev/null
+++ b/scripts/sh/stats_jobs_canfar.sh
@@ -0,0 +1,107 @@
+#!/usr/bin/env bash
+
+# Name: stats_jobs_canfar.sh
+# Author: Martin Kilbinger
+# Description: Handles headless jobs on canfar
+
+
+# Global variables
+
+## Temporary files
+tmpfile_jobs="jobinfo.txt"
+tmpfile_ids="ids.txt"
+tmpfile_running="jobs_running.txt"
+
+## curl options
+SSL=~/.ssl/cadcproxy.pem
+SESSION=https://ws-uv.canfar.net/skaha/v0/session
+
+
+# Command line arguments
+
+## Default values
+mode="count"
+
+## Help string
+usage="Usage: $(basename "$0") [OPTIONS]
+\n\nOptions:\n
+ -h\tthis message\n
+ -m, --mode MODE\n
+ \tmode, allowed are 'count' (default), 'delete'\n
+"
+
+## Parse command line
+while [ $# -gt 0 ]; do
+ case "$1" in
+ -h)
+ echo -ne $usage
+ exit 0
+ ;;
+ -m|--mode)
+ mode="$2"
+ shift
+ ;;
+ esac
+ shift
+done
+
+## Check options
+case $mode in
+ "count"|"delete")
+ # valid option
+ ;;
+ *)
+ echo "Invalid mode $mode"
+ exit 1
+ ;;
+esac
+
+
+# Main program
+
+# Get all instances
+#echo curl -E $SSL $SESSION
+curl -E $SSL $SESSION &> /dev/null > $tmpfile_jobs
+res=$?
+
+if [ "$res" == "0" ]; then
+ # Number of jobs
+ n_headless=`cat $tmpfile_ids | grep Running | wc -l`
+else
+ # Failure: set to very high number
+ n_headless=10000
+fi
+
+# Get headless job IDs
+#cat $tmpfile_jobs | grep headless -B 4 -A 12 | grep \"id | perl -F\" -ane 'print "$F[3]\n"' > $tmpfile_ids
+cat $tmpfile_jobs | grep headless -B 4 -A 2 | grep Running -A 1 > $tmpfile_ids
+
+
+# Get running job info
+cat $tmpfile_ids | grep name | perl -F\- -ane 'chomp; $F[4] =~ s/[",]//g; print "$F[3].$F[4]"' > $tmpfile_running
+
+
+if [ "$mode" == "count" ]; then
+
+ echo $n_headless
+
+elif [ "$mode" == "delete" ]; then
+
+ echo -n "Delete $n_headless jobs? [y|n] "
+ read answer
+ if [ "$answer" == "y" ]; then
+ cat $tmpfile_jobs | grep headless -B 34 -A 6 | grep Running -A 34 | grep id | grep -v user | perl -F\" -ane 'print "$F[3]\n"' > $tmpfile_ids
+ for ID in `cat $tmpfile_ids`; do
+ echo $ID
+ # Delete headless jobs
+ echo "curl -X DELETE -E $SSL $SESSION/$ID"
+ curl -X DELETE -E $SSL $SESSION/$ID
+ echo $?
+ done
+ fi
+
+fi
+
+
+# Remove temporary files
+#rm -f $tmpfile_jobs $tmpfile_ids
diff --git a/setup.py b/setup.py
index e5610581e..0d4c5c4c9 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
package_info = {}
infopath = os.path.abspath(
- os.path.join(os.path.dirname(__file__), 'shapepipe', 'info.py')
+ os.path.join(os.path.dirname(__file__), "shapepipe", "info.py")
)
with open(infopath) as open_file:
exec(open_file.read(), package_info)
@@ -15,8 +15,8 @@
def find_scripts():
scripts = []
- scripts_dir = package_info['__scripts_dir__']
- valid_extensions = package_info['__scripts_ext__']
+ scripts_dir = package_info["__scripts_dir__"]
+ valid_extensions = package_info["__scripts_ext__"]
sub_dirs = (
os.path.join(scripts_dir, sub_dir)
@@ -25,26 +25,29 @@ def find_scripts():
)
for sub_dir in sub_dirs:
- scripts.extend([
- os.path.join(sub_dir, val) for val in os.listdir(sub_dir)
- if os.path.isfile(os.path.join(sub_dir, val))
- and '__init__' not in val
- and val.endswith(valid_extensions)
- ])
+ scripts.extend(
+ [
+ os.path.join(sub_dir, val)
+ for val in os.listdir(sub_dir)
+ if os.path.isfile(os.path.join(sub_dir, val))
+ and "__init__" not in val
+ and val.endswith(valid_extensions)
+ ]
+ )
return scripts
setup(
- name=package_info['__name__'],
- author=package_info['__author__'],
- author_email=package_info['__email__'],
- version=package_info['__version__'],
+ name=package_info["__name__"],
+ author=package_info["__author__"],
+ author_email=package_info["__email__"],
+ version=package_info["__version__"],
packages=find_packages(),
scripts=find_scripts(),
- setup_requires=package_info['__setups__'],
- install_requires=package_info['__installs__'],
- description='Galaxy shape measurement pipeline.',
- long_description=package_info['__about__'],
- tests_require=package_info['__tests__'],
+ setup_requires=package_info["__setups__"],
+ install_requires=package_info["__installs__"],
+ description="Galaxy shape measurement pipeline.",
+ long_description=package_info["__about__"],
+ tests_require=package_info["__tests__"],
)
diff --git a/shapepipe/__init__.py b/shapepipe/__init__.py
index 88d7a1dfd..1957a353f 100644
--- a/shapepipe/__init__.py
+++ b/shapepipe/__init__.py
@@ -6,7 +6,7 @@
"""
-__all__ = ['modules', 'pipeline', 'utilities']
+__all__ = ["modules", "pipeline", "utilities"]
from . import *
from .info import __about__, __version__
diff --git a/shapepipe/info.py b/shapepipe/info.py
index d230bcd7f..7ce7f1d77 100644
--- a/shapepipe/info.py
+++ b/shapepipe/info.py
@@ -16,28 +16,24 @@
# Package Info
version_info = (1, 0, 1)
-__version__ = '.'.join(str(c) for c in version_info)
-__name__ = 'shapepipe'
-__author__ = 'Samuel Farrens'
-__email__ = 'samuel.farrens@cea.fr'
+__version__ = ".".join(str(c) for c in version_info)
+__name__ = "shapepipe"
+__author__ = "Samuel Farrens"
+__email__ = "samuel.farrens@cea.fr"
__about__ = (
- 'ShapePipe is a shape measurement pipeline developed with the'
- + 'CosmoStat lab at CEA Paris-Saclay.'
+ "ShapePipe is a shape measurement pipeline developed with the"
+ + "CosmoStat lab at CEA Paris-Saclay."
)
-__setups__ = ['pytest-runner']
-__installs__ = [
- 'joblib>=0.13',
- 'modopt>=1.2',
- 'numpy>=1.14'
-]
+__setups__ = ["pytest-runner"]
+__installs__ = ["joblib>=0.13", "modopt>=1.2", "numpy>=1.14"]
__tests__ = [
- 'pytest',
- 'pytest-cov',
- 'pytest-pycodestyle',
- 'pytest-pydocstyle',
+ "pytest",
+ "pytest-cov",
+ "pytest-pycodestyle",
+ "pytest-pydocstyle",
]
-__scripts_dir__ = 'scripts'
-__scripts_ext__ = ('.py', '.sh', '.bash')
+__scripts_dir__ = "scripts"
+__scripts_ext__ = (".py", ".sh", ".bash")
def shapepipe_logo(colour=False):
@@ -48,7 +44,7 @@ def shapepipe_logo(colour=False):
str logo string
"""
- shape = r'''
+ shape = r"""
_______ __ __ _______ _______ _______ _______ ___ _______ _______
| || | | || _ || || || || | | || |
| _____|| |_| || |_| || _ || ___|| _ || | | _ || ___|
@@ -56,12 +52,12 @@ def shapepipe_logo(colour=False):
|_____ || || || ___|| ___|| ___|| | | ___|| ___|
_____| || _ || _ || | | |___ | | | | | | | |___
|_______||__| |__||__| |__||___| |_______||___| |___| |___| |_______|
- '''
+ """
if not import_fail and colour:
- shape = colored(shape, 'cyan', attrs=['bold'])
+ shape = colored(shape, "cyan", attrs=["bold"])
- logo = r'''
+ logo = r"""
-------------------------------------------------------------------------------
{}
@@ -82,7 +78,9 @@ def shapepipe_logo(colour=False):
Version: {}
-------------------------------------------------------------------------------
- '''.format(shape, __version__)
+ """.format(
+ shape, __version__
+ )
return logo
@@ -95,8 +93,8 @@ def line():
str a horizontal line
"""
- line = r'''
+ line = r"""
-------------------------------------------------------------------------------
- '''
+ """
return line
diff --git a/shapepipe/modules/__init__.py b/shapepipe/modules/__init__.py
index c440b44cf..5f3847899 100644
--- a/shapepipe/modules/__init__.py
+++ b/shapepipe/modules/__init__.py
@@ -11,8 +11,6 @@
# Get a list of all files and directories in the modules directory
modules_dir = os.listdir(os.path.dirname(os.path.abspath(__file__)))
# List all ShapePipe module packages
-__all__ = [dir for dir in modules_dir if dir.endswith('_package')]
+__all__ = [dir for dir in modules_dir if dir.endswith("_package")]
# List all ShapePipe module runners
-__module_list__ = [
- file for file in modules_dir if file.endswith('_runner.py')
-]
+__module_list__ = [file for file in modules_dir if file.endswith("_runner.py")]
diff --git a/shapepipe/modules/execute_example_runner.py b/shapepipe/modules/execute_example_runner.py
index d1555ea5d..2872d608c 100644
--- a/shapepipe/modules/execute_example_runner.py
+++ b/shapepipe/modules/execute_example_runner.py
@@ -11,12 +11,12 @@
@module_runner(
- input_module='python_example_runner',
- version='1.0',
- file_pattern='pyex_output',
- file_ext='.cat',
- executes='head',
- run_method='parallel',
+ input_module="python_example_runner",
+ version="1.0",
+ file_pattern="pyex_output",
+ file_ext=".cat",
+ executes="head",
+ run_method="parallel",
)
def execute_example_runner(
input_file_list,
@@ -27,14 +27,14 @@ def execute_example_runner(
w_log,
):
"""Define The Execute Example Runner."""
- command_line = f'head {input_file_list[0]}'
+ command_line = f"head {input_file_list[0]}"
output_file_name = (
f'{run_dirs["output"]}/head_output{file_number_string}.txt'
)
stdout, stderr = execute(command_line)
- text_file = open(output_file_name, 'w')
+ text_file = open(output_file_name, "w")
text_file.write(stdout)
return stdout, stderr
diff --git a/shapepipe/modules/find_exposures_package/__init__.py b/shapepipe/modules/find_exposures_package/__init__.py
index 00653bf0b..6bb5d6344 100644
--- a/shapepipe/modules/find_exposures_package/__init__.py
+++ b/shapepipe/modules/find_exposures_package/__init__.py
@@ -32,4 +32,4 @@
Prefix of exposures
"""
-__all__ = ['find_exposures.py']
+__all__ = ["find_exposures.py"]
diff --git a/shapepipe/modules/find_exposures_package/find_exposures.py b/shapepipe/modules/find_exposures_package/find_exposures.py
index a3c8f7928..eab72801e 100644
--- a/shapepipe/modules/find_exposures_package/find_exposures.py
+++ b/shapepipe/modules/find_exposures_package/find_exposures.py
@@ -12,7 +12,7 @@
import astropy.io.fits as fits
-class FindExposures():
+class FindExposures:
"""Find Exposures.
This class finds exposures that are used for a given tile.
@@ -49,7 +49,7 @@ def process(self):
exp_list_uniq = self.get_exposure_list()
# Write list to output ascii file
- f_out = open(self._output_path, 'w')
+ f_out = open(self._output_path, "w")
if len(exp_list_uniq) > 0:
for exp in exp_list_uniq:
print(exp, file=f_out)
@@ -70,13 +70,13 @@ def get_exposure_list(self):
try:
# Get history from tiles FITS header
hdu = fits.open(self._img_tile_path)
- hist = hdu[0].header['HISTORY']
+ hist = hdu[0].header["HISTORY"]
except Exception:
# Key word not found -> raise error
self._w_log.info(
- 'Error while reading tile image FITS file '
- + f'{self._img_tile_path}, continuing...'
+ "Error while reading tile image FITS file "
+ + f"{self._img_tile_path}, continuing..."
)
exp_list = []
@@ -85,14 +85,14 @@ def get_exposure_list(self):
# History entries have format as the following example:
# "input image 2243881p.fits 6 extension(s)"
for _hist in hist:
- temp = _hist.split(' ')
+ temp = _hist.split(" ")
- pattern = r'(.*)\.{1}.*'
+ pattern = r"(.*)\.{1}.*"
pattern_match = re.search(pattern, temp[self._colnum])
if not pattern_match:
raise IndexError(
- f're match \'{pattern}\' failed for filename'
- + f' \'{temp[self._colnum]}\''
+ f"re match '{pattern}' failed for filename"
+ + f" '{temp[self._colnum]}'"
)
exp_name = pattern_match.group(1)
@@ -108,7 +108,7 @@ def get_exposure_list(self):
# For log output
n_exp_uniq = len(exp_list_uniq)
n_duplicate = len(exp_list) - n_exp_uniq
- self._w_log.info(f'Found {n_exp_uniq} exposures used in tile')
- self._w_log.info(f'{n_duplicate} duplicates were removed')
+ self._w_log.info(f"Found {n_exp_uniq} exposures used in tile")
+ self._w_log.info(f"{n_duplicate} duplicates were removed")
return exp_list_uniq
diff --git a/shapepipe/modules/find_exposures_runner.py b/shapepipe/modules/find_exposures_runner.py
index a7ea6b0be..a54d59dae 100644
--- a/shapepipe/modules/find_exposures_runner.py
+++ b/shapepipe/modules/find_exposures_runner.py
@@ -11,11 +11,11 @@
@module_runner(
- version='1.1',
- file_pattern=['image'],
- file_ext='.fits',
- depends=['numpy', 'astropy', 'sip_tpv'],
- numbering_scheme='_0',
+ version="1.1",
+ file_pattern=["image"],
+ file_ext=".fits",
+ depends=["numpy", "astropy", "sip_tpv"],
+ numbering_scheme="_0",
)
def find_exposures_runner(
input_file_list,
@@ -33,10 +33,10 @@ def find_exposures_runner(
output_path = f'{run_dirs["output"]}/exp_numbers{file_number_string}.txt'
# Give column number for exposure name in fits header
- colnum = config.getint(module_config_sec, 'COLNUM')
+ colnum = config.getint(module_config_sec, "COLNUM")
# Give the prefix of exposures
- exp_prefix = config.get(module_config_sec, 'EXP_PREFIX')
+ exp_prefix = config.get(module_config_sec, "EXP_PREFIX")
# Create find exposures class instance
find_exp_inst = find_exposures.FindExposures(
input_file_name,
diff --git a/shapepipe/modules/get_images_package/__init__.py b/shapepipe/modules/get_images_package/__init__.py
index 2c0b6b69c..d887b9f78 100644
--- a/shapepipe/modules/get_images_package/__init__.py
+++ b/shapepipe/modules/get_images_package/__init__.py
@@ -52,4 +52,4 @@
"""
-__all__ = ['get_images.py']
+__all__ = ["get_images.py"]
diff --git a/shapepipe/modules/get_images_package/get_images.py b/shapepipe/modules/get_images_package/get_images.py
index d465d0719..631a876f2 100644
--- a/shapepipe/modules/get_images_package/get_images.py
+++ b/shapepipe/modules/get_images_package/get_images.py
@@ -58,12 +58,12 @@ def in2out_pattern(number):
"""
# replace dots ('.') with dashes ('-') to avoid confusion
# with file extension delimiters
- number_final = re.sub(r'\.', '-', number)
+ number_final = re.sub(r"\.", "-", number)
# remove letters in number
- number_final = re.sub('[a-zA-Z]', '', number_final)
+ number_final = re.sub("[a-zA-Z]", "", number_final)
# make robust for more generalized file names
- number_final = re.sub(r'_', '', number_final)
+ number_final = re.sub(r"_", "", number_final)
return number_final
@@ -149,12 +149,12 @@ def process(self, input_dir, output_dir):
# List of unique input images
flat_list = [item for sublist in all_image_numbers for item in sublist]
- self._w_log.info(f'Number of total image IDs = {len(flat_list)}')
+ self._w_log.info(f"Number of total image IDs = {len(flat_list)}")
# Get unique number list
image_number_list = list(set(flat_list))
self._w_log.info(
- f'Number of unique image IDs = {len(image_number_list)}'
+ f"Number of unique image IDs = {len(image_number_list)}"
)
# Create array to make it compatible with input dir
@@ -165,36 +165,31 @@ def process(self, input_dir, output_dir):
# Check consistency of list lengths
if any(
- len(lst) != nitem for lst in [
+ len(lst) != nitem
+ for lst in [
input_dir,
self._input_file_pattern,
self._input_file_ext,
- self._output_file_pattern
+ self._output_file_pattern,
]
):
raise ValueError(
- f'Lists INPUT_PATH ({len(input_dir)}), '
- + f'INPUT_FILE_PATTERN ({len(self._input_file_pattern)}), '
- + f'INPUT_FILE_EXT ({len(self._input_file_ext)}), '
- + f'OUTPUT_FILE_PATTERN ({len(self._output_file_pattern)}) '
- + 'need to have equal length'
+ f"Lists INPUT_PATH ({len(input_dir)}), "
+ + f"INPUT_FILE_PATTERN ({len(self._input_file_pattern)}), "
+ + f"INPUT_FILE_EXT ({len(self._input_file_ext)}), "
+ + f"OUTPUT_FILE_PATTERN ({len(self._output_file_pattern)}) "
+ + "need to have equal length"
)
# Assemble input and output file lists
all_inputs = self.get_file_list(
- image_number_list,
- input_dir,
- use_output_file_pattern=False
+ image_number_list, input_dir, use_output_file_pattern=False
)
all_outputs_orig = self.get_file_list(
- image_number_list,
- output_dir,
- use_output_file_pattern=False
+ image_number_list, output_dir, use_output_file_pattern=False
)
all_outputs_renamed = self.get_file_list(
- image_number_list,
- output_dir,
- use_output_file_pattern=True
+ image_number_list, output_dir, use_output_file_pattern=True
)
# Retrieve files
@@ -242,24 +237,22 @@ def get_file_list(
# Keep initial dot in extension
x = in_ext[1:]
- x2 = re.sub(r'\.', '', x)
+ x2 = re.sub(r"\.", "", x)
ext_final = in_ext[0] + x2
- fbase = (
- f'{self._output_file_pattern[idx]}{number_final}'
- )
+ fbase = f"{self._output_file_pattern[idx]}{number_final}"
else:
fbase = re.sub(self._input_numbering, number, in_pattern)
ext_final = in_ext
if (
use_output_file_pattern
- and self._output_file_pattern[idx] == '*'
+ and self._output_file_pattern[idx] == "*"
):
# retrieve all input files to output dir, do not append
# extension
fpath = in_path
else:
- fpath = f'{in_path}/{fbase}{ext_final}'
+ fpath = f"{in_path}/{fbase}{ext_final}"
list_files_per_type.append(fpath)
list_all_files.append(list_files_per_type)
@@ -280,40 +273,38 @@ def retrieve(self, all_inputs, all_outputs_orig, all_outputs_renamed):
"""
for in_per_type, out_per_type_orig, out_per_type_renamed in zip(
- all_inputs,
- all_outputs_orig,
- all_outputs_renamed
+ all_inputs, all_outputs_orig, all_outputs_renamed
):
for idx in range(len(in_per_type)):
if self._check_existing_dir:
out_base = os.path.basename(out_per_type_orig[idx])
path = glob.glob(
- f'{self._check_existing_dir}/**/{out_base}',
+ f"{self._check_existing_dir}/**/{out_base}",
recursive=True,
)
if path:
if len(path) == self._n_expected:
self._w_log.info(
- f'{path[0]} found, skipping download'
+ f"{path[0]} found, skipping download"
)
continue
else:
self._w_log.info(
- f'{len(path)} instead of {self._n_expected} '
- + 'existing files found at'
- + f' {self._check_existing_dir}'
- + ', downloading images'
+ f"{len(path)} instead of {self._n_expected} "
+ + "existing files found at"
+ + f" {self._check_existing_dir}"
+ + ", downloading images"
)
else:
self._w_log.info(
- 'No existing images found at'
- + f' {self._check_existing_dir},'
- + ' downloading images'
+ "No existing images found at"
+ + f" {self._check_existing_dir},"
+ + " downloading images"
)
self.retrieve_one(
in_per_type[idx],
out_per_type_orig[idx],
- out_per_type_renamed[idx]
+ out_per_type_renamed[idx],
)
def retrieve_one(self, in_path, out_path_orig, out_path_renamed):
@@ -329,17 +320,17 @@ def retrieve_one(self, in_path, out_path_orig, out_path_renamed):
Output path
"""
- if self._retrieve_method == 'vos':
+ if self._retrieve_method == "vos":
sys.argv = []
- sys.argv.append('vcp')
+ sys.argv.append("vcp")
if self._retrieve_options:
- for opt in self._retrieve_options.split(' '):
+ for opt in self._retrieve_options.split(" "):
sys.argv.append(opt)
sys.argv.append(in_path)
sys.argv.append(out_path_orig)
- log_cmd = ' '.join(sys.argv)
- vcp = vosHandler('vcp')
+ log_cmd = " ".join(sys.argv)
+ vcp = vosHandler("vcp")
self._w_log.info(log_cmd)
# Download file from VOSpace
@@ -348,15 +339,15 @@ def retrieve_one(self, in_path, out_path_orig, out_path_renamed):
try:
vcp()
self._w_log.info(
- 'Success of command vcp after '
- + f'{attempt}/{self._n_try} attempts'
+ "Success of command vcp after "
+ + f"{attempt}/{self._n_try} attempts"
)
break
except Exception:
attempt += 1
self._w_log.info(
- 'Error with command vcp, attempt '
- + f'{attempt}/{self._n_try}'
+ "Error with command vcp, attempt "
+ + f"{attempt}/{self._n_try}"
)
sys.argv = None
@@ -365,14 +356,14 @@ def retrieve_one(self, in_path, out_path_orig, out_path_renamed):
# link name in ShapePipe numbering format
os.symlink(out_path_orig, out_path_renamed)
- elif self._retrieve_method == 'symlink':
+ elif self._retrieve_method == "symlink":
src = in_path
# Get all input file names if INPUT_FILE_PATTERN contains '*'
all_src = glob.glob(src)
if len(all_src) == 0:
raise IndexError(
- f'No input file found corresponding to \'{src}\''
+ f"No input file found corresponding to '{src}'"
)
dst = out_path_renamed
@@ -380,7 +371,7 @@ def retrieve_one(self, in_path, out_path_orig, out_path_renamed):
if os.path.isdir(dst):
# OUTPUT_FILE_PATTERN is '*', so dst is not regular file
# but directory. Append input file name
- dst_name = f'{dst}/{os.path.basename(src)}'
+ dst_name = f"{dst}/{os.path.basename(src)}"
else:
# dst is regular file
dst_name = dst
diff --git a/shapepipe/modules/get_images_runner.py b/shapepipe/modules/get_images_runner.py
index 2f5dbd1eb..fb25e0e8b 100644
--- a/shapepipe/modules/get_images_runner.py
+++ b/shapepipe/modules/get_images_runner.py
@@ -11,10 +11,10 @@
@module_runner(
- version='1.1',
- depends=['numpy'],
- run_method='serial',
- numbering_scheme='_0',
+ version="1.1",
+ depends=["numpy"],
+ run_method="serial",
+ numbering_scheme="_0",
)
def get_images_runner(
input_file_list,
@@ -28,57 +28,48 @@ def get_images_runner(
# Read config file section
# Copy/download method
- retrieve_method = config.get(module_config_sec, 'RETRIEVE')
- retrieve_ok = ['vos', 'symlink']
+ retrieve_method = config.get(module_config_sec, "RETRIEVE")
+ retrieve_ok = ["vos", "symlink"]
if retrieve_method not in retrieve_ok:
raise ValueError(
- f'key RETRIEVE={retrieve_method} is invalid, '
- + f'must be in {retrieve_ok}'
+ f"key RETRIEVE={retrieve_method} is invalid, "
+ + f"must be in {retrieve_ok}"
)
- if config.has_option(module_config_sec, 'RETRIEVE_OPTIONS'):
+ if config.has_option(module_config_sec, "RETRIEVE_OPTIONS"):
retrieve_options = config.getexpanded(
- module_config_sec,
- 'RETRIEVE_OPTIONS'
+ module_config_sec, "RETRIEVE_OPTIONS"
)
else:
retrieve_options = None
- if config.has_option(module_config_sec, 'N_TRY'):
- n_try = config.getint(module_config_sec, 'N_TRY')
+ if config.has_option(module_config_sec, "N_TRY"):
+ n_try = config.getint(module_config_sec, "N_TRY")
else:
n_try = 3
# Paths
- input_dir = config.getlist(module_config_sec, 'INPUT_PATH')
- input_file_pattern = config.getlist(
- module_config_sec,
- 'INPUT_FILE_PATTERN'
- )
- input_file_ext = config.getlist(
- module_config_sec,
- 'INPUT_FILE_EXT'
- )
+ input_dir = config.getlist(module_config_sec, "INPUT_PATH")
+ input_file_pattern = config.getlist(module_config_sec, "INPUT_FILE_PATTERN")
+ input_file_ext = config.getlist(module_config_sec, "INPUT_FILE_EXT")
output_file_pattern = config.getlist(
- module_config_sec,
- 'OUTPUT_FILE_PATTERN'
+ module_config_sec, "OUTPUT_FILE_PATTERN"
)
- input_numbering = config.get(module_config_sec, 'INPUT_NUMBERING')
+ input_numbering = config.get(module_config_sec, "INPUT_NUMBERING")
- if config.has_option(module_config_sec, 'OUTPUT_PATH'):
- output_dir = config.getexpanded(module_config_sec, 'OUTPUT_PATH')
+ if config.has_option(module_config_sec, "OUTPUT_PATH"):
+ output_dir = config.getexpanded(module_config_sec, "OUTPUT_PATH")
else:
- output_dir = run_dirs['output']
+ output_dir = run_dirs["output"]
# Flags to check for already retrieved files
- if config.has_option(module_config_sec, 'CHECK_EXISTING_DIR'):
+ if config.has_option(module_config_sec, "CHECK_EXISTING_DIR"):
check_existing_dir = config.getexpanded(
- module_config_sec,
- 'CHECK_EXISTING_DIR'
+ module_config_sec, "CHECK_EXISTING_DIR"
)
- if config.has_option(module_config_sec, 'N_EXPECTED'):
- n_expected = config.getint(module_config_sec, 'N_EXPECTED')
+ if config.has_option(module_config_sec, "N_EXPECTED"):
+ n_expected = config.getint(module_config_sec, "N_EXPECTED")
else:
n_expected = 1
else:
diff --git a/shapepipe/modules/make_cat_package/__init__.py b/shapepipe/modules/make_cat_package/__init__.py
index 53d802a9d..1bd1cee5b 100644
--- a/shapepipe/modules/make_cat_package/__init__.py
+++ b/shapepipe/modules/make_cat_package/__init__.py
@@ -52,4 +52,4 @@
"""
-__all__ = ['make_cat']
+__all__ = ["make_cat"]
diff --git a/shapepipe/modules/make_cat_package/make_cat.py b/shapepipe/modules/make_cat_package/make_cat.py
index 4e30e3552..e9b246a74 100644
--- a/shapepipe/modules/make_cat_package/make_cat.py
+++ b/shapepipe/modules/make_cat_package/make_cat.py
@@ -37,9 +37,7 @@ def prepare_final_cat_file(output_path, file_number_string):
Output FITS file
"""
- output_name = (
- f'{output_path}/final_cat{file_number_string}.fits'
- )
+ output_name = f"{output_path}/final_cat{file_number_string}.fits"
return file_io.FITSCatalogue(
output_name,
@@ -91,19 +89,23 @@ def save_sextractor_data(final_cat_file, sexcat_path, remove_vignet=True):
sexcat_file.open()
data = np.copy(sexcat_file.get_data())
if remove_vignet:
- data = remove_field_name(data, 'VIGNET')
+ data = remove_field_name(data, "VIGNET")
- final_cat_file.save_as_fits(data, ext_name='RESULTS')
+ final_cat_file.save_as_fits(data, ext_name="RESULTS")
cat_size = len(data)
- tile_id = float('.'.join(
- re.split('-', os.path.splitext(os.path.split(sexcat_path)[1])[0])[1:]
- ))
+ tile_id = float(
+ ".".join(
+ re.split("-", os.path.splitext(os.path.split(sexcat_path)[1])[0])[
+ 1:
+ ]
+ )
+ )
tile_id_array = np.ones(cat_size) * tile_id
final_cat_file.open()
- final_cat_file.add_col('TILE_ID', tile_id_array)
+ final_cat_file.add_col("TILE_ID", tile_id_array)
sexcat_file.close()
@@ -142,21 +144,21 @@ def save_sm_data(
sexcat_sm_file = file_io.FITSCatalogue(sexcat_sm_path, SEx_catalogue=True)
sexcat_sm_file.open()
- sm = np.copy(sexcat_sm_file.get_data()['SPREAD_MODEL'])
- sm_err = np.copy(sexcat_sm_file.get_data()['SPREADERR_MODEL'])
+ sm = np.copy(sexcat_sm_file.get_data()["SPREAD_MODEL"])
+ sm_err = np.copy(sexcat_sm_file.get_data()["SPREADERR_MODEL"])
sexcat_sm_file.close()
- final_cat_file.add_col('SPREAD_MODEL', sm)
- final_cat_file.add_col('SPREADERR_MODEL', sm_err)
+ final_cat_file.add_col("SPREAD_MODEL", sm)
+ final_cat_file.add_col("SPREADERR_MODEL", sm_err)
if do_classif:
- obj_flag = np.ones_like(sm, dtype='int16') * 2
+ obj_flag = np.ones_like(sm, dtype="int16") * 2
classif = sm + 2.0 * sm_err
obj_flag[np.where(np.abs(classif) < star_thresh)] = 0
obj_flag[np.where(classif > gal_thresh)] = 1
- final_cat_file.add_col('SPREAD_CLASS', obj_flag)
+ final_cat_file.add_col("SPREAD_CLASS", obj_flag)
final_cat_file.close()
@@ -179,7 +181,7 @@ def __init__(self, final_cat_file):
def process(
self,
- mode='',
+ mode="",
cat_path=None,
moments=False,
):
@@ -198,17 +200,17 @@ def process(
self._output_dict = {}
self.final_cat_file.open()
- self._obj_id = np.copy(self.final_cat_file.get_data()['NUMBER'])
+ self._obj_id = np.copy(self.final_cat_file.get_data()["NUMBER"])
- if mode == 'ngmix':
+ if mode == "ngmix":
self._save_ngmix_data(cat_path, moments)
- elif mode == 'galsim':
+ elif mode == "galsim":
self._save_galsim_shapes(cat_path)
- elif mode == 'psf':
+ elif mode == "psf":
self._save_psf_data(cat_path)
else:
raise ValueError(
- f'Invalid process mode ({mode}) for '
+ f"Invalid process mode ({mode}) for "
+ '``make_cat.Savecatalogue``. Options are "ngmix", '
+ '"galsim" or "psf".'
)
@@ -234,9 +236,9 @@ def _update_dict(self, key_string, value):
self._output_dict = {
**self._output_dict,
**{
- f'{key_string}{key_end}': np.copy(value)
+ f"{key_string}{key_end}": np.copy(value)
for key_end in self._key_ends
- }
+ },
}
def _add2dict(self, key, value, index=None):
@@ -270,55 +272,55 @@ def _save_ngmix_data(self, ngmix_cat_path, moments=False):
Path to NGMIX catalogue
"""
- self._key_ends = ['1M', '1P', '2M', '2P', 'NOSHEAR']
+ self._key_ends = ["1M", "1P", "2M", "2P", "NOSHEAR"]
ngmix_cat_file = file_io.FITSCatalogue(ngmix_cat_path)
ngmix_cat_file.open()
- ngmix_n_epoch = ngmix_cat_file.get_data()['n_epoch_model']
- ngmix_mom_fail = ngmix_cat_file.get_data()['moments_fail']
+ ngmix_n_epoch = ngmix_cat_file.get_data()["n_epoch_model"]
+ ngmix_mom_fail = ngmix_cat_file.get_data()["moments_fail"]
if moments:
- m = 'm'
+ m = "m"
else:
- m = ''
+ m = ""
- ngmix_mcal_flags = ngmix_cat_file.get_data()['mcal_flags']
- ngmix_id = ngmix_cat_file.get_data()['id']
+ ngmix_mcal_flags = ngmix_cat_file.get_data()["mcal_flags"]
+ ngmix_id = ngmix_cat_file.get_data()["id"]
- self._add2dict('NGMIX_N_EPOCH', np.zeros(len(self._obj_id)))
- self._add2dict('NGMIX_MOM_FAIL', np.zeros(len(self._obj_id)))
+ self._add2dict("NGMIX_N_EPOCH", np.zeros(len(self._obj_id)))
+ self._add2dict("NGMIX_MOM_FAIL", np.zeros(len(self._obj_id)))
- prefix = f'NGMIX{m}'
+ prefix = f"NGMIX{m}"
for key_str in (
- f'{prefix}_T_',
- f'{prefix}_Tpsf_',
- f'{prefix}_SNR_',
- f'{prefix}_FLUX_',
- f'{prefix}_MAG_',
- f'{prefix}_FLAGS_',
- f'{prefix}_T_PSFo_',
+ f"{prefix}_T_",
+ f"{prefix}_Tpsf_",
+ f"{prefix}_SNR_",
+ f"{prefix}_FLUX_",
+ f"{prefix}_MAG_",
+ f"{prefix}_FLAGS_",
+ f"{prefix}_T_PSFo_",
):
self._update_dict(key_str, np.zeros(len(self._obj_id)))
- for key_str in (f'NGMIX{m}_FLUX_ERR_', f'NGMIX{m}_MAG_ERR_'):
+ for key_str in (f"NGMIX{m}_FLUX_ERR_", f"NGMIX{m}_MAG_ERR_"):
self._update_dict(key_str, np.ones(len(self._obj_id)) * -1)
for key_str in (
- f'NGMIX{m}_ELL_',
- f'NGMIX{m}_ELL_ERR_',
- f'NGMIX{m}_ELL_PSFo_'
+ f"NGMIX{m}_ELL_",
+ f"NGMIX{m}_ELL_ERR_",
+ f"NGMIX{m}_ELL_PSFo_",
):
self._update_dict(key_str, np.ones((len(self._obj_id), 2)) * -10.0)
self._update_dict(
- f'NGMIX{m}_T_ERR_',
+ f"NGMIX{m}_T_ERR_",
np.ones(len(self._obj_id)) * 1e30,
)
- self._add2dict(f'NGMIX{m}_MCAL_FLAGS', np.zeros(len(self._obj_id)))
+ self._add2dict(f"NGMIX{m}_MCAL_FLAGS", np.zeros(len(self._obj_id)))
for idx, _ in enumerate(self._obj_id):
for key in self._key_ends:
- x = self._output_dict[f'NGMIX{m}_ELL_{key}'][idx]
- if np.all(x != np.array([-10., -10.])):
+ x = self._output_dict[f"NGMIX{m}_ELL_{key}"][idx]
+ if np.all(x != np.array([-10.0, -10.0])):
print(x)
for idx, id_tmp in enumerate(self._obj_id):
@@ -329,61 +331,61 @@ def _save_ngmix_data(self, ngmix_cat_path, moments=False):
ncf_data = ngmix_cat_file.get_data(key)
- g = (ncf_data['g1'][ind[0]], ncf_data['g2'][ind[0]])
+ g = (ncf_data["g1"][ind[0]], ncf_data["g2"][ind[0]])
g_err = (
- ncf_data['g1_err'][ind[0]],
- ncf_data['g2_err'][ind[0]]
+ ncf_data["g1_err"][ind[0]],
+ ncf_data["g2_err"][ind[0]],
)
- self._add2dict(f'NGMIX{m}_ELL_{key}', g, idx)
- self._add2dict(f'NGMIX{m}_ELL_ERR_{key}', g_err, idx)
+ self._add2dict(f"NGMIX{m}_ELL_{key}", g, idx)
+ self._add2dict(f"NGMIX{m}_ELL_ERR_{key}", g_err, idx)
- t = ncf_data['T'][ind[0]]
- t_err = ncf_data['T_err'][ind[0]]
- tpsf = ncf_data['Tpsf'][ind[0]]
- self._add2dict(f'NGMIX{m}_T_{key}', t, idx)
- self._add2dict(f'NGMIX{m}_T_ERR_{key}', t_err, idx)
- self._add2dict(f'NGMIX{m}_Tpsf_{key}', tpsf, idx)
+ t = ncf_data["T"][ind[0]]
+ t_err = ncf_data["T_err"][ind[0]]
+ tpsf = ncf_data["Tpsf"][ind[0]]
+ self._add2dict(f"NGMIX{m}_T_{key}", t, idx)
+ self._add2dict(f"NGMIX{m}_T_ERR_{key}", t_err, idx)
+ self._add2dict(f"NGMIX{m}_Tpsf_{key}", tpsf, idx)
- s2n = ncf_data['s2n'][ind[0]]
- self._add2dict(f'NGMIX{m}_SNR_{key}', s2n, idx)
+ s2n = ncf_data["s2n"][ind[0]]
+ self._add2dict(f"NGMIX{m}_SNR_{key}", s2n, idx)
- flux = ncf_data['flux'][ind[0]]
- flux_err = ncf_data['flux_err'][ind[0]]
- self._add2dict(f'NGMIX{m}_FLUX_{key}', flux, idx)
- self._add2dict(f'NGMIX{m}_FLUX_ERR_{key}', flux_err, idx)
+ flux = ncf_data["flux"][ind[0]]
+ flux_err = ncf_data["flux_err"][ind[0]]
+ self._add2dict(f"NGMIX{m}_FLUX_{key}", flux, idx)
+ self._add2dict(f"NGMIX{m}_FLUX_ERR_{key}", flux_err, idx)
- mag = ncf_data['mag'][ind[0]]
- mag_err = ncf_data['mag_err'][ind[0]]
- self._add2dict(f'NGMIX{m}_MAG_{key}', mag, idx)
- self._add2dict(f'NGMIX{m}_MAG_ERR_{key}', mag_err, idx)
+ mag = ncf_data["mag"][ind[0]]
+ mag_err = ncf_data["mag_err"][ind[0]]
+ self._add2dict(f"NGMIX{m}_MAG_{key}", mag, idx)
+ self._add2dict(f"NGMIX{m}_MAG_ERR_{key}", mag_err, idx)
- flags = ncf_data['flags'][ind[0]]
- self._add2dict(f'NGMIX{m}_FLAGS_{key}', flags, idx)
+ flags = ncf_data["flags"][ind[0]]
+ self._add2dict(f"NGMIX{m}_FLAGS_{key}", flags, idx)
g_psf = (
- ncf_data['g1_psfo_ngmix'][ind[0]],
- ncf_data['g2_psfo_ngmix'][ind[0]]
+ ncf_data["g1_psfo_ngmix"][ind[0]],
+ ncf_data["g2_psfo_ngmix"][ind[0]],
)
- self._add2dict(f'NGMIX{m}_ELL_PSFo_{key}', g_psf, idx)
+ self._add2dict(f"NGMIX{m}_ELL_PSFo_{key}", g_psf, idx)
- t_psfo = ncf_data['T_psfo_ngmix'][ind[0]]
- self._add2dict(f'NGMIX{m}_T_PSFo_{key}', t_psfo, idx)
+ t_psfo = ncf_data["T_psfo_ngmix"][ind[0]]
+ self._add2dict(f"NGMIX{m}_T_PSFo_{key}", t_psfo, idx)
self._add2dict(
- f'NGMIX{m}_MCAL_FLAGS',
+ f"NGMIX{m}_MCAL_FLAGS",
ngmix_mcal_flags[ind[0]],
idx,
)
if not moments:
self._add2dict(
- f'NGMIX{m}_N_EPOCH',
+ f"NGMIX{m}_N_EPOCH",
ngmix_n_epoch[ind[0]],
idx,
)
self._add2dict(
- f'NGMIX{m}_MOM_FAIL',
+ f"NGMIX{m}_MOM_FAIL",
ngmix_mom_fail[ind[0]],
idx,
)
@@ -406,27 +408,27 @@ def _save_galsim_shapes(self, galsim_cat_path):
self._key_ends = galsim_cat_file.get_ext_name()[1:]
- galsim_id = galsim_cat_file.get_data()['id']
+ galsim_id = galsim_cat_file.get_data()["id"]
for key_str in (
- 'GALSIM_GAL_SIGMA_',
- 'GALSIM_PSF_SIGMA_',
- 'GALSIM_FLUX_',
- 'GALSIM_MAG_',
+ "GALSIM_GAL_SIGMA_",
+ "GALSIM_PSF_SIGMA_",
+ "GALSIM_FLUX_",
+ "GALSIM_MAG_",
):
self._update_dict(key_str, np.zeros(len(self._obj_id)))
- for key_str in ('GALSIM_FLUX_ERR_', 'GALSIM_MAG_ERR_', 'GALSIM_RES_'):
+ for key_str in ("GALSIM_FLUX_ERR_", "GALSIM_MAG_ERR_", "GALSIM_RES_"):
self._update_dict(key_str, np.ones(len(self._obj_id)) * -1)
for key_str in (
- 'GALSIM_GAL_ELL_',
- 'GALSIM_GAL_ELL_ERR_',
- 'GALSIM_GAL_ELL_UNCORR_',
- 'GALSIM_PSF_ELL_'
+ "GALSIM_GAL_ELL_",
+ "GALSIM_GAL_ELL_ERR_",
+ "GALSIM_GAL_ELL_UNCORR_",
+ "GALSIM_PSF_ELL_",
):
self._update_dict(key_str, np.ones((len(self._obj_id), 2)) * -10.0)
self._update_dict(
- 'GALSIM_FLAGS_',
- np.ones(len(self._obj_id), dtype='int16'),
+ "GALSIM_FLAGS_",
+ np.ones(len(self._obj_id), dtype="int16"),
)
for idx, id_tmp in enumerate(self._obj_id):
@@ -437,69 +439,69 @@ def _save_galsim_shapes(self, galsim_cat_path):
gcf_data = galsim_cat_file.get_data(key)
- if key == 'ORIGINAL_PSF':
+ if key == "ORIGINAL_PSF":
uncorr_g = (
- gcf_data['gal_uncorr_g1'][ind[0]],
- gcf_data['gal_uncorr_g2'][ind[0]]
+ gcf_data["gal_uncorr_g1"][ind[0]],
+ gcf_data["gal_uncorr_g2"][ind[0]],
)
- psf_sig = gcf_data['gal_sigma'][ind[0]]
- self._add2dict(f'GALSIM_PSF_ELL_{key}', uncorr_g, idx)
- self._add2dict(f'GALSIM_PSF_SIGMA_{key}', psf_sig, idx)
+ psf_sig = gcf_data["gal_sigma"][ind[0]]
+ self._add2dict(f"GALSIM_PSF_ELL_{key}", uncorr_g, idx)
+ self._add2dict(f"GALSIM_PSF_SIGMA_{key}", psf_sig, idx)
else:
g = (
- gcf_data['gal_g1'][ind[0]],
- gcf_data['gal_g2'][ind[0]]
+ gcf_data["gal_g1"][ind[0]],
+ gcf_data["gal_g2"][ind[0]],
)
g_err = (
- gcf_data['gal_g1_err'][ind[0]],
- gcf_data['gal_g2_err'][ind[0]]
+ gcf_data["gal_g1_err"][ind[0]],
+ gcf_data["gal_g2_err"][ind[0]],
)
- self._add2dict(f'GALSIM_GAL_ELL_{key}', g, idx)
- self._add2dict(f'GALSIM_GAL_ELL_ERR_{key}', g_err, idx)
+ self._add2dict(f"GALSIM_GAL_ELL_{key}", g, idx)
+ self._add2dict(f"GALSIM_GAL_ELL_ERR_{key}", g_err, idx)
uncorr_g = (
- gcf_data['gal_uncorr_g1'][ind[0]],
- gcf_data['gal_uncorr_g2'][ind[0]],
+ gcf_data["gal_uncorr_g1"][ind[0]],
+ gcf_data["gal_uncorr_g2"][ind[0]],
)
self._add2dict(
- f'GALSIM_GAL_ELL_UNCORR_{key}',
+ f"GALSIM_GAL_ELL_UNCORR_{key}",
uncorr_g,
idx,
)
- sigma = gcf_data['gal_sigma'][ind[0]]
- self._add2dict(f'GALSIM_GAL_SIGMA_{key}', sigma, idx)
+ sigma = gcf_data["gal_sigma"][ind[0]]
+ self._add2dict(f"GALSIM_GAL_SIGMA_{key}", sigma, idx)
psf_g = (
- gcf_data['psf_g1'][ind[0]],
- gcf_data['psf_g2'][ind[0]]
+ gcf_data["psf_g1"][ind[0]],
+ gcf_data["psf_g2"][ind[0]],
)
- psf_sigma = gcf_data['psf_sigma'][ind[0]]
- self._add2dict(f'GALSIM_PSF_ELL_{key}', psf_g, idx)
+ psf_sigma = gcf_data["psf_sigma"][ind[0]]
+ self._add2dict(f"GALSIM_PSF_ELL_{key}", psf_g, idx)
self._add2dict(
- f'GALSIM_PSF_SIGMA_{key}',
+ f"GALSIM_PSF_SIGMA_{key}",
psf_sigma,
idx,
)
- flux = gcf_data['gal_flux'][ind[0]]
- flux_err = gcf_data['gal_flux_err'][ind[0]]
- self._add2dict(f'GALSIM_FLUX_{key}', flux, idx)
- self._add2dict(f'GALSIM_FLUX_ERR_{key}', flux_err, idx)
+ flux = gcf_data["gal_flux"][ind[0]]
+ flux_err = gcf_data["gal_flux_err"][ind[0]]
+ self._add2dict(f"GALSIM_FLUX_{key}", flux, idx)
+ self._add2dict(f"GALSIM_FLUX_ERR_{key}", flux_err, idx)
- mag = gcf_data['gal_mag'][ind[0]]
- mag_err = gcf_data['gal_mag_err'][ind[0]]
- self._add2dict(f'GALSIM_MAG_{key}', mag, idx)
- self._add2dict(f'GALSIM_MAG_ERR_{key}', mag_err, idx)
+ mag = gcf_data["gal_mag"][ind[0]]
+ mag_err = gcf_data["gal_mag_err"][ind[0]]
+ self._add2dict(f"GALSIM_MAG_{key}", mag, idx)
+ self._add2dict(f"GALSIM_MAG_ERR_{key}", mag_err, idx)
- flags = gcf_data['gal_flag'][ind[0]]
- self._add2dict(f'GALSIM_FLAGS_{key}', flags, idx)
+ flags = gcf_data["gal_flag"][ind[0]]
+ self._add2dict(f"GALSIM_FLAGS_{key}", flags, idx)
- res = gcf_data['gal_resolution'][ind[0]]
- self._add2dict(f'GALSIM_RES_{key}', res, idx)
+ res = gcf_data["gal_resolution"][ind[0]]
+ self._add2dict(f"GALSIM_RES_{key}", res, idx)
galsim_cat_file.close()
@@ -516,53 +518,51 @@ def _save_psf_data(self, galaxy_psf_path):
"""
galaxy_psf_cat = SqliteDict(galaxy_psf_path)
- max_epoch = np.max(self.final_cat_file.get_data()['N_EPOCH']) + 1
+ max_epoch = np.max(self.final_cat_file.get_data()["N_EPOCH"]) + 1
self._output_dict = {
- f'PSF_ELL_{idx + 1}': np.ones((len(self._obj_id), 2)) * -10.
+ f"PSF_ELL_{idx + 1}": np.ones((len(self._obj_id), 2)) * -10.0
for idx in range(max_epoch)
}
self._output_dict = {
**self._output_dict,
**{
- f'PSF_FWHM_{idx + 1}': np.zeros(len(self._obj_id))
+ f"PSF_FWHM_{idx + 1}": np.zeros(len(self._obj_id))
for idx in range(max_epoch)
- }
+ },
}
self._output_dict = {
**self._output_dict,
**{
- f'PSF_FLAG_{idx + 1}': np.ones(
- len(self._obj_id), dtype='int16'
- )
+ f"PSF_FLAG_{idx + 1}": np.ones(len(self._obj_id), dtype="int16")
for idx in range(max_epoch)
- }
+ },
}
for idx, id_tmp in enumerate(self._obj_id):
- if galaxy_psf_cat[str(id_tmp)] == 'empty':
+ if galaxy_psf_cat[str(id_tmp)] == "empty":
continue
for epoch, key in enumerate(galaxy_psf_cat[str(id_tmp)].keys()):
gpc_data = galaxy_psf_cat[str(id_tmp)][key]
- if gpc_data['SHAPES']['FLAG_PSF_HSM'] != 0:
+ if gpc_data["SHAPES"]["FLAG_PSF_HSM"] != 0:
continue
e_psf = (
- gpc_data['SHAPES']['E1_PSF_HSM'],
- gpc_data['SHAPES']['E2_PSF_HSM']
+ gpc_data["SHAPES"]["E1_PSF_HSM"],
+ gpc_data["SHAPES"]["E2_PSF_HSM"],
)
- self._add2dict(f'PSF_ELL_{epoch + 1}', e_psf, idx)
+ self._add2dict(f"PSF_ELL_{epoch + 1}", e_psf, idx)
psf_fwhm = galaxy.sigma_to_fwhm(
- gpc_data['SHAPES']['SIGMA_PSF_HSM']
+ gpc_data["SHAPES"]["SIGMA_PSF_HSM"]
)
- self._add2dict(f'PSF_FWHM_{epoch + 1}', psf_fwhm, idx)
+ self._add2dict(f"PSF_FWHM_{epoch + 1}", psf_fwhm, idx)
- flag_psf = gpc_data['SHAPES']['FLAG_PSF_HSM']
- self._add2dict(f'PSF_FLAG_{epoch + 1}', flag_psf, idx)
+ flag_psf = gpc_data["SHAPES"]["FLAG_PSF_HSM"]
+ self._add2dict(f"PSF_FLAG_{epoch + 1}", flag_psf, idx)
galaxy_psf_cat.close()
diff --git a/shapepipe/modules/make_cat_runner.py b/shapepipe/modules/make_cat_runner.py
index 8b6351e2e..f36209f42 100644
--- a/shapepipe/modules/make_cat_runner.py
+++ b/shapepipe/modules/make_cat_runner.py
@@ -11,21 +11,21 @@
@module_runner(
- version='1.1',
+ version="1.1",
input_module=[
- 'sextractor_runner',
- 'spread_model_runner',
- 'psfex_interp_runner',
- 'ngmix_runner',
+ "sextractor_runner",
+ "spread_model_runner",
+ "psfex_interp_runner",
+ "ngmix_runner",
],
file_pattern=[
- 'tile_sexcat',
- 'sexcat_sm',
- 'galaxy_psf',
- 'ngmix',
+ "tile_sexcat",
+ "sexcat_sm",
+ "galaxy_psf",
+ "ngmix",
],
- file_ext=['.fits', '.fits', '.sqlite', '.fits'],
- depends=['numpy', 'sqlitedict'],
+ file_ext=[".fits", ".fits", ".sqlite", ".fits"],
+ depends=["numpy", "sqlitedict"],
)
def make_cat_runner(
input_file_list,
@@ -49,11 +49,11 @@ def make_cat_runner(
# Fetch classification options
do_classif = config.getboolean(
module_config_sec,
- 'SM_DO_CLASSIFICATION',
+ "SM_DO_CLASSIFICATION",
)
if do_classif:
- star_thresh = config.getfloat(module_config_sec, 'SM_STAR_THRESH')
- gal_thresh = config.getfloat(module_config_sec, 'SM_GAL_THRESH')
+ star_thresh = config.getfloat(module_config_sec, "SM_STAR_THRESH")
+ gal_thresh = config.getfloat(module_config_sec, "SM_GAL_THRESH")
else:
star_thresh = None
gal_thresh = None
@@ -61,32 +61,32 @@ def make_cat_runner(
# Fetch shape measurement type
shape_type_list = config.getlist(
module_config_sec,
- 'SHAPE_MEASUREMENT_TYPE',
+ "SHAPE_MEASUREMENT_TYPE",
)
for shape_type in shape_type_list:
- if shape_type.lower() not in ['ngmix', 'galsim']:
+ if shape_type.lower() not in ["ngmix", "galsim"]:
raise ValueError(
- 'SHAPE_MEASUREMENT_TYPE must be in [ngmix, galsim]'
+ "SHAPE_MEASUREMENT_TYPE must be in [ngmix, galsim]"
)
# Fetch PSF data option
- if config.has_option(module_config_sec, 'SAVE_PSF_DATA'):
- save_psf = config.getboolean(module_config_sec, 'SAVE_PSF_DATA')
+ if config.has_option(module_config_sec, "SAVE_PSF_DATA"):
+ save_psf = config.getboolean(module_config_sec, "SAVE_PSF_DATA")
else:
save_psf = False
# Set final output file
final_cat_file = make_cat.prepare_final_cat_file(
- run_dirs['output'],
+ run_dirs["output"],
file_number_string,
)
# Save SExtractor data
- w_log.info('Save SExtractor data')
+ w_log.info("Save SExtractor data")
make_cat.save_sextractor_data(final_cat_file, tile_sexcat_path)
# Save spread-model data
- w_log.info('Save spread-model data')
+ w_log.info("Save spread-model data")
make_cat.save_sm_data(
final_cat_file,
sexcat_sm_path,
@@ -97,15 +97,15 @@ def make_cat_runner(
# Save shape data
sc_inst = make_cat.SaveCatalogue(final_cat_file)
- w_log.info('Save shape measurement data')
+ w_log.info("Save shape measurement data")
for shape_type in shape_type_list:
- w_log.info(f'Save {shape_type.lower()} data')
+ w_log.info(f"Save {shape_type.lower()} data")
cat_path = (
- shape2_cat_path if shape_type == 'galsim' else shape1_cat_path
+ shape2_cat_path if shape_type == "galsim" else shape1_cat_path
)
sc_inst.process(shape_type.lower(), cat_path)
if save_psf:
- sc_inst.process('psf', galaxy_psf_path)
+ sc_inst.process("psf", galaxy_psf_path)
# No return objects
return None, None
diff --git a/shapepipe/modules/mask_package/__init__.py b/shapepipe/modules/mask_package/__init__.py
index af2dc5c5c..bdfece65b 100644
--- a/shapepipe/modules/mask_package/__init__.py
+++ b/shapepipe/modules/mask_package/__init__.py
@@ -63,6 +63,9 @@
Prefix to be appended to output file name ``flag``;
helps to distinguish the file patterns of newly created and external
mask files
+CHECK_EXISTING_DIR : str, optional
+ If given, search this directory for existing mask files; the
+ corresponding images will then not be processed
Mask config file
================
@@ -179,4 +182,4 @@
"""
-__all__ = ['mask']
+__all__ = ["mask"]
diff --git a/shapepipe/modules/mask_package/mask.py b/shapepipe/modules/mask_package/mask.py
index 69a1c3c97..dfd68e4e3 100644
--- a/shapepipe/modules/mask_package/mask.py
+++ b/shapepipe/modules/mask_package/mask.py
@@ -45,6 +45,8 @@ class Mask(object):
Path to external flag file, default is ``None`` (not used)
outname_base : str, optional
Output file name base, default is ``flag``
+ check_existing_dir : str, optional
+ If not ``None`` (default), search path for existing mask files
star_cat_path : str, optional
Path to external star catalogue, default is ``None`` (not used;
instead the star catalogue is produced on the fly at run time)
@@ -63,7 +65,8 @@ def __init__(
output_dir,
w_log,
path_external_flag=None,
- outname_base='flag',
+ outname_base="flag",
+ check_existing_dir=None,
star_cat_path=None,
hdu=0,
):
@@ -75,10 +78,10 @@ def __init__(
self._weight_fullpath = weight_path
# Input image prefix
- if (image_prefix.lower() != 'none') and (image_prefix != ''):
- self._img_prefix = f'{image_prefix}_'
+ if (image_prefix.lower() != "none") and (image_prefix != ""):
+ self._img_prefix = f"{image_prefix}_"
else:
- self._img_prefix = ''
+ self._img_prefix = ""
# File number identified
self._img_number = image_num
@@ -98,6 +101,9 @@ def __init__(
# Output file base name
self._outname_base = outname_base
+ # Search path for existing mask files
+ self._check_existing_dir = check_existing_dir
+
# Set external star catalogue path if given
if star_cat_path is not None:
self._star_cat_path = star_cat_path
@@ -127,141 +133,136 @@ def _get_config(self):
"""
if self._config_filepath is None:
- raise ValueError('No path to config file given')
+ raise ValueError("No path to config file given")
if not os.path.exists(self._config_filepath):
- raise IOError(
- f'Config file "{self._config_filepath}" not found'
- )
+ raise IOError(f'Config file "{self._config_filepath}" not found')
conf = CustomParser()
conf.read(self._config_filepath)
self._config = {
- 'PATH': {},
- 'BORDER': {},
- 'HALO': {},
- 'SPIKE': {},
- 'MESSIER': {},
- 'NGC': {},
- 'MD': {},
+ "PATH": {},
+ "BORDER": {},
+ "HALO": {},
+ "SPIKE": {},
+ "MESSIER": {},
+ "NGC": {},
+ "MD": {},
}
- if conf.has_option('PROGRAM_PATH', 'WW_PATH'):
- self._config['PATH']['WW'] = (
- conf.getexpanded('PROGRAM_PATH', 'WW_PATH')
+ if conf.has_option("PROGRAM_PATH", "WW_PATH"):
+ self._config["PATH"]["WW"] = conf.getexpanded(
+ "PROGRAM_PATH", "WW_PATH"
)
else:
- self._config['PATH']['WW'] = 'ww'
- self._config['PATH']['WW_configfile'] = (
- conf.getexpanded('PROGRAM_PATH', 'WW_CONFIG_FILE')
+ self._config["PATH"]["WW"] = "ww"
+ self._config["PATH"]["WW_configfile"] = conf.getexpanded(
+ "PROGRAM_PATH", "WW_CONFIG_FILE"
)
- if conf.has_option('PROGRAM_PATH', 'CDSCLIENT_PATH'):
- self._config['PATH']['CDSclient'] = (
- conf.getexpanded('PROGRAM_PATH', 'CDSCLIENT_PATH')
+ if conf.has_option("PROGRAM_PATH", "CDSCLIENT_PATH"):
+ self._config["PATH"]["CDSclient"] = conf.getexpanded(
+ "PROGRAM_PATH", "CDSCLIENT_PATH"
)
elif self._star_cat_path is not None:
- self._config['PATH']['star_cat'] = self._star_cat_path
+ self._config["PATH"]["star_cat"] = self._star_cat_path
else:
raise ValueError(
- 'Either [PROGRAM_PATH]:CDSCLIENT_PATH in the mask config file '
- + ' or a star catalogue as module input needs to be present'
+ "Either [PROGRAM_PATH]:CDSCLIENT_PATH in the mask config file "
+ + " or a star catalogue as module input needs to be present"
)
- self._config['PATH']['temp_dir'] = self._get_temp_dir_path(
- conf.getexpanded('OTHER', 'TEMP_DIRECTORY')
+ self._config["PATH"]["temp_dir"] = self._get_temp_dir_path(
+ conf.getexpanded("OTHER", "TEMP_DIRECTORY")
)
- self._config['BORDER']['make'] = (
- conf.getboolean('BORDER_PARAMETERS', 'BORDER_MAKE')
+ self._config["BORDER"]["make"] = conf.getboolean(
+ "BORDER_PARAMETERS", "BORDER_MAKE"
)
- if self._config['BORDER']['make']:
- self._config['BORDER']['width'] = (
- conf.getint('BORDER_PARAMETERS', 'BORDER_WIDTH')
+ if self._config["BORDER"]["make"]:
+ self._config["BORDER"]["width"] = conf.getint(
+ "BORDER_PARAMETERS", "BORDER_WIDTH"
)
- self._config['BORDER']['flag'] = (
- conf.get('BORDER_PARAMETERS', 'BORDER_FLAG_VALUE')
+ self._config["BORDER"]["flag"] = conf.get(
+ "BORDER_PARAMETERS", "BORDER_FLAG_VALUE"
)
- for mask_shape in ['HALO', 'SPIKE']:
+ for mask_shape in ["HALO", "SPIKE"]:
- self._config[mask_shape]['make'] = conf.getboolean(
- f'{mask_shape}_PARAMETERS',
- f'{mask_shape}_MAKE',
+ self._config[mask_shape]["make"] = conf.getboolean(
+ f"{mask_shape}_PARAMETERS",
+ f"{mask_shape}_MAKE",
)
- self._config[mask_shape]['individual'] = (
- conf.getboolean('OTHER', 'KEEP_INDIVIDUAL_MASK')
+ self._config[mask_shape]["individual"] = conf.getboolean(
+ "OTHER", "KEEP_INDIVIDUAL_MASK"
)
- if self._config[mask_shape]['make']:
+ if self._config[mask_shape]["make"]:
- self._config[mask_shape]['maskmodel_path'] = conf.getexpanded(
- f'{mask_shape}_PARAMETERS',
- f'{mask_shape}_MASKMODEL_PATH',
+ self._config[mask_shape]["maskmodel_path"] = conf.getexpanded(
+ f"{mask_shape}_PARAMETERS",
+ f"{mask_shape}_MASKMODEL_PATH",
)
- self._config[mask_shape]['mag_lim'] = conf.getfloat(
- f'{mask_shape}_PARAMETERS',
- f'{mask_shape}_MAG_LIM',
+ self._config[mask_shape]["mag_lim"] = conf.getfloat(
+ f"{mask_shape}_PARAMETERS",
+ f"{mask_shape}_MAG_LIM",
)
- self._config[mask_shape]['scale_factor'] = conf.getfloat(
- f'{mask_shape}_PARAMETERS',
- f'{mask_shape}_SCALE_FACTOR',
+ self._config[mask_shape]["scale_factor"] = conf.getfloat(
+ f"{mask_shape}_PARAMETERS",
+ f"{mask_shape}_SCALE_FACTOR",
)
- self._config[mask_shape]['mag_pivot'] = conf.getfloat(
- f'{mask_shape}_PARAMETERS',
- f'{mask_shape}_MAG_PIVOT',
+ self._config[mask_shape]["mag_pivot"] = conf.getfloat(
+ f"{mask_shape}_PARAMETERS",
+ f"{mask_shape}_MAG_PIVOT",
)
- self._config[mask_shape]['flag'] = conf.getint(
- f'{mask_shape}_PARAMETERS',
- f'{mask_shape}_FLAG_VALUE',
+ self._config[mask_shape]["flag"] = conf.getint(
+ f"{mask_shape}_PARAMETERS",
+ f"{mask_shape}_FLAG_VALUE",
)
- if conf.getboolean('OTHER', 'KEEP_REG_FILE'):
+ if conf.getboolean("OTHER", "KEEP_REG_FILE"):
reg_file = conf.getexpanded(
- f'{mask_shape}_PARAMETERS',
- f'{mask_shape}_REG_FILE',
+ f"{mask_shape}_PARAMETERS",
+ f"{mask_shape}_REG_FILE",
)
- self._config[mask_shape]['reg_file'] = (
+ self._config[mask_shape]["reg_file"] = (
f'{self._config["PATH"]["temp_dir"]}/'
+ f'{re.split(".reg", reg_file)[0]}'
- + f'{self._img_number}.reg'
+ + f"{self._img_number}.reg"
)
else:
- self._config[mask_shape]['reg_file'] = None
+ self._config[mask_shape]["reg_file"] = None
- for mask_type in ['MESSIER', 'NGC']:
+ for mask_type in ["MESSIER", "NGC"]:
- self._config[mask_type]['make'] = conf.getboolean(
- f'{mask_type}_PARAMETERS',
- f'{mask_type}_MAKE'
+ self._config[mask_type]["make"] = conf.getboolean(
+ f"{mask_type}_PARAMETERS", f"{mask_type}_MAKE"
)
- if self._config[mask_type]['make']:
- self._config[mask_type]['cat_path'] = conf.getexpanded(
- f'{mask_type}_PARAMETERS',
- f'{mask_type}_CAT_PATH',
+ if self._config[mask_type]["make"]:
+ self._config[mask_type]["cat_path"] = conf.getexpanded(
+ f"{mask_type}_PARAMETERS",
+ f"{mask_type}_CAT_PATH",
)
- self._config[mask_type]['size_plus'] = conf.getfloat(
- f'{mask_type}_PARAMETERS',
- f'{mask_type}_SIZE_PLUS',
+ self._config[mask_type]["size_plus"] = conf.getfloat(
+ f"{mask_type}_PARAMETERS",
+ f"{mask_type}_SIZE_PLUS",
)
- self._config[mask_type]['flag'] = conf.getint(
- f'{mask_type}_PARAMETERS',
- f'{mask_type}_FLAG_VALUE',
+ self._config[mask_type]["flag"] = conf.getint(
+ f"{mask_type}_PARAMETERS",
+ f"{mask_type}_FLAG_VALUE",
)
- self._config['MD']['make'] = (
- conf.getboolean('MD_PARAMETERS', 'MD_MAKE')
- )
+ self._config["MD"]["make"] = conf.getboolean("MD_PARAMETERS", "MD_MAKE")
- if self._config['MD']['make']:
- self._config['MD']['thresh_flag'] = (
- conf.getfloat('MD_PARAMETERS', 'MD_THRESH_FLAG')
+ if self._config["MD"]["make"]:
+ self._config["MD"]["thresh_flag"] = conf.getfloat(
+ "MD_PARAMETERS", "MD_THRESH_FLAG"
)
- self._config['MD']['thresh_remove'] = (
- conf.getfloat('MD_PARAMETERS', 'MD_THRESH_REMOVE')
+ self._config["MD"]["thresh_remove"] = conf.getfloat(
+ "MD_PARAMETERS", "MD_THRESH_REMOVE"
)
- self._config['MD']['remove'] = (
- conf.getboolean('MD_PARAMETERS', 'MD_REMOVE')
+ self._config["MD"]["remove"] = conf.getboolean(
+ "MD_PARAMETERS", "MD_REMOVE"
)
def _set_image_coordinates(self):
@@ -286,9 +287,9 @@ def _set_image_coordinates(self):
pix_center = [img_shape[1] / 2.0, img_shape[0] / 2.0]
wcs_center = self._wcs.all_pix2world([pix_center], 1)[0]
self._fieldcenter = {}
- self._fieldcenter['pix'] = np.array(pix_center)
- self._fieldcenter['wcs'] = (
- SkyCoord(ra=wcs_center[0], dec=wcs_center[1], unit='deg')
+ self._fieldcenter["pix"] = np.array(pix_center)
+ self._fieldcenter["wcs"] = SkyCoord(
+ ra=wcs_center[0], dec=wcs_center[1], unit="deg"
)
# Get the four corners of the image
@@ -307,69 +308,78 @@ def make_mask(self):
Main function to create the mask.
"""
- if self._config['MD']['make']:
+ output_file_name = (
+ f"{self._img_prefix}"
+ + f"{self._outname_base}{self._img_number}.fits"
+ )
+ if os.path.exists(f"{self._check_existing_dir}//{output_file_name}"):
+ return None, None
+
+ if self._config["MD"]["make"]:
self.missing_data()
- if self._config['HALO']['make'] or self._config['SPIKE']['make']:
+ if self._config["HALO"]["make"] or self._config["SPIKE"]["make"]:
stars = self.find_stars(
- np.array([
- self._fieldcenter['wcs'].ra.value,
- self._fieldcenter['wcs'].dec.value
- ]),
+ np.array(
+ [
+ self._fieldcenter["wcs"].ra.value,
+ self._fieldcenter["wcs"].dec.value,
+ ]
+ ),
radius=self._img_radius,
)
if not self._err:
- for _type in ('HALO', 'SPIKE'):
- if self._config[_type]['make']:
+ for _type in ("HALO", "SPIKE"):
+ if self._config[_type]["make"]:
self._create_mask(
stars=stars,
types=_type,
- mag_limit=self._config[_type]['mag_lim'],
- scale_factor=self._config[_type]['scale_factor'],
- mag_pivot=self._config[_type]['mag_pivot'],
+ mag_limit=self._config[_type]["mag_lim"],
+ scale_factor=self._config[_type]["scale_factor"],
+ mag_pivot=self._config[_type]["mag_pivot"],
)
if not self._err:
mask_name = []
- if self._config['HALO']['make'] and self._config['SPIKE']['make']:
- self._exec_WW(types='ALL')
+ if self._config["HALO"]["make"] and self._config["SPIKE"]["make"]:
+ self._exec_WW(types="ALL")
mask_name.append(
f'{self._config["PATH"]["temp_dir"]}halo_spike_flag'
- + f'{self._img_number}.fits'
+ + f"{self._img_number}.fits"
)
mask_name.append(None)
else:
- for _type in ('HALO', 'SPIKE'):
- if self._config[_type]['make']:
+ for _type in ("HALO", "SPIKE"):
+ if self._config[_type]["make"]:
self._exec_WW(types=_type)
mask_name.append(
f'{self._config["PATH"]["temp_dir"]}'
- + f'{_type.lower()}_flag{self._img_number}.fits'
+ + f"{_type.lower()}_flag{self._img_number}.fits"
)
else:
mask_name.append(None)
masks_internal = {}
if not self._err:
- if self._config['BORDER']['make']:
- masks_internal['BORDER'] = self.mask_border(
- width=self._config['BORDER']['width']
+ if self._config["BORDER"]["make"]:
+ masks_internal["BORDER"] = self.mask_border(
+ width=self._config["BORDER"]["width"]
)
if not self._err:
- for _type in ('MESSIER', 'NGC'):
- if self._config[_type]['make']:
+ for _type in ("MESSIER", "NGC"):
+ if self._config[_type]["make"]:
masks_internal[_type] = self.mask_dso(
- self._config[_type]['cat_path'],
- size_plus=self._config[_type]['size_plus'],
- flag_value=self._config[_type]['flag'],
+ self._config[_type]["cat_path"],
+ size_plus=self._config[_type]["size_plus"],
+ flag_value=self._config[_type]["flag"],
obj_type=_type,
)
if not self._err:
try:
- im_pass = self._config['MD']['im_remove']
+ im_pass = self._config["MD"]["im_remove"]
except Exception:
im_pass = True
@@ -385,19 +395,19 @@ def make_mask(self):
path_external_flag=path_external_flag,
)
- if not self._config['HALO']['individual']:
+ if not self._config["HALO"]["individual"]:
if mask_name[0] is not None:
- self._rm_fits1_stdout, self._rm_fits1_stderr = (
- execute(f'rm {mask_name[0]}')
+ self._rm_fits1_stdout, self._rm_fits1_stderr = execute(
+ f"rm {mask_name[0]}"
)
if mask_name[1] is not None:
- self._rm_fits2_stdout, self._rm_fits2_stderr = (
- execute(f'rm {mask_name[1]}')
+ self._rm_fits2_stdout, self._rm_fits2_stderr = execute(
+ f"rm {mask_name[1]}"
)
output_file_name = (
- f'{self._output_dir}/{self._img_prefix}'
- + f'{self._outname_base}{self._img_number}.fits'
+ f"{self._output_dir}/{self._img_prefix}"
+ + f"{self._outname_base}{self._img_number}.fits"
)
self._mask_to_file(
@@ -406,32 +416,30 @@ def make_mask(self):
)
# Handle stdout / stderr
- general_stdout = f'\nCDSClient\n{self._CDS_stdout}'
- general_stderr = ''
- if self._CDS_stderr != '':
- general_stderr += f'\nCDSClient\n{self._CDS_stderr}'
- if hasattr(self, '_WW_stdout') or hasattr(self, '_WW_stdout'):
- general_stdout += f'\n\nWeightWatcher\n{self._WW_stdout}'
- if self._WW_stderr != '':
- general_stderr += f'\n\nWeightWatcher\n{self._WW_stderr}'
- if hasattr(self, '_rm_reg_stderr') or hasattr(self, '_rm_reg_stdout'):
- general_stdout += f'\n\nrm reg file\n{self._rm_reg_stdout}'
- if self._rm_reg_stderr != '':
- general_stderr += f'\n\nrm reg file\n{self._rm_reg_stderr}'
- if (
- hasattr(self, '_rm_fits1_stderr')
- or hasattr(self, '_rm_fits1_stdout')
+ general_stdout = f"\nCDSClient\n{self._CDS_stdout}"
+ general_stderr = ""
+ if self._CDS_stderr != "":
+ general_stderr += f"\nCDSClient\n{self._CDS_stderr}"
+ if hasattr(self, "_WW_stdout") or hasattr(self, "_WW_stdout"):
+ general_stdout += f"\n\nWeightWatcher\n{self._WW_stdout}"
+ if self._WW_stderr != "":
+ general_stderr += f"\n\nWeightWatcher\n{self._WW_stderr}"
+ if hasattr(self, "_rm_reg_stderr") or hasattr(self, "_rm_reg_stdout"):
+ general_stdout += f"\n\nrm reg file\n{self._rm_reg_stdout}"
+ if self._rm_reg_stderr != "":
+ general_stderr += f"\n\nrm reg file\n{self._rm_reg_stderr}"
+ if hasattr(self, "_rm_fits1_stderr") or hasattr(
+ self, "_rm_fits1_stdout"
):
- general_stdout += f'\n\nrm fits1 file\n{self._rm_fits1_stdout}'
- if self._rm_fits1_stderr != '':
- general_stderr += f'\n\nrm fits1 file\n{self._rm_fits1_stderr}'
- if (
- hasattr(self, '_rm_fits2_stderr')
- or hasattr(self, '_rm_fits2_stdout')
+ general_stdout += f"\n\nrm fits1 file\n{self._rm_fits1_stdout}"
+ if self._rm_fits1_stderr != "":
+ general_stderr += f"\n\nrm fits1 file\n{self._rm_fits1_stderr}"
+ if hasattr(self, "_rm_fits2_stderr") or hasattr(
+ self, "_rm_fits2_stdout"
):
- general_stdout += f'\n\nrm fits2 file\n{self._rm_fits2_stdout}'
- if self._rm_fits2_stderr != '':
- general_stderr += f'\n\nrm fits2 file\n{self._rm_fits2_stderr}'
+ general_stdout += f"\n\nrm fits2 file\n{self._rm_fits2_stdout}"
+ if self._rm_fits2_stderr != "":
+ general_stderr += f"\n\nrm fits2 file\n{self._rm_fits2_stderr}"
return general_stdout, general_stderr
@@ -459,35 +467,35 @@ def find_stars(self, position, radius):
For invalid configuration options
"""
- if 'CDSclient' in self._config['PATH']:
+ if "CDSclient" in self._config["PATH"]:
ra = position[0]
dec = position[1]
if dec > 0.0:
- sign = '+'
+ sign = "+"
else:
- sign = ''
+ sign = ""
cmd_line = (
f'{self._config["PATH"]["CDSclient"]} {ra} {sign}{dec} '
- + f'-r {radius} -n 1000000'
+ + f"-r {radius} -n 1000000"
)
self._CDS_stdout, self._CDS_stderr = execute(cmd_line)
- elif 'star_cat' in self._config['PATH']:
- f = open(self._config['PATH']['star_cat'], 'r')
+ elif "star_cat" in self._config["PATH"]:
+ f = open(self._config["PATH"]["star_cat"], "r")
self._CDS_stdout = f.read()
- self._CDS_stderr = ''
+ self._CDS_stderr = ""
f.close()
else:
raise ValueError(
- 'Either [PROGRAM_PATH]:CDSCLIENT_PATH in the mask config file '
- + ' or a star catalogue as module input needs to be present'
+ "Either [PROGRAM_PATH]:CDSCLIENT_PATH in the mask config file "
+ + " or a star catalogue as module input needs to be present"
)
- if self._CDS_stderr != '':
+ if self._CDS_stderr != "":
self._err = True
return None
@@ -517,15 +525,15 @@ def mask_border(self, width=100, flag_value=4):
"""
if width is None:
- raise ValueError('Width for border mask not provided')
+ raise ValueError("Width for border mask not provided")
# Note that python image array is [y, x]
flag = np.zeros(
(
- int(self._fieldcenter['pix'][1] * 2),
- int(self._fieldcenter['pix'][0] * 2)
+ int(self._fieldcenter["pix"][1] * 2),
+ int(self._fieldcenter["pix"][0] * 2),
),
- dtype='uint16',
+ dtype="uint16",
)
flag[0:width, :] = flag_value
@@ -540,7 +548,7 @@ def mask_dso(
cat_path,
size_plus=0.1,
flag_value=8,
- obj_type='Messier',
+ obj_type="Messier",
):
"""Mask DSO.
@@ -575,23 +583,23 @@ def mask_dso(
"""
if size_plus < 0:
raise ValueError(
- 'deep-sky mask size increase variable cannot be negative'
+ "deep-sky mask size increase variable cannot be negative"
)
if cat_path is None:
- raise ValueError('Path to deep-sky object catalogue not provided')
+ raise ValueError("Path to deep-sky object catalogue not provided")
m_cat, header = fits.getdata(cat_path, header=True)
- unit_ra = file_io.get_unit_from_fits_header(header, 'ra')
- unit_dec = file_io.get_unit_from_fits_header(header, 'dec')
+ unit_ra = file_io.get_unit_from_fits_header(header, "ra")
+ unit_dec = file_io.get_unit_from_fits_header(header, "dec")
m_sc = SkyCoord(
- ra=m_cat['ra'] * unit_ra,
- dec=m_cat['dec'] * unit_dec,
+ ra=m_cat["ra"] * unit_ra,
+ dec=m_cat["dec"] * unit_dec,
)
- unit_size_X = file_io.get_unit_from_fits_header(header, 'size_X')
- unit_size_Y = file_io.get_unit_from_fits_header(header, 'size_Y')
+ unit_size_X = file_io.get_unit_from_fits_header(header, "size_X")
+ unit_size_Y = file_io.get_unit_from_fits_header(header, "size_Y")
# Loop through all deep-sky objects and check whether any corner is
# closer than the object's radius
@@ -602,8 +610,8 @@ def mask_dso(
# DSO size
# r = max(m_obj['size']) * units.arcmin
r = max(
- m_obj['size_X'] * unit_size_X,
- m_obj['size_Y'] * unit_size_Y,
+ m_obj["size_X"] * unit_size_X,
+ m_obj["size_Y"] * unit_size_Y,
)
r_deg = r.to(units.degree)
size_max_deg.append(r_deg)
@@ -614,8 +622,7 @@ def mask_dso(
indices.append(idx)
self._w_log.info(
- f'Found {len(indices)} {obj_type} objects overlapping with'
- ' image'
+ f"Found {len(indices)} {obj_type} objects overlapping with" " image"
)
if len(indices) == 0:
@@ -628,42 +635,44 @@ def mask_dso(
for idx in indices:
in_img = self._wcs.footprint_contains(m_sc[idx])
self._w_log.info(
- '(obj_type, ra, dec, in_img) = '
- + f'({obj_type}, '
+ "(obj_type, ra, dec, in_img) = "
+ + f"({obj_type}, "
+ f'{m_cat["ra"][idx]}, '
+ f'{m_cat["dec"][idx]}, '
- + f'{in_img})'
+ + f"{in_img})"
)
# Note: python image array is [y, x]
flag = np.zeros(
(
- int(self._fieldcenter['pix'][1] * 2),
- int(self._fieldcenter['pix'][0] * 2)
+ int(self._fieldcenter["pix"][1] * 2),
+ int(self._fieldcenter["pix"][0] * 2),
),
- dtype='uint16',
+ dtype="uint16",
)
- nx = self._fieldcenter['pix'][0] * 2
- ny = self._fieldcenter['pix'][1] * 2
+ nx = self._fieldcenter["pix"][0] * 2
+ ny = self._fieldcenter["pix"][1] * 2
for idx in indices:
- m_center = np.hstack(self._wcs.all_world2pix(
- m_cat['ra'][idx],
- m_cat['dec'][idx],
- 0,
- ))
+ m_center = np.hstack(
+ self._wcs.all_world2pix(
+ m_cat["ra"][idx],
+ m_cat["dec"][idx],
+ 0,
+ )
+ )
r_pix = (
- size_max_deg[idx].to(units.deg).value * (1 + size_plus)
+ size_max_deg[idx].to(units.deg).value
+ * (1 + size_plus)
/ np.abs(self._wcs.pixel_scale_matrix[0][0])
)
# The following accounts for deep-sky centers outside of image,
# without creating masks for coordinates out of range
y_c, x_c = np.ogrid[0:ny, 0:nx]
- mask_tmp = (
- (x_c - m_center[0]) ** 2 + (y_c - m_center[1]) ** 2
- <= r_pix ** 2
- )
+ mask_tmp = (x_c - m_center[0]) ** 2 + (
+ y_c - m_center[1]
+ ) ** 2 <= r_pix**2
flag[mask_tmp] = flag_value
@@ -684,26 +693,26 @@ def missing_data(self):
tot = float(im_shape[0] * im_shape[1])
# Compute number and ratio of missing data (zero-valued pixels)
- missing = float(len(np.where(img.get_data() == 0.)[0]))
+ missing = float(len(np.where(img.get_data() == 0.0)[0]))
self._ratio = missing / tot
# Mark image as to be flagged if ratio larger than 'flag' threshold
- if self._ratio >= self._config['MD']['thresh_flag']:
- self._config['MD']['im_flagged'] = True
+ if self._ratio >= self._config["MD"]["thresh_flag"]:
+ self._config["MD"]["im_flagged"] = True
else:
- self._config['MD']['im_flagged'] = False
+ self._config["MD"]["im_flagged"] = False
# Mark image as to be removed if flag is True and
# ratio large than 'remove' threshold.
# Reset all other mask 'make' flags to False (no other mask needs
# to be created)
- if self._config['MD']['remove']:
- if self._ratio >= self._config['MD']['thresh_remove']:
- self._config['MD']['im_remove'] = True
- for idx in ['HALO', 'SPIKE', 'MESSIER', 'BORDER']:
- self._config[idx]['make'] = False
+ if self._config["MD"]["remove"]:
+ if self._ratio >= self._config["MD"]["thresh_remove"]:
+ self._config["MD"]["im_remove"] = True
+ for idx in ["HALO", "SPIKE", "MESSIER", "BORDER"]:
+ self._config[idx]["make"] = False
else:
- self._config['MD']['im_remove'] = False
+ self._config["MD"]["im_remove"] = False
img.close()
@@ -734,7 +743,7 @@ def sphere_dist(self, position1, position2):
type(position1) is not np.ndarray
or type(position2) is not np.ndarray
):
- raise ValueError('Object coordinates need to be a numpy.ndarray')
+ raise ValueError("Object coordinates need to be a numpy.ndarray")
p1 = (np.pi / 180.0) * np.hstack(
self._wcs.all_pix2world(position1[0], position1[1], 1)
@@ -747,10 +756,12 @@ def sphere_dist(self, position1, position2):
dLong = dTheta[0]
dLat = dTheta[1]
- dist = 2 * np.arcsin(np.sqrt(
- np.sin(dLat / 2.0) ** 2.0 + np.cos(p1[1]) * np.cos(p2[1])
- * np.sin(dLong / 2.0) ** 2.0
- ))
+ dist = 2 * np.arcsin(
+ np.sqrt(
+ np.sin(dLat / 2.0) ** 2.0
+ + np.cos(p1[1]) * np.cos(p2[1]) * np.sin(dLong / 2.0) ** 2.0
+ )
+ )
return dist * (180.0 / np.pi) * 3600.0
@@ -777,7 +788,7 @@ def _get_image_radius(self, center=None):
"""
if center is None:
return (
- self.sphere_dist(self._fieldcenter['pix'], np.zeros(2)) / 60.0
+ self.sphere_dist(self._fieldcenter["pix"], np.zeros(2)) / 60.0
)
else:
@@ -785,7 +796,7 @@ def _get_image_radius(self, center=None):
return self.sphere_dist(center, np.zeros(2)) / 60.0
else:
raise TypeError(
- 'Image center coordinates has to be a numpy.ndarray'
+ "Image center coordinates has to be a numpy.ndarray"
)
def _make_star_cat(self, CDSclient_output):
@@ -808,12 +819,12 @@ def _make_star_cat(self, CDSclient_output):
stars = {}
# get header
- for key in CDSclient_output.splitlines()[3].split(' '):
- if (key != '') and (key != ';'):
+ for key in CDSclient_output.splitlines()[3].split(" "):
+ if (key != "") and (key != ";"):
# cleaning output
- key = key.replace(' ', '')
- for key_split in re.split(',|#|;', key):
- if key_split != '':
+ key = key.replace(" ", "")
+ for key_split in re.split(",|#|;", key):
+ if key_split != "":
key = key_split
header.append(key)
stars[key] = []
@@ -821,19 +832,19 @@ def _make_star_cat(self, CDSclient_output):
# get data
for elem in range(4, len(CDSclient_output.splitlines()) - 5):
idx = 0
- for key in CDSclient_output.splitlines()[elem].split(' '):
- if (key != '') and (key != ';'):
+ for key in CDSclient_output.splitlines()[elem].split(" "):
+ if (key != "") and (key != ";"):
# cleaning output
- key = key.replace(' ', '')
- for key_split in re.split(',|#|;', key):
- if key_split != '':
+ key = key.replace(" ", "")
+ for key_split in re.split(",|#|;", key):
+ if key_split != "":
key = key_split
# handle missing data
try:
key = float(key)
stars[header[idx]].append(key)
except Exception:
- if key == '---':
+ if key == "---":
stars[header[idx]].append(None)
else:
stars[header[idx]].append(key)
@@ -844,7 +855,7 @@ def _make_star_cat(self, CDSclient_output):
def _create_mask(
self,
stars,
- types='HALO',
+ types="HALO",
mag_limit=18.0,
mag_pivot=13.8,
scale_factor=0.3,
@@ -875,34 +886,34 @@ def _create_mask(
"""
if stars is None:
- raise ValueError('Star catalogue dictionary not provided')
+ raise ValueError("Star catalogue dictionary not provided")
- if types not in ('HALO', 'SPIKE'):
+ if types not in ("HALO", "SPIKE"):
raise ValueError('Mask types need to be in ["HALO", "SPIKE"]')
- if self._config[types]['reg_file'] is None:
+ if self._config[types]["reg_file"] is None:
reg = (
f'{self._config["PATH"]["temp_dir"]}{types.lower()}'
- + f'{self._img_number}.reg'
+ + f"{self._img_number}.reg"
)
else:
- reg = self._config[types]['reg_file']
+ reg = self._config[types]["reg_file"]
mask_model = np.loadtxt(
- self._config[types]['maskmodel_path']
+ self._config[types]["maskmodel_path"]
).transpose()
- mask_reg = open(reg, 'w')
+ mask_reg = open(reg, "w")
stars_used = [[], [], []]
star_zip = zip(
- stars['RA(J2000)'],
- stars['Dec(J2000)'],
- stars['Fmag'],
- stars['Jmag'],
- stars['Vmag'],
- stars['Nmag'],
- stars['Clas'],
+ stars["RA(J2000)"],
+ stars["Dec(J2000)"],
+ stars["Fmag"],
+ stars["Jmag"],
+ stars["Vmag"],
+ stars["Nmag"],
+ stars["Clas"],
)
for ra, dec, Fmag, Jmag, Vmag, Nmag, clas in star_zip:
@@ -927,7 +938,9 @@ def _create_mask(
mag /= idx
if (
- ra is not None and dec is not None and mag is not None
+ ra is not None
+ and dec is not None
+ and mag is not None
and clas is not None
):
if (mag < mag_limit) and (clas == 0):
@@ -938,22 +951,22 @@ def _create_mask(
stars_used[2].append(scaling)
for idx in range(len(stars_used[0])):
- poly = 'polygon('
+ poly = "polygon("
for x, y in zip(mask_model[0], mask_model[1]):
angle = np.arctan2(y, x)
- ll = stars_used[2][idx] * np.sqrt(x ** 2 + y ** 2)
+ ll = stars_used[2][idx] * np.sqrt(x**2 + y**2)
xnew = ll * np.cos(angle)
ynew = ll * np.sin(angle)
poly = (
- f'{poly}{str(stars_used[0][idx] + xnew + 0.5)} '
- + f'{str(stars_used[1][idx] + ynew + 0.5)} '
+ f"{poly}{str(stars_used[0][idx] + xnew + 0.5)} "
+ + f"{str(stars_used[1][idx] + ynew + 0.5)} "
)
- poly = f'{poly})\n'
+ poly = f"{poly})\n"
mask_reg.write(poly)
mask_reg.close()
- def _exec_WW(self, types='HALO'):
+ def _exec_WW(self, types="HALO"):
"""Execute WeightWatcher.
Execute WeightWatcher to transform ``.reg`` to ``.fits`` flag map.
@@ -970,18 +983,18 @@ def _exec_WW(self, types='HALO'):
If catalogue file not found
"""
- if types in ('HALO', 'SPIKE'):
+ if types in ("HALO", "SPIKE"):
default_reg = (
f'{self._config["PATH"]["temp_dir"]}{types.lower()}'
- + f'{self._img_number}.reg'
+ + f"{self._img_number}.reg"
)
default_out = (
f'{self._config["PATH"]["temp_dir"]}{types.lower()}_flag'
- + f'{self._img_number}.fits'
+ + f"{self._img_number}.fits"
)
- if self._config[types]['reg_file'] is None:
+ if self._config[types]["reg_file"] is None:
reg = default_reg
if not file_io.BaseCatalogue(reg)._file_exists(reg):
@@ -990,20 +1003,18 @@ def _exec_WW(self, types='HALO'):
cmd = (
f'{self._config["PATH"]["WW"]} '
+ f'-c {self._config["PATH"]["WW_configfile"]} '
- + f'-WEIGHT_NAMES {self._weight_fullpath} '
- + f'-POLY_NAMES {reg} '
+ + f"-WEIGHT_NAMES {self._weight_fullpath} "
+ + f"-POLY_NAMES {reg} "
+ f'-POLY_OUTFLAGS {self._config[types]["flag"]} '
+ f'-FLAG_NAMES "" -OUTFLAG_NAME {default_out} '
+ '-OUTWEIGHT_NAME ""'
)
self._WW_stdout, self._WW_stderr = execute(cmd)
- self._rm_reg_stdout, self._rm_reg_stderr = (
- execute(f'rm {reg}')
- )
+ self._rm_reg_stdout, self._rm_reg_stderr = execute(f"rm {reg}")
else:
- reg = self._config[types]['reg_file']
+ reg = self._config[types]["reg_file"]
if not file_io.BaseCatalogue(reg)._file_exists(reg):
raise file_io.BaseCatalogue.CatalogFileNotFound(reg)
@@ -1011,8 +1022,8 @@ def _exec_WW(self, types='HALO'):
cmd = (
f'{self._config["PATH"]["WW"]} '
+ f'-c {self._config["PATH"]["WW_configfile"]} '
- + f'-WEIGHT_NAMES {self._weight_fullpath} '
- + f'-POLY_NAMES {reg} '
+ + f"-WEIGHT_NAMES {self._weight_fullpath} "
+ + f"-POLY_NAMES {reg} "
+ f'-POLY_OUTFLAGS {self._config[types]["flag"]} '
+ f'-FLAG_NAMES "" -OUTFLAG_NAME {default_out} '
+ '-OUTWEIGHT_NAME ""'
@@ -1020,24 +1031,24 @@ def _exec_WW(self, types='HALO'):
self._WW_stdout, self._WW_stderr = execute(cmd)
- elif types == 'ALL':
+ elif types == "ALL":
default_reg = [
(
f'{self._config["PATH"]["temp_dir"]}'
- + f'halo{self._img_number}.reg'
+ + f"halo{self._img_number}.reg"
),
(
f'{self._config["PATH"]["temp_dir"]}'
- + f'spike{self._img_number}.reg'
- )
+ + f"spike{self._img_number}.reg"
+ ),
]
default_out = (
f'{self._config["PATH"]["temp_dir"]}'
- + f'halo_spike_flag{self._img_number}.fits'
+ + f"halo_spike_flag{self._img_number}.fits"
)
- if self._config['HALO']['reg_file'] is None:
+ if self._config["HALO"]["reg_file"] is None:
reg = default_reg
for idx in range(2):
@@ -1051,8 +1062,8 @@ def _exec_WW(self, types='HALO'):
cmd = (
f'{self._config["PATH"]["WW"]} '
+ f'-c {self._config["PATH"]["WW_configfile"]} '
- + f'-WEIGHT_NAMES {self._weight_fullpath} '
- + f'-POLY_NAMES {reg[0]},{reg[1]} '
+ + f"-WEIGHT_NAMES {self._weight_fullpath} "
+ + f"-POLY_NAMES {reg[0]},{reg[1]} "
+ f'-POLY_OUTFLAGS {self._config["HALO"]["flag"]},'
+ f'{self._config["SPIKE"]["flag"]} '
+ f'-FLAG_NAMES "" -OUTFLAG_NAME {default_out} '
@@ -1060,14 +1071,14 @@ def _exec_WW(self, types='HALO'):
)
self._WW_stdout, self._WW_stderr = execute(cmd)
- self._rm_reg_stdout, self._rm_reg_stderr = (
- execute(f'rm {reg[0]} {reg[1]}')
+ self._rm_reg_stdout, self._rm_reg_stderr = execute(
+ f"rm {reg[0]} {reg[1]}"
)
else:
reg = [
- self._config['HALO']['reg_file'],
- self._config['SPIKE']['reg_file']
+ self._config["HALO"]["reg_file"],
+ self._config["SPIKE"]["reg_file"],
]
for idx in range(2):
@@ -1081,8 +1092,8 @@ def _exec_WW(self, types='HALO'):
cmd = (
f'{self._config["PATH"]["WW"]} '
+ f'-c {self._config["PATH"]["WW_configfile"]} '
- + f'-WEIGHT_NAMES {self._weight_fullpath} '
- + f'-POLY_NAMES {reg[0]},{reg[1]} '
+ + f"-WEIGHT_NAMES {self._weight_fullpath} "
+ + f"-POLY_NAMES {reg[0]},{reg[1]} "
+ f'-POLY_OUTFLAGS {self._config["HALO"]["flag"]},'
+ f'{self._config["SPIKE"]["flag"]} '
+ f'-FLAG_NAMES "" -OUTFLAG_NAME {default_out} '
@@ -1094,7 +1105,7 @@ def _exec_WW(self, types='HALO'):
else:
ValueError("Types must be in ['HALO','SPIKE','ALL']")
- if (self._WW_stderr != '') or (self._rm_reg_stderr != ''):
+ if (self._WW_stderr != "") or (self._rm_reg_stderr != ""):
self._err = True
def _build_final_mask(
@@ -1136,13 +1147,10 @@ def _build_final_mask(
"""
final_mask = None
- if (
- path_mask1 is None and path_mask2 is None
- and not masks_internal
- ):
+ if path_mask1 is None and path_mask2 is None and not masks_internal:
raise ValueError(
- 'No paths to mask files containing halos and/or spikes,'
- + ' borders, or deep-sky objects provided'
+ "No paths to mask files containing halos and/or spikes,"
+ + " borders, or deep-sky objects provided"
)
if path_mask1 is not None:
@@ -1168,8 +1176,8 @@ def _build_final_mask(
final_mask = masks_internal[typ]
else:
raise TypeError(
- f'internally created mask of type {typ} '
- + 'has to be numpy.ndarray'
+ f"internally created mask of type {typ} "
+ + "has to be numpy.ndarray"
)
if path_external_flag is not None:
@@ -1208,9 +1216,9 @@ def _mask_to_file(self, input_mask, output_fullpath):
"""
if input_mask is None:
- raise ValueError('input mask file path not provided')
+ raise ValueError("input mask file path not provided")
if output_fullpath is None:
- raise ValueError('output mask file path not provided')
+ raise ValueError("output mask file path not provided")
out = file_io.FITSCatalogue(
output_fullpath,
@@ -1219,16 +1227,16 @@ def _mask_to_file(self, input_mask, output_fullpath):
)
out.save_as_fits(data=input_mask, image=True)
- if self._config['MD']['make']:
+ if self._config["MD"]["make"]:
out.open()
out.add_header_card(
- 'MRATIO',
+ "MRATIO",
self._ratio,
- 'ratio missing_pixels/all_pixels',
+ "ratio missing_pixels/all_pixels",
)
out.add_header_card(
- 'MFLAG',
- self._config['MD']['im_flagged'],
+ "MFLAG",
+ self._config["MD"]["im_flagged"],
f'threshold value {self._config["MD"]["thresh_flag"]:.3}',
)
@@ -1266,14 +1274,14 @@ def _get_temp_dir_path(self, temp_dir_path):
"""
if temp_dir_path is None:
- raise ValueError('Temporary directory path not provided')
+ raise ValueError("Temporary directory path not provided")
- path = temp_dir_path.replace(' ', '')
+ path = temp_dir_path.replace(" ", "")
- if path == 'OUTPUT':
- path = f'{self._output_dir}/temp'
+ if path == "OUTPUT":
+ path = f"{self._output_dir}/temp"
- path += '/'
+ path += "/"
if not os.path.isdir(path):
mkdir(path)
diff --git a/shapepipe/modules/mask_runner.py b/shapepipe/modules/mask_runner.py
index 3683076e4..0cbec20e2 100644
--- a/shapepipe/modules/mask_runner.py
+++ b/shapepipe/modules/mask_runner.py
@@ -11,12 +11,12 @@
@module_runner(
- version='1.0',
- file_pattern=['image', 'weight', 'flag'],
- file_ext=['.fits', '.fits', '.fits'],
- depends=['numpy', 'astropy'],
- executes=['ww', 'findgsc2.2'],
- numbering_scheme='_0',
+ version="1.0",
+ file_pattern=["image", "weight", "flag"],
+ file_ext=[".fits", ".fits", ".fits"],
+ depends=["numpy", "astropy"],
+ executes=["ww", "findgsc2.2"],
+ numbering_scheme="_0",
)
def mask_runner(
input_file_list,
@@ -37,32 +37,31 @@ def mask_runner(
# Set options for 3 inputs
elif n_inputs == 3:
- if config.getboolean(module_config_sec, 'USE_EXT_FLAG'):
+ if config.getboolean(module_config_sec, "USE_EXT_FLAG"):
ext_flag_name = input_file_list[2]
ext_star_cat = None
- elif config.getboolean(module_config_sec, 'USE_EXT_STAR'):
+ elif config.getboolean(module_config_sec, "USE_EXT_STAR"):
ext_flag_name = None
ext_star_cat = input_file_list[2]
else:
raise ValueError(
- f'Found {n_inputs} inputs but was expecting external flag or '
- + 'external star catalogue in the MASK_RUNNER section of the '
- + 'config file.'
+ f"Found {n_inputs} inputs but was expecting external flag or "
+ + "external star catalogue in the MASK_RUNNER section of the "
+ + "config file."
)
# Set options for 4 inputs
elif n_inputs == 4:
- if (
- config.getboolean(module_config_sec, 'USE_EXT_FLAG')
- and config.getboolean(module_config_sec, 'USE_EXT_STAR')
- ):
+ if config.getboolean(
+ module_config_sec, "USE_EXT_FLAG"
+ ) and config.getboolean(module_config_sec, "USE_EXT_STAR"):
ext_flag_name = input_file_list[2]
ext_star_cat = input_file_list[3]
else:
raise ValueError(
- f'Found {n_inputs} inputs but was expecting external flag and '
- + 'external star catalogue in the MASK_RUNNER section of the '
- + 'config file.'
+ f"Found {n_inputs} inputs but was expecting external flag and "
+ + "external star catalogue in the MASK_RUNNER section of the "
+ + "config file."
)
# Raise error for invalid settings
@@ -70,37 +69,46 @@ def mask_runner(
raise ValueError(
f'Found {n_inputs} inputs and these must be "image", "weight" and '
+ '"ext_flags", "ext_star_cat" (optional). Check the MASK_RUNNER '
- + 'section of the config file to make sure you have the '
- + 'appropriate settings.'
+ + "section of the config file to make sure you have the "
+ + "appropriate settings."
)
# Get path to mask configuration options
- config_file = config.getexpanded(module_config_sec, 'MASK_CONFIG_PATH')
+ config_file = config.getexpanded(module_config_sec, "MASK_CONFIG_PATH")
# Get mask HDU number
- if config.has_option(module_config_sec, 'HDU'):
- hdu = config.getint(module_config_sec, 'HDU')
+ if config.has_option(module_config_sec, "HDU"):
+ hdu = config.getint(module_config_sec, "HDU")
else:
hdu = 0
# Get mask mask file name prefix
- if config.has_option(module_config_sec, 'PREFIX'):
- prefix = config.get(module_config_sec, 'PREFIX')
+ if config.has_option(module_config_sec, "PREFIX"):
+ prefix = config.get(module_config_sec, "PREFIX")
else:
- prefix = ''
+ prefix = ""
- outname_base = 'flag'
+ outname_base = "flag"
+
+ # Path to check for already created mask files
+ if config.has_option(module_config_sec, "CHECK_EXISTING_DIR"):
+ check_existing_dir = config.getexpanded(
+ module_config_sec, "CHECK_EXISTING_DIR"
+ )
+ else:
+ check_existing_dir = None
# Create instance of Mask
mask_inst = Mask(
*input_file_list[:2],
- image_prefix=prefix.replace(' ', ''),
+ image_prefix=prefix.replace(" ", ""),
image_num=file_number_string,
config_filepath=config_file,
- output_dir=run_dirs['output'],
+ output_dir=run_dirs["output"],
path_external_flag=ext_flag_name,
outname_base=outname_base,
star_cat_path=ext_star_cat,
+ check_existing_dir=check_existing_dir,
hdu=hdu,
w_log=w_log,
)
diff --git a/shapepipe/modules/match_external_package/__init__.py b/shapepipe/modules/match_external_package/__init__.py
index 950d84ca8..7fa68545c 100644
--- a/shapepipe/modules/match_external_package/__init__.py
+++ b/shapepipe/modules/match_external_package/__init__.py
@@ -46,4 +46,4 @@
"""
-__all__ = ['match_external']
+__all__ = ["match_external"]
diff --git a/shapepipe/modules/match_external_package/match_external.py b/shapepipe/modules/match_external_package/match_external.py
index 520bbb318..218a231e7 100644
--- a/shapepipe/modules/match_external_package/match_external.py
+++ b/shapepipe/modules/match_external_package/match_external.py
@@ -175,14 +175,14 @@ def process(self):
self._external_col_match[0],
self._external_col_match[1],
)
- external_coord = SkyCoord(ra=external_ra, dec=external_dec, unit='deg')
+ external_coord = SkyCoord(ra=external_ra, dec=external_dec, unit="deg")
data, col_names, ext_names = get_data(
self._input_file_list[0],
self._hdu_no,
)
ra, dec = get_ra_dec(data, self._col_match[0], self._col_match[1])
- coord = SkyCoord(ra=ra, dec=dec, unit='deg')
+ coord = SkyCoord(ra=ra, dec=dec, unit="deg")
# Match objects in external cat to internal cat. indices=indices to
# external object for each object in internal cat e.g.
@@ -198,17 +198,20 @@ def process(self):
if not any(indices_close):
self._w_log.info(
- f'No match for {self._input_file_list[0]} with distance < '
- + f'{self._tolerance} arcsec found, no output created.'
+ f"No match for {self._input_file_list[0]} with distance < "
+ + f"{self._tolerance} arcsec found, no output created."
)
else:
# Get indices in internal and external catalogues of pair-wise
# matches
- w = np.array([
- (idx, ide) for (idx, ide) in enumerate(indices)
- if indices_close[idx]
- ])
+ w = np.array(
+ [
+ (idx, ide)
+ for (idx, ide) in enumerate(indices)
+ if indices_close[idx]
+ ]
+ )
id_sub = w[:, 0]
id_ext_sub = w[:, 1]
id_all = np.arange(len(indices))
@@ -223,7 +226,7 @@ def process(self):
id_ext = id_ext_sub
self._w_log.info(
- f'{len(id_sub)} objects matched out of {len(indices)}.'
+ f"{len(id_sub)} objects matched out of {len(indices)}."
)
# Copy matched objects from internal catalogue to output data
@@ -242,7 +245,7 @@ def process(self):
# Output distance if desired
if self._output_distance:
# Output distance in arcsec
- matched['distance'] = d2d[id_data].to('arcsec').value
+ matched["distance"] = d2d[id_data].to("arcsec").value
# Write FITS file
out_cat = file_io.FITSCatalogue(
@@ -252,14 +255,13 @@ def process(self):
)
out_cat.save_as_fits(
data=matched,
- ext_name='MATCHED',
+ ext_name="MATCHED",
)
# Write all extensions if in multi-epoch mode
- if self._mode == 'MULTI-EPOCH':
+ if self._mode == "MULTI-EPOCH":
hdu_me_list = [
- idx for idx, name in enumerate(ext_names)
- if 'EPOCH' in name
+ idx for idx, name in enumerate(ext_names) if "EPOCH" in name
]
for hdu_me in hdu_me_list:
data_me, col_names_me, dummy = get_data(
diff --git a/shapepipe/modules/match_external_runner.py b/shapepipe/modules/match_external_runner.py
index 9f1060c11..4df5ac0c2 100644
--- a/shapepipe/modules/match_external_runner.py
+++ b/shapepipe/modules/match_external_runner.py
@@ -11,12 +11,12 @@
@module_runner(
- version='1.1',
- input_module='sextractor_runner',
- file_pattern='tile_sexcat',
- file_ext='.fits',
- depends=['numpy', 'astropy'],
- run_method='parallel',
+ version="1.1",
+ input_module="sextractor_runner",
+ file_pattern="tile_sexcat",
+ file_ext=".fits",
+ depends=["numpy", "astropy"],
+ run_method="parallel",
)
def match_external_runner(
input_file_list,
@@ -28,72 +28,71 @@ def match_external_runner(
):
"""Define The Match External Runner."""
# Get processing tolerance
- tolerance = config.getfloat(module_config_sec, 'TOLERANCE')
+ tolerance = config.getfloat(module_config_sec, "TOLERANCE")
# Internal data
- col_match = config.getlist(module_config_sec, 'COL_MATCH')
- if config.has_option(module_config_sec, 'HDU'):
- hdu_no = config.getint(module_config_sec, 'HDU')
+ col_match = config.getlist(module_config_sec, "COL_MATCH")
+ if config.has_option(module_config_sec, "HDU"):
+ hdu_no = config.getint(module_config_sec, "HDU")
else:
hdu_no = 2
# Set run mode
- mode = config.get(module_config_sec, 'MODE')
- valid_modes = ('CLASSIC', 'MULTI-EPOCH')
+ mode = config.get(module_config_sec, "MODE")
+ valid_modes = ("CLASSIC", "MULTI-EPOCH")
if mode not in valid_modes:
raise ValueError(
- f'mode \'{mode}\' is invalid, must be one of {valid_modes}.'
+ f"mode '{mode}' is invalid, must be one of {valid_modes}."
)
# External data
external_cat_path = config.getexpanded(
module_config_sec,
- 'EXTERNAL_CAT_PATH',
+ "EXTERNAL_CAT_PATH",
)
external_col_match = config.getlist(
module_config_sec,
- 'EXTERNAL_COL_MATCH',
+ "EXTERNAL_COL_MATCH",
)
# TODO: optional or 'none', 'all'
# Also TODO: change column name if already present in internal cat
- external_col_copy = config.getlist(module_config_sec, 'EXTERNAL_COL_COPY')
+ external_col_copy = config.getlist(module_config_sec, "EXTERNAL_COL_COPY")
- if config.has_option(module_config_sec, 'EXTERNAL_HDU'):
- external_hdu_no = config.getint(module_config_sec, 'EXTERNAL_HDU')
+ if config.has_option(module_config_sec, "EXTERNAL_HDU"):
+ external_hdu_no = config.getint(module_config_sec, "EXTERNAL_HDU")
else:
external_hdu_no = 1
# Output
- if config.has_option(module_config_sec, 'PREFIX'):
+ if config.has_option(module_config_sec, "PREFIX"):
prefix = config.get(
module_config_sec,
- 'PREFIX',
+ "PREFIX",
)
else:
- prefix = 'cat_matched'
+ prefix = "cat_matched"
- if config.has_option(module_config_sec, 'MARK_NON_MATCHED'):
+ if config.has_option(module_config_sec, "MARK_NON_MATCHED"):
mark_non_matched = config.getfloat(
module_config_sec,
- 'MARK_NON_MATCHED',
+ "MARK_NON_MATCHED",
)
else:
mark_non_matched = None
- if config.has_option(module_config_sec, 'OUTPUT_DISTANCE'):
+ if config.has_option(module_config_sec, "OUTPUT_DISTANCE"):
output_distance = config.getboolean(
module_config_sec,
- 'OUTPUT_DISTANCE',
+ "OUTPUT_DISTANCE",
)
else:
output_distance = False
# Set output file path
- file_ext = 'fits'
+ file_ext = "fits"
output_path = (
- f'{run_dirs["output"]}/{prefix}{file_number_string}.'
- + f'{file_ext}'
+ f'{run_dirs["output"]}/{prefix}{file_number_string}.' + f"{file_ext}"
)
# Create instance of MatchCats
diff --git a/shapepipe/modules/mccd_fit_runner.py b/shapepipe/modules/mccd_fit_runner.py
index 512364338..58e367231 100644
--- a/shapepipe/modules/mccd_fit_runner.py
+++ b/shapepipe/modules/mccd_fit_runner.py
@@ -13,13 +13,13 @@
@module_runner(
- version='1.1',
- input_module=['mccd_preprocessing_runner'],
- file_pattern=['train_star_selection'],
- file_ext=['.fits'],
- numbering_scheme='-0000000',
- depends=['numpy', 'mccd', 'galsim'],
- run_method='parallel',
+ version="1.1",
+ input_module=["mccd_preprocessing_runner"],
+ file_pattern=["train_star_selection"],
+ file_ext=[".fits"],
+ numbering_scheme="-0000000",
+ depends=["numpy", "mccd", "galsim"],
+ run_method="parallel",
)
def mccd_fit_runner(
input_file_list,
@@ -31,9 +31,9 @@ def mccd_fit_runner(
):
"""Define The MCCD Fit Runner."""
# Recover the MCCD config file and its params
- config_file_path = config.getexpanded(module_config_sec, 'CONFIG_PATH')
- mccd_mode = config.get(module_config_sec, 'MODE')
- verbose = config.getboolean(module_config_sec, 'VERBOSE')
+ config_file_path = config.getexpanded(module_config_sec, "CONFIG_PATH")
+ mccd_mode = config.get(module_config_sec, "MODE")
+ verbose = config.getboolean(module_config_sec, "VERBOSE")
# Parse MCCD config file
mccd_parser = mccd.auxiliary_fun.MCCDParamsParser(config_file_path)
@@ -41,10 +41,10 @@ def mccd_fit_runner(
# Prepare inputs to run the main fit function
trainstar_path = input_file_list[0]
- output_dir = run_dirs['output'] + '/'
- saving_name = 'fitted_model'
+ output_dir = run_dirs["output"] + "/"
+ saving_name = "fitted_model"
- if mccd_mode == 'FIT':
+ if mccd_mode == "FIT":
aux_mccd.mccd_fit_pipeline(
trainstar_path=trainstar_path,
file_number_string=file_number_string,
diff --git a/shapepipe/modules/mccd_fit_val_runner.py b/shapepipe/modules/mccd_fit_val_runner.py
index cb959e31c..26623c2a7 100644
--- a/shapepipe/modules/mccd_fit_val_runner.py
+++ b/shapepipe/modules/mccd_fit_val_runner.py
@@ -13,13 +13,13 @@
@module_runner(
- version='1.1',
- input_module=['mccd_preprocessing_runner'],
- file_pattern=['train_star_selection', 'test_star_selection'],
- file_ext=['.fits', '.fits'],
- numbering_scheme='-0000000',
- depends=['numpy', 'mccd', 'galsim'],
- run_method='parallel',
+ version="1.1",
+ input_module=["mccd_preprocessing_runner"],
+ file_pattern=["train_star_selection", "test_star_selection"],
+ file_ext=[".fits", ".fits"],
+ numbering_scheme="-0000000",
+ depends=["numpy", "mccd", "galsim"],
+ run_method="parallel",
)
def mccd_fit_val_runner(
input_file_list,
@@ -31,24 +31,24 @@ def mccd_fit_val_runner(
):
"""Define The MCCD Fit Validation Runner."""
# Recover the MCCD config file and its params
- config_file_path = config.getexpanded(module_config_sec, 'CONFIG_PATH')
- mccd_mode = config.get(module_config_sec, 'MODE')
- verbose = config.getboolean(module_config_sec, 'VERBOSE')
+ config_file_path = config.getexpanded(module_config_sec, "CONFIG_PATH")
+ mccd_mode = config.get(module_config_sec, "MODE")
+ verbose = config.getboolean(module_config_sec, "VERBOSE")
# Parse MCCD config file
mccd_parser = mccd.auxiliary_fun.MCCDParamsParser(config_file_path)
mccd_parser.parse_document()
# Prepare inputs to run the main fit function
- output_dir = run_dirs['output'] + '/'
- fit_saving_name = 'fitted_model'
- val_saving_name = 'validation_psf'
+ output_dir = run_dirs["output"] + "/"
+ fit_saving_name = "fitted_model"
+ val_saving_name = "validation_psf"
# Extract the training star catalog
trainstar_path = input_file_list[0]
# Validation stars are in the second position of the list
teststar_path = input_file_list[1]
- if mccd_mode == 'FIT_VALIDATION':
+ if mccd_mode == "FIT_VALIDATION":
aux_mccd.mccd_fit_pipeline(
trainstar_path=trainstar_path,
@@ -61,8 +61,9 @@ def mccd_fit_val_runner(
)
# Fitted model is found in the output directory
- mccd_model_path = output_dir + fit_saving_name + file_number_string \
- + '.npy'
+ mccd_model_path = (
+ output_dir + fit_saving_name + file_number_string + ".npy"
+ )
aux_mccd.mccd_validation_pipeline(
teststar_path=teststar_path,
diff --git a/shapepipe/modules/mccd_interp_runner.py b/shapepipe/modules/mccd_interp_runner.py
index 4856e562f..1428e44d6 100644
--- a/shapepipe/modules/mccd_interp_runner.py
+++ b/shapepipe/modules/mccd_interp_runner.py
@@ -10,19 +10,20 @@
from shapepipe.pipeline.run_log import get_last_dir
-from shapepipe.modules.mccd_package import \
- mccd_interpolation_script as mccd_interp
+from shapepipe.modules.mccd_package import (
+ mccd_interpolation_script as mccd_interp,
+)
from shapepipe.modules.mccd_package import shapepipe_auxiliary_mccd as aux_mccd
from shapepipe.modules.module_decorator import module_runner
@module_runner(
- version='1.0',
- input_module=['setools_runner'],
- file_pattern=['galaxy_selection'],
- file_ext=['.npy'],
- depends=['numpy', 'astropy', 'galsim', 'sqlitedict', 'mccd'],
- run_method='parallel',
+ version="1.0",
+ input_module=["setools_runner"],
+ file_pattern=["galaxy_selection"],
+ file_ext=[".npy"],
+ depends=["numpy", "astropy", "galsim", "sqlitedict", "mccd"],
+ run_method="parallel",
)
def mccd_interp_runner(
input_file_list,
@@ -33,37 +34,32 @@ def mccd_interp_runner(
w_log,
):
"""Define The MCCD Interpolation Runner."""
- mode = config.getexpanded(module_config_sec, 'MODE')
- pos_params = config.getlist(module_config_sec, 'POSITION_PARAMS')
- get_shapes = config.getboolean(module_config_sec, 'GET_SHAPES')
- mccd_model_extension = '.npy'
- output_dir = run_dirs['output']
-
- if mode == 'CLASSIC':
- module = config.getexpanded(
- module_config_sec,
- 'PSF_MODEL_DIR'
- )
- psf_model_dir = get_last_dir(run_dirs['run_log'], module)
- psf_model_pattern = config.get(
- module_config_sec,
- 'PSF_MODEL_PATTERN'
- )
- psf_separator = config.get(
- module_config_sec,
- 'PSF_MODEL_SEPARATOR'
- )
+ mode = config.getexpanded(module_config_sec, "MODE")
+ pos_params = config.getlist(module_config_sec, "POSITION_PARAMS")
+ get_shapes = config.getboolean(module_config_sec, "GET_SHAPES")
+ mccd_model_extension = ".npy"
+ output_dir = run_dirs["output"]
+
+ if mode == "CLASSIC":
+ module = config.getexpanded(module_config_sec, "PSF_MODEL_DIR")
+ psf_model_dir = get_last_dir(run_dirs["run_log"], module)
+ psf_model_pattern = config.get(module_config_sec, "PSF_MODEL_PATTERN")
+ psf_separator = config.get(module_config_sec, "PSF_MODEL_SEPARATOR")
galcat_path = input_file_list[0]
# verify that the MCCD model exists
ccd_id = file_number_string.split(psf_separator)[-1]
exposure_id = file_number_string.split(psf_separator)[-2]
- psf_model_path = psf_model_dir + psf_model_pattern + psf_separator +\
- exposure_id + mccd_model_extension
+ psf_model_path = (
+ psf_model_dir
+ + psf_model_pattern
+ + psf_separator
+ + exposure_id
+ + mccd_model_extension
+ )
- saving_path = output_dir + '/galaxy_psf' + file_number_string +\
- '.fits'
+ saving_path = output_dir + "/galaxy_psf" + file_number_string + ".fits"
if not os.path.exists(psf_model_path):
error_msg = "The corresponding PSF model was not not found."
@@ -74,7 +70,7 @@ def mccd_interp_runner(
return None, None
- w_log.info('Interpolating catalogue %s..' % file_number_string)
+ w_log.info("Interpolating catalogue %s.." % file_number_string)
output_msg = aux_mccd.mccd_interpolation_pipeline(
mccd_model_path=psf_model_path,
galcat_path=galcat_path,
@@ -90,20 +86,11 @@ def mccd_interp_runner(
+ f" id: {file_number_string}."
)
- elif mode == 'MULTI-EPOCH':
- module = config.getexpanded(
- module_config_sec,
- 'PSF_MODEL_DIR'
- )
- psf_model_dir = get_last_dir(run_dirs['run_log'], module)
- psf_model_pattern = config.get(
- module_config_sec,
- 'PSF_MODEL_PATTERN'
- )
- f_wcs_path = config.getexpanded(
- module_config_sec,
- 'ME_LOG_WCS'
- )
+ elif mode == "MULTI-EPOCH":
+ module = config.getexpanded(module_config_sec, "PSF_MODEL_DIR")
+ psf_model_dir = get_last_dir(run_dirs["run_log"], module)
+ psf_model_pattern = config.get(module_config_sec, "PSF_MODEL_PATTERN")
+ f_wcs_path = config.getexpanded(module_config_sec, "ME_LOG_WCS")
galcat_path = input_file_list[0]
@@ -119,7 +106,7 @@ def mccd_interp_runner(
inst.process_me(psf_model_dir, psf_model_pattern, f_wcs_path)
- elif mode == 'VALIDATION':
+ elif mode == "VALIDATION":
ValueError(
"MODE has to be in MULTI-EPOCH or CLASSIC. For validation"
+ " use MCCD validation runner."
diff --git a/shapepipe/modules/mccd_package/__init__.py b/shapepipe/modules/mccd_package/__init__.py
index dc6416c43..115cc0f86 100644
--- a/shapepipe/modules/mccd_package/__init__.py
+++ b/shapepipe/modules/mccd_package/__init__.py
@@ -190,7 +190,7 @@
"""
__all__ = [
- 'shapepipe_auxiliary_mccd',
- 'mccd_interpolation_script',
- 'mccd_plot_utilities',
+ "shapepipe_auxiliary_mccd",
+ "mccd_interpolation_script",
+ "mccd_plot_utilities",
]
diff --git a/shapepipe/modules/mccd_package/mccd_interpolation_script.py b/shapepipe/modules/mccd_package/mccd_interpolation_script.py
index 40e644e8b..6030fa657 100644
--- a/shapepipe/modules/mccd_package/mccd_interpolation_script.py
+++ b/shapepipe/modules/mccd_package/mccd_interpolation_script.py
@@ -23,9 +23,9 @@
import_fail = False
-NOT_ENOUGH_STARS = 'Fail_stars'
-BAD_CHI2 = 'Fail_chi2'
-FILE_NOT_FOUND = 'File_not_found'
+NOT_ENOUGH_STARS = "Fail_stars"
+BAD_CHI2 = "Fail_chi2"
+FILE_NOT_FOUND = "File_not_found"
def interp_MCCD(mccd_model_path, positions, ccd):
@@ -62,10 +62,12 @@ def interp_MCCD(mccd_model_path, positions, ccd):
# Positions to global coordinates
loc2glob = mccd.mccd_utils.Loc2Glob()
- glob_pos = np.array([
- loc2glob.loc2glob_img_coord(_ccd, _pos[0], _pos[1])
- for _ccd, _pos in zip(ccd_list, positions)
- ])
+ glob_pos = np.array(
+ [
+ loc2glob.loc2glob_img_coord(_ccd, _pos[0], _pos[1])
+ for _ccd, _pos in zip(ccd_list, positions)
+ ]
+ )
# Interpolate the model
PSFs = mccd_instance.interpolate_psf_pipeline(glob_pos, ccd)
@@ -116,16 +118,16 @@ def __init__(
img_number,
w_log,
pos_params=None,
- get_shapes=True
+ get_shapes=True,
):
# Path to PSFEx output file
self._dotpsf_path = dotpsf_path
# Path to catalogue containing galaxy positions
self._galcat_path = galcat_path
# Path to output file to be written
- self._output_path = output_path + '/galaxy_psf'
+ self._output_path = output_path + "/galaxy_psf"
# Path to output file to be written for validation
- self._output_path_validation = output_path + '/validation_psf'
+ self._output_path_validation = output_path + "/validation_psf"
# if required, compute and save shapes
self._compute_shape = get_shapes
@@ -142,8 +144,8 @@ def __init__(
if pos_params:
if not len(pos_params) == 2:
raise ValueError(
- f'{len(pos_params)} position parameters were passed on;'
- + f' there should be exactly two.'
+ f"{len(pos_params)} position parameters were passed on;"
+ + f" there should be exactly two."
)
self._pos_params = pos_params
else:
@@ -162,8 +164,8 @@ def _get_position_parameters(self):
dotpsf = file_io.FITSCatalogue(self._dotpsf_path)
dotpsf.open()
self._pos_params = [
- dotpsf.get_header()['POLNAME1'],
- dotpsf.get_header()['POLNAME2']
+ dotpsf.get_header()["POLNAME1"],
+ dotpsf.get_header()["POLNAME2"],
]
dotpsf.close()
@@ -180,20 +182,23 @@ def _get_galaxy_positions(self):
galcat.open()
try:
self.gal_pos = np.array(
- [[x, y] for x, y in zip(
- galcat.get_data()[self._pos_params[0]],
- galcat.get_data()[self._pos_params[1]]
- )]
+ [
+ [x, y]
+ for x, y in zip(
+ galcat.get_data()[self._pos_params[0]],
+ galcat.get_data()[self._pos_params[1]],
+ )
+ ]
)
except KeyError as detail:
# extract erroneous position parameter from original exception
err_pos_param = detail.args[0][4:-15]
pos_param_err = (
- f'Required position parameter {err_pos_param}'
- + 'was not found in galaxy catalog. Leave '
- + 'pos_params (or EXTRA_CODE_OPTION) blank to '
- + 'read them from .psf file.'
+ f"Required position parameter {err_pos_param}"
+ + "was not found in galaxy catalog. Leave "
+ + "pos_params (or EXTRA_CODE_OPTION) blank to "
+ + "read them from .psf file."
)
raise KeyError(pos_param_err)
galcat.close()
@@ -205,22 +210,24 @@ def _get_psfshapes(self):
"""
if import_fail:
- raise ImportError('Galsim is required to get shapes information')
+ raise ImportError("Galsim is required to get shapes information")
psf_moms = [
hsm.FindAdaptiveMom(Image(psf), strict=False)
for psf in self.interp_PSFs
]
- self.psf_shapes = np.array([
+ self.psf_shapes = np.array(
[
- moms.observed_shape.g1,
- moms.observed_shape.g2,
- moms.moments_sigma,
- int(bool(moms.error_message))
+ [
+ moms.observed_shape.g1,
+ moms.observed_shape.g2,
+ moms.moments_sigma,
+ int(bool(moms.error_message)),
+ ]
+ for moms in psf_moms
]
- for moms in psf_moms
- ])
+ )
def _write_output(self):
"""Write Output.
@@ -229,21 +236,21 @@ def _write_output(self):
"""
output = file_io.FITSCatalogue(
- self._output_path + self._img_number + '.fits',
+ self._output_path + self._img_number + ".fits",
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
- SEx_catalogue=True
+ SEx_catalogue=True,
)
if self._compute_shape:
data = {
- 'VIGNET': self.interp_PSFs,
- 'E1_PSF_HSM': self.psf_shapes[:, 0],
- 'E2_PSF_HSM': self.psf_shapes[:, 1],
- 'SIGMA_PSF_HSM': self.psf_shapes[:, 2],
- 'FLAG_PSF_HSM': self.psf_shapes[:, 3].astype(int)
+ "VIGNET": self.interp_PSFs,
+ "E1_PSF_HSM": self.psf_shapes[:, 0],
+ "E2_PSF_HSM": self.psf_shapes[:, 1],
+ "SIGMA_PSF_HSM": self.psf_shapes[:, 2],
+ "FLAG_PSF_HSM": self.psf_shapes[:, 3].astype(int),
}
else:
- data = {'VIGNET': self.interp_PSFs}
+ data = {"VIGNET": self.interp_PSFs}
output.save_as_fits(data, sex_cat_path=self._galcat_path)
def _get_starshapes(self, star_vign):
@@ -258,27 +265,27 @@ def _get_starshapes(self, star_vign):
"""
if import_fail:
- raise ImportError('Galsim is required to get shapes information')
+ raise ImportError("Galsim is required to get shapes information")
masks = np.zeros_like(star_vign)
masks[np.where(star_vign == -1e30)] = 1
- star_moms = [hsm.FindAdaptiveMom(
- Image(star),
- badpix=Image(mask),
- strict=False)
+ star_moms = [
+ hsm.FindAdaptiveMom(Image(star), badpix=Image(mask), strict=False)
for star, mask in zip(star_vign, masks)
]
- self.star_shapes = np.array([
+ self.star_shapes = np.array(
[
- moms.observed_shape.g1,
- moms.observed_shape.g2,
- moms.moments_sigma,
- int(bool(moms.error_message))
+ [
+ moms.observed_shape.g1,
+ moms.observed_shape.g2,
+ moms.moments_sigma,
+ int(bool(moms.error_message)),
+ ]
+ for moms in star_moms
]
- for moms in star_moms
- ])
+ )
def _get_psfexcatdict(self, psfex_cat_path):
"""Get PSFEx Catalogue Dictionary.
@@ -300,13 +307,16 @@ def _get_psfexcatdict(self, psfex_cat_path):
psfex_cat.open()
psfex_cat_dict = {}
- psfex_cat_dict['SOURCE_NUMBER'] = np.copy(
- psfex_cat.get_data()['SOURCE_NUMBER'])
- psfex_cat_dict['DELTAX_IMAGE'] = np.copy(
- psfex_cat.get_data()['DELTAX_IMAGE'])
- psfex_cat_dict['DELTAY_IMAGE'] = np.copy(
- psfex_cat.get_data()['DELTAY_IMAGE'])
- psfex_cat_dict['CHI2_PSF'] = np.copy(psfex_cat.get_data()['CHI2_PSF'])
+ psfex_cat_dict["SOURCE_NUMBER"] = np.copy(
+ psfex_cat.get_data()["SOURCE_NUMBER"]
+ )
+ psfex_cat_dict["DELTAX_IMAGE"] = np.copy(
+ psfex_cat.get_data()["DELTAX_IMAGE"]
+ )
+ psfex_cat_dict["DELTAY_IMAGE"] = np.copy(
+ psfex_cat.get_data()["DELTAY_IMAGE"]
+ )
+ psfex_cat_dict["CHI2_PSF"] = np.copy(psfex_cat.get_data()["CHI2_PSF"])
return psfex_cat_dict
@@ -324,28 +334,29 @@ def _write_output_validation(self, star_dict, psfex_cat_dict):
"""
output = file_io.FITSCatalogue(
- self._output_path_validation + self._img_number + '.fits',
+ self._output_path_validation + self._img_number + ".fits",
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
- SEx_catalogue=True)
+ SEx_catalogue=True,
+ )
data = {
- 'E1_PSF_HSM': self.psf_shapes[:, 0],
- 'E2_PSF_HSM': self.psf_shapes[:, 1],
- 'SIGMA_PSF_HSM': self.psf_shapes[:, 2],
- 'FLAG_PSF_HSM': self.psf_shapes[:, 3].astype(int),
- 'E1_STAR_HSM': self.star_shapes[:, 0],
- 'E2_STAR_HSM': self.star_shapes[:, 1],
- 'SIGMA_STAR_HSM': self.star_shapes[:, 2],
- 'FLAG_STAR_HSM': self.star_shapes[:, 3].astype(int)
+ "E1_PSF_HSM": self.psf_shapes[:, 0],
+ "E2_PSF_HSM": self.psf_shapes[:, 1],
+ "SIGMA_PSF_HSM": self.psf_shapes[:, 2],
+ "FLAG_PSF_HSM": self.psf_shapes[:, 3].astype(int),
+ "E1_STAR_HSM": self.star_shapes[:, 0],
+ "E2_STAR_HSM": self.star_shapes[:, 1],
+ "SIGMA_STAR_HSM": self.star_shapes[:, 2],
+ "FLAG_STAR_HSM": self.star_shapes[:, 3].astype(int),
}
data = {**data, **star_dict}
- data['ACCEPTED'] = np.ones_like(data['NUMBER'], dtype='int16')
- star_used = psfex_cat_dict.pop('SOURCE_NUMBER')
+ data["ACCEPTED"] = np.ones_like(data["NUMBER"], dtype="int16")
+ star_used = psfex_cat_dict.pop("SOURCE_NUMBER")
- for i in range(len(data['NUMBER'])):
+ for i in range(len(data["NUMBER"])):
if i + 1 not in star_used:
- data['ACCEPTED'][i] = 0
+ data["ACCEPTED"][i] = 0
output.save_as_fits(data, sex_cat_path=self._galcat_path)
@@ -395,22 +406,23 @@ def _interpolate_me(self):
all_id = np.copy(cat.get_data()['NUMBER'])
key_ne = 'N_EPOCH'
- if key_ne not in cat.get_data():
+ if key_ne not in cat.get_data().dtype.names:
raise KeyError(
- f'Key {key_ne} not found in input galaxy catalogue, needed for'
- + ' PSF interpolation to multi-epoch data; run previous module'
- + ' (SExtractor) in multi-epoch mode'
+ f"Key {key_ne} not found in input galaxy catalogue, needed for"
+ + " PSF interpolation to multi-epoch data; run previous module"
+ + " (SExtractor) in multi-epoch mode"
)
n_epoch = np.copy(cat.get_data()[key_ne])
list_ext_name = cat.get_ext_name()
- hdu_ind = [i for i in range(len(list_ext_name)) if
- 'EPOCH' in list_ext_name[i]]
+ hdu_ind = [
+ i for i in range(len(list_ext_name)) if "EPOCH" in list_ext_name[i]
+ ]
final_list = []
for hdu_index in hdu_ind:
- exp_name = cat.get_data(hdu_index)['EXP_NAME'][0]
- ccd_list = list(set(cat.get_data(hdu_index)['CCD_N']))
+ exp_name = cat.get_data(hdu_index)["EXP_NAME"][0]
+ ccd_list = list(set(cat.get_data(hdu_index)["CCD_N"]))
array_psf = None
array_id = None
array_shape = None
@@ -421,53 +433,54 @@ def _interpolate_me(self):
# dot_psf_path = self._dot_psf_dir + '/' +\
# self._dot_psf_pattern + '-' + exp_name + '-' + str(ccd) +\
# '.psf'
- mccd_model_path = self._dot_psf_dir + '/' +\
- self._dot_psf_pattern + '-' + exp_name + '.npy'
+ mccd_model_path = (
+ self._dot_psf_dir
+ + "/"
+ + self._dot_psf_pattern
+ + "-"
+ + exp_name
+ + ".npy"
+ )
- ind_obj = np.where(cat.get_data(hdu_index)['CCD_N'] == ccd)[0]
+ ind_obj = np.where(cat.get_data(hdu_index)["CCD_N"] == ccd)[0]
obj_id = all_id[ind_obj]
gal_pos = np.array(
- self._f_wcs_file[exp_name][ccd]['WCS'].all_world2pix(
+ self._f_wcs_file[exp_name][ccd]["WCS"].all_world2pix(
self.gal_pos[:, 0][ind_obj],
self.gal_pos[:, 1][ind_obj],
- 0
+ 0,
)
).T
self.interp_PSFs = interp_MCCD(mccd_model_path, gal_pos, ccd)
- # self.interp_PSFs = interpsfex(
- # dot_psf_path, gal_pos, self._star_thresh, self._chi2_thresh)
- if (
- isinstance(self.interp_PSFs, str)
- and (self.interp_PSFs == NOT_ENOUGH_STARS)
+ if isinstance(self.interp_PSFs, str) and (
+ self.interp_PSFs == NOT_ENOUGH_STARS
):
self._w_log.info(
- f'Not enough stars find in the ccd {ccd} of the'
- + f' exposure {exp_name}. Object inside this '
- + f'ccd will lose an epoch.'
+ f"Not enough stars find in the ccd {ccd} of the"
+ + f" exposure {exp_name}. Object inside this "
+ + f"ccd will lose an epoch."
)
continue
- if (
- isinstance(self.interp_PSFs, str)
- and (self.interp_PSFs == BAD_CHI2)
+ if isinstance(self.interp_PSFs, str) and (
+ self.interp_PSFs == BAD_CHI2
):
self._w_log.info(
- f'Bad chi2 for the psf model in the ccd {ccd} of the'
- + f' exposure {exp_name}. Object inside this ccd'
- + f' will lose an epoch.'
+ f"Bad chi2 for the psf model in the ccd {ccd} of the"
+ + f" exposure {exp_name}. Object inside this ccd"
+ + f" will lose an epoch."
)
continue
- if (
- isinstance(self.interp_PSFs, str)
- and (self.interp_PSFs == FILE_NOT_FOUND)
+ if isinstance(self.interp_PSFs, str) and (
+ self.interp_PSFs == FILE_NOT_FOUND
):
self._w_log.info(
- f'Psf model file {self._dotpsf_path} not found.'
- + f' Object inside this ccd will lose an epoch.'
+ f"Psf model file {self._dotpsf_path} not found."
+ + f" Object inside this ccd will lose an epoch."
)
continue
@@ -475,7 +488,8 @@ def _interpolate_me(self):
array_psf = np.copy(self.interp_PSFs)
else:
array_psf = np.concatenate(
- (array_psf, np.copy(self.interp_PSFs)))
+ (array_psf, np.copy(self.interp_PSFs))
+ )
if array_id is None:
array_id = np.copy(obj_id)
@@ -488,20 +502,24 @@ def _interpolate_me(self):
array_shape = np.copy(self.psf_shapes)
else:
array_shape = np.concatenate(
- (array_shape, np.copy(self.psf_shapes)))
+ (array_shape, np.copy(self.psf_shapes))
+ )
else:
array_shape = None
exp_name_tmp = np.array(
- [exp_name + '-' + str(ccd) for i in range(len(obj_id))])
+ [exp_name + "-" + str(ccd) for i in range(len(obj_id))]
+ )
if array_exp_name is None:
array_exp_name = exp_name_tmp
else:
array_exp_name = np.concatenate(
- (array_exp_name, exp_name_tmp))
+ (array_exp_name, exp_name_tmp)
+ )
final_list.append(
- [array_id, array_psf, array_shape, array_exp_name])
+ [array_id, array_psf, array_shape, array_exp_name]
+ )
self._f_wcs_file.close()
cat.close()
@@ -515,22 +533,28 @@ def _interpolate_me(self):
if len(where_res) != 0:
output_dict[id_tmp][final_list[j][3][where_res[0]]] = {}
output_dict[id_tmp][final_list[j][3][where_res[0]]][
- 'VIGNET'] = final_list[j][1][where_res[0]]
+ "VIGNET"
+ ] = final_list[j][1][where_res[0]]
if self._compute_shape:
shape_dict = {}
- shape_dict['E1_PSF_HSM'] = \
- final_list[j][2][where_res[0]][0]
- shape_dict['E2_PSF_HSM'] = \
- final_list[j][2][where_res[0]][1]
- shape_dict['SIGMA_PSF_HSM'] = \
- final_list[j][2][where_res[0]][2]
- shape_dict['FLAG_PSF_HSM'] = \
- final_list[j][2][where_res[0]][3]
+ shape_dict["E1_PSF_HSM"] = final_list[j][2][
+ where_res[0]
+ ][0]
+ shape_dict["E2_PSF_HSM"] = final_list[j][2][
+ where_res[0]
+ ][1]
+ shape_dict["SIGMA_PSF_HSM"] = final_list[j][2][
+ where_res[0]
+ ][2]
+ shape_dict["FLAG_PSF_HSM"] = final_list[j][2][
+ where_res[0]
+ ][3]
output_dict[id_tmp][final_list[j][3][where_res[0]]][
- 'SHAPES'] = shape_dict
+ "SHAPES"
+ ] = shape_dict
counter += 1
if counter == 0:
- output_dict[id_tmp] = 'empty'
+ output_dict[id_tmp] = "empty"
return output_dict
@@ -548,7 +572,8 @@ def _write_output_me(self, output_dict):
# np.save(self._output_path+self._img_number, output_dict)
output_file = SqliteDict(
- self._output_path + self._img_number + '.sqlite')
+ self._output_path + self._img_number + ".sqlite"
+ )
for i in output_dict.keys():
output_file[str(i)] = output_dict[i]
output_file.commit()
diff --git a/shapepipe/modules/mccd_package/mccd_plot_utilities.py b/shapepipe/modules/mccd_package/mccd_plot_utilities.py
index 1d3eb9f14..c7a65b5bd 100644
--- a/shapepipe/modules/mccd_package/mccd_plot_utilities.py
+++ b/shapepipe/modules/mccd_package/mccd_plot_utilities.py
@@ -5,7 +5,7 @@
It can also plot the rho statistics provided that the required packages are
installed.
-:Author: Tobias Liaudat
+:Authors: Tobias Liaudat, Martin Kilbinger
"""
@@ -21,11 +21,13 @@
from astropy.io import fits
from stile.sys_tests import BaseCorrelationFunctionSysTest
+from shear_psf_leakage.rho_tau_stat import RhoStat
+
# Define the backend for matplotlib
-mpl.use('agg')
+mpl.use("agg")
# MegaCam -> plt.subplot correspondance, as given by:
-''' 'COMMENT Unique detector IDs for MegaCam',
+""" 'COMMENT Unique detector IDs for MegaCam',
'COMMENT (North on top, East to the left)',
'COMMENT --------------------------',
'COMMENT ba ba ba ba ba ba ba ba ba',
@@ -40,7 +42,7 @@
'COMMENT 27 28 29 30 31 32 33 34 35',
'COMMENT ab ab ab ab ab ab ab ab ab',
'COMMENT __________________________'
-'''
+"""
def megacam_pos(index):
@@ -136,12 +138,7 @@ def megacam_flip_2(xbins, ybins, ccd_nb, nb_pixel):
def mean_shapes_plot(
- ccd_maps,
- filename,
- title='',
- colorbar_ampl=1.0,
- wind=None,
- cmap='bwr'
+ ccd_maps, filename, title="", colorbar_ampl=1.0, wind=None, cmap="bwr"
):
r"""Mean Shapes Plot.
@@ -166,8 +163,10 @@ def mean_shapes_plot(
"""
# colorbar amplitude
if wind is None:
- vmax = max(
- np.nanmax(ccd_maps), np.abs(np.nanmin(ccd_maps))) * colorbar_ampl
+ vmax = (
+ max(np.nanmax(ccd_maps), np.abs(np.nanmin(ccd_maps)))
+ * colorbar_ampl
+ )
vmin = -vmax * colorbar_ampl
else:
vmin, vmax = wind[0] * colorbar_ampl, wind[1] * colorbar_ampl
@@ -176,24 +175,20 @@ def mean_shapes_plot(
fig, axes = plt.subplots(nrows=4, ncols=11, figsize=(18, 12), dpi=400)
# remove corner axes (above and below ears)
for j in [0, 10, -1, -11]:
- axes.flat[j].axis('off')
+ axes.flat[j].axis("off")
for ccd_nb, ccd_map in enumerate(ccd_maps):
ax = axes.flat[megacam_pos(ccd_nb)]
im = ax.imshow(
- ccd_map.T,
- cmap=cmap,
- interpolation='Nearest',
- vmin=vmin,
- vmax=vmax
+ ccd_map.T, cmap=cmap, interpolation="Nearest", vmin=vmin, vmax=vmax
)
ax.set_xticks([])
ax.set_yticks([])
- ax.set_title(f'rmse={np.sqrt(np.nanmean(ccd_map ** 2)):.3e}', size=8)
+ ax.set_title(f"rmse={np.sqrt(np.nanmean(ccd_map ** 2)):.3e}", size=8)
plt.suptitle(title, size=20) # TODO: fix title
fig.subplots_adjust(right=0.8)
cbar_ax = fig.add_axes([0.85, 0.15, 0.05, 0.7])
fig.colorbar(im, cax=cbar_ax)
- plt.savefig(f'{filename}.png')
+ plt.savefig(f"{filename}.png")
plt.close()
@@ -206,7 +201,7 @@ def plot_meanshapes(
remove_outliers=False,
plot_meanshapes=True,
plot_histograms=True,
- psf_model_type='mccd',
+ psf_model_type="mccd",
max_e=None,
max_de=None,
min_r2=None,
@@ -260,38 +255,43 @@ def plot_meanshapes(
starcat = fits.open(starcat_path, memmap=False)
auto_colorbar = False
- colorbar_ampl = 1.
+ colorbar_ampl = 1.0
loc2glob = mccd_utils.Loc2Glob()
# MegaCam: each CCD is 2048x4612
- grid = np.linspace(0, loc2glob.x_npix, nb_pixel[0] + 1), \
- np.linspace(0, loc2glob.y_npix, nb_pixel[1] + 1)
+ grid = np.linspace(0, loc2glob.x_npix, nb_pixel[0] + 1), np.linspace(
+ 0, loc2glob.y_npix, nb_pixel[1] + 1
+ )
# Flag mask
- star_flags = starcat[hdu_no].data['FLAG_STAR_HSM']
- psf_flags = starcat[hdu_no].data['FLAG_PSF_HSM']
+ star_flags = starcat[hdu_no].data["FLAG_STAR_HSM"]
+ psf_flags = starcat[hdu_no].data["FLAG_PSF_HSM"]
flagmask = np.abs(star_flags - 1) * np.abs(psf_flags - 1)
# convert sigma to R^2's
- all_star_shapes = np.array([
- starcat[hdu_no].data['E1_STAR_HSM'],
- starcat[hdu_no].data['E2_STAR_HSM'],
- 2. * starcat[hdu_no].data['SIGMA_STAR_HSM'] ** 2
- ])
- all_psf_shapes = np.array([
- starcat[hdu_no].data['E1_PSF_HSM'],
- starcat[hdu_no].data['E2_PSF_HSM'],
- 2. * starcat[hdu_no].data['SIGMA_PSF_HSM'] ** 2
- ])
- all_CCDs = starcat[hdu_no].data['CCD_NB']
- all_X = starcat[hdu_no].data['X']
- all_Y = starcat[hdu_no].data['Y']
+ all_star_shapes = np.array(
+ [
+ starcat[hdu_no].data["E1_STAR_HSM"],
+ starcat[hdu_no].data["E2_STAR_HSM"],
+ 2.0 * starcat[hdu_no].data["SIGMA_STAR_HSM"] ** 2,
+ ]
+ )
+ all_psf_shapes = np.array(
+ [
+ starcat[hdu_no].data["E1_PSF_HSM"],
+ starcat[hdu_no].data["E2_PSF_HSM"],
+ 2.0 * starcat[hdu_no].data["SIGMA_PSF_HSM"] ** 2,
+ ]
+ )
+ all_CCDs = starcat[hdu_no].data["CCD_NB"]
+ all_X = starcat[hdu_no].data["X"]
+ all_Y = starcat[hdu_no].data["Y"]
# Remove stars/PSFs where the measured size is zero
# Sometimes the HSM shape measurement gives objects with measured
# size equals to zero without an error Flag.
- bad_stars = (abs(all_star_shapes[2, :]) < 0.1)
- bad_psfs = (abs(all_psf_shapes[2, :]) < 0.1)
+ bad_stars = abs(all_star_shapes[2, :]) < 0.1
+ bad_psfs = abs(all_psf_shapes[2, :]) < 0.1
size_mask = np.abs(bad_stars) * np.abs(bad_psfs)
# Remove outlier stars/PSFs
all_star_shapes = all_star_shapes[:, ~size_mask]
@@ -304,8 +304,8 @@ def plot_meanshapes(
# Remove stars/PSFs where the measured size is zero
# Sometimes the HSM shape measurement gives objects with measured
# size equals to zero without an error Flag.
- bad_stars = (abs(all_star_shapes[2, :]) < 0.1)
- bad_psfs = (abs(all_psf_shapes[2, :]) < 0.1)
+ bad_stars = abs(all_star_shapes[2, :]) < 0.1
+ bad_psfs = abs(all_psf_shapes[2, :]) < 0.1
size_mask = np.abs(bad_stars) * np.abs(bad_psfs)
# Remove outlier stars/PSFs
all_star_shapes = all_star_shapes[:, ~size_mask]
@@ -316,14 +316,13 @@ def plot_meanshapes(
flagmask = flagmask[~size_mask]
if remove_outliers:
- shape_std_max = 5.
+ shape_std_max = 5.0
# Outlier rejection based on the size
- R2_thresh = (
- shape_std_max * np.std(all_star_shapes[2, :])
- + np.mean(all_star_shapes[2, :])
+ R2_thresh = shape_std_max * np.std(all_star_shapes[2, :]) + np.mean(
+ all_star_shapes[2, :]
)
- bad_stars = (abs(all_star_shapes[2, :]) > R2_thresh)
- w_log.info(f'Nb of outlier stars: {np.sum(bad_stars):d}')
+ bad_stars = abs(all_star_shapes[2, :]) > R2_thresh
+ w_log.info(f"Nb of outlier stars: {np.sum(bad_stars):d}")
# Remove outlier PSFs
all_star_shapes = all_star_shapes[:, ~bad_stars]
all_psf_shapes = all_psf_shapes[:, ~bad_stars]
@@ -351,17 +350,17 @@ def plot_meanshapes(
for ccd_nb, ccd_map in enumerate(ccd_maps):
# handle different input catalogue types
- if psf_model_type == 'mccd':
+ if psf_model_type == "mccd":
- ccd_mask = (
- ((all_CCDs.astype(int) == ccd_nb) * flagmask).astype(bool)
+ ccd_mask = ((all_CCDs.astype(int) == ccd_nb) * flagmask).astype(
+ bool
)
# Calculate shift to go from global coordinates to local
# coordinates
x_shift, y_shift = loc2glob.shift_coord(ccd_nb)
- elif psf_model_type == 'psfex':
+ elif psf_model_type == "psfex":
ccd_mask = ((all_CCDs == str(ccd_nb)) * flagmask).astype(bool)
@@ -370,14 +369,14 @@ def plot_meanshapes(
else:
- raise ValueError(f'Invalid psf model type {psf_model_type}')
+ raise ValueError(f"Invalid psf model type {psf_model_type}")
star_shapes = all_star_shapes[:, ccd_mask]
psf_shapes = all_psf_shapes[:, ccd_mask]
xs_loc, ys_loc = all_X[ccd_mask] - x_shift, all_Y[ccd_mask] - y_shift
- if psf_model_type == 'mccd':
+ if psf_model_type == "mccd":
# swap axes to match CCD orientation and origin convention
ys_loc = loc2glob.y_npix - ys_loc + 1
@@ -385,7 +384,7 @@ def plot_meanshapes(
xbins = np.digitize(xs_loc, grid[0])
ybins = np.digitize(ys_loc, grid[1])
- if psf_model_type == 'psfex':
+ if psf_model_type == "psfex":
xbins, ybins = megacam_flip(xbins, ybins, ccd_nb, nb_pixel)
for xb in range(nb_pixel[0]):
@@ -407,38 +406,32 @@ def plot_meanshapes(
else:
vmax = max(
np.nanmax(ccd_maps[:, :, 0]),
- np.abs(np.nanmin(ccd_maps[:, :, 0]))
+ np.abs(np.nanmin(ccd_maps[:, :, 0])),
)
vmin = -vmax
wind = [vmin, vmax]
title = (
- f'e_1 (stars), std={np.nanstd(ccd_maps[:, 0, 0]):.5e}\n'
- + f'vmax={np.nanmax(abs(ccd_maps[:, 0, 0])):.4e}'
+ f"e_1 (stars), std={np.nanstd(ccd_maps[:, 0, 0]):.5e}\n"
+ + f"vmax={np.nanmax(abs(ccd_maps[:, 0, 0])):.4e}"
)
mean_shapes_plot(
- ccd_maps[:, 0, 0],
- output_path + 'e1s',
- title,
- wind=wind
+ ccd_maps[:, 0, 0], output_path + "e1s", title, wind=wind
)
title = (
- f'e_1 (model), std={np.nanstd(ccd_maps[:, 1, 0]):.5e}\n'
- + f'vmax={np.nanmax(abs(ccd_maps[:, 1, 0])):.4e}'
+ f"e_1 (model), std={np.nanstd(ccd_maps[:, 1, 0]):.5e}\n"
+ + f"vmax={np.nanmax(abs(ccd_maps[:, 1, 0])):.4e}"
)
mean_shapes_plot(
- ccd_maps[:, 1, 0],
- output_path + 'e1m',
- title,
- wind=wind
+ ccd_maps[:, 1, 0], output_path + "e1m", title, wind=wind
)
if auto_colorbar:
wind = None
e1_res = ccd_maps[:, 0, 0] - ccd_maps[:, 1, 0]
e1_res = e1_res[~np.isnan(e1_res)]
- rmse_e1 = np.sqrt(np.mean(e1_res ** 2))
- w_log.info(f'Bins: e1 residual RMSE: {rmse_e1:.6f}\n')
+ rmse_e1 = np.sqrt(np.mean(e1_res**2))
+ w_log.info(f"Bins: e1 residual RMSE: {rmse_e1:.6f}\n")
if max_de:
vmax = max_de
else:
@@ -446,15 +439,15 @@ def plot_meanshapes(
vmin = -vmax
wind = [vmin, vmax]
title = (
- f'e_1 res, rmse={rmse_e1:.5e}\nvmax={vmax:.4e} , '
- + f'std={np.nanstd(ccd_maps[:, 0, 0] - ccd_maps[:, 1, 0]):.5e}'
+ f"e_1 res, rmse={rmse_e1:.5e}\nvmax={vmax:.4e} , "
+ + f"std={np.nanstd(ccd_maps[:, 0, 0] - ccd_maps[:, 1, 0]):.5e}"
)
mean_shapes_plot(
ccd_maps[:, 0, 0] - ccd_maps[:, 1, 0],
- output_path + 'e1res',
+ output_path + "e1res",
title,
wind=wind,
- colorbar_ampl=colorbar_ampl
+ colorbar_ampl=colorbar_ampl,
)
# e_2
@@ -463,39 +456,33 @@ def plot_meanshapes(
else:
vmax = max(
np.nanmax(ccd_maps[:, :, 1]),
- np.abs(np.nanmin(ccd_maps[:, :, 1]))
+ np.abs(np.nanmin(ccd_maps[:, :, 1])),
)
vmin = -vmax
wind = [vmin, vmax]
title = (
- f'e_2 (stars), std={np.nanstd(ccd_maps[:, 0, 1]):.5e}\n'
- + f'vmax={np.nanmax(abs(ccd_maps[:, 0, 1])):.4e}'
+ f"e_2 (stars), std={np.nanstd(ccd_maps[:, 0, 1]):.5e}\n"
+ + f"vmax={np.nanmax(abs(ccd_maps[:, 0, 1])):.4e}"
)
mean_shapes_plot(
- ccd_maps[:, 0, 1],
- output_path + 'e2s',
- title,
- wind=wind
+ ccd_maps[:, 0, 1], output_path + "e2s", title, wind=wind
)
title = (
- f'e_2 (model), std={np.nanstd(ccd_maps[:, 1, 1]):.5e}\n'
- + f'vmax={np.nanmax(abs(ccd_maps[:, 1, 1])):.4e}'
+ f"e_2 (model), std={np.nanstd(ccd_maps[:, 1, 1]):.5e}\n"
+ + f"vmax={np.nanmax(abs(ccd_maps[:, 1, 1])):.4e}"
)
mean_shapes_plot(
- ccd_maps[:, 1, 1],
- output_path + 'e2m',
- title,
- wind=wind
+ ccd_maps[:, 1, 1], output_path + "e2m", title, wind=wind
)
if auto_colorbar:
wind = None
- colorbar_ampl = 1.
+ colorbar_ampl = 1.0
e2_res = ccd_maps[:, 0, 1] - ccd_maps[:, 1, 1]
e2_res = e2_res[~np.isnan(e2_res)]
- rmse_e2 = np.sqrt(np.mean(e2_res ** 2))
- w_log.info(f'Bins: e2 residual RMSE: {rmse_e2:.6f}\n')
+ rmse_e2 = np.sqrt(np.mean(e2_res**2))
+ w_log.info(f"Bins: e2 residual RMSE: {rmse_e2:.6f}\n")
if max_de:
vmax = max_de
else:
@@ -503,15 +490,15 @@ def plot_meanshapes(
vmin = -vmax
wind = [vmin, vmax]
title = (
- f'e_2 res, rmse={rmse_e2:.5e}\nvmax={vmax:.4e} , '
- + f'std={np.nanstd(ccd_maps[:, 0, 1] - ccd_maps[:, 1, 1]):.5e}'
+ f"e_2 res, rmse={rmse_e2:.5e}\nvmax={vmax:.4e} , "
+ + f"std={np.nanstd(ccd_maps[:, 0, 1] - ccd_maps[:, 1, 1]):.5e}"
)
mean_shapes_plot(
ccd_maps[:, 0, 1] - ccd_maps[:, 1, 1],
- output_path + 'e2res',
+ output_path + "e2res",
title,
wind=wind,
- colorbar_ampl=colorbar_ampl
+ colorbar_ampl=colorbar_ampl,
)
# R^2
@@ -526,47 +513,48 @@ def plot_meanshapes(
wind = [vmin, vmax]
colorbar_ampl = 1
title = (
- f'R_2 (stars), std={np.nanstd(ccd_maps[:, 0, 2]):.5e}\n'
- + f'vmax={np.nanmax(abs(ccd_maps[:, 0, 2])):.4e}'
+ f"R_2 (stars), std={np.nanstd(ccd_maps[:, 0, 2]):.5e}\n"
+ + f"vmax={np.nanmax(abs(ccd_maps[:, 0, 2])):.4e}"
)
mean_shapes_plot(
ccd_maps[:, 0, 2],
- output_path + 'R2s',
+ output_path + "R2s",
title,
wind=wind,
- cmap='Reds'
+ cmap="Reds",
)
title = (
- f'R_2 (model), std={np.nanstd(ccd_maps[:, 1, 2]):.5e}\n'
- + f'vmax={np.nanmax(abs(ccd_maps[:, 1, 2])):.4e}'
+ f"R_2 (model), std={np.nanstd(ccd_maps[:, 1, 2]):.5e}\n"
+ + f"vmax={np.nanmax(abs(ccd_maps[:, 1, 2])):.4e}"
)
mean_shapes_plot(
ccd_maps[:, 1, 2],
- output_path + 'R2m',
+ output_path + "R2m",
title,
wind=wind,
- cmap='Reds'
+ cmap="Reds",
)
if auto_colorbar:
wind = [
0,
- np.nanmax(np.abs(
- (ccd_maps[:, 0, 2] - ccd_maps[:, 1, 2]) / ccd_maps[:, 0, 2]
- ))
+ np.nanmax(
+ np.abs(
+ (ccd_maps[:, 0, 2] - ccd_maps[:, 1, 2])
+ / ccd_maps[:, 0, 2]
+ )
+ ),
]
- colorbar_ampl = 1.
+ colorbar_ampl = 1.0
R2_res = (ccd_maps[:, 0, 2] - ccd_maps[:, 1, 2]) / ccd_maps[:, 0, 2]
R2_res = R2_res[~np.isnan(R2_res)]
- rmse_r2 = np.sqrt(np.mean(R2_res ** 2))
+ rmse_r2 = np.sqrt(np.mean(R2_res**2))
w_log.info(f"Bins: R2 residual RMSE: {rmse_r2:.6f}\n")
if max_dr2:
vmax = max_dr2
else:
vmax = np.nanmax(
- abs(
- (ccd_maps[:, 0, 2] - ccd_maps[:, 1, 2]) / ccd_maps[:, 0, 2]
- )
+ abs((ccd_maps[:, 0, 2] - ccd_maps[:, 1, 2]) / ccd_maps[:, 0, 2])
)
wind = [0, vmax]
std_title = np.nanstd(
@@ -580,26 +568,23 @@ def plot_meanshapes(
title = "Outliers removed\n" + title
mean_shapes_plot(
- np.abs(
- (ccd_maps[:, 0, 2] - ccd_maps[:, 1, 2])
- / ccd_maps[:, 0, 2]
- ),
- output_path + 'R2res',
+ np.abs((ccd_maps[:, 0, 2] - ccd_maps[:, 1, 2]) / ccd_maps[:, 0, 2]),
+ output_path + "R2res",
title,
wind=wind,
colorbar_ampl=colorbar_ampl,
- cmap='Reds'
+ cmap="Reds",
)
# nstars
wind = (0, np.max(ccd_maps[:, 0, 3]))
- title = f'Number of stars\nTotal={np.nansum(ccd_maps[:, 0, 3]):.0f}'
+ title = f"Number of stars\nTotal={np.nansum(ccd_maps[:, 0, 3]):.0f}"
mean_shapes_plot(
ccd_maps[:, 0, 3],
- f'{output_path}nstar',
+ f"{output_path}nstar",
title,
wind=wind,
- cmap='magma'
+ cmap="magma",
)
# Histograms
@@ -610,19 +595,19 @@ def plot_meanshapes(
all_star_shapes[0, :],
bins=hist_bins,
range=[-0.2, 0.2],
- label='stars',
- alpha=0.5
+ label="stars",
+ alpha=0.5,
)
plt.hist(
all_psf_shapes[0, :],
bins=hist_bins,
range=[-0.2, 0.2],
- label='PSFs',
- alpha=0.5
+ label="PSFs",
+ alpha=0.5,
)
- plt.legend(loc='best', fontsize=16)
- plt.title('e1', fontsize=24)
- plt.savefig(f'{output_path}e1_hist.png')
+ plt.legend(loc="best", fontsize=16)
+ plt.title("e1", fontsize=24)
+ plt.savefig(f"{output_path}e1_hist.png")
plt.close()
plt.figure(figsize=(12, 6), dpi=300)
@@ -631,12 +616,12 @@ def plot_meanshapes(
data_hist,
bins=hist_bins,
range=[np.min(data_hist), np.max(data_hist)],
- label='err(star - psf)',
- alpha=0.5
+ label="err(star - psf)",
+ alpha=0.5,
)
- plt.legend(loc='best', fontsize=16)
- plt.title('e1 err', fontsize=24)
- plt.savefig(output_path + 'err_e1_hist.png')
+ plt.legend(loc="best", fontsize=16)
+ plt.title("e1 err", fontsize=24)
+ plt.savefig(output_path + "err_e1_hist.png")
plt.close()
plt.figure(figsize=(12, 6), dpi=300)
@@ -644,19 +629,19 @@ def plot_meanshapes(
all_star_shapes[1, :],
bins=hist_bins,
range=[-0.2, 0.2],
- label='stars',
- alpha=0.5
+ label="stars",
+ alpha=0.5,
)
plt.hist(
all_psf_shapes[1, :],
bins=hist_bins,
range=[-0.2, 0.2],
- label='PSFs',
- alpha=0.5
+ label="PSFs",
+ alpha=0.5,
)
- plt.legend(loc='best', fontsize=16)
- plt.title('e2', fontsize=24)
- plt.savefig(output_path + 'e2_hist.png')
+ plt.legend(loc="best", fontsize=16)
+ plt.title("e2", fontsize=24)
+ plt.savefig(output_path + "e2_hist.png")
plt.close()
plt.figure(figsize=(12, 6), dpi=300)
@@ -665,12 +650,12 @@ def plot_meanshapes(
data_hist,
bins=hist_bins,
range=[np.min(data_hist), np.max(data_hist)],
- label='err(star - psf)',
- alpha=0.5
+ label="err(star - psf)",
+ alpha=0.5,
)
- plt.legend(loc='best', fontsize=16)
- plt.title('e2 err', fontsize=24)
- plt.savefig(output_path + 'err_e2_hist.png')
+ plt.legend(loc="best", fontsize=16)
+ plt.title("e2 err", fontsize=24)
+ plt.savefig(output_path + "err_e2_hist.png")
plt.close()
plt.figure(figsize=(12, 6), dpi=300)
@@ -680,36 +665,35 @@ def plot_meanshapes(
all_star_shapes[2, :],
bins=hist_bins,
range=wind,
- label='stars',
- alpha=0.5
+ label="stars",
+ alpha=0.5,
)
plt.hist(
all_psf_shapes[2, :],
bins=hist_bins,
range=wind,
- label='PSFs',
- alpha=0.5
+ label="PSFs",
+ alpha=0.5,
)
- plt.legend(loc='best', fontsize=16)
- plt.title('R2', fontsize=24)
- plt.savefig(output_path + 'R2_hist.png')
+ plt.legend(loc="best", fontsize=16)
+ plt.title("R2", fontsize=24)
+ plt.savefig(output_path + "R2_hist.png")
plt.close()
plt.figure(figsize=(12, 6), dpi=300)
data_hist = (
- (all_star_shapes[2, :] - all_psf_shapes[2, :])
- / all_star_shapes[2, :]
- )
+ all_star_shapes[2, :] - all_psf_shapes[2, :]
+ ) / all_star_shapes[2, :]
plt.hist(
data_hist,
bins=hist_bins,
range=[np.min(data_hist), np.max(data_hist)],
- label='err(star - psf)/star',
- alpha=0.5
+ label="err(star - psf)/star",
+ alpha=0.5,
)
- plt.legend(loc='best', fontsize=16)
- plt.title('R2 err', fontsize=24)
- plt.savefig(output_path + 'err_R2_hist.png')
+ plt.legend(loc="best", fontsize=16)
+ plt.title("R2 err", fontsize=24)
+ plt.savefig(output_path + "err_R2_hist.png")
plt.close()
starcat.close()
@@ -720,15 +704,15 @@ def neg_dash(
x_in,
y_in,
yerr_in,
- plot_name='',
+ plot_name="",
vertical_lines=True,
- xlabel='',
- ylabel='',
- rho_nb='',
+ xlabel="",
+ ylabel="",
+ rho_nb="",
ylim=None,
semilogx=False,
semilogy=False,
- **kwargs
+ **kwargs,
):
r"""Neg Dash.
@@ -770,14 +754,19 @@ def neg_dash(
# catch and separate errorbar-specific keywords from Lines2D ones
safekwargs = dict(kwargs)
errbkwargs = dict()
- if 'linestyle' in kwargs.keys():
+ if "linestyle" in kwargs.keys():
print(
- 'Warning: linestyle was provided but that would kind of defeat'
- + 'the purpose, so I will just ignore it. Sorry.'
+ "Warning: linestyle was provided but that would kind of defeat"
+ + "the purpose, so I will just ignore it. Sorry."
)
- del safekwargs['linestyle']
+ del safekwargs["linestyle"]
for errorbar_kword in [
- 'fmt', 'ecolor', 'elinewidth', 'capsize', 'barsabove', 'errorevery'
+ "fmt",
+ "ecolor",
+ "elinewidth",
+ "capsize",
+ "barsabove",
+ "errorevery",
]:
if errorbar_kword in kwargs.keys():
# posfmt = '-'+kwargs['fmt']
@@ -795,7 +784,7 @@ def neg_dash(
x[:first_change],
y[:first_change],
yerr=yerr[:first_change],
- linestyle='-',
+ linestyle="-",
**errbkwargs,
)
if vertical_lines:
@@ -803,14 +792,14 @@ def neg_dash(
x[first_change - 1],
0,
y[first_change - 1],
- linestyle='-',
+ linestyle="-",
**safekwargs,
)
plt.vlines(
x[first_change],
0,
np.abs(y[first_change]),
- linestyle='--',
+ linestyle="--",
**safekwargs,
)
else:
@@ -818,7 +807,7 @@ def neg_dash(
x[:first_change],
np.abs(y[:first_change]),
yerr=yerr[:first_change],
- linestyle='--',
+ linestyle="--",
**errbkwargs,
)
if vertical_lines:
@@ -826,14 +815,14 @@ def neg_dash(
x[first_change - 1],
0,
np.abs(y[first_change - 1]),
- linestyle='--',
+ linestyle="--",
**safekwargs,
)
plt.vlines(
x[first_change],
0,
y[first_change],
- linestyle='-',
+ linestyle="-",
**safekwargs,
)
x = x[first_change:]
@@ -843,18 +832,19 @@ def neg_dash(
first_change = np.argmax(current_sign * y < 0)
# one last time when `first_change'==0 ie no more changes:
if rho_nb:
- lab = fr'$\rho_{rho_nb}(\theta)$'
+ lab = rf"$\rho_{rho_nb}(\theta)$"
else:
- lab = ''
+ lab = ""
if current_sign > 0:
- plt.errorbar(x, y, yerr=yerr, linestyle='-', label=lab, **errbkwargs)
+ plt.errorbar(x, y, yerr=yerr, linestyle="-", label=lab, **errbkwargs)
else:
- plt.errorbar(x, np.abs(y), yerr=yerr, linestyle='--', label=lab,
- **errbkwargs)
+ plt.errorbar(
+ x, np.abs(y), yerr=yerr, linestyle="--", label=lab, **errbkwargs
+ )
if semilogx:
- plt.xscale('log')
+ plt.xscale("log")
if semilogy:
- plt.yscale('log')
+ plt.yscale("log")
if ylim is not None:
plt.ylim(ylim)
plt.xlabel(xlabel)
@@ -872,11 +862,7 @@ class new_BaseCorrelationFunctionSysTest(BaseCorrelationFunctionSysTest):
"""
def make_catalogue(
- self,
- data,
- config=None,
- use_as_k=None,
- use_chip_coords=False
+ self, data, config=None, use_as_k=None, use_chip_coords=False
):
"""Make Catalogue.
@@ -911,43 +897,45 @@ def make_catalogue(
catalog_kwargs = {}
fields = data.dtype.names
- if 'ra' in fields and 'dec' in fields:
+ if "ra" in fields and "dec" in fields:
if not use_chip_coords:
- catalog_kwargs['ra'] = data['ra']
- catalog_kwargs['dec'] = data['dec']
- elif 'x' in fields and 'y' in fields:
- catalog_kwargs['x'] = data['x']
- catalog_kwargs['y'] = data['y']
+ catalog_kwargs["ra"] = data["ra"]
+ catalog_kwargs["dec"] = data["dec"]
+ elif "x" in fields and "y" in fields:
+ catalog_kwargs["x"] = data["x"]
+ catalog_kwargs["y"] = data["y"]
else:
raise ValueError(
"Chip coordinates requested, but 'x' and 'y' fields"
- "not found in data")
- elif 'x' in fields and 'y' in fields:
- catalog_kwargs['x'] = data['x']
- catalog_kwargs['y'] = data['y']
+ "not found in data"
+ )
+ elif "x" in fields and "y" in fields:
+ catalog_kwargs["x"] = data["x"]
+ catalog_kwargs["y"] = data["y"]
else:
raise ValueError(
"Data must contain (ra,dec) or (x,y) in order to do"
- "correlation function tests.")
- if 'g1' in fields and 'g2' in fields:
- catalog_kwargs['g1'] = data['g1']
- catalog_kwargs['g2'] = data['g2']
- if 'w' in fields:
- catalog_kwargs['w'] = data['w']
+ "correlation function tests."
+ )
+ if "g1" in fields and "g2" in fields:
+ catalog_kwargs["g1"] = data["g1"]
+ catalog_kwargs["g2"] = data["g2"]
+ if "w" in fields:
+ catalog_kwargs["w"] = data["w"]
if use_as_k:
if use_as_k in fields:
- catalog_kwargs['k'] = data[use_as_k]
- elif 'k' in fields:
- catalog_kwargs['k'] = data['k']
+ catalog_kwargs["k"] = data[use_as_k]
+ elif "k" in fields:
+ catalog_kwargs["k"] = data["k"]
# Quirk of length-1 formatted arrays: the fields will be floats, not
# arrays, which would break the Catalog init.
try:
len(data)
except Exception:
- if not hasattr(data, 'len') and isinstance(data, np.ndarray):
+ if not hasattr(data, "len") and isinstance(data, np.ndarray):
for key in catalog_kwargs:
catalog_kwargs[key] = np.array([catalog_kwargs[key]])
- catalog_kwargs['config'] = config
+ catalog_kwargs["config"] = config
return treecorr.Catalog(**catalog_kwargs)
@@ -959,19 +947,13 @@ class Rho1SysTest(new_BaseCorrelationFunctionSysTest):
"""
- short_name = 'rho1'
- long_name = 'Rho1 statistics (Auto-correlation of star-PSF shapes)'
- objects_list = ['star PSF']
- required_quantities = [('ra', 'dec', 'g1', 'g2', 'psf_g1', 'psf_g2', 'w')]
+ short_name = "rho1"
+ long_name = "Rho1 statistics (Auto-correlation of star-PSF shapes)"
+ objects_list = ["star PSF"]
+ required_quantities = [("ra", "dec", "g1", "g2", "psf_g1", "psf_g2", "w")]
def __call__(
- self,
- data,
- data2=None,
- random=None,
- random2=None,
- config=None,
- **kwargs
+ self, data, data2=None, random=None, random2=None, config=None, **kwargs
):
"""Call Method.
@@ -996,28 +978,28 @@ def __call__(
"""
new_data = data.copy()
- new_data['g1'] = new_data['g1'] - new_data['psf_g1']
- new_data['g2'] = new_data['g2'] - new_data['psf_g2']
+ new_data["g1"] = new_data["g1"] - new_data["psf_g1"]
+ new_data["g2"] = new_data["g2"] - new_data["psf_g2"]
if data2 is not None:
new_data2 = data2.copy()
- new_data2['g1'] = new_data2['g1'] - new_data2['psf_g1']
- new_data2['g2'] = new_data2['g2'] - new_data2['psf_g2']
+ new_data2["g1"] = new_data2["g1"] - new_data2["psf_g1"]
+ new_data2["g2"] = new_data2["g2"] - new_data2["psf_g2"]
else:
new_data2 = data2
if random is not None:
new_random = random.copy()
- new_random['g1'] = new_random['g1'] - new_random['psf_g1']
- new_random['g2'] = new_random['g2'] - new_random['psf_g2']
+ new_random["g1"] = new_random["g1"] - new_random["psf_g1"]
+ new_random["g2"] = new_random["g2"] - new_random["psf_g2"]
else:
new_random = random
if random2 is not None:
new_random2 = random2.copy()
- new_random2['g1'] = new_random2['g1'] - new_random2['psf_g1']
- new_random2['g2'] = new_random2['g2'] - new_random2['psf_g2']
+ new_random2["g1"] = new_random2["g1"] - new_random2["psf_g1"]
+ new_random2["g2"] = new_random2["g2"] - new_random2["psf_g2"]
else:
new_random2 = random2
return self.getCF(
- 'gg',
+ "gg",
new_data,
new_data2,
new_random,
@@ -1035,19 +1017,13 @@ class DESRho2SysTest(new_BaseCorrelationFunctionSysTest):
"""
- short_name = 'rho2des'
- long_name = 'Rho2 statistics (as defined in DES shape catalogue papers)'
- objects_list = ['star PSF']
- required_quantities = [('ra', 'dec', 'g1', 'g2', 'psf_g1', 'psf_g2', 'w')]
+ short_name = "rho2des"
+ long_name = "Rho2 statistics (as defined in DES shape catalogue papers)"
+ objects_list = ["star PSF"]
+ required_quantities = [("ra", "dec", "g1", "g2", "psf_g1", "psf_g2", "w")]
def __call__(
- self,
- data,
- data2=None,
- random=None,
- random2=None,
- config=None,
- **kwargs
+ self, data, data2=None, random=None, random2=None, config=None, **kwargs
):
"""Call Method.
@@ -1072,31 +1048,31 @@ def __call__(
"""
new_data = np.rec.fromarrays(
- [data['ra'], data['dec'], data['g1'], data['g2'], data['w']],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ [data["ra"], data["dec"], data["g1"], data["g2"], data["w"]],
+ names=["ra", "dec", "g1", "g2", "w"],
)
if data2 is None:
data2 = data
new_data2 = np.rec.fromarrays(
[
- data2['ra'],
- data2['dec'],
- data2['g1'] - data2['psf_g1'],
- data2['g2'] - data2['psf_g2'],
- data2['w']
+ data2["ra"],
+ data2["dec"],
+ data2["g1"] - data2["psf_g1"],
+ data2["g2"] - data2["psf_g2"],
+ data2["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ names=["ra", "dec", "g1", "g2", "w"],
)
if random is not None:
new_random = np.rec.fromarrays(
[
- random['ra'],
- random['dec'],
- random['g1'],
- random['g2'],
- random['w']
+ random["ra"],
+ random["dec"],
+ random["g1"],
+ random["g2"],
+ random["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ names=["ra", "dec", "g1", "g2", "w"],
)
else:
@@ -1106,24 +1082,24 @@ def __call__(
if random2 is not None:
new_random2 = np.rec.fromarrays(
[
- data2['ra'],
- data2['dec'],
- data2['g1'] - data2['psf_g1'],
- data2['g2'] - data2['psf_g2'],
- data2['w']
+ data2["ra"],
+ data2["dec"],
+ data2["g1"] - data2["psf_g1"],
+ data2["g2"] - data2["psf_g2"],
+ data2["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ names=["ra", "dec", "g1", "g2", "w"],
)
else:
new_random2 = random2
return self.getCF(
- 'gg',
+ "gg",
new_data,
new_data2,
new_random,
new_random2,
config=config,
- **kwargs
+ **kwargs,
)
@@ -1134,24 +1110,16 @@ class DESRho3SysTest(new_BaseCorrelationFunctionSysTest):
"""
- short_name = 'rho3'
+ short_name = "rho3"
long_name = (
- 'Rho3 statistics (Auto-correlation of star shapes weighted by '
- + 'the residual size)'
+ "Rho3 statistics (Auto-correlation of star shapes weighted by "
+ + "the residual size)"
)
- objects_list = ['star PSF']
- required_quantities = [
- ('ra', 'dec', 'sigma', 'g1', 'g2', 'psf_sigma', 'w')
- ]
+ objects_list = ["star PSF"]
+ required_quantities = [("ra", "dec", "sigma", "g1", "g2", "psf_sigma", "w")]
def __call__(
- self,
- data,
- data2=None,
- random=None,
- random2=None,
- config=None,
- **kwargs
+ self, data, data2=None, random=None, random2=None, config=None, **kwargs
):
"""Call Method.
@@ -1176,24 +1144,33 @@ def __call__(
"""
new_data = np.rec.fromarrays(
- [data['ra'], data['dec'],
- data['g1'] * (data['sigma'] - data[
- 'psf_sigma']) / data['sigma'],
- data['g2'] * (data['sigma'] - data[
- 'psf_sigma']) / data['sigma'],
- data['w']],
- names=['ra', 'dec', 'g1', 'g2', 'w']
+ [
+ data["ra"],
+ data["dec"],
+ data["g1"]
+ * (data["sigma"] - data["psf_sigma"])
+ / data["sigma"],
+ data["g2"]
+ * (data["sigma"] - data["psf_sigma"])
+ / data["sigma"],
+ data["w"],
+ ],
+ names=["ra", "dec", "g1", "g2", "w"],
)
if data2 is not None:
new_data2 = np.rec.fromarrays(
[
- data2['ra'], data2['dec'],
- data2['g1'] * (data2['sigma'] - data2['psf_sigma'])
- / data2['sigma'],
- data2['g2'] * (data2['sigma'] - data2['psf_sigma'])
- / data2['sigma'],
- data2['w']],
- names=['ra', 'dec', 'g1', 'g2', 'w']
+ data2["ra"],
+ data2["dec"],
+ data2["g1"]
+ * (data2["sigma"] - data2["psf_sigma"])
+ / data2["sigma"],
+ data2["g2"]
+ * (data2["sigma"] - data2["psf_sigma"])
+ / data2["sigma"],
+ data2["w"],
+ ],
+ names=["ra", "dec", "g1", "g2", "w"],
)
else:
@@ -1201,14 +1178,17 @@ def __call__(
if random is not None:
new_random = np.rec.fromarrays(
[
- random['ra'], random['dec'],
- random['g1'] * (random['sigma'] - random['psf_sigma'])
- / random['sigma'],
- random['g2'] * (random['sigma'] - random['psf_sigma'])
- / random['sigma'],
- random['w']
+ random["ra"],
+ random["dec"],
+ random["g1"]
+ * (random["sigma"] - random["psf_sigma"])
+ / random["sigma"],
+ random["g2"]
+ * (random["sigma"] - random["psf_sigma"])
+ / random["sigma"],
+ random["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w']
+ names=["ra", "dec", "g1", "g2", "w"],
)
else:
new_random = random
@@ -1216,27 +1196,30 @@ def __call__(
if random2 is not None:
new_random2 = np.rec.fromarrays(
[
- random2['ra'], random2['dec'],
- random2['g1'] * (random2['sigma'] - random2['psf_sigma'])
- / random2['sigma'],
- random2['g2'] * (random2['sigma'] - random2['psf_sigma'])
- / random2['sigma'],
- random2['w']
+ random2["ra"],
+ random2["dec"],
+ random2["g1"]
+ * (random2["sigma"] - random2["psf_sigma"])
+ / random2["sigma"],
+ random2["g2"]
+ * (random2["sigma"] - random2["psf_sigma"])
+ / random2["sigma"],
+ random2["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w']
+ names=["ra", "dec", "g1", "g2", "w"],
)
else:
new_random2 = random2
return self.getCF(
- 'gg',
+ "gg",
new_data,
new_data2,
new_random,
new_random2,
config=config,
- **kwargs
+ **kwargs,
)
@@ -1247,24 +1230,18 @@ class DESRho4SysTest(new_BaseCorrelationFunctionSysTest):
"""
- short_name = 'rho4'
+ short_name = "rho4"
long_name = (
- 'Rho4 statistics (Correlation of residual star shapes weighted '
- + 'by residual size)'
+ "Rho4 statistics (Correlation of residual star shapes weighted "
+ + "by residual size)"
)
- objects_list = ['star PSF']
- required_quantities = [(
- 'ra', 'dec', 'g1', 'g2', 'sigma', 'psf_g1', 'psf_g2', 'psf_sigma', 'w'
- )]
+ objects_list = ["star PSF"]
+ required_quantities = [
+ ("ra", "dec", "g1", "g2", "sigma", "psf_g1", "psf_g2", "psf_sigma", "w")
+ ]
def __call__(
- self,
- data,
- data2=None,
- random=None,
- random2=None,
- config=None,
- **kwargs
+ self, data, data2=None, random=None, random2=None, config=None, **kwargs
):
"""Call Method.
@@ -1290,38 +1267,40 @@ def __call__(
"""
new_data = np.rec.fromarrays(
[
- data['ra'],
- data['dec'],
- data['g1'] - data['psf_g1'],
- data['g2'] - data['psf_g2'],
- data['w']
+ data["ra"],
+ data["dec"],
+ data["g1"] - data["psf_g1"],
+ data["g2"] - data["psf_g2"],
+ data["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ names=["ra", "dec", "g1", "g2", "w"],
)
if data2 is None:
data2 = data
new_data2 = np.rec.fromarrays(
[
- data2['ra'],
- data2['dec'],
- data2['g1'] * (data2['sigma'] - data2['psf_sigma'])
- / data2['sigma'],
- data2['g2'] * (data2['sigma'] - data2['psf_sigma'])
- / data2['sigma'],
- data2['w']
+ data2["ra"],
+ data2["dec"],
+ data2["g1"]
+ * (data2["sigma"] - data2["psf_sigma"])
+ / data2["sigma"],
+ data2["g2"]
+ * (data2["sigma"] - data2["psf_sigma"])
+ / data2["sigma"],
+ data2["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ names=["ra", "dec", "g1", "g2", "w"],
)
if random is not None:
new_random = np.rec.fromarrays(
[
- random['ra'],
- random['dec'],
- random['g1'] - random['psf_g1'],
- random['g2'] - random['psf_g2'],
- random['w']
+ random["ra"],
+ random["dec"],
+ random["g1"] - random["psf_g1"],
+ random["g2"] - random["psf_g2"],
+ random["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ names=["ra", "dec", "g1", "g2", "w"],
)
else:
new_random = random
@@ -1330,25 +1309,28 @@ def __call__(
if random2 is not None:
new_random2 = np.rec.fromarrays(
[
- random2['ra'], random2['dec'],
- random2['g1'] * (random2['sigma'] - random2['psf_sigma'])
- / random2['sigma'],
- random2['g2'] * (random2['sigma'] - random2['psf_sigma'])
- / random2['sigma'],
- random2['w']
+ random2["ra"],
+ random2["dec"],
+ random2["g1"]
+ * (random2["sigma"] - random2["psf_sigma"])
+ / random2["sigma"],
+ random2["g2"]
+ * (random2["sigma"] - random2["psf_sigma"])
+ / random2["sigma"],
+ random2["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w']
+ names=["ra", "dec", "g1", "g2", "w"],
)
else:
new_random2 = random2
return self.getCF(
- 'gg',
+ "gg",
new_data,
new_data2,
new_random,
new_random2,
config=config,
- **kwargs
+ **kwargs,
)
@@ -1359,24 +1341,16 @@ class DESRho5SysTest(new_BaseCorrelationFunctionSysTest):
"""
- short_name = 'rho5'
+ short_name = "rho5"
long_name = (
- 'Rho5 statistics (Correlation of star and PSF shapes weighted by '
- 'residual size)'
+ "Rho5 statistics (Correlation of star and PSF shapes weighted by "
+ "residual size)"
)
- objects_list = ['star PSF']
- required_quantities = [
- ('ra', 'dec', 'sigma', 'g1', 'g2', 'psf_sigma', 'w')
- ]
+ objects_list = ["star PSF"]
+ required_quantities = [("ra", "dec", "sigma", "g1", "g2", "psf_sigma", "w")]
def __call__(
- self,
- data,
- data2=None,
- random=None,
- random2=None,
- config=None,
- **kwargs
+ self, data, data2=None, random=None, random2=None, config=None, **kwargs
):
"""Call Method.
@@ -1402,34 +1376,36 @@ def __call__(
"""
new_data = np.rec.fromarrays(
- [data['ra'], data['dec'], data['g1'], data['g2'], data['w']],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ [data["ra"], data["dec"], data["g1"], data["g2"], data["w"]],
+ names=["ra", "dec", "g1", "g2", "w"],
)
if data2 is None:
data2 = data
new_data2 = np.rec.fromarrays(
[
- data2['ra'],
- data2['dec'],
- data2['g1'] * (data2['sigma'] - data2['psf_sigma'])
- / data2['sigma'],
- data2['g2'] * (data2['sigma'] - data2['psf_sigma'])
- / data2['sigma'],
- data2['w']
+ data2["ra"],
+ data2["dec"],
+ data2["g1"]
+ * (data2["sigma"] - data2["psf_sigma"])
+ / data2["sigma"],
+ data2["g2"]
+ * (data2["sigma"] - data2["psf_sigma"])
+ / data2["sigma"],
+ data2["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ names=["ra", "dec", "g1", "g2", "w"],
)
if random is not None:
new_random = np.rec.fromarrays(
[
- random['ra'],
- random['dec'],
- random['g1'],
- random['g2'],
- random['w']
+ random["ra"],
+ random["dec"],
+ random["g1"],
+ random["g2"],
+ random["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ names=["ra", "dec", "g1", "g2", "w"],
)
else:
new_random = random
@@ -1438,38 +1414,64 @@ def __call__(
if random2 is not None:
new_random2 = np.rec.fromarrays(
[
- random2['ra'],
- random2['dec'],
- random2['g1'] * (random2['sigma'] - random2['psf_sigma'])
- / random2['sigma'],
- random2['g2'] * (random2['sigma'] - random2['psf_sigma'])
- / random2['sigma'],
- random2['w']
+ random2["ra"],
+ random2["dec"],
+ random2["g1"]
+ * (random2["sigma"] - random2["psf_sigma"])
+ / random2["sigma"],
+ random2["g2"]
+ * (random2["sigma"] - random2["psf_sigma"])
+ / random2["sigma"],
+ random2["w"],
],
- names=['ra', 'dec', 'g1', 'g2', 'w'],
+ names=["ra", "dec", "g1", "g2", "w"],
)
else:
new_random2 = random2
return self.getCF(
- 'gg',
+ "gg",
new_data,
new_data2,
new_random,
new_random2,
config=config,
- **kwargs
+ **kwargs,
)
+def get_params_rho():
+
+ params = {}
+
+ params["patch_number"] = 50
+
+ params["ra_col"] = "RA"
+ params["dec_col"] = "DEC"
+ params["e1_PSF_col"] = "E1_PSF_HSM"
+ params["e2_PSF_col"] = "E2_PSF_HSM"
+ params["e1_star_col"] = "E1_STAR_HSM"
+ params["e2_star_col"] = "E2_STAR_HSM"
+ params["PSF_size"] = "SIGMA_PSF_HSM"
+ params["star_size"] = "SIGMA_STAR_HSM"
+ params["PSF_flag"] = "FLAG_PSF_HSM"
+ params["star_flag"] = "FLAG_STAR_HSM"
+ params["ra_units"] = "deg"
+ params["dec_units"] = "deg"
+
+ params["w_col"] = None
+
+ return params
+
+
def rho_stats(
starcat_path,
output_path,
- rho_def='HSC',
+ rho_def="HSC",
hdu_no=2,
ylim_l=None,
ylim_r=None,
- print_fun=lambda x: print(x)
+ print_fun=lambda x: print(x),
):
"""Rho Statistics.
@@ -1491,58 +1493,57 @@ def rho_stats(
Output message function; default is ``print``
"""
- # Read starcat
- starcat = fits.open(starcat_path, memmap=False)
-
- rho_stats_fun = None
-
- # Convert HSM flags to 0/1 weights
- star_flags = starcat[hdu_no].data['FLAG_STAR_HSM']
- psf_flags = starcat[hdu_no].data['FLAG_PSF_HSM']
- w = np.abs(star_flags - 1) * np.abs(psf_flags - 1)
-
- # Convert to Stile-compatible and change sigmas to R^2 (up to constant)
- stilecat = np.rec.fromarrays(
- [
- w,
- starcat[hdu_no].data['RA'],
- starcat[hdu_no].data['DEC'],
- starcat[hdu_no].data['E1_STAR_HSM'],
- starcat[hdu_no].data['E2_STAR_HSM'],
- starcat[hdu_no].data['SIGMA_STAR_HSM'] ** 2,
- starcat[hdu_no].data['E1_PSF_HSM'],
- starcat[hdu_no].data['E2_PSF_HSM'],
- starcat[hdu_no].data['SIGMA_PSF_HSM'] ** 2
- ],
- names=[
- 'w',
- 'ra',
- 'dec',
- 'g1',
- 'g2',
- 'sigma',
- 'psf_g1',
- 'psf_g2',
- 'psf_sigma'
- ],
- )
+ if rho_def != "UNIONS":
+ # Read starcat
+ starcat = fits.open(starcat_path, memmap=False)
+ rho_stats_fun = None
+ # Convert HSM flags to 0/1 weights
+ star_flags = starcat[hdu_no].data["FLAG_STAR_HSM"]
+ psf_flags = starcat[hdu_no].data["FLAG_PSF_HSM"]
+ w = np.abs(star_flags - 1) * np.abs(psf_flags - 1)
+
+ # Convert to Stile-compatible and change sigmas to R^2 (up to constant)
+ stilecat = np.rec.fromarrays(
+ [
+ w,
+ starcat[hdu_no].data["RA"],
+ starcat[hdu_no].data["DEC"],
+ starcat[hdu_no].data["E1_STAR_HSM"],
+ starcat[hdu_no].data["E2_STAR_HSM"],
+ starcat[hdu_no].data["SIGMA_STAR_HSM"] ** 2,
+ starcat[hdu_no].data["E1_PSF_HSM"],
+ starcat[hdu_no].data["E2_PSF_HSM"],
+ starcat[hdu_no].data["SIGMA_PSF_HSM"] ** 2,
+ ],
+ names=[
+ "w",
+ "ra",
+ "dec",
+ "g1",
+ "g2",
+ "sigma",
+ "psf_g1",
+ "psf_g2",
+ "psf_sigma",
+ ],
+ )
# TreeCorr config:
TreeCorrConfig = {
- 'ra_units': 'degrees',
- 'dec_units': 'degrees',
- 'max_sep': 3e2,
- 'min_sep': 5e-1,
- 'sep_units': 'arcmin',
- 'nbins': 32
+ "ra_units": "degrees",
+ "dec_units": "degrees",
+ "max_sep": 3e2,
+ "min_sep": 5e-1,
+ "sep_units": "arcmin",
+ "nbins": 32,
}
# Ininitialize all 5 rho stats
- if rho_def == 'HSC':
+ if rho_def == "HSC":
rho_stats_fun = [
- stile.CorrelationFunctionSysTest(f'Rho{j}') for j in range(1, 6)
+ stile.CorrelationFunctionSysTest(f"Rho{j}") for j in range(1, 6)
]
- elif rho_def == 'DES':
+ elif rho_def == "DES":
rho_stats_fun = [
Rho1SysTest(),
DESRho2SysTest(),
@@ -1550,36 +1551,79 @@ def rho_stats(
DESRho4SysTest(),
DESRho5SysTest(),
]
+ elif rho_def == "UNIONS":
+ rho_stat_handler = RhoStat(
+ output=output_path,
+ treecorr_config=TreeCorrConfig,
+ verbose=False,
+ )
+
+ # Set parameters
+ params = get_params_rho()
+ rho_stat_handler.catalogs.set_params(params, output_path)
+
+ # Build catalogues
+ mask = True
+ square_size = True
+ ver = "id"
+ out_base = f"rho_stats_{ver}.fits"
+ # TODO: deal with flags
+ rho_stat_handler.build_cat_to_compute_rho(
+ starcat_path,
+ catalog_id=ver,
+ square_size=square_size,
+ mask=mask,
+ hdu=hdu_no,
+ )
+
+ # Compute and save rho stats
+ def only_p(corrs):
+ return np.array([corr.xip for corr in corrs]).flatten()
+
+ rho_stat_handler.compute_rho_stats(
+ ver, out_base, save_cov=True, func=only_p, var_method="bootstrap"
+ )
+
+ rho_stat_handler.plot_rho_stats(
+ [out_base],
+ ["b"],
+ [ver],
+ abs=False,
+ savefig="rho_stats.png",
+ legend="outside",
+ )
+
+ if rho_def == "UNIONS":
+ return
for rho in rho_stats_fun:
print_fun(rho.required_quantities)
# Compute them!
- print_fun(' > Computing rho statistics...')
+ print_fun(" > Computing rho statistics...")
start = time.time()
rho_results = [
- rho_stat(stilecat, config=TreeCorrConfig)
- for rho_stat in rho_stats_fun
+ rho_stat(stilecat, config=TreeCorrConfig) for rho_stat in rho_stats_fun
]
- print_fun(f' > Done in {time.time() - start}s.')
- np.save(output_path + 'rho_stat_results.npy', np.array(rho_results))
+ print_fun(f" > Done in {time.time() - start}s.")
+ np.save(output_path + "rho_stat_results.npy", np.array(rho_results))
# Plots
ylims = [ylim_l, ylim_r, ylim_l, ylim_l, ylim_r]
- colors = ['blue', 'red', 'green', 'orange', 'cyan']
- markers = ['o', 'd', 'v', '^', 's']
+ colors = ["blue", "red", "green", "orange", "cyan"]
+ markers = ["o", "d", "v", "^", "s"]
- xlabel = r'$\theta$ [arcmin]'
- ylabel = r'$\rho$-statistics'
+ xlabel = r"$\theta$ [arcmin]"
+ ylabel = r"$\rho$-statistics"
capsize = 3
alpha = 0.7
for j, rhores in enumerate(rho_results):
neg_dash(
- rhores['meanr'],
- rhores['xip'],
- rhores['sigma_xip'],
- f'{output_path}/rho_{j+1}.png',
+ rhores["meanr"],
+ rhores["xip"],
+ rhores["sigma_xip"],
+ f"{output_path}/rho_{j+1}.png",
semilogx=True,
semilogy=True,
color=colors[j],
@@ -1588,15 +1632,15 @@ def rho_stats(
alpha=alpha,
ylim=ylims[j],
xlabel=xlabel,
- ylabel=ylabel
+ ylabel=ylabel,
)
for j, rhores in enumerate(rho_results):
if j in [0, 2, 3]:
neg_dash(
- rhores['meanr'],
- rhores['xip'],
- rhores['sigma_xip'],
+ rhores["meanr"],
+ rhores["xip"],
+ rhores["sigma_xip"],
semilogx=True,
semilogy=True,
rho_nb=j + 1,
@@ -1606,18 +1650,18 @@ def rho_stats(
alpha=alpha,
ylim=ylims[j],
xlabel=xlabel,
- ylabel=ylabel
+ ylabel=ylabel,
)
plt.legend()
- plt.savefig(f'{output_path}/lefthand_rhos.pdf')
+ plt.savefig(f"{output_path}/lefthand_rhos.pdf")
plt.close()
for j, rhores in enumerate(rho_results):
if j in [1, 4]:
neg_dash(
- rhores['meanr'],
- rhores['xip'],
- rhores['sigma_xip'],
+ rhores["meanr"],
+ rhores["xip"],
+ rhores["sigma_xip"],
semilogx=True,
semilogy=True,
rho_nb=j + 1,
@@ -1627,10 +1671,10 @@ def rho_stats(
alpha=alpha,
ylim=ylims[j],
xlabel=xlabel,
- ylabel=ylabel
+ ylabel=ylabel,
)
plt.legend()
- plt.savefig(f'{output_path}/righthand_rhos.pdf')
+ plt.savefig(f"{output_path}/righthand_rhos.pdf")
plt.close()
starcat.close()
diff --git a/shapepipe/modules/mccd_package/shapepipe_auxiliary_mccd.py b/shapepipe/modules/mccd_package/shapepipe_auxiliary_mccd.py
index 1877719fa..44b7cf55b 100644
--- a/shapepipe/modules/mccd_package/shapepipe_auxiliary_mccd.py
+++ b/shapepipe/modules/mccd_package/shapepipe_auxiliary_mccd.py
@@ -17,7 +17,7 @@
from shapepipe.pipeline import file_io
-NOT_ENOUGH_STARS = 'Not enough stars to train the model.'
+NOT_ENOUGH_STARS = "Not enough stars to train the model."
def mccd_preprocessing_pipeline(
@@ -25,14 +25,14 @@ def mccd_preprocessing_pipeline(
output_path,
input_file_position=0,
min_n_stars=20,
- separator='-',
+ separator="-",
CCD_id_filter_list=None,
- outlier_std_max=100.,
+ outlier_std_max=100.0,
save_masks=True,
- save_name='train_star_selection',
- save_extension='.fits',
+ save_name="train_star_selection",
+ save_extension=".fits",
verbose=True,
- print_fun=None
+ print_fun=None,
):
r"""Preprocess Input Catalogue.
@@ -86,38 +86,55 @@ def mccd_preprocessing_pipeline(
if verbose:
if print_fun is None:
+
def print_fun(x):
print(x)
+
else:
+
def print_fun(x):
pass
- print_fun('Processing dataset..')
+ print_fun("Processing dataset..")
mccd_inputs = mccd.mccd_utils.MccdInputs(separator=separator)
catalog_ids = mccd_inputs.proprocess_pipeline_data(
- input_file_list,
- element_position=input_file_position
+ input_file_list, element_position=input_file_position
)
# Loop over the catalogs
for it in range(catalog_ids.shape[0]):
# For each observation position
catalog_id = catalog_ids[it]
- star_list, pos_list, mask_list, ccd_list, SNR_list, RA_list, \
- DEC_list = mccd_inputs.get_inputs(catalog_id)
-
- star_list, pos_list, mask_list, ccd_list, SNR_list, RA_list, \
- DEC_list, _ = mccd_inputs.outlier_rejection(
- star_list,
- pos_list,
- mask_list,
- ccd_list,
- SNR_list,
- RA_list,
- DEC_list,
- shape_std_max=outlier_std_max,
- print_fun=print_fun
- )
+ (
+ star_list,
+ pos_list,
+ mask_list,
+ ccd_list,
+ SNR_list,
+ RA_list,
+ DEC_list,
+ ) = mccd_inputs.get_inputs(catalog_id)
+
+ (
+ star_list,
+ pos_list,
+ mask_list,
+ ccd_list,
+ SNR_list,
+ RA_list,
+ DEC_list,
+ _,
+ ) = mccd_inputs.outlier_rejection(
+ star_list,
+ pos_list,
+ mask_list,
+ ccd_list,
+ SNR_list,
+ RA_list,
+ DEC_list,
+ shape_std_max=outlier_std_max,
+ print_fun=print_fun,
+ )
mccd_star_list = []
mccd_pos_list = []
@@ -163,13 +180,15 @@ def print_fun(x):
# Concatenate, as fits can't handle list of numpy arrays and
# turn into reg format
mccd_stars = mccd.utils.reg_format(
- np.concatenate(mccd_star_list, axis=2))
+ np.concatenate(mccd_star_list, axis=2)
+ )
mccd_poss = np.concatenate(mccd_pos_list, axis=0)
mccd_ccds = np.concatenate(mccd_ccd_list, axis=0)
if save_masks is True:
mccd_masks = mccd.utils.reg_format(
- np.concatenate(mccd_mask_list, axis=2))
+ np.concatenate(mccd_mask_list, axis=2)
+ )
else:
# Send an array of False (None cannot be used in .fits)
mccd_masks = np.zeros((mccd_poss.shape[0]), dtype=bool)
@@ -191,20 +210,25 @@ def print_fun(x):
# Save the fits file
train_dic = {
- 'VIGNET_LIST': mccd_stars,
- 'GLOB_POSITION_IMG_LIST': mccd_poss,
- 'MASK_LIST': mccd_masks,
- 'CCD_ID_LIST': mccd_ccds,
- 'SNR_WIN_LIST': mccd_SNRs,
- 'RA_LIST': mccd_RAs,
- 'DEC_LIST': mccd_DECs
+ "VIGNET_LIST": mccd_stars,
+ "GLOB_POSITION_IMG_LIST": mccd_poss,
+ "MASK_LIST": mccd_masks,
+ "CCD_ID_LIST": mccd_ccds,
+ "SNR_WIN_LIST": mccd_SNRs,
+ "RA_LIST": mccd_RAs,
+ "DEC_LIST": mccd_DECs,
}
- saving_path = output_path + save_name + separator \
- + catalog_id + save_extension
+ saving_path = (
+ output_path
+ + save_name
+ + separator
+ + catalog_id
+ + save_extension
+ )
mccd.mccd_utils.save_to_fits(train_dic, saving_path)
- print_fun('Finished the training dataset processing.')
+ print_fun("Finished the training dataset processing.")
print_fun(f"Total stars processed = {mccd_star_nb:d}")
return mccd_inputs
@@ -216,8 +240,8 @@ def mccd_fit_pipeline(
mccd_parser,
output_dir,
verbose,
- saving_name='fitted_model',
- w_log=None
+ saving_name="fitted_model",
+ w_log=None,
):
r"""Fit MCCD Model.
@@ -244,20 +268,20 @@ def mccd_fit_pipeline(
# Extract the MCCD parameters from the parser
mccd_inst_kw = mccd_parser.get_instance_kw()
mccd_fit_kw = mccd_parser.get_fit_kw()
- use_SNR_weight = mccd_parser.get_extra_kw('use_SNR_weight')
+ use_SNR_weight = mccd_parser.get_extra_kw("use_SNR_weight")
# Print the model configuration so that it is saved in log files
- w_log.info('MCCD configuration parameters:')
- w_log.info('[INPUTS]')
- inputs_dict_str = pprint.pformat({'use_SNR_weight': use_SNR_weight})
+ w_log.info("MCCD configuration parameters:")
+ w_log.info("[INPUTS]")
+ inputs_dict_str = pprint.pformat({"use_SNR_weight": use_SNR_weight})
w_log.info(inputs_dict_str)
- w_log.info('[INSTANCE]')
+ w_log.info("[INSTANCE]")
inst_dict_str = pprint.pformat(mccd_inst_kw)
w_log.info(inst_dict_str)
- w_log.info('[FIT]')
+ w_log.info("[FIT]")
fit_dict_str = pprint.pformat(mccd_fit_kw)
w_log.info(fit_dict_str)
- w_log.info('End of MCCD configuration parameters.')
+ w_log.info("End of MCCD configuration parameters.")
# Open fits file
starcat = fits.open(trainstar_path, memmap=False)
@@ -271,7 +295,7 @@ def mccd_fit_pipeline(
sex_thresh=-1e5,
use_SNR_weight=use_SNR_weight,
verbose=verbose,
- saving_name=saving_name
+ saving_name=saving_name,
)
starcat.close()
@@ -284,7 +308,7 @@ def mccd_validation_pipeline(
output_dir,
file_number_string,
w_log,
- val_saving_name
+ val_saving_name,
):
r"""Validate MCCD Pipeline.
@@ -311,7 +335,7 @@ def mccd_validation_pipeline(
w_log.info(f"Validating catalogue {file_number_string}..")
# Get MCCD parameters
- save_extension = '.fits'
+ save_extension = ".fits"
mccd_val_kw = mccd_parser.get_val_kw()
testcat = fits.open(teststar_path, memmap=False)
@@ -322,13 +346,14 @@ def mccd_validation_pipeline(
mccd_model_path=mccd_model_path,
testcat=testcat[1],
**mccd_val_kw,
- sex_thresh=-1e5
+ sex_thresh=-1e5,
)
testcat.close()
- val_saving_path = output_dir + val_saving_name + \
- file_number_string + save_extension
+ val_saving_path = (
+ output_dir + val_saving_name + file_number_string + save_extension
+ )
# Save validation dictionary to fits file
mccd.mccd_utils.save_to_fits(val_dict, val_saving_path)
@@ -343,12 +368,7 @@ def mccd_validation_pipeline(
def mccd_interpolation_pipeline(
- mccd_model_path,
- galcat_path,
- pos_params,
- ccd_id,
- saving_path,
- get_shapes
+ mccd_model_path, galcat_path, pos_params, ccd_id, saving_path, get_shapes
):
r"""Interpolate the MCCD Model.
@@ -395,22 +415,24 @@ def mccd_interpolation_pipeline(
for psf in interp_PSFs
]
- PSF_shapes = np.array([
+ PSF_shapes = np.array(
[
- moms.observed_shape.g1,
- moms.observed_shape.g2,
- moms.moments_sigma,
- int(bool(moms.error_message))
+ [
+ moms.observed_shape.g1,
+ moms.observed_shape.g2,
+ moms.moments_sigma,
+ int(bool(moms.error_message)),
+ ]
+ for moms in PSF_moms
]
- for moms in PSF_moms
- ])
+ )
shapepipe_write_output(
saving_path=saving_path,
example_fits_path=galcat_path,
get_shapes=get_shapes,
interp_PSFs=interp_PSFs,
- PSF_shapes=PSF_shapes
+ PSF_shapes=PSF_shapes,
)
return None
@@ -419,11 +441,7 @@ def mccd_interpolation_pipeline(
def shapepipe_write_output(
- saving_path,
- example_fits_path,
- get_shapes,
- interp_PSFs,
- PSF_shapes=None
+ saving_path, example_fits_path, get_shapes, interp_PSFs, PSF_shapes=None
):
r"""Write ShapePipe Output.
@@ -447,18 +465,18 @@ def shapepipe_write_output(
output = file_io.FITSCatalogue(
saving_path,
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
- SEx_catalogue=True
+ SEx_catalogue=True,
)
if get_shapes:
data = {
- 'VIGNET': interp_PSFs,
- 'E1_PSF_HSM': PSF_shapes[:, 0],
- 'E2_PSF_HSM': PSF_shapes[:, 1],
- 'SIGMA_PSF_HSM': PSF_shapes[:, 2],
- 'FLAG_PSF_HSM': PSF_shapes[:, 3].astype(int)
+ "VIGNET": interp_PSFs,
+ "E1_PSF_HSM": PSF_shapes[:, 0],
+ "E2_PSF_HSM": PSF_shapes[:, 1],
+ "SIGMA_PSF_HSM": PSF_shapes[:, 2],
+ "FLAG_PSF_HSM": PSF_shapes[:, 3].astype(int),
}
else:
- data = {'VIGNET': interp_PSFs}
+ data = {"VIGNET": interp_PSFs}
output.save_as_fits(data, sex_cat_path=example_fits_path)
diff --git a/shapepipe/modules/mccd_plots_runner.py b/shapepipe/modules/mccd_plots_runner.py
index 1c80505b7..9c23537d3 100644
--- a/shapepipe/modules/mccd_plots_runner.py
+++ b/shapepipe/modules/mccd_plots_runner.py
@@ -19,6 +19,7 @@
import stile
import stile.stile_utils
from stile.sys_tests import BaseCorrelationFunctionSysTest
+
has_stile = True
except ImportError:
@@ -27,6 +28,7 @@
try:
import treecorr
from treecorr.corr2 import corr2_valid_params
+
has_treecorr = True
except ImportError:
@@ -37,7 +39,7 @@
import matplotlib.pyplot as plt
# Define the backend for matplotlib
- mpl.use('agg')
+ mpl.use("agg")
has_mpl = True
except ImportError:
@@ -45,13 +47,13 @@
@module_runner(
- version='1.1',
- input_module=['merge_starcat_runner'],
- file_pattern=['full_starcat'],
- file_ext=['.fits'],
- numbering_scheme='-0000000',
- depends=['numpy', 'mccd', 'astropy', 'matplotlib', 'stile', 'treecorr'],
- run_method='serial',
+ version="1.1",
+ input_module=["merge_starcat_runner"],
+ file_pattern=["full_starcat"],
+ file_ext=[".fits"],
+ numbering_scheme="-0000000",
+ depends=["numpy", "mccd", "astropy", "matplotlib", "stile", "treecorr"],
+ run_method="serial",
)
def mccd_plots_runner(
input_file_list,
@@ -63,63 +65,63 @@ def mccd_plots_runner(
):
"""Define The MCCD Plots Runner."""
# Input parameters
- if config.has_option(module_config_sec, 'HDU'):
- hdu_no = config.getint(module_config_sec, 'HDU')
+ if config.has_option(module_config_sec, "HDU"):
+ hdu_no = config.getint(module_config_sec, "HDU")
else:
hdu_no = 2
# Get parameters for meanshapes plots
- psf_model_type = config.get(module_config_sec, 'PSF')
+ psf_model_type = config.get(module_config_sec, "PSF")
- if config.has_option(module_config_sec, 'MAX_E'):
+ if config.has_option(module_config_sec, "MAX_E"):
max_e = config.getfloat(module_config_sec, "MAX_E")
else:
max_e = None
- if config.has_option(module_config_sec, 'MAX_DE'):
+ if config.has_option(module_config_sec, "MAX_DE"):
max_de = config.getfloat(module_config_sec, "MAX_DE")
else:
max_de = None
- if config.has_option(module_config_sec, 'MIN_R2'):
+ if config.has_option(module_config_sec, "MIN_R2"):
min_r2 = config.getfloat(module_config_sec, "MIN_R2")
else:
min_r2 = None
- if config.has_option(module_config_sec, 'MAX_R2'):
+ if config.has_option(module_config_sec, "MAX_R2"):
max_r2 = config.getfloat(module_config_sec, "MAX_R2")
else:
max_r2 = None
- if config.has_option(module_config_sec, 'MAX_DR2'):
+ if config.has_option(module_config_sec, "MAX_DR2"):
max_dr2 = config.getfloat(module_config_sec, "MAX_DR2")
else:
max_dr2 = None
- x_nb_bins = config.getint(module_config_sec, 'X_GRID')
- y_nb_bins = config.getint(module_config_sec, 'Y_GRID')
- remove_outliers = config.getboolean(module_config_sec, 'REMOVE_OUTLIERS')
- plot_meanshapes = config.getboolean(module_config_sec, 'PLOT_MEANSHAPES')
- plot_histograms = config.getboolean(module_config_sec, 'PLOT_HISTOGRAMS')
+ x_nb_bins = config.getint(module_config_sec, "X_GRID")
+ y_nb_bins = config.getint(module_config_sec, "Y_GRID")
+ remove_outliers = config.getboolean(module_config_sec, "REMOVE_OUTLIERS")
+ plot_meanshapes = config.getboolean(module_config_sec, "PLOT_MEANSHAPES")
+ plot_histograms = config.getboolean(module_config_sec, "PLOT_HISTOGRAMS")
# Get parameters for rho stats plots
- plot_rho_stats = config.getboolean(module_config_sec, 'PLOT_RHO_STATS')
- rho_stat_plot_style = config.get(module_config_sec, 'RHO_STATS_STYLE')
+ plot_rho_stats = config.getboolean(module_config_sec, "PLOT_RHO_STATS")
+ rho_stat_plot_style = config.get(module_config_sec, "RHO_STATS_STYLE")
- if config.has_option(module_config_sec, 'RHO_STATS_YLIM_L'):
- str_list = config.getlist(module_config_sec, 'RHO_STATS_YLIM_L')
+ if config.has_option(module_config_sec, "RHO_STATS_YLIM_L"):
+ str_list = config.getlist(module_config_sec, "RHO_STATS_YLIM_L")
ylim_l = [float(s) for s in str_list]
else:
ylim_l = None
- if config.has_option(module_config_sec, 'RHO_STATS_YLIM_R'):
- str_list = config.getlist(module_config_sec, 'RHO_STATS_YLIM_R')
+ if config.has_option(module_config_sec, "RHO_STATS_YLIM_R"):
+ str_list = config.getlist(module_config_sec, "RHO_STATS_YLIM_R")
ylim_r = [float(s) for s in str_list]
else:
ylim_r = None
nb_pixel = x_nb_bins, y_nb_bins
starcat_path = input_file_list[0][0]
- output_path = run_dirs['output'] + '/'
+ output_path = run_dirs["output"] + "/"
if plot_meanshapes or plot_histograms:
if has_mpl:
@@ -141,10 +143,10 @@ def mccd_plots_runner(
)
else:
msg = (
- '[!] In order to plot the Meanshapes the package '
- + '_matplotlib_ has to be correctly imported. This was not'
- + ' the case, so the task is aborted. For the next time make'
- + ' sure the package is installed.'
+ "[!] In order to plot the Meanshapes the package "
+ + "_matplotlib_ has to be correctly imported. This was not"
+ + " the case, so the task is aborted. For the next time make"
+ + " sure the package is installed."
)
warnings.warn(msg)
w_log.info(msg)
@@ -152,18 +154,16 @@ def mccd_plots_runner(
if plot_rho_stats:
if has_stile is False or has_treecorr is False:
msg = (
- '[!] In order to calculate the Rho stats the packages '
- + '_stile_ and _treecorr_ have to be correctly imported.'
- + ' This was not the case, so the rho stat calculation is'
- + 'aborted. For the next time make sure both of the'
- + 'packages are installed.'
+ "[!] To calculate the rho stats the packages "
+ + "stile and treecorr are required. However, "
+ + f" treecorr: {has_treecorr}, stile: {has_stile}."
)
warnings.warn(msg)
w_log.info(msg)
- elif rho_stat_plot_style != 'HSC' and rho_stat_plot_style != 'DES':
+ elif rho_stat_plot_style not in ("HSC", "DES", "UNIONS"):
msg = (
- 'The rho stat definition should be HSC or DES. An unknown'
- + ' definition was used. Rho stat calculation aborted.'
+ f"Invalid flag RHO_STAT_STYLE={rho_stat_plot_style}, allowed"
+ + " are 'HSC', 'DES', 'UNIONS'."
)
warnings.warn(msg)
w_log.info(msg)
diff --git a/shapepipe/modules/mccd_preprocessing_runner.py b/shapepipe/modules/mccd_preprocessing_runner.py
index 7a5ac53cb..f15287cf5 100644
--- a/shapepipe/modules/mccd_preprocessing_runner.py
+++ b/shapepipe/modules/mccd_preprocessing_runner.py
@@ -6,6 +6,7 @@
:Author: Tobias Liaudat
"""
+
import mccd
from shapepipe.modules.mccd_package import shapepipe_auxiliary_mccd as aux_mccd
@@ -13,12 +14,12 @@
@module_runner(
- version='1.1',
- input_module=['setools_runner'],
- file_pattern=['star_split_ratio_80', 'star_split_ratio_20'],
- file_ext=['.fits', '.fits'],
- depends=['numpy', 'mccd', 'galsim', 'astropy'],
- run_method='serial',
+ version="1.1",
+ input_module=["setools_runner"],
+ file_pattern=["star_split_ratio_80", "star_split_ratio_20"],
+ file_ext=[".fits", ".fits"],
+ depends=["numpy", "mccd", "galsim", "astropy"],
+ run_method="serial",
)
def mccd_preprocessing_runner(
input_file_list,
@@ -30,9 +31,9 @@ def mccd_preprocessing_runner(
):
"""Define The MCCD Pre-processing Runner."""
# Recover the MCCD config file and its params
- config_file_path = config.getexpanded(module_config_sec, 'CONFIG_PATH')
- mccd_mode = config.get(module_config_sec, 'MODE')
- verbose = config.getboolean(module_config_sec, 'VERBOSE')
+ config_file_path = config.getexpanded(module_config_sec, "CONFIG_PATH")
+ mccd_mode = config.get(module_config_sec, "MODE")
+ verbose = config.getboolean(module_config_sec, "VERBOSE")
# Parse MCCD config file
mccd_parser = mccd.auxiliary_fun.MCCDParamsParser(config_file_path)
@@ -40,28 +41,28 @@ def mccd_preprocessing_runner(
input_dict = mccd_parser.get_inputs_kw()
# Extract useful parameters
- separator = input_dict['separator']
- min_n_stars = input_dict['min_n_stars']
- outlier_std_max = input_dict['outlier_std_max']
+ separator = input_dict["separator"]
+ min_n_stars = input_dict["min_n_stars"]
+ outlier_std_max = input_dict["outlier_std_max"]
- if mccd_mode == 'FIT':
+ if mccd_mode == "FIT":
input_file_pos_list = [0]
- save_name_list = ['train_star_selection']
+ save_name_list = ["train_star_selection"]
min_n_stars_list = [min_n_stars]
- elif mccd_mode == 'FIT_VALIDATION':
+ elif mccd_mode == "FIT_VALIDATION":
if len(input_file_list[0]) == 1:
input_file_pos_list = [0]
- save_name_list = ['train_star_selection']
+ save_name_list = ["train_star_selection"]
min_n_stars_list = [min_n_stars]
else:
input_file_pos_list = [0, 1]
- save_name_list = ['train_star_selection', 'test_star_selection']
+ save_name_list = ["train_star_selection", "test_star_selection"]
min_n_stars_list = [min_n_stars, 1]
- elif mccd_mode == 'VALIDATION':
+ elif mccd_mode == "VALIDATION":
input_file_pos_list = [0]
- save_name_list = ['test_star_selection']
+ save_name_list = ["test_star_selection"]
min_n_stars_list = [1]
else:
@@ -72,7 +73,7 @@ def mccd_preprocessing_runner(
# Use the outfile from the pipeline and ignore the output directory from
# the MCCD config file
# Output paths for both newly generates datasets
- output_mccd_path = run_dirs['output'] + '/'
+ output_mccd_path = run_dirs["output"] + "/"
[
aux_mccd.mccd_preprocessing_pipeline(
@@ -85,12 +86,13 @@ def mccd_preprocessing_runner(
outlier_std_max=outlier_std_max,
save_masks=False,
save_name=_save_name,
- save_extension='.fits',
+ save_extension=".fits",
verbose=verbose,
print_fun=w_log.info,
)
- for _input_pos, _save_name, _min_stars in
- zip(input_file_pos_list, save_name_list, min_n_stars_list)
+ for _input_pos, _save_name, _min_stars in zip(
+ input_file_pos_list, save_name_list, min_n_stars_list
+ )
]
# No return objects
diff --git a/shapepipe/modules/mccd_val_runner.py b/shapepipe/modules/mccd_val_runner.py
index 73f1bcd07..dc0811fc1 100644
--- a/shapepipe/modules/mccd_val_runner.py
+++ b/shapepipe/modules/mccd_val_runner.py
@@ -13,13 +13,13 @@
@module_runner(
- version='1.1',
- input_module=['mccd_preprocessing_runner'],
- file_pattern=['fitted_model', 'test_star_selection'],
- file_ext=['.npy', '.fits'],
- numbering_scheme='-0000000',
- depends=['numpy', 'mccd', 'galsim'],
- run_method='parallel',
+ version="1.1",
+ input_module=["mccd_preprocessing_runner"],
+ file_pattern=["fitted_model", "test_star_selection"],
+ file_ext=[".npy", ".fits"],
+ numbering_scheme="-0000000",
+ depends=["numpy", "mccd", "galsim"],
+ run_method="parallel",
)
def mccd_val_runner(
input_file_list,
@@ -31,24 +31,24 @@ def mccd_val_runner(
):
"""Define The MCCD Validation Runner."""
# Recover the MCCD config file and its params
- config_file_path = config.getexpanded(module_config_sec, 'CONFIG_PATH')
- mccd_mode = config.get(module_config_sec, 'MODE')
- verbose = config.getboolean(module_config_sec, 'VERBOSE')
+ config_file_path = config.getexpanded(module_config_sec, "CONFIG_PATH")
+ mccd_mode = config.get(module_config_sec, "MODE")
+ verbose = config.getboolean(module_config_sec, "VERBOSE")
# Parse MCCD config file
mccd_parser = mccd.auxiliary_fun.MCCDParamsParser(config_file_path)
mccd_parser.parse_document()
# Prepare inputs to run the main fit function
- output_dir = run_dirs['output'] + '/'
- val_saving_name = 'validation_psf'
+ output_dir = run_dirs["output"] + "/"
+ val_saving_name = "validation_psf"
# Extract the MCCD model path
mccd_model_path = input_file_list[0]
# Validation stars are in the second position of the list
teststar_path = input_file_list[1]
- if mccd_mode == 'VALIDATION':
+ if mccd_mode == "VALIDATION":
aux_mccd.mccd_validation_pipeline(
teststar_path=teststar_path,
@@ -62,7 +62,7 @@ def mccd_val_runner(
else:
raise ValueError(
- 'The mccd_val_runner should only be called when the MODE is '
+ "The mccd_val_runner should only be called when the MODE is "
+ '"VALIDATION".'
)
diff --git a/shapepipe/modules/merge_headers_package/__init__.py b/shapepipe/modules/merge_headers_package/__init__.py
index 48a972c14..ed8416790 100644
--- a/shapepipe/modules/merge_headers_package/__init__.py
+++ b/shapepipe/modules/merge_headers_package/__init__.py
@@ -25,4 +25,4 @@
"""
-__all__ = ['merge_headers']
+__all__ = ["merge_headers"]
diff --git a/shapepipe/modules/merge_headers_package/merge_headers.py b/shapepipe/modules/merge_headers_package/merge_headers.py
index 95d3e9acc..5c0a2213e 100644
--- a/shapepipe/modules/merge_headers_package/merge_headers.py
+++ b/shapepipe/modules/merge_headers_package/merge_headers.py
@@ -36,14 +36,14 @@ def merge_headers(input_file_list, output_dir):
"""
if not isinstance(output_dir, str):
raise TypeError(
- 'Output directory for merge headers must be a string '
- + f'not {type(output_dir)}.'
+ "Output directory for merge headers must be a string "
+ + f"not {type(output_dir)}."
)
# Open SqliteDict file
- final_file = SqliteDict(f'{output_dir}/log_exp_headers.sqlite')
+ final_file = SqliteDict(f"{output_dir}/log_exp_headers.sqlite")
# Set matching pattern
- pattern = 'headers-'
+ pattern = "headers-"
for file_path in input_file_list:
# Extract file path
diff --git a/shapepipe/modules/merge_headers_runner.py b/shapepipe/modules/merge_headers_runner.py
index 9e692bba7..bfedc8a89 100644
--- a/shapepipe/modules/merge_headers_runner.py
+++ b/shapepipe/modules/merge_headers_runner.py
@@ -11,12 +11,12 @@
@module_runner(
- input_module='split_exp_runner',
- version='1.1',
- file_pattern=['headers'],
- file_ext=['.npy'],
- depends=['numpy', 'sqlitedict'],
- run_method='serial',
+ input_module="split_exp_runner",
+ version="1.1",
+ file_pattern=["headers"],
+ file_ext=[".npy"],
+ depends=["numpy", "sqlitedict"],
+ run_method="serial",
)
def merge_headers_runner(
input_file_list,
@@ -28,15 +28,17 @@ def merge_headers_runner(
):
"""Define The Merge Headers Runner."""
# Set output directory
- output_dir = run_dirs['output']
- if config.has_option(module_config_sec, 'OUTPUT_PATH'):
- output_dir = config.getexpanded(module_config_sec, 'OUTPUT_PATH')
+ output_dir = run_dirs["output"]
+ if config.has_option(module_config_sec, "OUTPUT_PATH"):
+ output_dir = config.getexpanded(module_config_sec, "OUTPUT_PATH")
# Log output directory
- w_log.info(f'output_dir = {output_dir}')
+ w_log.info(f"output_dir = {output_dir}")
# Merge header files
merge_headers(input_file_list, output_dir)
+ w_log.info(f"Merged {len(input_file_list)} input file headers")
+
# No return objects
return None, None
diff --git a/shapepipe/modules/merge_sep_cats_package/__init__.py b/shapepipe/modules/merge_sep_cats_package/__init__.py
index d99553bf4..333e3d24c 100644
--- a/shapepipe/modules/merge_sep_cats_package/__init__.py
+++ b/shapepipe/modules/merge_sep_cats_package/__init__.py
@@ -34,4 +34,4 @@
"""
-__all__ = ['merge_sep_cats.py']
+__all__ = ["merge_sep_cats.py"]
diff --git a/shapepipe/modules/merge_sep_cats_package/merge_sep_cats.py b/shapepipe/modules/merge_sep_cats_package/merge_sep_cats.py
index 85f7e194f..be7477c81 100644
--- a/shapepipe/modules/merge_sep_cats_package/merge_sep_cats.py
+++ b/shapepipe/modules/merge_sep_cats_package/merge_sep_cats.py
@@ -51,7 +51,7 @@ def __init__(
output_dir,
n_split_max,
warning,
- w_log
+ w_log,
):
self._input_file_list = input_file_list
@@ -79,21 +79,47 @@ def process(self):
input_path_n = []
input_path_n.append(input_file)
for n in range(2, self._n_split_max + 1):
- res = re.sub('1', str(n), input_file, 1)
+ res = re.sub("1", str(n), input_file, 1)
input_path_n.append(res)
# Open first catalogue, read number of extensions and columns
cat0 = file_io.FITSCatalogue(input_file, SEx_catalogue=True)
cat0.open()
list_ext_name = cat0.get_ext_name()
+
+ # Inupt ngmix files sometimes have not all sheared versions
+ # (HDUs 1 - 5 = 1M, 1P, 2M, 2P, NOSHEAR) due to IO errors
+ if len(list_ext_name) < 6:
+ raise IndexError(
+ f"Input ngmix catalogue {input_file} has only"
+ + f" {len(list_ext_name)} HDUs, required are 6"
+ )
+
list_col_name = cat0.get_col_names()
+
+ # Some older input ngmix catalogues have multiple of 5 HDUs
+ # if reprocessed and not deleted but appended.
+ # The following log message should be replaced by raising
+ # and error in future
+ if len(list_ext_name) > 6:
+ wmsg = f"Cropping input HDUs from {len(list_ext_name)} to 5"
+ self._w_log.info(wmsg)
+ list_ext_name = list_ext_name[:6]
cat0.close()
+ # Check that exactly 6 (1 primary + secondary HDUs) exist
+ if len(list_ext_name) != 6:
+ msg = f"Number of HDUs is {len(list_ext_name)}, expected 6"
+ #raise ValueError(msg)
+ print(f"warning: {msg}; setting to 6")
+ list_ext_name = list_ext_name[:6]
+ list_col_name = list_col_name[:6]
+
# Create empty dictionary
# data dimension = n_extension x n_column x n_obj
data = {}
for hdu_ind, ext_name in enumerate(list_ext_name):
- if ext_name == 'PRIMARY':
+ if ext_name == "PRIMARY":
continue
data[ext_name] = {}
for col_name in list_col_name:
@@ -106,38 +132,47 @@ def process(self):
cat = file_io.FITSCatalogue(cat_path, SEx_catalogue=True)
cat.open()
+ list_ext_name_n = cat.get_ext_name()
+ if len(list_ext_name_n) < 6:
+ raise IndexError(
+ f"Input ngmix catalogue {cat_path} has only"
+ + f" {len(list_ext_name_n)} HDUs, required are 6"
+ )
for hdu_ind, ext_name in enumerate(list_ext_name):
- if ext_name == 'PRIMARY':
+ if ext_name == "PRIMARY":
continue
+ if not ext_name in data:
+ raise IndexError(
+ f"Extension {ext_name} not found in file "
+ + f"{cat_path}"
+ )
for col_name in list_col_name:
+ # print("MKDEBUG ", cat_path, ext_name, col_name)
data[ext_name][col_name] += list(
cat.get_data(hdu_ind)[col_name]
)
cat.close()
else:
- msg = f'Input catalogue \'{cat_path}\' not found'
+ msg = f"Input catalogue '{cat_path}' not found"
warnings.warn(msg)
- wmsg = f'Warning: {msg}'
+ wmsg = f"Warning: {msg}"
self._w_log.info(wmsg)
print(wmsg)
# Save combined catalogue
output_name = (
- f'{self._output_dir}/{self._file_pattern[idx]}'
- + f'{self._file_number_string}{self._file_ext[idx]}'
+ f"{self._output_dir}/{self._file_pattern[idx]}"
+ + f"{self._file_number_string}{self._file_ext[idx]}"
)
output = file_io.FITSCatalogue(
- output_name,
- open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
+ output_name, open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
)
for hdu_ind, ext_name in enumerate(list_ext_name):
- if ext_name == 'PRIMARY':
+ if ext_name == "PRIMARY":
continue
output.save_as_fits(
- data[ext_name],
- names=list_col_name,
- ext_name=ext_name
+ data[ext_name], names=list_col_name, ext_name=ext_name
)
return None, None
diff --git a/shapepipe/modules/merge_sep_cats_runner.py b/shapepipe/modules/merge_sep_cats_runner.py
index 5cae71a2a..927c79b76 100644
--- a/shapepipe/modules/merge_sep_cats_runner.py
+++ b/shapepipe/modules/merge_sep_cats_runner.py
@@ -12,11 +12,12 @@
@module_runner(
- version='1.1',
- input_module='ngmix_runner',
- file_pattern=['ngmix'],
- file_ext=['.fits'],
- depends=['numpy'])
+ version="1.1",
+ input_module="ngmix_runner",
+ file_pattern=["ngmix"],
+ file_ext=[".fits"],
+ depends=["numpy"],
+)
def merge_sep_cats_runner(
input_file_list,
run_dirs,
@@ -27,15 +28,15 @@ def merge_sep_cats_runner(
):
"""Define The Merge SEP Catalogues Runner."""
# Get config entries
- n_split_max = config.getint(module_config_sec, 'N_SPLIT_MAX')
+ n_split_max = config.getint(module_config_sec, "N_SPLIT_MAX")
- file_pattern = config.getlist(module_config_sec, 'FILE_PATTERN')
- file_ext = config.getlist(module_config_sec, 'FILE_EXT')
+ file_pattern = config.getlist(module_config_sec, "FILE_PATTERN")
+ file_ext = config.getlist(module_config_sec, "FILE_EXT")
- if config.has_option(module_config_sec, 'WARNING'):
- warning = config.get(module_config_sec, 'WARNING')
+ if config.has_option(module_config_sec, "WARNING"):
+ warning = config.get(module_config_sec, "WARNING")
else:
- warning = 'error'
+ warning = "error"
# Create merge sep cat class instance
merge_sep_inst = MergeSep(
@@ -43,7 +44,7 @@ def merge_sep_cats_runner(
file_number_string,
file_pattern,
file_ext,
- run_dirs['output'],
+ run_dirs["output"],
n_split_max,
warning,
w_log,
diff --git a/shapepipe/modules/merge_starcat_package/__init__.py b/shapepipe/modules/merge_starcat_package/__init__.py
index c75a9c863..f407ac72c 100644
--- a/shapepipe/modules/merge_starcat_package/__init__.py
+++ b/shapepipe/modules/merge_starcat_package/__init__.py
@@ -21,8 +21,11 @@
===================================
PSF_MODEL : str
- PSF model used; options are ``psfex`` or ``mccd``
+ PSF model used; options are ``psfex`` or ``mccd``, ``setools''
+HDU : int, optional
+ HDU number of input catalogue table, default is ``1`` for ``mccd``
+ and ``2`` for ``psfex`` and ``setools``
"""
-__all__ = ['merge_starcat']
+__all__ = ["merge_starcat"]
diff --git a/shapepipe/modules/merge_starcat_package/merge_starcat.py b/shapepipe/modules/merge_starcat_package/merge_starcat.py
index 924c46aab..67c258f96 100644
--- a/shapepipe/modules/merge_starcat_package/merge_starcat.py
+++ b/shapepipe/modules/merge_starcat_package/merge_starcat.py
@@ -45,7 +45,7 @@ def __init__(
w_log,
stamp_size=51,
rad=10,
- hdu_table=1
+ hdu_table=1,
):
self._input_file_list = input_file_list
@@ -136,9 +136,7 @@ def mean_calc(values, sizes):
Mean
"""
- mean = (
- np.nansum(np.array(values)) / np.nansum(np.array(sizes))
- )
+ mean = np.nansum(np.array(values)) / np.nansum(np.array(sizes))
return mean
@@ -186,7 +184,7 @@ def stats_calculator(val_ref, val_model):
"""
residual = val_ref - val_model
- rmse = np.sqrt(np.mean(residual ** 2))
+ rmse = np.sqrt(np.mean(residual**2))
mean = np.mean(residual)
std_dev = np.std(residual)
@@ -227,22 +225,26 @@ def process(self):
idx = np.arange(0, shap[0])
jdx = np.arange(0, shap[1])
- inside_circle = np.sqrt(
- (idx[np.newaxis, :] - cent[0]) ** 2
- + (jdx[:, np.newaxis] - cent[1]) ** 2
- ) <= self._rad
+ inside_circle = (
+ np.sqrt(
+ (idx[np.newaxis, :] - cent[0]) ** 2
+ + (jdx[:, np.newaxis] - cent[1]) ** 2
+ )
+ <= self._rad
+ )
my_mask[inside_circle] = True
for name in self._input_file_list:
- starcat_j = fits.open(name[0], memmap=False)
-
try:
- stars = np.copy(starcat_j[self._hdu_table].data['VIGNET_LIST'])
+ starcat_j = fits.open(name[0], memmap=False, ignore_missing_simple=True)
except ValueError:
- print(f'Error for file {name[0]}, check FITS file integrity')
- raise
+ print(f"Error for file {name[0]}, check FITS file integrity")
+ #raise
+ continue
+
+ stars = np.copy(starcat_j[self._hdu_table].data["VIGNET_LIST"])
stars[stars < -1e6] = 0
- psfs = np.copy(starcat_j[self._hdu_table].data['PSF_VIGNET_LIST'])
+ psfs = np.copy(starcat_j[self._hdu_table].data["PSF_VIGNET_LIST"])
# Pixel mse calculation
pix_val = np.sum((stars - psfs) ** 2)
@@ -250,7 +252,7 @@ def process(self):
masked_diffs = np.array(
[(_star - _psf)[my_mask] for _star, _psf in zip(stars, psfs)]
)
- masked_pix_val = np.sum(masked_diffs ** 2)
+ masked_pix_val = np.sum(masked_diffs**2)
masked_pix_sum = np.sum(masked_diffs)
# Star noise variance (using masked stars)
@@ -268,12 +270,11 @@ def process(self):
# if pix_val < 1e20:
# Normalised pixel mse calculation
- stars_norm_vals = np.sqrt(np.sum(stars ** 2, axis=(1, 2)))
- psfs_norm_vals = np.sqrt(np.sum(psfs ** 2, axis=(1, 2)))
+ stars_norm_vals = np.sqrt(np.sum(stars**2, axis=(1, 2)))
+ psfs_norm_vals = np.sqrt(np.sum(psfs**2, axis=(1, 2)))
# Select non zero stars & psfs
non_zero_elems = np.logical_and(
- (psfs_norm_vals != 0),
- (stars_norm_vals != 0)
+ (psfs_norm_vals != 0), (stars_norm_vals != 0)
)
# Calculate the filtered mse calculation
pix_filt_val = np.sum(
@@ -286,7 +287,8 @@ def process(self):
(
stars[non_zero_elems] / stars_norm_vals
- psfs[non_zero_elems] / psfs_norm_vals
- ) ** 2
+ )
+ ** 2
)
# Calculate sizes
filt_size = stars[non_zero_elems].size
@@ -313,56 +315,60 @@ def process(self):
# positions
x += list(
- starcat_j[self._hdu_table].data['GLOB_POSITION_IMG_LIST'][:, 0]
+ starcat_j[self._hdu_table].data["GLOB_POSITION_IMG_LIST"][:, 0]
)
y += list(
- starcat_j[self._hdu_table].data['GLOB_POSITION_IMG_LIST'][:, 1]
+ starcat_j[self._hdu_table].data["GLOB_POSITION_IMG_LIST"][:, 1]
)
# RA and DEC positions
try:
- ra += list(starcat_j[self._hdu_table].data['RA_LIST'][:])
- dec += list(starcat_j[self._hdu_table].data['DEC_LIST'][:])
+ ra += list(starcat_j[self._hdu_table].data["RA_LIST"][:])
+ dec += list(starcat_j[self._hdu_table].data["DEC_LIST"][:])
except Exception:
- ra += list(np.zeros(
- starcat_j[self._hdu_table].data[
- 'GLOB_POSITION_IMG_LIST'
- ][:, 0].shape,
- dtype=int,
- ))
- dec += list(np.zeros(
- starcat_j[self._hdu_table].data[
- 'GLOB_POSITION_IMG_LIST'
- ][:, 0].shape,
- dtype=int,
- ))
+ ra += list(
+ np.zeros(
+ starcat_j[self._hdu_table]
+ .data["GLOB_POSITION_IMG_LIST"][:, 0]
+ .shape,
+ dtype=int,
+ )
+ )
+ dec += list(
+ np.zeros(
+ starcat_j[self._hdu_table]
+ .data["GLOB_POSITION_IMG_LIST"][:, 0]
+ .shape,
+ dtype=int,
+ )
+ )
# shapes (convert sigmas to R^2)
g1_psf += list(
- starcat_j[self._hdu_table].data['PSF_MOM_LIST'][:, 0]
+ starcat_j[self._hdu_table].data["PSF_MOM_LIST"][:, 0]
)
g2_psf += list(
- starcat_j[self._hdu_table].data['PSF_MOM_LIST'][:, 1]
+ starcat_j[self._hdu_table].data["PSF_MOM_LIST"][:, 1]
)
size_psf += list(
- starcat_j[self._hdu_table].data['PSF_MOM_LIST'][:, 2] ** 2
+ starcat_j[self._hdu_table].data["PSF_MOM_LIST"][:, 2] ** 2
)
- g1 += list(starcat_j[self._hdu_table].data['STAR_MOM_LIST'][:, 0])
- g2 += list(starcat_j[self._hdu_table].data['STAR_MOM_LIST'][:, 1])
+ g1 += list(starcat_j[self._hdu_table].data["STAR_MOM_LIST"][:, 0])
+ g2 += list(starcat_j[self._hdu_table].data["STAR_MOM_LIST"][:, 1])
size += list(
- starcat_j[self._hdu_table].data['STAR_MOM_LIST'][:, 2] ** 2
+ starcat_j[self._hdu_table].data["STAR_MOM_LIST"][:, 2] ** 2
)
# flags
flag_psf += list(
- starcat_j[self._hdu_table].data['PSF_MOM_LIST'][:, 3]
+ starcat_j[self._hdu_table].data["PSF_MOM_LIST"][:, 3]
)
flag_star += list(
- starcat_j[self._hdu_table].data['STAR_MOM_LIST'][:, 3]
+ starcat_j[self._hdu_table].data["STAR_MOM_LIST"][:, 3]
)
# ccd id list
- ccd_nb += list(starcat_j[self._hdu_table].data['CCD_ID_LIST'])
+ ccd_nb += list(starcat_j[self._hdu_table].data["CCD_ID_LIST"])
starcat_j.close()
@@ -372,43 +378,43 @@ def process(self):
# Regular pixel RMSE
tot_pixel_rmse = MSC.rmse_calc(pixel_mse, size_mse)
self._w_log.info(
- f'MCCD_merge_starcat: Regular Total pixel RMSE ='
- + f' {tot_pixel_rmse:.5e}\n'
+ f"MCCD_merge_starcat: Regular Total pixel RMSE ="
+ + f" {tot_pixel_rmse:.5e}\n"
)
# Regular Total pixel mean
tot_pixel_mean = MSC.mean_calc(pixel_sum, size_mse)
self._w_log.info(
- f'MCCD_merge_starcat: Regular Total pixel mean ='
- + f' {tot_pixel_mean:.5e}\n'
+ f"MCCD_merge_starcat: Regular Total pixel mean ="
+ + f" {tot_pixel_mean:.5e}\n"
)
# Regular Total MASKED pixel RMSE
tot_masked_pixel_rmse = MSC.rmse_calc(masked_pixel_mse, masked_size)
self._w_log.info(
- f'MCCD_merge_starcat: Regular Total MASKED pixel RMSE ='
- + f' {tot_masked_pixel_rmse:.5e}\n'
+ f"MCCD_merge_starcat: Regular Total MASKED pixel RMSE ="
+ + f" {tot_masked_pixel_rmse:.5e}\n"
)
# Regular Total MASKED pixel mean
tot_masked_pixel_mean = MSC.mean_calc(masked_pixel_sum, masked_size)
self._w_log.info(
- f'MCCD_merge_starcat: Regular Total MASKED pixel mean ='
- + f' {tot_masked_pixel_mean:.5e}\n'
+ f"MCCD_merge_starcat: Regular Total MASKED pixel mean ="
+ + f" {tot_masked_pixel_mean:.5e}\n"
)
# Normalized pixel RMSE
tot_pix_norm_rmse = MSC.rmse_calc(pix_norm_mse, size_norm_mse)
self._w_log.info(
- 'MCCD_merge_starcat: Normalized Total pixel RMSE ='
- + f' {tot_pix_norm_rmse:.5e}\n'
+ "MCCD_merge_starcat: Normalized Total pixel RMSE ="
+ + f" {tot_pix_norm_rmse:.5e}\n"
)
# Normalized filtered pixel RMSE
tot_pix_filt_rmse = MSC.rmse_calc(pix_filt_mse, size_filt_mse)
self._w_log.info(
- 'MCCD_merge_starcat: Filtered Total pixel RMSE ='
- + f' {tot_pix_filt_rmse:.5e}\n'
+ "MCCD_merge_starcat: Filtered Total pixel RMSE ="
+ + f" {tot_pix_filt_rmse:.5e}\n"
)
concat_model_var = np.concatenate(np.array(model_var))
@@ -419,9 +425,9 @@ def process(self):
std_model_var = MSC.std_calc(concat_model_var)
rmse_model_var = MSC.rmse_calc_2(concat_model_var, model_var_size)
self._w_log.info(
- f'MCCD-RCA variance:\nMean Variance= {mean_model_var:.5e}\n'
- + f'Std Variance= {std_model_var:.5e}\n'
- + f'RMSE Variance= {rmse_model_var:.5e}\n'
+ f"MCCD-RCA variance:\nMean Variance= {mean_model_var:.5e}\n"
+ + f"Std Variance= {std_model_var:.5e}\n"
+ + f"RMSE Variance= {rmse_model_var:.5e}\n"
)
# Star Noise Variance
@@ -429,14 +435,14 @@ def process(self):
std_star_var = MSC.std_calc(concat_star_noise_var)
rmse_star_var = MSC.rmse_calc_2(concat_star_noise_var, star_noise_size)
self._w_log.info(
- f'Masked stars variance:\nMean Variance= {mean_star_var:.5e}\n'
- + f'Std Variance= {std_star_var:.5e}\n'
- + f'RMSE Variance= {rmse_star_var:.5e}\n'
+ f"Masked stars variance:\nMean Variance= {mean_star_var:.5e}\n"
+ + f"Std Variance= {std_star_var:.5e}\n"
+ + f"RMSE Variance= {rmse_star_var:.5e}\n"
)
# Mask and transform to numpy arrays
- flagmask = (
- np.abs(np.array(flag_star) - 1) * np.abs(np.array(flag_psf) - 1)
+ flagmask = np.abs(np.array(flag_star) - 1) * np.abs(
+ np.array(flag_psf) - 1
)
psf_e1 = np.array(g1_psf)[flagmask.astype(bool)]
psf_e2 = np.array(g2_psf)[flagmask.astype(bool)]
@@ -447,47 +453,47 @@ def process(self):
rmse, mean, std_dev = MSC.stats_calculator(star_e1, psf_e1)
self._w_log.info(
- f'Moment residual e1:\nMean= {mean:.5e}\nStd Dev= {std_dev:.5e}\n'
- + f'RMSE= {rmse:.5e}\n'
+ f"Moment residual e1:\nMean= {mean:.5e}\nStd Dev= {std_dev:.5e}\n"
+ + f"RMSE= {rmse:.5e}\n"
)
rmse, mean, std_dev = MSC.stats_calculator(star_e2, psf_e2)
self._w_log.info(
- f'Moment residual e2:\nMean= {mean:.5e}\nStd Dev= {std_dev:.5e}\n'
- + f'RMSE= {rmse:.5e}\n'
+ f"Moment residual e2:\nMean= {mean:.5e}\nStd Dev= {std_dev:.5e}\n"
+ + f"RMSE= {rmse:.5e}\n"
)
rmse, mean, std_dev = MSC.stats_calculator(star_r2, psf_r2)
self._w_log.info(
- f'Moment residual R2:\nMean= {mean:.5e}\nStd Dev= {std_dev:.5e}\n'
- + f'RMSE= {rmse:.5e}\n'
+ f"Moment residual R2:\nMean= {mean:.5e}\nStd Dev= {std_dev:.5e}\n"
+ + f"RMSE= {rmse:.5e}\n"
)
- self._w_log.info(f'MCCD: Number of stars: {star_e1.shape[0]:d}')
+ self._w_log.info(f"MCCD: Number of stars: {star_e1.shape[0]:d}")
# Prepare output FITS catalogue
output = file_io.FITSCatalogue(
- f'{self._output_dir}/full_starcat-0000000.fits',
+ f"{self._output_dir}/full_starcat-0000000.fits",
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
- SEx_catalogue=True
+ SEx_catalogue=True,
)
# Collect columns
# convert back to sigma for consistency
data = {
- 'X': x,
- 'Y': y,
- 'RA': ra,
- 'DEC': dec,
- 'E1_PSF_HSM': g1_psf,
- 'E2_PSF_HSM': g2_psf,
- 'SIGMA_PSF_HSM': np.sqrt(size_psf),
- 'E1_STAR_HSM': g1,
- 'E2_STAR_HSM': g2,
- 'SIGMA_STAR_HSM': np.sqrt(size),
- 'FLAG_PSF_HSM': flag_psf,
- 'FLAG_STAR_HSM': flag_star,
- 'CCD_NB': ccd_nb
+ "X": x,
+ "Y": y,
+ "RA": ra,
+ "DEC": dec,
+ "E1_PSF_HSM": g1_psf,
+ "E2_PSF_HSM": g2_psf,
+ "SIGMA_PSF_HSM": np.sqrt(size_psf),
+ "E1_STAR_HSM": g1,
+ "E2_STAR_HSM": g2,
+ "SIGMA_STAR_HSM": np.sqrt(size),
+ "FLAG_PSF_HSM": flag_psf,
+ "FLAG_STAR_HSM": flag_star,
+ "CCD_NB": ccd_nb,
}
# Write file
@@ -533,76 +539,96 @@ def process(self):
ccd_nb = []
self._w_log.info(
- f'Merging {len(self._input_file_list)} star catalogues'
+ f"Merging {len(self._input_file_list)} star catalogues"
)
for name in self._input_file_list:
- starcat_j = fits.open(name[0], memmap=False)
+ try:
+ starcat_j = fits.open(name[0], memmap=False, ignore_missing_simple=True)
+ except OSError as e:
+ print(f"Error while opening file '{name[0]}'")
+ #raise
+ continue
data_j = starcat_j[self._hdu_table].data
# positions
- x += list(data_j['X'])
- y += list(data_j['Y'])
- ra += list(data_j['RA'])
- dec += list(data_j['DEC'])
+ x += list(data_j["X"])
+ y += list(data_j["Y"])
+ ra += list(data_j["RA"])
+ dec += list(data_j["DEC"])
# shapes (convert sigmas to R^2)
- g1_psf += list(data_j['E1_PSF_HSM'])
- g2_psf += list(data_j['E2_PSF_HSM'])
- size_psf += list(data_j['SIGMA_PSF_HSM']**2)
- g1 += list(data_j['E1_STAR_HSM'])
- g2 += list(data_j['E2_STAR_HSM'])
- size += list(data_j['SIGMA_STAR_HSM']**2)
+ g1_psf += list(data_j["E1_PSF_HSM"])
+ g2_psf += list(data_j["E2_PSF_HSM"])
+ size_psf += list(data_j["SIGMA_PSF_HSM"] ** 2)
+ g1 += list(data_j["E1_STAR_HSM"])
+ g2 += list(data_j["E2_STAR_HSM"])
+ size += list(data_j["SIGMA_STAR_HSM"] ** 2)
# flags
- flag_psf += list(data_j['FLAG_PSF_HSM'])
- flag_star += list(data_j['FLAG_STAR_HSM'])
+ flag_psf += list(data_j["FLAG_PSF_HSM"])
+ flag_star += list(data_j["FLAG_STAR_HSM"])
# misc
- mag += list(data_j['MAG'])
- snr += list(data_j['SNR'])
- psfex_acc += list(data_j['ACCEPTED'])
+
+ # MKDEBUG: The following columns do not exist (yet)
+ # for psf converted (pix2wcs) files.
+ try:
+ mag += list(data_j["MAG"])
+ except:
+ mag += list(np.zeros_like(data_j["X"]))
+ try:
+ snr += list(data_j["SNR"])
+ except:
+ snr += list(np.zeros_like(data_j["X"]))
+ try:
+ psfex_acc += list(data_j["ACCEPTED"])
+ except:
+ psfex_acc += list(np.zeros_like(data_j["X"]))
# CCD number
- ccd_nb += [
- re.split(r"\-([0-9]*)\-([0-9]+)\.", name[0])[-2]
- ] * len(data_j['RA'])
+ ccd_nb += [re.split(r"\-([0-9]*)\-([0-9]+)\.", name[0])[-2]] * len(
+ data_j["RA"]
+ )
# Prepare output FITS catalogue
+ # MKDEBUG: SEx_cat=True -> False
output = file_io.FITSCatalogue(
- f'{self._output_dir}/full_starcat-0000000.fits',
+ f"{self._output_dir}/full_starcat-0000000.fits",
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
- SEx_catalogue=True
+ SEx_catalogue=False,
)
# Collect columns
# convert back to sigma for consistency
data = {
- 'X': x,
- 'Y': y,
- 'RA': ra,
- 'DEC': dec,
- 'E1_PSF_HSM': g1_psf,
- 'E2_PSF_HSM': g2_psf,
- 'SIGMA_PSF_HSM': np.sqrt(size_psf),
- 'E1_STAR_HSM': g1,
- 'E2_STAR_HSM': g2,
- 'SIGMA_STAR_HSM': np.sqrt(size),
- 'FLAG_PSF_HSM': flag_psf,
- 'FLAG_STAR_HSM': flag_star,
- 'MAG': mag,
- 'SNR': snr,
- 'ACCEPTED': psfex_acc,
- 'CCD_NB': ccd_nb
+ "X": x,
+ "Y": y,
+ "RA": ra,
+ "DEC": dec,
+ "E1_PSF_HSM": g1_psf,
+ "E2_PSF_HSM": g2_psf,
+ "SIGMA_PSF_HSM": np.sqrt(size_psf),
+ "E1_STAR_HSM": g1,
+ "E2_STAR_HSM": g2,
+ "SIGMA_STAR_HSM": np.sqrt(size),
+ "FLAG_PSF_HSM": flag_psf,
+ "FLAG_STAR_HSM": flag_star,
+ "MAG": mag,
+ "SNR": snr,
+ "ACCEPTED": psfex_acc,
+ "CCD_NB": ccd_nb,
}
# Write file
+ # MKDEBUG for psf conv (pix2WCS) files do not write as SExtractorCat;
+ # we do not want to copy the first input data content to HDU #1.
output.save_as_fits(
data,
overwrite=True,
- sex_cat_path=self._input_file_list[0][0],
)
+ # sex_cat_path=self._input_file_list[0][0],
class MergeStarCatSetools(object):
@@ -653,9 +679,9 @@ def get_moments(cls, data):
"""
# SExtractor output. First and second moments are normalised.
# Second moments are centred.
- q11 = 'X2WIN_IMAGE'
- q22 = 'Y2WIN_IMAGE'
- q12 = 'XYWIN_IMAGE'
+ q11 = "X2WIN_IMAGE"
+ q22 = "Y2WIN_IMAGE"
+ q12 = "XYWIN_IMAGE"
# Second moments
m11 = data[q12]
@@ -687,13 +713,13 @@ def get_ellipticity(cls, m11, m20, m02, typ):
ellipticity components
"""
- if typ == 'epsilon':
+ if typ == "epsilon":
# Determinant = (Q_11 Q_22 - Q_12^2)^(1/2)
det = np.sqrt(m20 * m02 - m11 * m11)
- elif typ == 'chi':
+ elif typ == "chi":
det = 0
else:
- raise ValueError(f'Invalid ellipticity type {type}')
+ raise ValueError(f"Invalid ellipticity type {type}")
# Denominator = Q_11 + Q_22 [ + 2 * det]
den = m20 + m02 + 2 * det
@@ -701,7 +727,7 @@ def get_ellipticity(cls, m11, m20, m02, typ):
# Ellipticity = (Q_11 - Q_22 + 2 i Q_12) / den
ell = (m20 - m02 + 1j * 2 * m11) / den
- if type == 'chi':
+ if type == "chi":
# chi estimates 2*g, so to get g we have to divide by 2
ell = ell / 2
@@ -720,7 +746,7 @@ def process(self):
ccd_nb = []
self._w_log.info(
- f'Merging {len(self._input_file_list)} star catalogues'
+ f"Merging {len(self._input_file_list)} star catalogues"
)
for name in self._input_file_list:
@@ -729,54 +755,54 @@ def process(self):
data_j = starcat_j[self._hdu_table].data
# positions
- x += list(data_j['XWIN_IMAGE'])
- y += list(data_j['YWIN_IMAGE'])
- ra += list(data_j['XWIN_WORLD'])
- dec += list(data_j['YWIN_WORLD'])
+ x += list(data_j["XWIN_IMAGE"])
+ y += list(data_j["YWIN_IMAGE"])
+ ra += list(data_j["XWIN_WORLD"])
+ dec += list(data_j["YWIN_WORLD"])
m11, m20, m02 = self.get_moments(data_j)
- eps1, eps2 = self.get_ellipticity(m11, m20, m02, 'epsilon')
- chi1, chi2 = self.get_ellipticity(m11, m20, m02, 'chi')
+ eps1, eps2 = self.get_ellipticity(m11, m20, m02, "epsilon")
+ chi1, chi2 = self.get_ellipticity(m11, m20, m02, "chi")
- size += list(data_j['FLUX_RADIUS'])
+ size += list(data_j["FLUX_RADIUS"])
# flags
- flags += list(data_j['FLAGS_WIN'])
- flags_ext += list(data_j['IMAFLAGS_ISO'])
+ flags += list(data_j["FLAGS_WIN"])
+ flags_ext += list(data_j["IMAFLAGS_ISO"])
# misc
- mag += list(data_j['MAG_WIN'])
- snr += list(data_j['SNR_WIN'])
+ mag += list(data_j["MAG_WIN"])
+ snr += list(data_j["SNR_WIN"])
# CCD number
- ccd_nb += [
- re.split(r"\-([0-9]*)\-([0-9]+)\.", name[0])[-2]
- ] * len(data_j['XWIN_IMAGE'])
+ ccd_nb += [re.split(r"\-([0-9]*)\-([0-9]+)\.", name[0])[-2]] * len(
+ data_j["XWIN_IMAGE"]
+ )
# Prepare output FITS catalogue
output = file_io.FITSCatalogue(
- f'{self._output_dir}/full_starcat-0000000.fits',
+ f"{self._output_dir}/full_starcat-0000000.fits",
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
- SEx_catalogue=True
+ SEx_catalogue=True,
)
# Collect columns
# convert back to sigma for consistency
data = {
- 'X': x,
- 'Y': y,
- 'RA': ra,
- 'DEC': dec,
- 'EPS1': eps1,
- 'EPS2': eps2,
- 'CHI1': chi1,
- 'CHI2': chi2,
- 'SIZE': size,
- 'FLAGS': flags,
- 'FLAGS_EXT': flags_ext,
- 'MAG': mag,
- 'SNR': snr,
- 'CCD_NB': ccd_nb,
+ "X": x,
+ "Y": y,
+ "RA": ra,
+ "DEC": dec,
+ "EPS1": eps1,
+ "EPS2": eps2,
+ "CHI1": chi1,
+ "CHI2": chi2,
+ "SIZE": size,
+ "FLAGS": flags,
+ "FLAGS_EXT": flags_ext,
+ "MAG": mag,
+ "SNR": snr,
+ "CCD_NB": ccd_nb,
}
# Write file
diff --git a/shapepipe/modules/merge_starcat_runner.py b/shapepipe/modules/merge_starcat_runner.py
index 5d0b43f6d..5213809a6 100644
--- a/shapepipe/modules/merge_starcat_runner.py
+++ b/shapepipe/modules/merge_starcat_runner.py
@@ -11,13 +11,13 @@
@module_runner(
- version='1.1',
- input_module=['mccd_fit_val_runner'],
- file_pattern=['validation_psf'],
- file_ext=['.fits'],
- numbering_scheme='-0000000',
- depends=['numpy', 'astropy'],
- run_method='serial',
+ version="1.1",
+ input_module=["mccd_fit_val_runner"],
+ file_pattern=["validation_psf"],
+ file_ext=[".fits"],
+ numbering_scheme="-0000000",
+ depends=["numpy", "astropy"],
+ run_method="serial",
)
def merge_starcat_runner(
input_file_list,
@@ -29,27 +29,33 @@ def merge_starcat_runner(
):
"""Define The Merge Star Catalogues Runner."""
# Read config file options
- psf_model = config.get(module_config_sec, 'PSF_MODEL')
- allowed_psf_models = ('psfex', 'mccd', 'setools')
+ psf_model = config.get(module_config_sec, "PSF_MODEL")
+ allowed_psf_models = ("psfex", "mccd", "setools")
if psf_model not in allowed_psf_models:
raise ValueError(
- f'Invalid config entry PSF_MODEL={psf_model} found, '
- + f'needs to be one of {allowed_psf_models}'
+ f"Invalid config entry PSF_MODEL={psf_model} found, "
+ + f"needs to be one of {allowed_psf_models}"
)
+ # Get input catalogue HDU number
+ if config.has_option(module_config_sec, "HDU"):
+ hdu = config.getint(module_config_sec, "HDU")
+ else:
+ hdu = 1
+
# Set output directory
- output_dir = run_dirs['output']
+ output_dir = run_dirs["output"]
# Set merge class to use
- if psf_model == 'mccd':
+ if psf_model == "mccd":
MSC = merge_starcat.MergeStarCatMCCD
- elif psf_model == 'psfex':
+ elif psf_model == "psfex":
MSC = merge_starcat.MergeStarCatPSFEX
- elif psf_model == 'setools':
+ elif psf_model == "setools":
MSC = merge_starcat.MergeStarCatSetools
# Create instance of merge class
- merge_inst = MSC(input_file_list, output_dir, w_log)
+ merge_inst = MSC(input_file_list, output_dir, w_log, hdu_table=hdu)
# Run processing
merge_inst.process()
diff --git a/shapepipe/modules/module_decorator.py b/shapepipe/modules/module_decorator.py
index 17911b49d..1ad480465 100644
--- a/shapepipe/modules/module_decorator.py
+++ b/shapepipe/modules/module_decorator.py
@@ -8,14 +8,14 @@
def module_runner(
- version='0.0',
+ version="0.0",
input_module=None,
- file_pattern='',
- file_ext='',
+ file_pattern="",
+ file_ext="",
depends=[],
executes=[],
numbering_scheme=None,
- run_method='parallel',
+ run_method="parallel",
):
"""Wrap Module Runners.
@@ -63,41 +63,39 @@ def module_runner(
"""
if not isinstance(version, str):
- raise TypeError('Module version must be a string.')
+ raise TypeError("Module version must be a string.")
if isinstance(input_module, str):
input_module = [input_module]
elif not isinstance(input_module, (list, type(None))):
- raise TypeError('Input module must be a list or a string.')
+ raise TypeError("Input module must be a list or a string.")
if isinstance(file_pattern, str):
file_pattern = [file_pattern]
elif not isinstance(file_pattern, list):
- raise TypeError('File pattern must be a string or a list of strings.')
+ raise TypeError("File pattern must be a string or a list of strings.")
if isinstance(file_ext, str):
file_ext = [file_ext]
elif not isinstance(file_ext, list):
- raise TypeError(
- 'File extension must be a string or a list of strings.'
- )
+ raise TypeError("File extension must be a string or a list of strings.")
if isinstance(depends, str):
depends = [depends]
elif not isinstance(depends, list):
- raise TypeError('Dependencies must be a string or a list of strings.')
+ raise TypeError("Dependencies must be a string or a list of strings.")
if isinstance(executes, str):
executes = [executes]
elif not isinstance(executes, list):
- raise TypeError('Executables must be a string or a list of strings.')
+ raise TypeError("Executables must be a string or a list of strings.")
if not isinstance(numbering_scheme, (str, type(None))):
raise TypeError(
- f'Numbering scheme must be a string, found \'{numbering_scheme}\'.'
+ f"Numbering scheme must be a string, found '{numbering_scheme}'."
)
- if run_method not in {'parallel', 'serial'}:
+ if run_method not in {"parallel", "serial"}:
raise ValueError('Run method must be a "parallel" or "serial".')
if (len(file_ext) == 1) and (len(file_pattern) > 1):
@@ -105,9 +103,9 @@ def module_runner(
if len(file_ext) != len(file_pattern):
raise ValueError(
- f'The number of file_ext values ({len(file_ext)}) does not match '
- + f'the number of file_pattern values ({len(file_pattern)}) in '
- + 'the module decorator.'
+ f"The number of file_ext values ({len(file_ext)}) does not match "
+ + f"the number of file_pattern values ({len(file_pattern)}) in "
+ + "the module decorator."
)
def decorator(func):
diff --git a/shapepipe/modules/module_runners.py b/shapepipe/modules/module_runners.py
index 74a48ce50..eddee6eb0 100644
--- a/shapepipe/modules/module_runners.py
+++ b/shapepipe/modules/module_runners.py
@@ -25,17 +25,19 @@ def get_module_runners(modules):
Dictionary of module runners
"""
- package = 'shapepipe.modules'
+ package = "shapepipe.modules"
- module_runners = dict([
- (
- module,
- getattr(
- import_module(f'.{module}', package=package),
+ module_runners = dict(
+ [
+ (
module,
+ getattr(
+ import_module(f".{module}", package=package),
+ module,
+ ),
)
- )
- for module in modules
- ])
+ for module in modules
+ ]
+ )
return module_runners
diff --git a/shapepipe/modules/ngmix_package/__init__.py b/shapepipe/modules/ngmix_package/__init__.py
index e74d71f76..909631097 100644
--- a/shapepipe/modules/ngmix_package/__init__.py
+++ b/shapepipe/modules/ngmix_package/__init__.py
@@ -41,4 +41,4 @@
"""
-__all__ = ['ngmix']
+__all__ = ["ngmix"]
diff --git a/shapepipe/modules/ngmix_package/ngmix.py b/shapepipe/modules/ngmix_package/ngmix.py
index 7cb614a42..9a731d66e 100644
--- a/shapepipe/modules/ngmix_package/ngmix.py
+++ b/shapepipe/modules/ngmix_package/ngmix.py
@@ -66,13 +66,13 @@ def __init__(
f_wcs_path,
w_log,
id_obj_min=-1,
- id_obj_max=-1
+ id_obj_max=-1,
):
if len(input_file_list) != 6:
raise IndexError(
- f'Input file list has length {len(input_file_list)},'
- + ' required is 6'
+ f"Input file list has length {len(input_file_list)},"
+ + " required is 6"
)
self._tile_cat_path = input_file_list[0]
@@ -95,9 +95,9 @@ def __init__(
self._w_log = w_log
# Initiatlise random generator
- seed = int(''.join(re.findall(r'\d+', self._file_number_string)))
+ seed = int("".join(re.findall(r"\d+", self._file_number_string)))
np.random.seed(seed)
- self._w_log.info(f'Random generator initialisation seed = {seed}')
+ self._w_log.info(f"Random generator initialisation seed = {seed}")
@classmethod
def MegaCamFlip(self, vign, ccd_nb):
@@ -153,21 +153,18 @@ def get_prior(self):
# Size prior. Instead of flat, two-sided error function (TwoSidedErf)
# could be used
Tminval = -10.0 # arcsec squared
- Tmaxval = 1.e6
+ Tmaxval = 1.0e6
T_prior = ngmix.priors.FlatPrior(Tminval, Tmaxval)
# Flux prior. Bounds need to make sense for
# images in question
- Fminval = -1.e4
- Fmaxval = 1.e9
+ Fminval = -1.0e4
+ Fmaxval = 1.0e9
F_prior = ngmix.priors.FlatPrior(Fminval, Fmaxval)
# Joint prior, combine all individual priors
prior = ngmix.joint_prior.PriorSimpleSep(
- cen_prior,
- g_prior,
- T_prior,
- F_prior
+ cen_prior, g_prior, T_prior, F_prior
)
return prior
@@ -193,112 +190,107 @@ def compile_results(self, results):
If SNR key not found
"""
- names = ['1m', '1p', '2m', '2p', 'noshear']
+ names = ["1m", "1p", "2m", "2p", "noshear"]
names2 = [
- 'id',
- 'n_epoch_model',
- 'moments_fail',
- 'ntry_fit',
- 'g1_psfo_ngmix',
- 'g2_psfo_ngmix',
- 'T_psfo_ngmix',
- 'g1_err_psfo_ngmix',
- 'g2_err_psfo_ngmix',
- 'T_err_psfo_ngmix',
- 'g1',
- 'g1_err',
- 'g2',
- 'g2_err',
- 'T',
- 'T_err',
- 'Tpsf',
- 'g1_psf',
- 'g2_psf',
- 'flux',
- 'flux_err',
- 's2n',
- 'mag',
- 'mag_err',
- 'flags',
- 'mcal_flags'
+ "id",
+ "n_epoch_model",
+ "moments_fail",
+ "ntry_fit",
+ "g1_psfo_ngmix",
+ "g2_psfo_ngmix",
+ "T_psfo_ngmix",
+ "g1_err_psfo_ngmix",
+ "g2_err_psfo_ngmix",
+ "T_err_psfo_ngmix",
+ "g1",
+ "g1_err",
+ "g2",
+ "g2_err",
+ "T",
+ "T_err",
+ "Tpsf",
+ "g1_psf",
+ "g2_psf",
+ "flux",
+ "flux_err",
+ "s2n",
+ "mag",
+ "mag_err",
+ "flags",
+ "mcal_flags",
]
output_dict = {k: {kk: [] for kk in names2} for k in names}
for idx in range(len(results)):
for name in names:
mag = (
- -2.5 * np.log10(results[idx][name]['flux'])
+ -2.5 * np.log10(results[idx][name]["flux"])
+ self._zero_point
)
mag_err = np.abs(
- -2.5 * results[idx][name]['flux_err']
- / (results[idx][name]['flux'] * np.log(10))
+ -2.5
+ * results[idx][name]["flux_err"]
+ / (results[idx][name]["flux"] * np.log(10))
)
- output_dict[name]['id'].append(results[idx]['obj_id'])
- output_dict[name]['n_epoch_model'].append(
- results[idx]['n_epoch_model']
+ output_dict[name]["id"].append(results[idx]["obj_id"])
+ output_dict[name]["n_epoch_model"].append(
+ results[idx]["n_epoch_model"]
)
- output_dict[name]['moments_fail'].append(
- results[idx]['moments_fail']
+ output_dict[name]["moments_fail"].append(
+ results[idx]["moments_fail"]
)
- output_dict[name]['ntry_fit'].append(
- results[idx][name]['ntry']
+ output_dict[name]["ntry_fit"].append(results[idx][name]["ntry"])
+ output_dict[name]["g1_psfo_ngmix"].append(
+ results[idx]["g_PSFo"][0]
)
- output_dict[name]['g1_psfo_ngmix'].append(
- results[idx]['g_PSFo'][0]
+ output_dict[name]["g2_psfo_ngmix"].append(
+ results[idx]["g_PSFo"][1]
)
- output_dict[name]['g2_psfo_ngmix'].append(
- results[idx]['g_PSFo'][1]
+ output_dict[name]["g1_err_psfo_ngmix"].append(
+ results[idx]["g_err_PSFo"][0]
)
- output_dict[name]['g1_err_psfo_ngmix'].append(
- results[idx]['g_err_PSFo'][0]
+ output_dict[name]["g2_err_psfo_ngmix"].append(
+ results[idx]["g_err_PSFo"][1]
)
- output_dict[name]['g2_err_psfo_ngmix'].append(
- results[idx]['g_err_PSFo'][1]
+ output_dict[name]["T_psfo_ngmix"].append(results[idx]["T_PSFo"])
+ output_dict[name]["T_err_psfo_ngmix"].append(
+ results[idx]["T_err_PSFo"]
)
- output_dict[name]['T_psfo_ngmix'].append(
- results[idx]['T_PSFo']
+ output_dict[name]["g1"].append(results[idx][name]["g"][0])
+ output_dict[name]["g1_err"].append(
+ results[idx][name]["pars_err"][2]
)
- output_dict[name]['T_err_psfo_ngmix'].append(
- results[idx]['T_err_PSFo']
+ output_dict[name]["g2"].append(results[idx][name]["g"][1])
+ output_dict[name]["g2_err"].append(
+ results[idx][name]["pars_err"][3]
)
- output_dict[name]['g1'].append(results[idx][name]['g'][0])
- output_dict[name]['g1_err'].append(
- results[idx][name]['pars_err'][2]
+ output_dict[name]["T"].append(results[idx][name]["T"])
+ output_dict[name]["T_err"].append(results[idx][name]["T_err"])
+ output_dict[name]["Tpsf"].append(results[idx][name]["Tpsf"])
+ output_dict[name]["g1_psf"].append(
+ results[idx][name]["gpsf"][0]
)
- output_dict[name]['g2'].append(results[idx][name]['g'][1])
- output_dict[name]['g2_err'].append(
- results[idx][name]['pars_err'][3]
+ output_dict[name]["g2_psf"].append(
+ results[idx][name]["gpsf"][1]
)
- output_dict[name]['T'].append(results[idx][name]['T'])
- output_dict[name]['T_err'].append(results[idx][name]['T_err'])
- output_dict[name]['Tpsf'].append(results[idx][name]['Tpsf'])
- output_dict[name]['g1_psf'].append(
- results[idx][name]['gpsf'][0]
+ output_dict[name]["flux"].append(results[idx][name]["flux"])
+ output_dict[name]["flux_err"].append(
+ results[idx][name]["flux_err"]
)
- output_dict[name]['g2_psf'].append(
- results[idx][name]['gpsf'][1]
- )
- output_dict[name]['flux'].append(results[idx][name]['flux'])
- output_dict[name]['flux_err'].append(
- results[idx][name]['flux_err']
- )
- output_dict[name]['mag'].append(mag)
- output_dict[name]['mag_err'].append(mag_err)
-
- if 's2n' in results[idx][name]:
- output_dict[name]['s2n'].append(results[idx][name]['s2n'])
- elif 's2n_r' in results[idx][name]:
- output_dict[name]['s2n'].append(
- results[idx][name]['s2n_r']
- )
+ output_dict[name]["mag"].append(mag)
+ output_dict[name]["mag_err"].append(mag_err)
+
+ if "s2n" in results[idx][name]:
+ output_dict[name]["s2n"].append(results[idx][name]["s2n"])
+ elif "s2n_r" in results[idx][name]:
+ output_dict[name]["s2n"].append(results[idx][name]["s2n_r"])
else:
- raise KeyError('No SNR key (s2n, s2n_r) found in results')
+ raise KeyError("No SNR key (s2n, s2n_r) found in results")
- output_dict[name]['flags'].append(results[idx][name]['flags'])
- output_dict[name]['mcal_flags'].append(
- results[idx]['mcal_flags']
+ output_dict[name]["flags"].append(results[idx][name]["flags"])
+ output_dict[name]["mcal_flags"].append(
+ results[idx]["mcal_flags"]
)
return output_dict
@@ -314,18 +306,31 @@ def save_results(self, output_dict):
Dictionary containing the results
"""
- output_name = (
- f'{self._output_dir}/ngmix{self._file_number_string}.fits'
- )
+ output_name = f"{self._output_dir}/ngmix{self._file_number_string}.fits"
f = file_io.FITSCatalogue(
- output_name,
- open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
+ output_name, open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
)
+ n_hdu = len(output_dict.keys())
+ if n_hdu != 5:
+ raise IndexError(
+ f"FITS output file data has {n_hdu} HDUs,"
+ + " expected are 5"
+ )
for key in output_dict.keys():
f.save_as_fits(output_dict[key], ext_name=key.upper())
+
+ @classmethod
+ def check_key(self, expccd_name_tmp, vign_cat, vignet_path):
+ if expccd_name_tmp not in vign_cat:
+ raise KeyError(
+ f"Key '{expccd_name_tmp}' (exposure CCD ID from PSF postage stamp list)"
+ + " not found in postage stamp database"
+ + f" file '{vignet_path}'"
+ )
+
def process(self):
"""Process.
@@ -342,10 +347,10 @@ def process(self):
SEx_catalogue=True,
)
tile_cat.open()
- obj_id = np.copy(tile_cat.get_data()['NUMBER'])
- tile_vign = np.copy(tile_cat.get_data()['VIGNET'])
- tile_ra = np.copy(tile_cat.get_data()['XWIN_WORLD'])
- tile_dec = np.copy(tile_cat.get_data()['YWIN_WORLD'])
+ obj_id = np.copy(tile_cat.get_data()["NUMBER"])
+ tile_vign = np.copy(tile_cat.get_data()["VIGNET"])
+ tile_ra = np.copy(tile_cat.get_data()["XWIN_WORLD"])
+ tile_dec = np.copy(tile_cat.get_data()["YWIN_WORLD"])
tile_cat.close()
f_wcs_file = SqliteDict(self._f_wcs_path)
@@ -362,6 +367,7 @@ def process(self):
id_first = -1
id_last = -1
+ self._w_log.info(f"Processing objects # {self._id_obj_min} ... {self._id_obj_max}")
for i_tile, id_tmp in enumerate(obj_id):
if self._id_obj_min > 0 and id_tmp < self._id_obj_min:
@@ -372,8 +378,7 @@ def process(self):
if id_first == -1:
id_first = id_tmp
id_last = id_tmp
-
- count = count + 1
+ str_id_tmp = str(id_tmp)
gal_vign = []
psf_vign = []
@@ -381,70 +386,94 @@ def process(self):
weight_vign = []
flag_vign = []
jacob_list = []
- if (
- (psf_vign_cat[str(id_tmp)] == 'empty')
- or (gal_vign_cat[str(id_tmp)] == 'empty')
- ):
+ if psf_vign_cat[str_id_tmp] == "empty":
+ self._w_log.info(f"Skipping object {id_tmp}: empty PSF vignet")
continue
+
+ self.check_key(str_id_tmp, gal_vign_cat, self._gal_vignet_path)
+ self.check_key(str_id_tmp, bkg_vign_cat, self._bkg_vignet_path)
+ self.check_key(str_id_tmp, flag_vign_cat, self._flag_vignet_path)
+ self.check_key(str_id_tmp, weight_vign_cat, self._weight_vignet_path)
+ if gal_vign_cat[str_id_tmp] == "empty":
+ self._w_log.info(
+ f"Skipping object {id_tmp}: empty galaxy vignet"
+ )
+ continue
+
psf_expccd_name = list(psf_vign_cat[str(id_tmp)].keys())
for expccd_name_tmp in psf_expccd_name:
- exp_name, ccd_n = re.split('-', expccd_name_tmp)
- gal_vign_tmp = (
- gal_vign_cat[str(id_tmp)][expccd_name_tmp]['VIGNET']
- )
+ self.check_key(expccd_name_tmp, gal_vign_cat[str_id_tmp], self._gal_vignet_path)
+ self.check_key(expccd_name_tmp, bkg_vign_cat[str_id_tmp], self._bkg_vignet_path)
+ self.check_key(expccd_name_tmp, flag_vign_cat[str_id_tmp], self._flag_vignet_path)
+ self.check_key(expccd_name_tmp, weight_vign_cat[str_id_tmp], self._weight_vignet_path)
+
+ exp_name, ccd_n = re.split("-", expccd_name_tmp)
+
+ gal_vign_tmp = gal_vign_cat[str_id_tmp][expccd_name_tmp][
+ "VIGNET"
+ ]
if len(np.where(gal_vign_tmp.ravel() == 0)[0]) != 0:
+ self._w_log.info(
+ f"Skipping exp {expccd_name_tmp} for object {id_tmp}: zero-length galaxy vignet"
+ )
continue
- bkg_vign_tmp = (
- bkg_vign_cat[str(id_tmp)][expccd_name_tmp]['VIGNET']
- )
+ bkg_vign_tmp = bkg_vign_cat[str_id_tmp][expccd_name_tmp][
+ "VIGNET"
+ ]
gal_vign_sub_bkg = gal_vign_tmp - bkg_vign_tmp
- tile_vign_tmp = (
- Ngmix.MegaCamFlip(np.copy(tile_vign[i_tile]), int(ccd_n))
+ tile_vign_tmp = Ngmix.MegaCamFlip(
+ np.copy(tile_vign[i_tile]), int(ccd_n)
)
- flag_vign_tmp = (
- flag_vign_cat[str(id_tmp)][expccd_name_tmp]['VIGNET']
- )
+ flag_vign_tmp = flag_vign_cat[str_id_tmp][expccd_name_tmp][
+ "VIGNET"
+ ]
flag_vign_tmp[np.where(tile_vign_tmp == -1e30)] = 2**10
v_flag_tmp = flag_vign_tmp.ravel()
if len(np.where(v_flag_tmp != 0)[0]) / (51 * 51) > 1 / 3.0:
+ self._w_log.info(
+ f"Skipping exp {expccd_name_tmp} for object {id_tmp}: mask > 1/3"
+ )
continue
- weight_vign_tmp = (
- weight_vign_cat[str(id_tmp)][expccd_name_tmp]['VIGNET']
- )
+ weight_vign_tmp = weight_vign_cat[str_id_tmp][expccd_name_tmp][
+ "VIGNET"
+ ]
jacob_tmp = get_jacob(
- f_wcs_file[exp_name][int(ccd_n)]['WCS'],
+ f_wcs_file[exp_name][int(ccd_n)]["WCS"],
tile_ra[i_tile],
- tile_dec[i_tile]
+ tile_dec[i_tile],
)
header_tmp = fits.Header.fromstring(
- f_wcs_file[exp_name][int(ccd_n)]['header']
+ f_wcs_file[exp_name][int(ccd_n)]["header"]
)
- Fscale = header_tmp['FSCALE']
+ Fscale = header_tmp["FSCALE"]
gal_vign_scaled = gal_vign_sub_bkg * Fscale
- weight_vign_scaled = weight_vign_tmp * 1 / Fscale ** 2
+ weight_vign_scaled = weight_vign_tmp * 1 / Fscale**2
gal_vign.append(gal_vign_scaled)
psf_vign.append(
- psf_vign_cat[str(id_tmp)][expccd_name_tmp]['VIGNET']
+ psf_vign_cat[str_id_tmp][expccd_name_tmp]["VIGNET"]
)
sigma_psf.append(
- psf_vign_cat[
- str(id_tmp)
- ][expccd_name_tmp]['SHAPES']['SIGMA_PSF_HSM']
+ psf_vign_cat[str_id_tmp][expccd_name_tmp]["SHAPES"][
+ "SIGMA_PSF_HSM"
+ ]
)
weight_vign.append(weight_vign_scaled)
flag_vign.append(flag_vign_tmp)
jacob_list.append(jacob_tmp)
if len(gal_vign) == 0:
+ self._w_log.info(
+ f"Skipping object {id_tmp}: no exposure vignets added"
+ )
continue
try:
res = do_ngmix_metacal(
@@ -455,21 +484,23 @@ def process(self):
flag_vign,
jacob_list,
prior,
- self._pixel_scale
+ self._pixel_scale,
)
except Exception as ee:
self._w_log.info(
- f'ngmix failed for object ID={id_tmp}.\nMessage: {ee}'
+ f"ngmix failed for object ID={id_tmp}.\nMessage: {ee}"
)
continue
- res['obj_id'] = id_tmp
- res['n_epoch_model'] = len(gal_vign)
+ count = count + 1
+
+ res["obj_id"] = id_tmp
+ res["n_epoch_model"] = len(gal_vign)
final_res.append(res)
self._w_log.info(
- f'ngmix loop over objects finished, processed {count} '
- + f'objects, id first/last={id_first}/{id_last}'
+ f"ngmix loop over objects finished, measured {count} "
+ + f"objects, id first/last={id_first}/{id_last}"
)
f_wcs_file.close()
@@ -489,11 +520,11 @@ def process(self):
def get_guess(
img,
pixel_scale,
- guess_flux_unit='img',
- guess_size_type='T',
- guess_size_unit='sky',
+ guess_flux_unit="img",
+ guess_size_type="T",
+ guess_size_unit="sky",
guess_centroid=True,
- guess_centroid_unit='sky'
+ guess_centroid_unit="sky",
):
r"""Get Guess.
@@ -543,61 +574,56 @@ def get_guess(
error_msg = hsm_shape.error_message
- if error_msg != '':
+ if error_msg != "":
raise galsim.hsm.GalSimHSMError(
- f'Error in adaptive moments :\n{error_msg}'
+ f"Error in adaptive moments :\n{error_msg}"
)
- if guess_flux_unit == 'img':
+ if guess_flux_unit == "img":
guess_flux = hsm_shape.moments_amp
- elif guess_flux_unit == 'sky':
- guess_flux = hsm_shape.moments_amp / pixel_scale ** 2
+ elif guess_flux_unit == "sky":
+ guess_flux = hsm_shape.moments_amp / pixel_scale**2
else:
raise ValueError(
- f'invalid guess_flux_unit \'{guess_flux_unit}\','
- + ' must be one of \'img\', \'sky\''
+ f"invalid guess_flux_unit '{guess_flux_unit}',"
+ + " must be one of 'img', 'sky'"
)
- if guess_size_unit == 'img':
- size_unit = 1.
- elif guess_size_unit == 'sky':
+ if guess_size_unit == "img":
+ size_unit = 1.0
+ elif guess_size_unit == "sky":
size_unit = pixel_scale
else:
raise ValueError(
- 'invalid guess_size_unit \'{guess_size_unit}\','
- + 'must be one of \'img\', \'sky\''
+ "invalid guess_size_unit '{guess_size_unit}',"
+ + "must be one of 'img', 'sky'"
)
- if guess_size_type == 'sigma':
+ if guess_size_type == "sigma":
guess_size = hsm_shape.moments_sigma * size_unit
- elif guess_size_type == 'T':
+ elif guess_size_type == "T":
guess_size = 2 * (hsm_shape.moments_sigma * size_unit) ** 2
- if guess_centroid_unit == 'img':
+ if guess_centroid_unit == "img":
centroid_unit = 1
- elif guess_centroid_unit == 'sky':
+ elif guess_centroid_unit == "sky":
centroid_unit = pixel_scale
else:
raise ValueError(
- f'invalid guess_centroid_unit \'{guess_centroid_unit}\','
- + ' must be one of \'img\', \'sky\''
+ f"invalid guess_centroid_unit '{guess_centroid_unit}',"
+ + " must be one of 'img', 'sky'"
)
if guess_centroid:
guess_centroid = (
- (hsm_shape.moments_centroid - galsim_img.center) * centroid_unit
- )
+ hsm_shape.moments_centroid - galsim_img.center
+ ) * centroid_unit
else:
guess_centroid = galsim_img.center * centroid_unit
- guess = np.array([
- guess_centroid.x,
- guess_centroid.y,
- 0.,
- 0.,
- guess_size,
- guess_flux
- ])
+ guess = np.array(
+ [guess_centroid.x, guess_centroid.y, 0.0, 0.0, guess_size, guess_flux]
+ )
return guess
@@ -637,8 +663,8 @@ def make_galsimfit(obs, model, guess0, prior=None, ntry=5):
fres = {}
for it in range(ntry):
guess[0:5] += urand(low=-limit, high=limit)
- guess[5:] *= (1 + urand(low=-limit, high=limit))
- fres['flags'] = 1
+ guess[5:] *= 1 + urand(low=-limit, high=limit)
+ fres["flags"] = 1
try:
fitter = ngmix.galsimfit.GalsimSimple(
obs,
@@ -650,15 +676,15 @@ def make_galsimfit(obs, model, guess0, prior=None, ntry=5):
except Exception:
continue
- if fres['flags'] == 0:
+ if fres["flags"] == 0:
break
- if fres['flags'] != 0:
+ if fres["flags"] != 0:
raise ngmix.gexceptions.BootGalFailure(
- 'Failed to fit galaxy image with galsimfit'
+ "Failed to fit galaxy image with galsimfit"
)
- fres['ntry'] = it + 1
+ fres["ntry"] = it + 1
return fres
@@ -730,9 +756,7 @@ def get_noise(gal, weight, guess, pixel_scale, thresh=1.2):
gauss_win = galsim.Gaussian(sigma=np.sqrt(guess[4] / 2), flux=guess[5])
gauss_win = gauss_win.shear(g1=guess[2], g2=guess[3])
gauss_win = gauss_win.drawImage(
- nx=img_shape[0],
- ny=img_shape[1],
- scale=pixel_scale
+ nx=img_shape[0], ny=img_shape[1], scale=pixel_scale
).array
m_weight = weight[gauss_win < thresh * sig_tmp] != 0
@@ -743,14 +767,7 @@ def get_noise(gal, weight, guess, pixel_scale, thresh=1.2):
def do_ngmix_metacal(
- gals,
- psfs,
- psfs_sigma,
- weights,
- flags,
- jacob_list,
- prior,
- pixel_scale
+ gals, psfs, psfs_sigma, weights, flags, jacob_list, prior, pixel_scale
):
"""Do Ngmix Metacal.
@@ -791,10 +808,10 @@ def do_ngmix_metacal(
gal_obs_list = ObsList()
T_guess_psf = []
psf_res_gT = {
- 'g_PSFo': np.array([0., 0.]),
- 'g_err_PSFo': np.array([0., 0.]),
- 'T_PSFo': 0.,
- 'T_err_PSFo': 0.
+ "g_PSFo": np.array([0.0, 0.0]),
+ "g_err_PSFo": np.array([0.0, 0.0]),
+ "T_PSFo": 0.0,
+ "T_err_PSFo": 0.0,
}
gal_guess = []
gal_guess_flag = True
@@ -804,7 +821,7 @@ def do_ngmix_metacal(
psf_jacob = ngmix.Jacobian(
row=(psfs[0].shape[0] - 1) / 2,
col=(psfs[0].shape[1] - 1) / 2,
- wcs=jacob_list[n_e]
+ wcs=jacob_list[n_e],
)
psf_obs = Observation(psfs[n_e], jacobian=psf_jacob)
@@ -812,31 +829,29 @@ def do_ngmix_metacal(
psf_T = psfs_sigma[n_e] * 1.17741 * pixel_scale
weight_map = np.copy(weights[n_e])
- weight_map[np.where(flags[n_e] != 0)] = 0.
+ weight_map[np.where(flags[n_e] != 0)] = 0.0
weight_map[weight_map != 0] = 1
- psf_guess = np.array([0., 0., 0., 0., psf_T, 1.])
+ psf_guess = np.array([0.0, 0.0, 0.0, 0.0, psf_T, 1.0])
try:
- psf_res = make_galsimfit(psf_obs, 'gauss', psf_guess)
+ psf_res = make_galsimfit(psf_obs, "gauss", psf_guess)
except Exception:
continue
# Gal guess
try:
gal_guess_tmp = get_guess(
- gals[n_e],
- pixel_scale,
- guess_size_type='sigma'
+ gals[n_e], pixel_scale, guess_size_type="sigma"
)
except Exception:
gal_guess_flag = False
- gal_guess_tmp = np.array([0., 0., 0., 0., 1, 100])
+ gal_guess_tmp = np.array([0.0, 0.0, 0.0, 0.0, 1, 100])
# Recenter jacobian if necessary
gal_jacob = ngmix.Jacobian(
row=(gals[0].shape[0] - 1) / 2 + gal_guess_tmp[0],
col=(gals[0].shape[1] - 1) / 2 + gal_guess_tmp[1],
- wcs=jacob_list[n_e]
+ wcs=jacob_list[n_e],
)
# Noise handling
@@ -854,20 +869,19 @@ def do_ngmix_metacal(
noise_img_gal = np.random.randn(*gals[n_e].shape) * sig_noise
gal_masked = np.copy(gals[n_e])
- if (len(np.where(weight_map == 0)[0]) != 0):
+ if len(np.where(weight_map == 0)[0]) != 0:
gal_masked[weight_map == 0] = noise_img_gal[weight_map == 0]
- weight_map *= 1 / sig_noise ** 2
+ weight_map *= 1 / sig_noise**2
# Original PSF fit
w_tmp = np.sum(weight_map)
- psf_res_gT['g_PSFo'] += psf_res['g'] * w_tmp
- psf_res_gT['g_err_PSFo'] += np.array([
- psf_res['pars_err'][2],
- psf_res['pars_err'][3]
- ]) * w_tmp
- psf_res_gT['T_PSFo'] += psf_res['T'] * w_tmp
- psf_res_gT['T_err_PSFo'] += psf_res['T_err'] * w_tmp
+ psf_res_gT["g_PSFo"] += psf_res["g"] * w_tmp
+ psf_res_gT["g_err_PSFo"] += (
+ np.array([psf_res["pars_err"][2], psf_res["pars_err"][3]]) * w_tmp
+ )
+ psf_res_gT["T_PSFo"] += psf_res["T"] * w_tmp
+ psf_res_gT["T_err_PSFo"] += psf_res["T_err"] * w_tmp
wsum += w_tmp
gal_obs = Observation(
@@ -875,7 +889,7 @@ def do_ngmix_metacal(
weight=weight_map,
jacobian=gal_jacob,
psf=psf_obs,
- noise=noise_img
+ noise=noise_img,
)
if gal_guess_flag:
@@ -887,7 +901,7 @@ def do_ngmix_metacal(
gal_guess_flag = True
if wsum == 0:
- raise ZeroDivisionError('Sum of weights = 0, division by zero')
+ raise ZeroDivisionError("Sum of weights = 0, division by zero")
# Normalize PSF fit output
for key in psf_res_gT.keys():
@@ -897,22 +911,22 @@ def do_ngmix_metacal(
fail_get_guess = False
if len(gal_guess) == 0:
fail_get_guess = True
- gal_pars = [0., 0., 0., 0., 1, 100]
+ gal_pars = [0.0, 0.0, 0.0, 0.0, 1, 100]
else:
gal_pars = np.mean(gal_guess, 0)
- psf_model = 'gauss'
- gal_model = 'gauss'
+ psf_model = "gauss"
+ gal_model = "gauss"
# metacal specific parameters
metacal_pars = {
- 'types': ['noshear', '1p', '1m', '2p', '2m'],
- 'step': 0.01,
- 'psf': 'gauss',
- 'fixnoise': True,
- 'cheatnoise': False,
- 'symmetrize_psf': False,
- 'use_noise_image': True
+ "types": ["noshear", "1p", "1m", "2p", "2m"],
+ "step": 0.01,
+ "psf": "gauss",
+ "fixnoise": True,
+ "cheatnoise": False,
+ "symmetrize_psf": False,
+ "use_noise_image": True,
}
Tguess = np.mean(T_guess_psf)
@@ -921,25 +935,22 @@ def do_ngmix_metacal(
ntry = 2
obs_dict_mcal = ngmix.metacal.get_all_metacal(gal_obs_list, **metacal_pars)
- res = {'mcal_flags': 0}
+ res = {"mcal_flags": 0}
ntry = 5
for key in sorted(obs_dict_mcal):
fres = make_galsimfit(
- obs_dict_mcal[key],
- gal_model,
- gal_pars,
- prior=prior
+ obs_dict_mcal[key], gal_model, gal_pars, prior=prior
)
- res['mcal_flags'] |= fres['flags']
+ res["mcal_flags"] |= fres["flags"]
tres = {}
for name in fres.keys():
tres[name] = fres[name]
- tres['flags'] = fres['flags']
+ tres["flags"] = fres["flags"]
wsum = 0
Tpsf_sum = 0
@@ -947,29 +958,29 @@ def do_ngmix_metacal(
npsf = 0
for obs in obs_dict_mcal[key]:
- if hasattr(obs, 'psf_nopix'):
+ if hasattr(obs, "psf_nopix"):
try:
psf_res = make_galsimfit(
obs.psf_nopix,
psf_model,
- np.array([0., 0., 0., 0., Tguess, 1.]),
- ntry=ntry
+ np.array([0.0, 0.0, 0.0, 0.0, Tguess, 1.0]),
+ ntry=ntry,
)
except Exception:
continue
- g1, g2 = psf_res['g']
- T = psf_res['T']
+ g1, g2 = psf_res["g"]
+ T = psf_res["T"]
else:
try:
psf_res = make_galsimfit(
obs.psf,
psf_model,
- np.array([0., 0., 0., 0., Tguess, 1.]),
+ np.array([0.0, 0.0, 0.0, 0.0, Tguess, 1.0]),
)
except Exception:
continue
- g1, g2 = psf_res['g']
- T = psf_res['T']
+ g1, g2 = psf_res["g"]
+ T = psf_res["T"]
# TODO we sometimes use other weights
twsum = obs.weight.sum()
@@ -980,8 +991,8 @@ def do_ngmix_metacal(
Tpsf_sum += T * twsum
npsf += 1
- tres['gpsf'] = gpsf_sum / wsum
- tres['Tpsf'] = Tpsf_sum / wsum
+ tres["gpsf"] = gpsf_sum / wsum
+ tres["Tpsf"] = Tpsf_sum / wsum
res[key] = tres
@@ -989,6 +1000,6 @@ def do_ngmix_metacal(
metacal_res = res
metacal_res.update(psf_res_gT)
- metacal_res['moments_fail'] = fail_get_guess
+ metacal_res["moments_fail"] = fail_get_guess
return metacal_res
diff --git a/shapepipe/modules/ngmix_runner.py b/shapepipe/modules/ngmix_runner.py
index 432008793..9c2c5ca08 100644
--- a/shapepipe/modules/ngmix_runner.py
+++ b/shapepipe/modules/ngmix_runner.py
@@ -11,22 +11,22 @@
@module_runner(
- version='0.0.1',
+ version="0.0.1",
input_module=[
- 'sextractor_runner',
- 'psfex_interp_runner',
- 'vignetmaker_runner'
+ "sextractor_runner",
+ "psfex_interp_runner",
+ "vignetmaker_runner",
],
file_pattern=[
- 'tile_sexcat',
- 'image',
- 'exp_background',
- 'galaxy_psf',
- 'weight',
- 'flag'
+ "tile_sexcat",
+ "image",
+ "exp_background",
+ "galaxy_psf",
+ "weight",
+ "flag",
],
- file_ext=['.fits', '.sqlite', '.sqlite', '.sqlite', '.sqlite', '.sqlite'],
- depends=['numpy', 'ngmix', 'galsim', 'sqlitedict', 'astropy'],
+ file_ext=[".fits", ".sqlite", ".sqlite", ".sqlite", ".sqlite", ".sqlite"],
+ depends=["numpy", "ngmix", "galsim", "sqlitedict", "astropy"],
)
def ngmix_runner(
input_file_list,
@@ -40,22 +40,22 @@ def ngmix_runner(
# Read config file entries
# Photometric zero point
- zero_point = config.getfloat(module_config_sec, 'MAG_ZP')
+ zero_point = config.getfloat(module_config_sec, "MAG_ZP")
# Pixel scale
- pixel_scale = config.getfloat(module_config_sec, 'PIXEL_SCALE')
+ pixel_scale = config.getfloat(module_config_sec, "PIXEL_SCALE")
# Path to merged single-exposure single-HDU headers
- f_wcs_path = config.getexpanded(module_config_sec, 'LOG_WCS')
+ f_wcs_path = config.getexpanded(module_config_sec, "LOG_WCS")
# First and last galaxy ID to process
- id_obj_min = config.getint(module_config_sec, 'ID_OBJ_MIN')
- id_obj_max = config.getint(module_config_sec, 'ID_OBJ_MAX')
+ id_obj_min = config.getint(module_config_sec, "ID_OBJ_MIN")
+ id_obj_max = config.getint(module_config_sec, "ID_OBJ_MAX")
# Initialise class instance
ngmix_inst = Ngmix(
input_file_list,
- run_dirs['output'],
+ run_dirs["output"],
file_number_string,
zero_point,
pixel_scale,
@@ -66,7 +66,9 @@ def ngmix_runner(
)
# Process ngmix shape measurement and metacalibration
+ w_log.info("ngmix processing start")
ngmix_inst.process()
+ w_log.info("ngmix end")
# No return objects
return None, None
diff --git a/shapepipe/modules/pastecat_package/__init__.py b/shapepipe/modules/pastecat_package/__init__.py
index 62838d8e4..b5bcfdcc0 100644
--- a/shapepipe/modules/pastecat_package/__init__.py
+++ b/shapepipe/modules/pastecat_package/__init__.py
@@ -32,4 +32,4 @@
"""
-__all__ = ['pastecat']
+__all__ = ["pastecat"]
diff --git a/shapepipe/modules/pastecat_package/pastecat.py b/shapepipe/modules/pastecat_package/pastecat.py
index c1a4b07c6..35941018a 100644
--- a/shapepipe/modules/pastecat_package/pastecat.py
+++ b/shapepipe/modules/pastecat_package/pastecat.py
@@ -49,7 +49,7 @@ def __init__(
w_log,
ext_name=None,
check_col_name=None,
- hdu_no=None
+ hdu_no=None,
):
self._input_file_list = input_file_list
@@ -71,12 +71,12 @@ def process(self):
# Create output catalogue
pasted_cat = file_io.FITSCatalogue(
self._output_path,
- open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
+ open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
)
for idx, input_file in enumerate(self._input_file_list):
- self._w_log.info(f'Pasting catalogue \'{input_file}\'')
+ self._w_log.info(f"Pasting catalogue '{input_file}'")
# Read input data
cat = file_io.FITSCatalogue(input_file)
@@ -90,18 +90,18 @@ def process(self):
if idx > 0:
if self._check_col_name not in col_names:
raise KeyError(
- f'CHECK_COL_NAME key \'{self._check_col_name}\''
- + 'not found in input catalogue'
+ f"CHECK_COL_NAME key '{self._check_col_name}'"
+ + "not found in input catalogue"
)
if not (
data[self._check_col_name]
== data_prev[self._check_col_name]
).all():
raise Exception(
- f'Column check using key'
- + '\'{self._check_col_name}\''
- + 'failed for input catalogues '
- + f'#{idx - 1} and #{idx}'
+ f"Column check using key"
+ + "'{self._check_col_name}'"
+ + "failed for input catalogues "
+ + f"#{idx - 1} and #{idx}"
)
data_prev = data
diff --git a/shapepipe/modules/pastecat_runner.py b/shapepipe/modules/pastecat_runner.py
index 247a44f46..4f659bffa 100644
--- a/shapepipe/modules/pastecat_runner.py
+++ b/shapepipe/modules/pastecat_runner.py
@@ -11,12 +11,12 @@
@module_runner(
- version='1.1',
- input_module='sextractor_runner',
- file_pattern='tile_sexcat',
- file_ext='.fits',
- depends=['numpy', 'astropy'],
- run_method='parallel',
+ version="1.1",
+ input_module="sextractor_runner",
+ file_pattern="tile_sexcat",
+ file_ext=".fits",
+ depends=["numpy", "astropy"],
+ run_method="parallel",
)
def paste_cat_runner(
input_file_list,
@@ -28,48 +28,44 @@ def paste_cat_runner(
):
"""Define The Paste Catalogue Runner."""
# Get config options
- if config.has_option(module_config_sec, 'CHECK_COL_NAME'):
- check_col_name = config.get(module_config_sec, 'CHECK_COL_NAME')
+ if config.has_option(module_config_sec, "CHECK_COL_NAME"):
+ check_col_name = config.get(module_config_sec, "CHECK_COL_NAME")
else:
check_col_name = None
- if config.has_option(module_config_sec, 'HDU'):
- tmp = config.getlist(module_config_sec, 'HDU')
+ if config.has_option(module_config_sec, "HDU"):
+ tmp = config.getlist(module_config_sec, "HDU")
hdu_no = [int(idx) for idx in tmp]
if len(hdu_no) != len(input_file_list):
raise IndexError(
- 'Different lengths for input file list '
- + f'({len(input_file_list)}) and HDU ({len(hdu_no)}).'
+ "Different lengths for input file list "
+ + f"({len(input_file_list)}) and HDU ({len(hdu_no)})."
)
else:
hdu_no = None
- if config.has_option(module_config_sec, 'PREFIX'):
- prefix = config.get(
- module_config_sec,
- 'PREFIX'
- )
+ if config.has_option(module_config_sec, "PREFIX"):
+ prefix = config.get(module_config_sec, "PREFIX")
else:
- prefix = 'cat_pasted'
+ prefix = "cat_pasted"
- if config.has_option(module_config_sec, 'EXT_NAME'):
- ext_name_list = config.getlist(module_config_sec, 'EXT_NAME')
+ if config.has_option(module_config_sec, "EXT_NAME"):
+ ext_name_list = config.getlist(module_config_sec, "EXT_NAME")
if len(ext_name_list) != len(input_file_list):
raise ValueError(
- f'Input file list length ({len(input_file_list)}) '
- + f'and EXT_NAME list ({len(ext_name_list)})'
- + 'need to be equal.'
+ f"Input file list length ({len(input_file_list)}) "
+ + f"and EXT_NAME list ({len(ext_name_list)})"
+ + "need to be equal."
)
else:
ext_name_list = None
# Set file extension
- file_ext = 'fits'
+ file_ext = "fits"
# Set output path
output_path = (
- f'{run_dirs["output"]}/{prefix}'
- + f'{file_number_string}.{file_ext}'
+ f'{run_dirs["output"]}/{prefix}' + f"{file_number_string}.{file_ext}"
)
# Create rand cat class instance
@@ -79,7 +75,7 @@ def paste_cat_runner(
w_log,
ext_name=ext_name_list,
check_col_name=check_col_name,
- hdu_no=hdu_no
+ hdu_no=hdu_no,
)
# Run processing
diff --git a/shapepipe/modules/psfex_interp_package/__init__.py b/shapepipe/modules/psfex_interp_package/__init__.py
index afda4d2e2..1c3b51ca4 100644
--- a/shapepipe/modules/psfex_interp_package/__init__.py
+++ b/shapepipe/modules/psfex_interp_package/__init__.py
@@ -43,4 +43,4 @@
"""
-__all__ = ['psfex_interp']
+__all__ = ["psfex_interp"]
diff --git a/shapepipe/modules/psfex_interp_package/psfex_interp.py b/shapepipe/modules/psfex_interp_package/psfex_interp.py
index 3ac1b25ea..dc18a0339 100644
--- a/shapepipe/modules/psfex_interp_package/psfex_interp.py
+++ b/shapepipe/modules/psfex_interp_package/psfex_interp.py
@@ -2,7 +2,7 @@
This module computes the PSFs from a PSFEx model at several galaxy positions.
-:Authors: Morgan Schmitz and Axel Guinot
+:Authors: Morgan Schmitz, Axel Guinot, Martin Kilbinger
"""
@@ -24,86 +24,9 @@
import_fail = False
-NOT_ENOUGH_STARS = 'Fail_stars'
-BAD_CHI2 = 'Fail_chi2'
-FILE_NOT_FOUND = 'File_not_found'
-
-
-def interpsfex(dotpsfpath, pos, thresh_star, thresh_chi2):
- """Interpolate PSFEx.
-
- Use PSFEx generated model to perform spatial PSF interpolation.
-
- Parameters
- ----------
- dotpsfpath : str
- Path to ``.psf`` file (PSFEx output)
- pos : numpy.ndarray
- Positions where the PSF model should be evaluated
- thresh_star : int
- Threshold of stars under which the PSF is not interpolated
- thresh_chi2 : int
- Threshold for chi squared
-
- Returns
- -------
- numpy.ndarray
- Array of PSFs, each row is the PSF image at the corresponding position
- requested
-
- """
- if not os.path.exists(dotpsfpath):
- return FILE_NOT_FOUND
-
- # read PSF model and extract basis and polynomial degree and scale position
- PSF_model = fits.open(dotpsfpath)[1]
-
- # Check number of stars used to compute the PSF
- if PSF_model.header['ACCEPTED'] < thresh_star:
- return NOT_ENOUGH_STARS
- if PSF_model.header['CHI2'] > thresh_chi2:
- return BAD_CHI2
-
- PSF_basis = np.array(PSF_model.data)[0][0]
- try:
- deg = PSF_model.header['POLDEG1']
- except KeyError:
- # constant PSF model
- return PSF_basis[0, :, :]
-
- # scale coordinates
- x_interp, x_scale = (
- PSF_model.header['POLZERO1'],
- PSF_model.header['POLSCAL1']
- )
- y_interp, y_scale = (
- PSF_model.header['POLZERO2'],
- PSF_model.header['POLSCAL2']
-
- )
- xs, ys = (pos[:, 0] - x_interp) / x_scale, (pos[:, 1] - y_interp) / y_scale
-
- # compute polynomial coefficients
- coeffs = np.array([[x ** idx for idx in range(deg + 1)] for x in xs])
- cross_coeffs = np.array([
- np.concatenate([
- [(x ** idx_j) * (y ** idx_i) for idx_j in range(deg - idx_i + 1)]
- for idx_i in range(1, deg + 1)
- ])
- for x, y in zip(xs, ys)
- ])
- coeffs = np.hstack((coeffs, cross_coeffs))
-
- # compute interpolated PSF
- PSFs = np.array([
- np.sum(
- [coeff * atom for coeff, atom in zip(coeffs_posi, PSF_basis)],
- axis=0,
- )
- for coeffs_posi in coeffs
- ])
-
- return PSFs
+NOT_ENOUGH_STARS = "Fail_stars"
+BAD_CHI2 = "Fail_chi2"
+FILE_NOT_FOUND = "File_not_found"
class PSFExInterpolator(object):
@@ -115,7 +38,7 @@ class PSFExInterpolator(object):
Parameters
----------
dotpsf_path : str
- Path to PSFEx output file
+ Path to PSFEx output file; can be `None` in multi-epoch mode
galcat_path : str
Path to SExtractor-like galaxy catalogue
output_path : str
@@ -151,22 +74,22 @@ def __init__(
):
# Path to PSFEx output file
- if (
- isinstance(dotpsf_path, type(None))
- or os.path.isfile(dotpsf_path)
+ self._dotpsf_path = dotpsf_path
+ if not isinstance(dotpsf_path, type(None)) and not os.path.isfile(
+ dotpsf_path
):
- self._dotpsf_path = dotpsf_path
- else:
- raise ValueError(f'Cound not find file {dotpsf_path}.')
+ raise ValueError(f"Cound not find file {dotpsf_path}.")
+
# Path to catalogue containing galaxy positions
if os.path.isfile(galcat_path):
self._galcat_path = galcat_path
else:
- raise ValueError(f'Cound not find file {galcat_path}.')
+ raise ValueError(f"Cound not find file {galcat_path}.")
+
# Path to output file to be written
- self._output_path = output_path + '/galaxy_psf'
+ self._output_path = output_path + "/galaxy_psf"
# Path to output file to be written for validation
- self._output_path_validation = output_path + '/validation_psf'
+ self._output_path_validation = output_path + "/validation_psf"
# if required, compute and save shapes
self._compute_shape = get_shapes
# Number of stars under which we don't interpolate the PSF
@@ -182,8 +105,8 @@ def __init__(
if pos_params:
if not len(pos_params) == 2:
raise ValueError(
- f'{len(pos_params)} position parameters were passed on; '
- + 'there should be exactly two.'
+ f"{len(pos_params)} position parameters were passed on; "
+ + "there should be exactly two."
)
self._pos_params = pos_params
else:
@@ -210,21 +133,18 @@ def process(self):
and self.interp_PSFs == NOT_ENOUGH_STARS
):
self._w_log.info(
- 'Not enough stars to interpolate the psf in the file '
- + f'{self._dotpsf_path}.'
+ "Not enough stars to interpolate the psf in the file "
+ + f"{self._dotpsf_path}."
)
- elif (
- isinstance(self.interp_PSFs, str)
- and self.interp_PSFs == BAD_CHI2
- ):
+ elif isinstance(self.interp_PSFs, str) and self.interp_PSFs == BAD_CHI2:
self._w_log.info(
- f'Bad chi2 for the psf model in the file {self._dotpsf_path}.'
+ f"Bad chi2 for the psf model in the file {self._dotpsf_path}."
)
elif (
isinstance(self.interp_PSFs, str)
and self.interp_PSFs == FILE_NOT_FOUND
):
- self._w_log.info(f'Psf model file {self._dotpsf_path} not found.')
+ self._w_log.info(f"Psf model file {self._dotpsf_path} not found.")
else:
if self._compute_shape:
self._get_psfshapes()
@@ -240,8 +160,8 @@ def _get_position_parameters(self):
dotpsf = file_io.FITSCatalogue(self._dotpsf_path)
dotpsf.open()
self._pos_params = [
- dotpsf.get_header()['POLNAME1'],
- dotpsf.get_header()['POLNAME2']
+ dotpsf.get_header()["POLNAME1"],
+ dotpsf.get_header()["POLNAME2"],
]
dotpsf.close()
@@ -258,28 +178,125 @@ def _get_galaxy_positions(self):
galcat.open()
try:
- self.gal_pos = np.array([
- [x, y] for x, y in zip(
- galcat.get_data()[self._pos_params[0]],
- galcat.get_data()[self._pos_params[1]]
- )
- ])
+ self.gal_pos = np.array(
+ [
+ [x, y]
+ for x, y in zip(
+ galcat.get_data()[self._pos_params[0]],
+ galcat.get_data()[self._pos_params[1]],
+ )
+ ]
+ )
self._w_log.info(
- f'Read {self.gal_pos.shape[0]} positions from galaxy catalog'
+ f"Read {self.gal_pos.shape[0]} positions from galaxy catalog"
)
except KeyError as detail:
# extract erroneous position parameter from original exception
err_pos_param = detail.args[0][4:-15]
pos_param_err = (
- f'Required position parameter {err_pos_param}'
- + 'was not found in galaxy catalog. Leave '
- + 'pos_params (or EXTRA_CODE_OPTION) blank to '
- + 'read them from .psf file.'
+ f"Required position parameter {err_pos_param}"
+ + "was not found in galaxy catalog. Leave "
+ + "pos_params (or EXTRA_CODE_OPTION) blank to "
+ + "read them from .psf file."
)
raise KeyError(pos_param_err)
galcat.close()
+ def interpsfex(self, dotpsfpath, pos):
+ """Interpolate PSFEx.
+
+ Use PSFEx generated model to perform spatial PSF interpolation.
+
+ Parameters
+ ----------
+ dotpsfpath : str
+ Path to ``.psf`` file (PSFEx output)
+ pos : numpy.ndarray
+ Positions where the PSF model should be evaluated
+
+ Returns
+ -------
+ numpy.ndarray
+ Array of PSFs, each row is the PSF image at the corresponding position
+ requested
+
+ """
+ if not os.path.exists(dotpsfpath):
+ return FILE_NOT_FOUND
+
+ # read PSF model and extract basis and polynomial degree and scale position
+ try:
+ PSF_model = fits.open(dotpsfpath)[1]
+ except OSError as err:
+ msg = f"Psf model file {dotpsfpath} empty or corrupt."
+ self._w_log.info(msg)
+ self._w_log.info(f"Error: {err=}, {type(err)=}")
+ raise
+
+ # Check number of stars used to compute the PSF
+ thresh_star = self._star_thresh
+ thresh_chi2 = self._chi2_thresh
+
+ if PSF_model.header["ACCEPTED"] < thresh_star:
+ return NOT_ENOUGH_STARS
+ if PSF_model.header["CHI2"] > thresh_chi2:
+ return BAD_CHI2
+
+ PSF_basis = np.array(PSF_model.data)[0][0]
+ try:
+ deg = PSF_model.header["POLDEG1"]
+ except KeyError:
+ # constant PSF model
+ return PSF_basis[0, :, :]
+
+ # scale coordinates
+ x_interp, x_scale = (
+ PSF_model.header["POLZERO1"],
+ PSF_model.header["POLSCAL1"],
+ )
+ y_interp, y_scale = (
+ PSF_model.header["POLZERO2"],
+ PSF_model.header["POLSCAL2"],
+ )
+ xs, ys = (pos[:, 0] - x_interp) / x_scale, (
+ pos[:, 1] - y_interp
+ ) / y_scale
+
+ # compute polynomial coefficients
+ coeffs = np.array([[x**idx for idx in range(deg + 1)] for x in xs])
+ cross_coeffs = np.array(
+ [
+ np.concatenate(
+ [
+ [
+ (x**idx_j) * (y**idx_i)
+ for idx_j in range(deg - idx_i + 1)
+ ]
+ for idx_i in range(1, deg + 1)
+ ]
+ )
+ for x, y in zip(xs, ys)
+ ]
+ )
+ coeffs = np.hstack((coeffs, cross_coeffs))
+
+ # compute interpolated PSF
+ PSFs = np.array(
+ [
+ np.sum(
+ [
+ coeff * atom
+ for coeff, atom in zip(coeffs_posi, PSF_basis)
+ ],
+ axis=0,
+ )
+ for coeffs_posi in coeffs
+ ]
+ )
+
+ return PSFs
+
def _interpolate(self):
"""Interpolate.
@@ -287,11 +304,9 @@ def _interpolate(self):
positions.
"""
- self.interp_PSFs = interpsfex(
+ self.interp_PSFs = self.interpsfex(
self._dotpsf_path,
self.gal_pos,
- self._star_thresh,
- self._chi2_thresh,
)
def _get_psfshapes(self):
@@ -301,22 +316,24 @@ def _get_psfshapes(self):
"""
if import_fail:
- raise ImportError('Galsim is required to get shapes information')
+ raise ImportError("Galsim is required to get shapes information")
psf_moms = [
hsm.FindAdaptiveMom(Image(psf), strict=False)
for psf in self.interp_PSFs
]
- self.psf_shapes = np.array([
+ self.psf_shapes = np.array(
[
- moms.observed_shape.g1,
- moms.observed_shape.g2,
- moms.moments_sigma,
- int(bool(moms.error_message))
+ [
+ moms.observed_shape.g1,
+ moms.observed_shape.g2,
+ moms.moments_sigma,
+ int(bool(moms.error_message)),
+ ]
+ for moms in psf_moms
]
- for moms in psf_moms
- ])
+ )
def _write_output(self):
"""Write Output.
@@ -325,21 +342,21 @@ def _write_output(self):
"""
output = file_io.FITSCatalogue(
- self._output_path + self._img_number + '.fits',
+ self._output_path + self._img_number + ".fits",
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
SEx_catalogue=True,
)
if self._compute_shape:
data = {
- 'VIGNET': self.interp_PSFs,
- 'E1_PSF_HSM': self.psf_shapes[:, 0],
- 'E2_PSF_HSM': self.psf_shapes[:, 1],
- 'SIGMA_PSF_HSM': self.psf_shapes[:, 2],
- 'FLAG_PSF_HSM': self.psf_shapes[:, 3].astype(int)
+ "VIGNET": self.interp_PSFs,
+ "E1_PSF_HSM": self.psf_shapes[:, 0],
+ "E2_PSF_HSM": self.psf_shapes[:, 1],
+ "SIGMA_PSF_HSM": self.psf_shapes[:, 2],
+ "FLAG_PSF_HSM": self.psf_shapes[:, 3].astype(int),
}
else:
- data = {'VIGNET': self.interp_PSFs}
+ data = {"VIGNET": self.interp_PSFs}
output.save_as_fits(data, sex_cat_path=self._galcat_path)
def process_validation(self, psfex_cat_path):
@@ -354,7 +371,7 @@ def process_validation(self, psfex_cat_path):
"""
if not os.path.isfile(psfex_cat_path):
- raise ValueError(f'Cound not find file {psfex_cat_path}.')
+ raise ValueError(f"Cound not find file {psfex_cat_path}.")
if self.gal_pos is None:
self._get_galaxy_positions()
@@ -367,21 +384,18 @@ def process_validation(self, psfex_cat_path):
and self.interp_PSFs == NOT_ENOUGH_STARS
):
self._w_log.info(
- 'Not enough stars to interpolate the psf in the file '
- + f'{self._dotpsf_path}.'
+ "Not enough stars to interpolate the psf in the file "
+ + f"{self._dotpsf_path}."
)
- elif (
- isinstance(self.interp_PSFs, str)
- and self.interp_PSFs == BAD_CHI2
- ):
+ elif isinstance(self.interp_PSFs, str) and self.interp_PSFs == BAD_CHI2:
self._w_log.info(
- f'Bad chi2 for the psf model in the file {self._dotpsf_path}.'
+ f"Bad chi2 for the psf model in the file {self._dotpsf_path}."
)
elif (
isinstance(self.interp_PSFs, str)
and self.interp_PSFs == FILE_NOT_FOUND
):
- self._w_log.info(f'Psf model file {self._dotpsf_path} not found.')
+ self._w_log.info(f"Psf model file {self._dotpsf_path} not found.")
else:
star_cat = file_io.FITSCatalogue(
self._galcat_path,
@@ -389,14 +403,14 @@ def process_validation(self, psfex_cat_path):
)
star_cat.open()
star_dict = {}
- star_vign = np.copy(star_cat.get_data()['VIGNET'])
- star_dict['NUMBER'] = np.copy(star_cat.get_data()['NUMBER'])
- star_dict['X'] = np.copy(star_cat.get_data()['XWIN_IMAGE'])
- star_dict['Y'] = np.copy(star_cat.get_data()['YWIN_IMAGE'])
- star_dict['RA'] = np.copy(star_cat.get_data()['XWIN_WORLD'])
- star_dict['DEC'] = np.copy(star_cat.get_data()['YWIN_WORLD'])
- star_dict['MAG'] = np.copy(star_cat.get_data()['MAG_AUTO'])
- star_dict['SNR'] = np.copy(star_cat.get_data()['SNR_WIN'])
+ star_vign = np.copy(star_cat.get_data()["VIGNET"])
+ star_dict["NUMBER"] = np.copy(star_cat.get_data()["NUMBER"])
+ star_dict["X"] = np.copy(star_cat.get_data()["XWIN_IMAGE"])
+ star_dict["Y"] = np.copy(star_cat.get_data()["YWIN_IMAGE"])
+ star_dict["RA"] = np.copy(star_cat.get_data()["XWIN_WORLD"])
+ star_dict["DEC"] = np.copy(star_cat.get_data()["YWIN_WORLD"])
+ star_dict["MAG"] = np.copy(star_cat.get_data()["MAG_AUTO"])
+ star_dict["SNR"] = np.copy(star_cat.get_data()["SNR_WIN"])
star_cat.close()
self._get_psfshapes()
@@ -417,7 +431,7 @@ def _get_starshapes(self, star_vign):
"""
if import_fail:
- raise ImportError('Galsim is required to get shapes information')
+ raise ImportError("Galsim is required to get shapes information")
masks = np.zeros_like(star_vign)
masks[np.where(star_vign == -1e30)] = 1
@@ -427,15 +441,17 @@ def _get_starshapes(self, star_vign):
for star, mask in zip(star_vign, masks)
]
- self.star_shapes = np.array([
+ self.star_shapes = np.array(
[
- moms.observed_shape.g1,
- moms.observed_shape.g2,
- moms.moments_sigma,
- int(bool(moms.error_message))
+ [
+ moms.observed_shape.g1,
+ moms.observed_shape.g2,
+ moms.moments_sigma,
+ int(bool(moms.error_message)),
+ ]
+ for moms in star_moms
]
- for moms in star_moms
- ])
+ )
def _get_psfexcatdict(self, psfex_cat_path):
"""Get PSFEx Catalogue Dictionary.
@@ -457,18 +473,16 @@ def _get_psfexcatdict(self, psfex_cat_path):
psfex_cat.open()
psfex_cat_dict = {}
- psfex_cat_dict['SOURCE_NUMBER'] = np.copy(
- psfex_cat.get_data()['SOURCE_NUMBER']
- )
- psfex_cat_dict['DELTAX_IMAGE'] = np.copy(
- psfex_cat.get_data()['DELTAX_IMAGE']
+ psfex_cat_dict["SOURCE_NUMBER"] = np.copy(
+ psfex_cat.get_data()["SOURCE_NUMBER"]
)
- psfex_cat_dict['DELTAY_IMAGE'] = np.copy(
- psfex_cat.get_data()['DELTAY_IMAGE']
+ psfex_cat_dict["DELTAX_IMAGE"] = np.copy(
+ psfex_cat.get_data()["DELTAX_IMAGE"]
)
- psfex_cat_dict['CHI2_PSF'] = np.copy(
- psfex_cat.get_data()['CHI2_PSF']
+ psfex_cat_dict["DELTAY_IMAGE"] = np.copy(
+ psfex_cat.get_data()["DELTAY_IMAGE"]
)
+ psfex_cat_dict["CHI2_PSF"] = np.copy(psfex_cat.get_data()["CHI2_PSF"])
return psfex_cat_dict
@@ -486,58 +500,58 @@ def _write_output_validation(self, star_dict, psfex_cat_dict):
"""
output = file_io.FITSCatalogue(
- self._output_path_validation + self._img_number + '.fits',
+ self._output_path_validation + self._img_number + ".fits",
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
SEx_catalogue=True,
)
data = {
- 'E1_PSF_HSM': self.psf_shapes[:, 0],
- 'E2_PSF_HSM': self.psf_shapes[:, 1],
- 'SIGMA_PSF_HSM': self.psf_shapes[:, 2],
- 'FLAG_PSF_HSM': self.psf_shapes[:, 3].astype(int),
- 'E1_STAR_HSM': self.star_shapes[:, 0],
- 'E2_STAR_HSM': self.star_shapes[:, 1],
- 'SIGMA_STAR_HSM': self.star_shapes[:, 2],
- 'FLAG_STAR_HSM': self.star_shapes[:, 3].astype(int)
+ "E1_PSF_HSM": self.psf_shapes[:, 0],
+ "E2_PSF_HSM": self.psf_shapes[:, 1],
+ "SIGMA_PSF_HSM": self.psf_shapes[:, 2],
+ "FLAG_PSF_HSM": self.psf_shapes[:, 3].astype(int),
+ "E1_STAR_HSM": self.star_shapes[:, 0],
+ "E2_STAR_HSM": self.star_shapes[:, 1],
+ "SIGMA_STAR_HSM": self.star_shapes[:, 2],
+ "FLAG_STAR_HSM": self.star_shapes[:, 3].astype(int),
}
data = {**data, **star_dict}
- data['ACCEPTED'] = np.ones_like(data['NUMBER'], dtype='int16')
- star_used = psfex_cat_dict.pop('SOURCE_NUMBER')
+ data["ACCEPTED"] = np.ones_like(data["NUMBER"], dtype="int16")
+ star_used = psfex_cat_dict.pop("SOURCE_NUMBER")
- for idx in range(len(data['NUMBER'])):
+ for idx in range(len(data["NUMBER"])):
if idx + 1 not in star_used:
- data['ACCEPTED'][idx] = 0
+ data["ACCEPTED"][idx] = 0
output.save_as_fits(data, sex_cat_path=self._galcat_path)
- def process_me(self, dot_psf_dir, dot_psf_pattern, f_wcs_path):
+ def process_me(self, dot_psf_dirs, dot_psf_pattern, f_wcs_path):
"""Process Multi-Epoch.
- Process the multi-epoch.
+ Process multi-epoc PSF interpolation.
Parameters
----------
- dot_psf_dir : str
- Path to the directory containing the ``.psf`` files
+ dot_psf_dirs : list
+ Paths to the directory containing the ``.psf`` files
dot_psf_pattern : str
Common pattern of the ``.psf`` files
f_wcs_path : str
Path to the log file containing the WCS for each CCDs
"""
- if os.path.exists(dot_psf_dir):
- self._dot_psf_dir = dot_psf_dir
- else:
- raise ValueError(f'Cound not find directory {dot_psf_dir}.')
+ if not any(os.path.exists(dot_psf_dir) for dot_psf_dir in dot_psf_dirs):
+ raise ValueError("Cound not find any dot psf directory.")
+
+ self._dot_psf_dirs = dot_psf_dirs
self._dot_psf_pattern = dot_psf_pattern
if os.path.isfile(f_wcs_path):
self._f_wcs_file = SqliteDict(f_wcs_path)
else:
- raise ValueError(f'Cound not find file {f_wcs_path}.')
+ raise ValueError(f"Cound not find file {f_wcs_path}.")
if self.gal_pos is None:
self._get_galaxy_positions()
@@ -566,26 +580,28 @@ def _interpolate_me(self):
cat = file_io.FITSCatalogue(self._galcat_path, SEx_catalogue=True)
cat.open()
- all_id = np.copy(cat.get_data()['NUMBER'])
- key_ne = 'N_EPOCH'
- if key_ne not in cat.get_data():
+ all_id = np.copy(cat.get_data()["NUMBER"])
+ key_ne = "N_EPOCH"
+ if key_ne not in cat.get_data().dtype.names:
raise KeyError(
- f'Key {key_ne} not found in input galaxy catalogue, needed for'
- + ' PSF interpolation to multi-epoch data; run previous module'
- + ' (SExtractor) in multi-epoch mode'
+ f"Key {key_ne} not found in input galaxy catalogue"
+ + f" {self._galcat_path}, needed for"
+ + " PSF interpolation to multi-epoch data; run previous module"
+ + " (SExtractor) in multi-epoch mode"
)
- n_epoch = np.copy(cat.get_data()[key_me])
+ n_epoch = np.copy(cat.get_data()[key_ne])
list_ext_name = cat.get_ext_name()
hdu_ind = [
- idx for idx in range(len(list_ext_name))
- if 'EPOCH' in list_ext_name[idx]
+ idx
+ for idx in range(len(list_ext_name))
+ if "EPOCH" in list_ext_name[idx]
]
final_list = []
for hdu_index in hdu_ind:
- exp_name = cat.get_data(hdu_index)['EXP_NAME'][0]
- ccd_list = list(set(cat.get_data(hdu_index)['CCD_N']))
+ exp_name = cat.get_data(hdu_index)["EXP_NAME"][0]
+ ccd_list = list(set(cat.get_data(hdu_index)["CCD_N"]))
array_psf = None
array_id = None
array_shape = None
@@ -593,25 +609,35 @@ def _interpolate_me(self):
for ccd in ccd_list:
if ccd == -1:
continue
- dot_psf_path = (
- f'{self._dot_psf_dir}/{self._dot_psf_pattern}-{exp_name}'
- + f'-{ccd}.psf'
- )
- ind_obj = np.where(cat.get_data(hdu_index)['CCD_N'] == ccd)[0]
+ found = False
+ for dot_psf_dir in self._dot_psf_dirs:
+ dot_psf_path = (
+ f"{dot_psf_dir}/{self._dot_psf_pattern}-{exp_name}"
+ + f"-{ccd}.psf"
+ )
+ if os.path.exists(dot_psf_path):
+ found = True
+ break
+ if not found:
+ self._w_log.info(
+ f"No .psf file found for exposure {exp_name} and"
+ + f" ccd {ccd}"
+ )
+ continue
+
+ ind_obj = np.where(cat.get_data(hdu_index)["CCD_N"] == ccd)[0]
obj_id = all_id[ind_obj]
gal_pos = np.array(
- self._f_wcs_file[exp_name][ccd]['WCS'].all_world2pix(
+ self._f_wcs_file[exp_name][ccd]["WCS"].all_world2pix(
self.gal_pos[:, 0][ind_obj],
self.gal_pos[:, 1][ind_obj],
0,
)
).T
- self.interp_PSFs = interpsfex(
+ self.interp_PSFs = self.interpsfex(
dot_psf_path,
gal_pos,
- self._star_thresh,
- self._chi2_thresh,
)
if (
@@ -619,9 +645,9 @@ def _interpolate_me(self):
and self.interp_PSFs == NOT_ENOUGH_STARS
):
self._w_log.info(
- f'Not enough stars find in the ccd {ccd} of the '
- + f'exposure {exp_name}. Object inside this ccd will '
- + 'lose an epoch.'
+ f"Not enough stars found on ccd {ccd} of "
+ + f"exposure {exp_name}. Object inside this ccd will "
+ + "lose an epoch."
)
continue
if (
@@ -629,9 +655,9 @@ def _interpolate_me(self):
and self.interp_PSFs == BAD_CHI2
):
self._w_log.info(
- f'Bad chi2 for the psf model in the ccd {ccd} of the '
- + f'exposure {exp_name}. Object inside this ccd will '
- + 'lose an epoch.'
+ f"Bad chi2 for the psf model in the ccd {ccd} of the "
+ + f"exposure {exp_name}. Object inside this ccd will "
+ + "lose an epoch."
)
continue
if (
@@ -639,8 +665,8 @@ def _interpolate_me(self):
and self.interp_PSFs == FILE_NOT_FOUND
):
self._w_log.info(
- f'Psf model file {self._dotpsf_path} not found. '
- + 'Object inside this ccd will lose an epoch.'
+ f"Psf model file {dot_psf_path} not found. "
+ + "Object inside this ccd will lose an epoch."
)
continue
@@ -661,16 +687,18 @@ def _interpolate_me(self):
if array_shape is None:
array_shape = np.copy(self.psf_shapes)
else:
- array_shape = np.concatenate((
- array_shape,
- np.copy(self.psf_shapes),
- ))
+ array_shape = np.concatenate(
+ (
+ array_shape,
+ np.copy(self.psf_shapes),
+ )
+ )
else:
array_shape = None
- exp_name_tmp = np.array([
- exp_name + '-' + str(ccd) for _ in range(len(obj_id))
- ])
+ exp_name_tmp = np.array(
+ [exp_name + "-" + str(ccd) for _ in range(len(obj_id))]
+ )
if array_exp_name is None:
array_exp_name = exp_name_tmp
else:
@@ -678,12 +706,9 @@ def _interpolate_me(self):
(array_exp_name, exp_name_tmp)
)
- final_list.append([
- array_id,
- array_psf,
- array_shape,
- array_exp_name
- ])
+ final_list.append(
+ [array_id, array_psf, array_shape, array_exp_name]
+ )
self._f_wcs_file.close()
cat.close()
@@ -695,34 +720,34 @@ def _interpolate_me(self):
counter = 0
for j in range(len(final_list)):
where_res = np.where(final_list[j][0] == id_tmp)[0]
- if (len(where_res) != 0):
+ if len(where_res) != 0:
output_dict[id_tmp][final_list[j][3][where_res[0]]] = {}
- output_dict[id_tmp][
- final_list[j][3][where_res[0]]
- ]['VIGNET'] = final_list[j][1][where_res[0]]
+ output_dict[id_tmp][final_list[j][3][where_res[0]]][
+ "VIGNET"
+ ] = final_list[j][1][where_res[0]]
if self._compute_shape:
shape_dict = {}
- shape_dict['E1_PSF_HSM'] = (
- final_list[j][2][where_res[0]][0]
- )
- shape_dict['E2_PSF_HSM'] = (
- final_list[j][2][where_res[0]][1]
- )
- shape_dict['SIGMA_PSF_HSM'] = (
- final_list[j][2][where_res[0]][2]
- )
- shape_dict['FLAG_PSF_HSM'] = (
- final_list[j][2][where_res[0]][3]
- )
- output_dict[id_tmp][
- final_list[j][3][where_res[0]]
- ]['SHAPES'] = shape_dict
+ shape_dict["E1_PSF_HSM"] = final_list[j][2][
+ where_res[0]
+ ][0]
+ shape_dict["E2_PSF_HSM"] = final_list[j][2][
+ where_res[0]
+ ][1]
+ shape_dict["SIGMA_PSF_HSM"] = final_list[j][2][
+ where_res[0]
+ ][2]
+ shape_dict["FLAG_PSF_HSM"] = final_list[j][2][
+ where_res[0]
+ ][3]
+ output_dict[id_tmp][final_list[j][3][where_res[0]]][
+ "SHAPES"
+ ] = shape_dict
counter += 1
if counter == 0:
- output_dict[id_tmp] = 'empty'
+ output_dict[id_tmp] = "empty"
n_empty += 1
- self._w_log.info(f'{n_empty}/{len(all_id)} PSFs are empty')
+ self._w_log.info(f"{n_empty}/{len(all_id)} PSFs are empty")
return output_dict
@@ -738,7 +763,7 @@ def _write_output_me(self, output_dict):
"""
output_file = SqliteDict(
- self._output_path + self._img_number + '.sqlite'
+ self._output_path + self._img_number + ".sqlite"
)
for idx in output_dict.keys():
output_file[str(idx)] = output_dict[idx]
diff --git a/shapepipe/modules/psfex_interp_runner.py b/shapepipe/modules/psfex_interp_runner.py
index f18b543fb..55d8d73c1 100644
--- a/shapepipe/modules/psfex_interp_runner.py
+++ b/shapepipe/modules/psfex_interp_runner.py
@@ -2,22 +2,22 @@
Module runner for ``psfex_interp``.
-:Author: Axel Guinot
+:Author: Axel Guinot, Martin Kilbinger
"""
from shapepipe.modules.module_decorator import module_runner
from shapepipe.modules.psfex_interp_package import psfex_interp
-from shapepipe.pipeline.run_log import get_last_dir
+from shapepipe.pipeline.run_log import get_last_dir, get_all_dirs
@module_runner(
- version='1.1',
- input_module=['psfex_runner', 'setools_runner'],
- file_pattern=['star_selection', 'galaxy_selection'],
- file_ext=['.psf', '.fits'],
- depends=['numpy', 'astropy', 'galsim', 'sqlitedict'],
+ version="1.1",
+ input_module=["psfex_runner", "setools_runner"],
+ file_pattern=["star_selection", "galaxy_selection"],
+ file_ext=[".psf", ".fits"],
+ depends=["numpy", "astropy", "galsim", "sqlitedict"],
)
def psfex_interp_runner(
input_file_list,
@@ -29,15 +29,15 @@ def psfex_interp_runner(
):
"""Define The PSFEx Interpolation Runner."""
# Fetch interpolation run mode
- mode = config.get(module_config_sec, 'MODE')
+ mode = config.get(module_config_sec, "MODE")
# Fetch parameter values
- pos_params = config.getlist(module_config_sec, 'POSITION_PARAMS')
- get_shapes = config.getboolean(module_config_sec, 'GET_SHAPES')
- star_thresh = config.getint(module_config_sec, 'STAR_THRESH')
- chi2_thresh = config.getint(module_config_sec, 'CHI2_THRESH')
+ pos_params = config.getlist(module_config_sec, "POSITION_PARAMS")
+ get_shapes = config.getboolean(module_config_sec, "GET_SHAPES")
+ star_thresh = config.getint(module_config_sec, "STAR_THRESH")
+ chi2_thresh = config.getint(module_config_sec, "CHI2_THRESH")
# Run in CLASSIC mode
- if mode == 'CLASSIC':
+ if mode == "CLASSIC":
# Set input paths
psfcat_path, galcat_path = input_file_list
@@ -46,7 +46,7 @@ def psfex_interp_runner(
pi_inst = psfex_interp.PSFExInterpolator(
psfcat_path,
galcat_path,
- run_dirs['output'],
+ run_dirs["output"],
file_number_string,
w_log,
pos_params,
@@ -59,19 +59,29 @@ def psfex_interp_runner(
pi_inst.process()
# Run in MULTI-EPOCH mode
- elif mode == 'MULTI-EPOCH':
+ elif mode == "MULTI-EPOCH":
# Fetch multi-epoch parameters
module = config.getexpanded(
module_config_sec,
- 'ME_DOT_PSF_DIR',
+ "ME_DOT_PSF_DIR",
)
- dot_psf_dir = get_last_dir(run_dirs['run_log'], module)
+ module_name = module.split(":")[-1]
+ if "last" in module:
+ dot_psf_dirs = [get_last_dir(run_dirs["run_log"], module_name)]
+ elif "all" in module:
+ dot_psf_dirs = get_all_dirs(run_dirs["run_log"], module_name)
+ else:
+ raise ValueError(
+ "Expected qualifier 'last:' or 'all' before module"
+ + f" '{module}' in config entry 'ME_DOT_PSF_DIR'"
+ )
+
dot_psf_pattern = config.get(
module_config_sec,
- 'ME_DOT_PSF_PATTERN',
+ "ME_DOT_PSF_PATTERN",
)
- f_wcs_path = config.getexpanded(module_config_sec, 'ME_LOG_WCS')
+ f_wcs_path = config.getexpanded(module_config_sec, "ME_LOG_WCS")
# Set input paths
galcat_path = input_file_list[0]
@@ -80,7 +90,7 @@ def psfex_interp_runner(
psfex_interp_inst = psfex_interp.PSFExInterpolator(
None,
galcat_path,
- run_dirs['output'],
+ run_dirs["output"],
file_number_string,
w_log,
pos_params,
@@ -90,10 +100,10 @@ def psfex_interp_runner(
)
# Process inputs multi-epoch
- psfex_interp_inst.process_me(dot_psf_dir, dot_psf_pattern, f_wcs_path)
+ psfex_interp_inst.process_me(dot_psf_dirs, dot_psf_pattern, f_wcs_path)
# Run in VALIDATION mode
- elif mode == 'VALIDATION':
+ elif mode == "VALIDATION":
# Set input paths
psfcat_path, galcat_path, psfex_cat_path = input_file_list
@@ -102,7 +112,7 @@ def psfex_interp_runner(
psfex_interp_inst = psfex_interp.PSFExInterpolator(
psfcat_path,
galcat_path,
- run_dirs['output'],
+ run_dirs["output"],
file_number_string,
w_log,
pos_params,
@@ -116,7 +126,7 @@ def psfex_interp_runner(
else:
# Raise error for invalid run mode
- ValueError('MODE has to be in : [CLASSIC, MULTI-EPOCH, VALIDATION]')
+ ValueError("MODE has to be in : [CLASSIC, MULTI-EPOCH, VALIDATION]")
# No return objects
return None, None
diff --git a/shapepipe/modules/psfex_package/__init__.py b/shapepipe/modules/psfex_package/__init__.py
index 81cdd2e69..63e7590d0 100644
--- a/shapepipe/modules/psfex_package/__init__.py
+++ b/shapepipe/modules/psfex_package/__init__.py
@@ -35,4 +35,4 @@
"""
-__all__ = ['psfex_script']
+__all__ = ["psfex_script"]
diff --git a/shapepipe/modules/psfex_package/psfex_script.py b/shapepipe/modules/psfex_package/psfex_script.py
index 7e8866426..bde7b4a5d 100644
--- a/shapepipe/modules/psfex_package/psfex_script.py
+++ b/shapepipe/modules/psfex_package/psfex_script.py
@@ -39,7 +39,7 @@ def __init__(
psfex_config_file,
output_dir,
outcatalog_name,
- check_image_list
+ check_image_list,
):
self.psfex_executable_path = psfex_executable_path
self.input_file_path = input_file_path
@@ -61,19 +61,16 @@ def generate_command(self):
"""
# Prepare command line
command_line = (
- f'{self.psfex_executable_path} '
- + f'{self.input_file_path} '
- + f'-c {self.psfex_config_file} '
- + f'-PSF_DIR {self.output_dir} '
- + f'-OUTCAT_NAME {self.outcatalog_name}'
+ f"{self.psfex_executable_path} "
+ + f"{self.input_file_path} "
+ + f"-c {self.psfex_config_file} "
+ + f"-PSF_DIR {self.output_dir} "
+ + f"-OUTCAT_NAME {self.outcatalog_name}"
)
- if (
- (len(self.check_image_list) == 1)
- & (self.check_image_list[0] == '')
- ):
- check_type_list = ['NONE']
- check_name_list = ['none']
+ if (len(self.check_image_list) == 1) & (self.check_image_list[0] == ""):
+ check_type_list = ["NONE"]
+ check_name_list = ["none"]
else:
# Get pattern for filenaming from file in list
input_file_name = os.path.split(input_file_path)[-1]
@@ -85,10 +82,10 @@ def generate_command(self):
for check_image in self.check_image_list:
check_type_list.append(check_image.upper())
check_name_list.append(
- f'{output_dir}'
- + f'/{suffix}'
- + f'{check_image.lower()}'
- + f'{file_number_string}.fits'
+ f"{output_dir}"
+ + f"/{suffix}"
+ + f"{check_image.lower()}"
+ + f"{file_number_string}.fits"
)
# Add checks to command line
@@ -120,11 +117,11 @@ def parse_errors(stderr, stdout):
Updated standard output and error
"""
- check_error = re.findall('error', stdout.lower())
- check_error2 = re.findall('all done', stdout.lower())
+ check_error = re.findall("error", stdout.lower())
+ check_error2 = re.findall("all done", stdout.lower())
if check_error == []:
- stderr2 = ''
+ stderr2 = ""
else:
stderr2 = stdout
diff --git a/shapepipe/modules/psfex_runner.py b/shapepipe/modules/psfex_runner.py
index 0398c46c8..d9c515e58 100644
--- a/shapepipe/modules/psfex_runner.py
+++ b/shapepipe/modules/psfex_runner.py
@@ -12,45 +12,41 @@
@module_runner(
- input_module='setools_runner',
- version='1.0',
- file_pattern=['star_selection'],
- file_ext=['.fits'],
- executes='psfex',
+ input_module="setools_runner",
+ version="1.0",
+ file_pattern=["star_selection"],
+ file_ext=[".fits"],
+ executes="psfex",
)
def psfex_runner(
- input_file_list,
- run_dirs,
- file_number_string,
- config,
- module_config_sec,
- w_log,
+ input_file_list,
+ run_dirs,
+ file_number_string,
+ config,
+ module_config_sec,
+ w_log,
):
"""Define The PSFEx Runner."""
# Extract psfex run configurations
- if config.has_option(module_config_sec, 'EXEC_PATH'):
+ if config.has_option(module_config_sec, "EXEC_PATH"):
psfex_executable_path = config.getexpanded(
- module_config_sec,
- 'EXEC_PATH'
+ module_config_sec, "EXEC_PATH"
)
else:
- psfex_executable_path = 'psfex'
- output_dir = run_dirs['output']
+ psfex_executable_path = "psfex"
+ output_dir = run_dirs["output"]
- outcatalog_name = f'{output_dir}/psfex_cat{file_number_string}.cat'
+ outcatalog_name = f"{output_dir}/psfex_cat{file_number_string}.cat"
- psfex_config_file = config.getexpanded(
- module_config_sec,
- 'DOT_PSFEX_FILE'
- )
+ psfex_config_file = config.getexpanded(module_config_sec, "DOT_PSFEX_FILE")
input_file_path = input_file_list[0]
# Check image options
- if config.has_option(module_config_sec, 'CHECKIMAGE'):
- check_image_list = config.getlist(module_config_sec, 'CHECKIMAGE')
+ if config.has_option(module_config_sec, "CHECKIMAGE"):
+ check_image_list = config.getlist(module_config_sec, "CHECKIMAGE")
else:
- check_image_list = ['']
+ check_image_list = [""]
# Create psfex caller class instance
psfex_inst = PSFExCaller(
@@ -64,7 +60,7 @@ def psfex_runner(
# Generate psfex command line
command_line = psfex_inst.generate_command()
- w_log.info(f'Running command \'{command_line}\'')
+ w_log.info(f"Running command '{command_line}'")
# Execute command line
stderr, stdout = execute(command_line)
diff --git a/shapepipe/modules/python_example_package/__init__.py b/shapepipe/modules/python_example_package/__init__.py
index ecc47860d..41bce721e 100644
--- a/shapepipe/modules/python_example_package/__init__.py
+++ b/shapepipe/modules/python_example_package/__init__.py
@@ -27,4 +27,4 @@
"""
-__all__ = ['python_example']
+__all__ = ["python_example"]
diff --git a/shapepipe/modules/python_example_package/python_example.py b/shapepipe/modules/python_example_package/python_example.py
index d9ea2a22c..5bbe9a968 100644
--- a/shapepipe/modules/python_example_package/python_example.py
+++ b/shapepipe/modules/python_example_package/python_example.py
@@ -60,7 +60,7 @@ def _read_file(self, file_name):
"""
with open(file_name) as data_file:
- content = data_file.read().replace('\n', '')
+ content = data_file.read().replace("\n", "")
return content
@@ -81,7 +81,7 @@ def read_files(self, file_name1, file_name2):
content1 = self._read_file(file_name1)
content2 = self._read_file(file_name2)
- self.content = f'{content1} and {content2}'
+ self.content = f"{content1} and {content2}"
def write_file(self, file_name, message):
"""Write File.
@@ -98,6 +98,6 @@ def write_file(self, file_name, message):
"""
new_content = message + str(self.content)
- text_file = open(file_name, 'w')
+ text_file = open(file_name, "w")
text_file.write(new_content)
text_file.close()
diff --git a/shapepipe/modules/python_example_runner.py b/shapepipe/modules/python_example_runner.py
index d468c10e0..f5016f08a 100644
--- a/shapepipe/modules/python_example_runner.py
+++ b/shapepipe/modules/python_example_runner.py
@@ -11,25 +11,25 @@
@module_runner(
- version='1.1',
- file_pattern=['numbers', 'letters'],
- file_ext='.txt',
+ version="1.1",
+ file_pattern=["numbers", "letters"],
+ file_ext=".txt",
depends=[
- 'numpy',
- 'astropy',
- 'galsim',
- 'joblib',
- 'mccd',
- 'ngmix',
- 'pandas',
- 'pysap',
- 'scipy',
- 'sf_tools',
- 'sip_tpv',
- 'sqlitedict',
- 'treecorr',
+ "numpy",
+ "astropy",
+ "galsim",
+ "joblib",
+ "mccd",
+ "ngmix",
+ "pandas",
+ "pysap",
+ "scipy",
+ "sf_tools",
+ "sip_tpv",
+ "sqlitedict",
+ "treecorr",
],
- run_method='parallel',
+ run_method="parallel",
)
def python_example_runner(
input_file_list,
@@ -46,7 +46,7 @@ def python_example_runner(
)
# Retrieve log message from config file
- message = config.get(module_config_sec, 'MESSAGE')
+ message = config.get(module_config_sec, "MESSAGE")
# Create an instance of the Python example class
py_ex_inst = python_example.PythonExample(0)
diff --git a/shapepipe/modules/random_cat_package/__init__.py b/shapepipe/modules/random_cat_package/__init__.py
index b3a1cf21e..32c6f64b2 100644
--- a/shapepipe/modules/random_cat_package/__init__.py
+++ b/shapepipe/modules/random_cat_package/__init__.py
@@ -34,4 +34,4 @@
"""
-__all__ = ['random_cat.py']
+__all__ = ["random_cat.py"]
diff --git a/shapepipe/modules/random_cat_package/random_cat.py b/shapepipe/modules/random_cat_package/random_cat.py
index 3bdb6ba6d..feb69ff90 100644
--- a/shapepipe/modules/random_cat_package/random_cat.py
+++ b/shapepipe/modules/random_cat_package/random_cat.py
@@ -22,7 +22,7 @@
from shapepipe.utilities import cfis
-class RandomCat():
+class RandomCat:
"""Random Catalogue.
This class creates a random catalogue given a mask FITS file.
@@ -90,24 +90,24 @@ def save_as_healpix(self, mask, header):
return
# Tranform config entry from str to int
- nside = int(self._healpix_options['NSIDE'])
+ nside = int(self._healpix_options["NSIDE"])
mask_1d, footprint = reproject_to_healpix(
(mask, header),
- 'galactic',
+ "galactic",
nside=nside,
)
t = Table()
- t['flux'] = mask_1d
- t.meta['ORDERING'] = 'RING'
- t.meta['COORDSYS'] = 'G'
- t.meta['NSIDE'] = nside
- t.meta['INDXSCHM'] = 'IMPLICIT'
+ t["flux"] = mask_1d
+ t.meta["ORDERING"] = "RING"
+ t.meta["COORDSYS"] = "G"
+ t.meta["NSIDE"] = nside
+ t.meta["INDXSCHM"] = "IMPLICIT"
output_path = (
f'{self._output_dir}/{self._healpix_options["FILE_BASE"]}-'
- + f'{self._file_number_string}.fits'
+ + f"{self._file_number_string}.fits"
)
t.write(output_path)
@@ -174,14 +174,14 @@ def process(self):
# Check that a reasonably large number of pixels is not masked
if n_unmasked < n_obj:
raise ValueError(
- f'Number of un-masked pixels {n_unmasked} is smaller '
- + f'than number of random objects requested {n_obj}'
+ f"Number of un-masked pixels {n_unmasked} is smaller "
+ + f"than number of random objects requested {n_obj}"
)
else:
n_obj = 0
- self._w_log.info(f'Creating {n_obj} random objects')
+ self._w_log.info(f"Creating {n_obj} random objects")
# Draw points until n are in mask
n_found = 0
@@ -213,35 +213,28 @@ def process(self):
# Tile ID
output_path = (
- f'{self._output_dir}/{self._output_file_pattern}-'
- + f'{self._file_number_string}.fits'
+ f"{self._output_dir}/{self._output_file_pattern}-"
+ + f"{self._file_number_string}.fits"
)
file_name = os.path.split(output_path)[1]
file_base = os.path.splitext(file_name)[0]
- tile_ID_str = re.split('-', file_base)[1:]
- tile_id = float('.'.join(tile_ID_str))
+ tile_ID_str = re.split("-", file_base)[1:]
+ tile_id = float(".".join(tile_ID_str))
tile_id_array = np.ones(n_obj) * tile_id
# Write to output
- cat_out = [
- ra_rand,
- dec_rand,
- x_rand,
- y_rand,
- tile_id_array
- ]
- column_names = ['RA', 'DEC', 'x', 'y', 'TILE_ID']
+ cat_out = [ra_rand, dec_rand, x_rand, y_rand, tile_id_array]
+ column_names = ["RA", "DEC", "x", "y", "TILE_ID"]
# TODO: Add units to header
output = file_io.FITSCatalogue(
- output_path,
- open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
+ output_path, open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
)
output.save_as_fits(cat_out, names=column_names)
# Write area information to log file
- self._w_log.info(f'Total area = {area_deg2:.4f} deg^2')
- self._w_log.info(f'Unmasked area = {area_deg2_eff:.4f} deg^2')
+ self._w_log.info(f"Total area = {area_deg2:.4f} deg^2")
+ self._w_log.info(f"Unmasked area = {area_deg2_eff:.4f} deg^2")
self._w_log.info(
- f'Ratio masked to total pixels = {n_unmasked / n_pix:.3f}'
+ f"Ratio masked to total pixels = {n_unmasked / n_pix:.3f}"
)
diff --git a/shapepipe/modules/random_cat_runner.py b/shapepipe/modules/random_cat_runner.py
index 5595a53ad..665792fec 100644
--- a/shapepipe/modules/random_cat_runner.py
+++ b/shapepipe/modules/random_cat_runner.py
@@ -11,11 +11,11 @@
@module_runner(
- version='1.1',
- file_pattern=['image', 'pipeline_flag'],
- file_ext=['.fits', 'fits'],
- depends=['astropy'],
- numbering_scheme='_0',
+ version="1.1",
+ file_pattern=["image", "pipeline_flag"],
+ file_ext=[".fits", "fits"],
+ depends=["astropy"],
+ numbering_scheme="_0",
)
def random_cat_runner(
input_file_list,
@@ -31,42 +31,39 @@ def random_cat_runner(
input_mask_name = input_file_list[1]
# Set output file name
- if config.has_option(module_config_sec, 'OUTPUT_FILE_PATTERN'):
+ if config.has_option(module_config_sec, "OUTPUT_FILE_PATTERN"):
output_file_pattern = config.get(
- module_config_sec,
- 'OUTPUT_FILE_PATTERN'
+ module_config_sec, "OUTPUT_FILE_PATTERN"
)
else:
- output_file_pattern = 'random_cat'
+ output_file_pattern = "random_cat"
# Get number of random objects requested on output
- n_rand = config.getfloat(module_config_sec, 'N_RANDOM')
+ n_rand = config.getfloat(module_config_sec, "N_RANDOM")
# Flag whether n_rand is total (DENSITY=False, default)
# or per square degree (DENSITY=True)
- if config.has_option(module_config_sec, 'DENSITY'):
- density = config.getboolean(module_config_sec, 'DENSITY')
+ if config.has_option(module_config_sec, "DENSITY"):
+ density = config.getboolean(module_config_sec, "DENSITY")
else:
density = False
# Get healpix output options
save_mask_as_healpix = config.getboolean(
- module_config_sec,
- 'SAVE_MASK_AS_HEALPIX'
+ module_config_sec, "SAVE_MASK_AS_HEALPIX"
)
if save_mask_as_healpix:
healpix_options = {}
- for option_trunc in ['FILE_BASE', 'NSIDE']:
- option = f'HEALPIX_OUT_{option_trunc}'
+ for option_trunc in ["FILE_BASE", "NSIDE"]:
+ option = f"HEALPIX_OUT_{option_trunc}"
healpix_options[option_trunc] = config.get(
- module_config_sec,
- option
+ module_config_sec, option
)
# Create rand cat class instance
rand_cat_inst = RandomCat(
input_image_name,
input_mask_name,
- run_dirs['output'],
+ run_dirs["output"],
file_number_string,
output_file_pattern,
n_rand,
diff --git a/shapepipe/modules/serial_example_runner.py b/shapepipe/modules/serial_example_runner.py
index 3baced6ee..61cfc3edf 100644
--- a/shapepipe/modules/serial_example_runner.py
+++ b/shapepipe/modules/serial_example_runner.py
@@ -19,13 +19,13 @@ def __init__(self):
def _read_file(self, file_name):
"""Read File."""
with open(file_name) as data_file:
- content = data_file.read().replace('\n', '')
+ content = data_file.read().replace("\n", "")
return content
def read_files(self, input_file_list):
"""Read Files."""
- self.content = ''
+ self.content = ""
for file_list in input_file_list:
for file_name in file_list:
@@ -33,18 +33,18 @@ def read_files(self, input_file_list):
def write_file(self, file_name):
"""Write Files."""
- text_file = open(file_name, 'w')
+ text_file = open(file_name, "w")
text_file.write(self.content)
text_file.close()
@module_runner(
- version='1.1',
- input_module='python_example_runner',
- file_pattern=['numbers', 'letters', 'pyex_output'],
- file_ext=['.txt', '.txt', '.cat'],
- depends='numpy',
- run_method='serial',
+ version="1.1",
+ input_module="python_example_runner",
+ file_pattern=["numbers", "letters", "pyex_output"],
+ file_ext=[".txt", ".txt", ".cat"],
+ depends="numpy",
+ run_method="serial",
)
def serial_example_runner(
input_file_list,
diff --git a/shapepipe/modules/setools_package/__init__.py b/shapepipe/modules/setools_package/__init__.py
index 0414a9db7..502df0ae8 100644
--- a/shapepipe/modules/setools_package/__init__.py
+++ b/shapepipe/modules/setools_package/__init__.py
@@ -203,4 +203,4 @@
"""
-__all__ = ['setools']
+__all__ = ["setools"]
diff --git a/shapepipe/modules/setools_package/setools.py b/shapepipe/modules/setools_package/setools.py
index 78feae3d1..c430b52b1 100644
--- a/shapepipe/modules/setools_package/setools.py
+++ b/shapepipe/modules/setools_package/setools.py
@@ -12,6 +12,9 @@
import re
import string
+import matplotlib
+matplotlib.use('Agg')
+
import matplotlib.pylab as plt
import numpy as np
@@ -58,7 +61,10 @@ def __init__(
SEx_catalogue=True,
)
cat_file.open()
- self._data = cat_file.get_data()
+ try:
+ self._data = cat_file.get_data()
+ except:
+ raise IOError(f"Could not load catalogue data from {cat}")
cat_file.close()
else:
@@ -85,39 +91,39 @@ def process(self, w_log):
if self._is_file:
file_number = self._file_number_string
else:
- file_number = ''
+ file_number = ""
self.read()
# Processing: Create mask = filter input
if len(self._mask) != 0:
- direc = f'{self._output_dir}/mask'
+ direc = f"{self._output_dir}/mask"
mkdir(direc)
self._make_mask()
for key in self.mask.keys():
- if 'NO_SAVE' in self._mask[key]:
+ if "NO_SAVE" in self._mask[key]:
continue
- file_name = f'{direc}/{key}{file_number}.fits'
+ file_name = f"{direc}/{key}{file_number}.fits"
self.save_mask(self.mask[key], file_name)
if len(self._plot) != 0:
- direc = f'{self._output_dir}/plot'
+ direc = f"{self._output_dir}/plot"
mkdir(direc)
self._make_plot()
for key in self.plot.keys():
- output_path = f'{direc}/{key}{file_number}'
+ output_path = f"{direc}/{key}{file_number}"
SEPlot(self.plot[key], self._data, output_path, self.mask)
if len(self._new_cat) != 0:
- direc = f'{self._output_dir}/new_cat'
+ direc = f"{self._output_dir}/new_cat"
mkdir(direc)
self._make_new_cat()
for key in self.new_cat.keys():
- file_name = f'{direc}/{key}{file_number}'
+ file_name = f"{direc}/{key}{file_number}"
self.save_new_cat(self.new_cat[key], file_name)
if len(self._rand_split) != 0:
- direc = f'{self._output_dir}/rand_split'
+ direc = f"{self._output_dir}/rand_split"
mkdir(direc)
self._make_rand_split()
@@ -131,12 +137,13 @@ def process(self, w_log):
empty_found = True
if empty_found:
w_log.info(
- 'At least one random-split catalogue is empty, no '
- + 'random sub-samples written for sample_type='
- + f'{sample_type}')
+ "At least one random-split catalogue is empty, no "
+ + "random sub-samples written for sample_type="
+ + f"{sample_type}"
+ )
continue
- output_dir = f'{direc}/{sample_type}_'
+ output_dir = f"{direc}/{sample_type}_"
self.save_rand_split(
self.rand_split[sample_type],
output_dir,
@@ -144,11 +151,11 @@ def process(self, w_log):
)
if len(self._stat) != 0:
- direc = f'{self._output_dir}/stat'
+ direc = f"{self._output_dir}/stat"
mkdir(direc)
self._make_stat()
for key in self.stat.keys():
- output_path = f'{direc}/{key}{file_number}.txt'
+ output_path = f"{direc}/{key}{file_number}.txt"
self.save_stat(self.stat[key], output_path)
def read(self):
@@ -177,7 +184,7 @@ def read(self):
while True:
line_tmp = self._config_file.readline()
- if line_tmp == '':
+ if line_tmp == "":
break
line_tmp = self._clean_line(line_tmp)
@@ -189,49 +196,49 @@ def read(self):
# [SECTION_TYPE:OBJECT_NAME], e.g.
# [MASK:star_selection]
- if (in_section != 0) & (re.split(r'\[', line_tmp)[0] == ''):
+ if (in_section != 0) & (re.split(r"\[", line_tmp)[0] == ""):
in_section = 0
if not in_section:
- if (re.split(r'\[', line_tmp)[0] != ''):
- raise RuntimeError('No section found')
+ if re.split(r"\[", line_tmp)[0] != "":
+ raise RuntimeError("No section found")
- sec = re.split(r'\[|\]', line_tmp)[1]
- if re.split(':', sec)[0] == 'MASK':
+ sec = re.split(r"\[|\]", line_tmp)[1]
+ if re.split(":", sec)[0] == "MASK":
in_section = 1
try:
- mask_name = re.split(':', sec)[1]
+ mask_name = re.split(":", sec)[1]
except Exception:
- mask_name = f'mask_{len(self._mask) + 1}'
+ mask_name = f"mask_{len(self._mask) + 1}"
self._mask_key.append(mask_name)
self._mask[mask_name] = []
- elif re.split(':', sec)[0] == 'PLOT':
+ elif re.split(":", sec)[0] == "PLOT":
in_section = 2
try:
- plot_name = re.split(':', sec)[1]
+ plot_name = re.split(":", sec)[1]
except Exception:
- plot_name = f'plot_{len(self._plot) + 1}'
+ plot_name = f"plot_{len(self._plot) + 1}"
self._plot[plot_name] = []
- elif re.split(':', sec)[0] == 'STAT':
+ elif re.split(":", sec)[0] == "STAT":
in_section = 3
try:
- stat_name = re.split(':', sec)[1]
+ stat_name = re.split(":", sec)[1]
except Exception:
- stat_name = f'stat_{len(self._stat) + 1}'
+ stat_name = f"stat_{len(self._stat) + 1}"
self._stat[stat_name] = []
- elif re.split(':', sec)[0] == 'NEW_CAT':
+ elif re.split(":", sec)[0] == "NEW_CAT":
in_section = 4
try:
- new_cat_name = re.split(':', sec)[1]
+ new_cat_name = re.split(":", sec)[1]
except Exception:
- new_cat_name = f'new_cat_{len(self._new_cat) + 1}'
+ new_cat_name = f"new_cat_{len(self._new_cat) + 1}"
self._new_cat[new_cat_name] = []
- elif re.split(':', sec)[0] == 'RAND_SPLIT':
+ elif re.split(":", sec)[0] == "RAND_SPLIT":
in_section = 5
try:
- rand_split_name = re.split(':', sec)[1]
+ rand_split_name = re.split(":", sec)[1]
except Exception:
rand_split_name = (
- f'rand_split_{len(self._rand_split) + 1}'
+ f"rand_split_{len(self._rand_split) + 1}"
)
self._rand_split[rand_split_name] = []
else:
@@ -271,23 +278,23 @@ def _clean_line(self, line):
"""
s = re.split('"', line)
if len(s) == 3:
- line_tmp = s[0].replace(' ', '') + s[1] + s[2].replace(' ', '')
+ line_tmp = s[0].replace(" ", "") + s[1] + s[2].replace(" ", "")
else:
- line_tmp = line.replace(' ', '')
+ line_tmp = line.replace(" ", "")
- if re.split('#', line_tmp)[0] == '':
+ if re.split("#", line_tmp)[0] == "":
return None
- line_tmp = line_tmp.replace('\n', '')
- line_tmp = line_tmp.replace('\t', '')
- line_tmp = re.split('#', line_tmp)[0]
+ line_tmp = line_tmp.replace("\n", "")
+ line_tmp = line_tmp.replace("\t", "")
+ line_tmp = re.split("#", line_tmp)[0]
- if line_tmp != '':
+ if line_tmp != "":
return line_tmp
else:
return None
- def save_mask(self, mask, output_path, ext_name='LDAC_OBJECTS'):
+ def save_mask(self, mask, output_path, ext_name="LDAC_OBJECTS"):
"""Save Mask.
This function will apply a mask to the data and save them into a new
@@ -312,12 +319,12 @@ def save_mask(self, mask, output_path, ext_name='LDAC_OBJECTS'):
"""
if mask is None:
- raise ValueError('mask not provided')
+ raise ValueError("mask not provided")
if len(mask) == 0:
pass
if output_path is None:
- raise ValueError('output path not provided')
+ raise ValueError("output path not provided")
mask_file = file_io.FITSCatalogue(
output_path,
@@ -330,7 +337,7 @@ def save_mask(self, mask, output_path, ext_name='LDAC_OBJECTS'):
sex_cat_path=self._cat_filepath,
)
- def save_new_cat(self, new_cat, output_path, ext_name='LDAC_OBJECTS'):
+ def save_new_cat(self, new_cat, output_path, ext_name="LDAC_OBJECTS"):
"""Save New Catalogue.
This function creates a new catalogue with a specific format
@@ -354,19 +361,19 @@ def save_new_cat(self, new_cat, output_path, ext_name='LDAC_OBJECTS'):
"""
try:
- output_format = new_cat.pop('OUTPUT_FORMAT')
+ output_format = new_cat.pop("OUTPUT_FORMAT")
except Exception:
- raise ValueError('OUTPUT_FORMAT not provided')
+ raise ValueError("OUTPUT_FORMAT not provided")
- if output_format == 'fits':
+ if output_format == "fits":
new_file = file_io.FITSCatalogue(
- output_path + '.fits',
+ output_path + ".fits",
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
)
new_file.save_as_fits(data=new_cat, ext_name=ext_name)
- elif output_format == 'SEx_cat':
+ elif output_format == "SEx_cat":
new_file = file_io.FITSCatalogue(
- output_path + '.fits',
+ output_path + ".fits",
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
SEx_catalogue=(self._cat_filepath is not None),
)
@@ -375,23 +382,23 @@ def save_new_cat(self, new_cat, output_path, ext_name='LDAC_OBJECTS'):
ext_name=ext_name,
sex_cat_path=self._cat_filepath,
)
- elif (output_format == 'txt') | (output_format == 'ascii'):
- new_file = open(output_path + '.txt', 'w')
- new_file.write('# HEADER\n')
- new_file.write('# ')
+ elif (output_format == "txt") | (output_format == "ascii"):
+ new_file = open(output_path + ".txt", "w")
+ new_file.write("# HEADER\n")
+ new_file.write("# ")
n_max = -1
for key in new_cat.keys():
if len(new_cat[key]) > n_max:
n_max = len(new_cat[key])
- new_file.write(f'{key}\t')
- new_file.write('\n')
+ new_file.write(f"{key}\t")
+ new_file.write("\n")
for idx in range(n_max):
for key in new_cat.keys():
try:
- new_file.write(f'{new_cat[key][idx]}\t')
+ new_file.write(f"{new_cat[key][idx]}\t")
except Exception:
- new_file.write('\t')
- new_file.write('\n')
+ new_file.write("\t")
+ new_file.write("\n")
new_file.close()
else:
raise ValueError("Format should be in ['fits', 'SEx_cat', 'txt']")
@@ -401,7 +408,7 @@ def save_rand_split(
rand_split,
output_path,
file_number,
- ext_name='LDAC_OBJECTS',
+ ext_name="LDAC_OBJECTS",
):
"""Save Random Split Catalogues.
@@ -429,18 +436,18 @@ def save_rand_split(
"""
if rand_split is None:
- raise ValueError('rand_split not provided')
+ raise ValueError("rand_split not provided")
if output_path is None:
- raise ValueError('output path not provided')
+ raise ValueError("output path not provided")
if file_number is None:
- raise ValueError('file_number path not provided')
+ raise ValueError("file_number path not provided")
- mask = rand_split.pop('mask')
+ mask = rand_split.pop("mask")
data = self._data[mask]
for idx in rand_split.keys():
rand_split_file = file_io.FITSCatalogue(
- f'{output_path}{idx}{file_number}.fits',
+ f"{output_path}{idx}{file_number}.fits",
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
SEx_catalogue=(self._cat_filepath is not None),
)
@@ -471,15 +478,15 @@ def save_stat(self, stat, output_path):
"""
if stat is None:
- raise ValueError('stat not provided')
+ raise ValueError("stat not provided")
if output_path is None:
- raise ValueError('output path not provided')
+ raise ValueError("output path not provided")
- file = open(output_path, 'w')
- file.write('# Statistics\n')
+ file = open(output_path, "w")
+ file.write("# Statistics\n")
for key in stat.keys():
- file.write(f'{key} = {str(stat[key])}\n')
+ file.write(f"{key} = {str(stat[key])}\n")
file.close()
@@ -504,8 +511,8 @@ def _make_mask(self):
global_mask = np.ones(self._cat_size, dtype=bool)
global_ind = np.where(global_mask)[0]
for idx in self._mask[key]:
- s = re.split('{|}', idx)
- if s[0] == '':
+ s = re.split("{|}", idx)
+ if s[0] == "":
try:
global_mask &= self.mask[s[1]]
global_ind = np.where(global_mask)[0]
@@ -515,7 +522,7 @@ def _make_mask(self):
mask_tmp = None
for idx in self._mask[key]:
- if idx == 'NO_SAVE':
+ if idx == "NO_SAVE":
continue
tmp = StrInterpreter(
idx,
@@ -553,23 +560,23 @@ def _make_plot(self):
for key in self._plot.keys():
self.plot[key] = {}
for idx in self._plot[key]:
- s = re.split('=', idx)
+ s = re.split("=", idx)
if len(s) != 2:
raise ValueError(
- 'Plot option keyword/value not in correct format '
- + f'(key=val): {idx}'
+ "Plot option keyword/value not in correct format "
+ + f"(key=val): {idx}"
)
- ss = re.split('_', s[0])
+ ss = re.split("_", s[0])
if len(ss) == 1:
- self.plot[key][ss[0]] = {'0': s[1]}
+ self.plot[key][ss[0]] = {"0": s[1]}
elif len(ss) == 2:
if ss[0] not in self.plot[key].keys():
self.plot[key][ss[0]] = {}
self.plot[key][ss[0]][ss[1]] = s[1]
else:
raise ValueError(
- 'Plot keyword not in correct format (key or key_i)'
- + f': {idx}'
+ "Plot keyword not in correct format (key or key_i)"
+ + f": {idx}"
)
def _make_new_cat(self):
@@ -591,9 +598,9 @@ def _make_new_cat(self):
for key in self._new_cat.keys():
self.new_cat[key] = {}
for idx in self._new_cat[key]:
- s = re.split('=', j)
+ s = re.split("=", j)
if len(s) == 2:
- if s[0] == 'OUTPUT_FORMAT':
+ if s[0] == "OUTPUT_FORMAT":
self.new_cat[key][s[0]] = s[1]
else:
self.new_cat[key][s[0]] = StrInterpreter(
@@ -603,7 +610,7 @@ def _make_new_cat(self):
mask_dict=self.mask,
).result
else:
- raise ValueError(f'Not a valid format : {idx}')
+ raise ValueError(f"Not a valid format : {idx}")
def _make_rand_split(self):
"""Make Random Split.
@@ -629,25 +636,25 @@ def _make_rand_split(self):
for key in self._rand_split.keys():
self.rand_split[key] = {}
for idx in self._rand_split[key]:
- s = re.split('=', idx)
+ s = re.split("=", idx)
if len(s) != 2:
raise ValueError(
- f'Not a valid format : {self._rand_split[key][0]}'
+ f"Not a valid format : {self._rand_split[key][0]}"
)
- if s[0] == 'RATIO':
+ if s[0] == "RATIO":
try:
ratio = float(s[1])
except Exception:
- raise ValueError('RATIO is not a number')
+ raise ValueError("RATIO is not a number")
if ratio >= 1:
- ratio /= 100.
- elif s[0] == 'MASK':
- ss = re.split(',', s[1])
+ ratio /= 100.0
+ elif s[0] == "MASK":
+ ss = re.split(",", s[1])
for k in ss:
try:
mask &= self.mask[k]
except Exception:
- raise ValueError(f'mask {k} does not exist')
+ raise ValueError(f"mask {k} does not exist")
cat_size = len(np.where(mask)[0])
n_keep = int(np.ceil(cat_size * ratio))
@@ -658,9 +665,9 @@ def _make_rand_split(self):
mask_ratio.append(mask_left.pop(idx))
mask_ratio = np.array(mask_ratio)
mask_left = np.array(mask_left)
- self.rand_split[key]['mask'] = mask
- self.rand_split[key][f'ratio_{int(ratio * 100)}'] = mask_ratio
- self.rand_split[key][f'ratio_{100 - int(ratio * 100)}'] = mask_left
+ self.rand_split[key]["mask"] = mask
+ self.rand_split[key][f"ratio_{int(ratio * 100)}"] = mask_ratio
+ self.rand_split[key][f"ratio_{100 - int(ratio * 100)}"] = mask_left
def _make_stat(self):
"""Make Statistics.
@@ -680,9 +687,9 @@ def _make_stat(self):
for key in self._stat.keys():
self.stat[key] = {}
for idx in self._stat[key]:
- s = re.split('=', idx)
+ s = re.split("=", idx)
if len(s) != 2:
- raise ValueError(f'Not a valid format : {idx}')
+ raise ValueError(f"Not a valid format : {idx}")
self.stat[key][s[0]] = StrInterpreter(
s[1],
self._data,
@@ -729,33 +736,33 @@ class SEPlot(object):
def __init__(self, plot_dict, catalogue, output_path, mask_dict=None):
if plot_dict is None:
- raise ValueError('plot_dict not provided')
+ raise ValueError("plot_dict not provided")
if catalogue is None:
- raise ValueError('catalogue not provided')
+ raise ValueError("catalogue not provided")
if output_path is None:
- raise ValueError('output_path not provided')
+ raise ValueError("output_path not provided")
self._plot = plot_dict
self._output_path = output_path
self._cat = catalogue
self._mask_dict = mask_dict
- if 'TYPE' not in self._plot.keys():
- raise ValueError('Plot type not specified')
+ if "TYPE" not in self._plot.keys():
+ raise ValueError("Plot type not specified")
- if self._plot['TYPE']['0'] in ['plot', 'PLOT']:
- self._check_key_for_plot(['X', 'Y'])
+ if self._plot["TYPE"]["0"] in ["plot", "PLOT"]:
+ self._check_key_for_plot(["X", "Y"])
self._make_plot()
- elif self._plot['TYPE']['0'] in ['scatter', 'SCATTER']:
- self._check_key_for_plot(['X', 'Y'])
+ elif self._plot["TYPE"]["0"] in ["scatter", "SCATTER"]:
+ self._check_key_for_plot(["X", "Y"])
self._make_scatter()
- elif self._plot['TYPE']['0'] in [
- 'histogram',
- 'hist',
- 'HISTOGRAM',
- 'HIST'
+ elif self._plot["TYPE"]["0"] in [
+ "histogram",
+ "hist",
+ "HISTOGRAM",
+ "HIST",
]:
- self._check_key_for_plot(['Y'])
+ self._check_key_for_plot(["Y"])
self._make_hist()
else:
raise ValueError(f'Type : {self._plot["TYPE"]["0"]} not available')
@@ -779,7 +786,7 @@ def _check_key_for_plot(self, key_list):
for key in key_list:
if key not in self._plot.keys():
raise ValueError(
- f'Key \'{key}\' not provided for plot of type '
+ f"Key '{key}' not provided for plot of type "
+ f'\'{self._plot["TYPE"]["0"]}\''
)
@@ -802,9 +809,9 @@ def _make_plot(self):
"""
self._fig = plt.figure()
- if 'TITLE' in self._plot.keys():
- title = self._plot['TITLE']['0']
- s = re.split('@', title)
+ if "TITLE" in self._plot.keys():
+ title = self._plot["TITLE"]["0"]
+ s = re.split("@", title)
if len(s) >= 3:
title = s[0]
ii = 1
@@ -812,23 +819,25 @@ def _make_plot(self):
if ii % 2 == 0:
title += idx
else:
- title += str(StrInterpreter(
- idx,
- self._cat,
- make_compare=False,
- mask_dict=self._mask_dict,
- ).result)
+ title += str(
+ StrInterpreter(
+ idx,
+ self._cat,
+ make_compare=False,
+ mask_dict=self._mask_dict,
+ ).result
+ )
ii += 1
else:
- title = ''
+ title = ""
self._fig.suptitle(title)
- for key in self._plot['Y'].keys():
- if 'LABEL' in self._plot.keys():
+ for key in self._plot["Y"].keys():
+ if "LABEL" in self._plot.keys():
try:
- label = self._plot['LABEL'][key]
- s = re.split('@', label)
+ label = self._plot["LABEL"][key]
+ s = re.split("@", label)
if len(s) >= 3:
label = s[0]
jj = 1
@@ -836,68 +845,70 @@ def _make_plot(self):
if jj % 2 == 0:
label += j
else:
- label += str(StrInterpreter(
- j,
- self._cat,
- make_compare=False,
- mask_dict=self._mask_dict,
- ).result)
+ label += str(
+ StrInterpreter(
+ j,
+ self._cat,
+ make_compare=False,
+ mask_dict=self._mask_dict,
+ ).result
+ )
jj += 1
except Exception:
label = None
else:
label = None
- if 'COLOR' in self._plot.keys():
+ if "COLOR" in self._plot.keys():
try:
- color = self._plot['COLOR'][key]
+ color = self._plot["COLOR"][key]
except Exception:
color = None
else:
color = None
- if 'MARKER' in self._plot.keys():
+ if "MARKER" in self._plot.keys():
try:
- marker = self._plot['MARKER'][key]
+ marker = self._plot["MARKER"][key]
except Exception:
- marker = '+'
+ marker = "+"
else:
- marker = '+'
- if 'MARKERSIZE' in self._plot.keys():
+ marker = "+"
+ if "MARKERSIZE" in self._plot.keys():
try:
- markersize = self._plot['MARKERSIZE'][key]
+ markersize = self._plot["MARKERSIZE"][key]
except Exception:
markersize = 1
else:
markersize = 1
- if 'LINE' in self._plot.keys():
+ if "LINE" in self._plot.keys():
try:
- line = self._plot['LINE'][key]
+ line = self._plot["LINE"][key]
except Exception:
- line = ''
+ line = ""
else:
- line = ''
- if 'ALPHA' in self._plot.keys():
+ line = ""
+ if "ALPHA" in self._plot.keys():
try:
- alpha = self._plot['ALPHA'][key]
+ alpha = self._plot["ALPHA"][key]
except Exception:
alpha = None
else:
alpha = None
try:
- x = self._plot['X'][key]
+ x = self._plot["X"][key]
except Exception:
- if len(self._plot['X']) == 1:
- x = self._plot['X'][self._plot['X'].keys()[0]]
+ if len(self._plot["X"]) == 1:
+ x = self._plot["X"][self._plot["X"].keys()[0]]
else:
raise ValueError(
- 'You need to specify X for each Y provided if they '
- + 'dont have the same'
+ "You need to specify X for each Y provided if they "
+ + "dont have the same"
)
plt.plot(
StrInterpreter(x, self._cat, mask_dict=self._mask_dict).result,
StrInterpreter(
- self._plot['Y'][key],
+ self._plot["Y"][key],
self._cat,
mask_dict=self._mask_dict,
).result,
@@ -911,33 +922,33 @@ def _make_plot(self):
)
# Set ploy limits for x and y
- for (lim, set_lim) in zip(['XLIM', 'YLIM'], [plt.xlim, plt.ylim]):
+ for lim, set_lim in zip(["XLIM", "YLIM"], [plt.xlim, plt.ylim]):
if lim in self._plot.keys():
try:
- val = re.split(',', self._plot[lim]['0'])
+ val = re.split(",", self._plot[lim]["0"])
except Exception:
raise ValueError(
- f'Plot {lim} keyword/value not in correct format '
+ f"Plot {lim} keyword/value not in correct format "
+ f'({lim}=lower,upper): {self._plot[lim]["0"]}'
)
set_lim(float(val[0]), float(val[1]))
- if 'LABEL' in self._plot.keys():
+ if "LABEL" in self._plot.keys():
plt.legend()
- if 'XLABEL' in self._plot.keys():
- plt.xlabel(self._plot['XLABEL']['0'])
- if 'YLABEL' in self._plot.keys():
- plt.ylabel(self._plot['YLABEL']['0'])
+ if "XLABEL" in self._plot.keys():
+ plt.xlabel(self._plot["XLABEL"]["0"])
+ if "YLABEL" in self._plot.keys():
+ plt.ylabel(self._plot["YLABEL"]["0"])
- if 'FORMAT' in self._plot.keys():
- out_format = self._plot['FORMAT']['0']
+ if "FORMAT" in self._plot.keys():
+ out_format = self._plot["FORMAT"]["0"]
else:
out_format = "PNG"
self._fig.savefig(
- f'{self._output_path}.{out_format.lower()}',
+ f"{self._output_path}.{out_format.lower()}",
format=out_format,
)
plt.close()
@@ -961,9 +972,9 @@ def _make_scatter(self):
"""
self._fig = plt.figure()
- if 'TITLE' in self._plot.keys():
- title = self._plot['TITLE']['0']
- s = re.split('@', title)
+ if "TITLE" in self._plot.keys():
+ title = self._plot["TITLE"]["0"]
+ s = re.split("@", title)
if len(s) >= 3:
title = s[0]
counter = 1
@@ -971,23 +982,25 @@ def _make_scatter(self):
if counter % 2 == 0:
title += idx
else:
- title += str(StrInterpreter(
- idx,
- self._cat,
- make_compare=False,
- mask_dict=self._mask_dict,
- ).result)
+ title += str(
+ StrInterpreter(
+ idx,
+ self._cat,
+ make_compare=False,
+ mask_dict=self._mask_dict,
+ ).result
+ )
counter += 1
else:
- title = ''
+ title = ""
self._fig.suptitle(title)
- for key in self._plot['SCATTER'].keys():
- if 'LABEL' in self._plot.keys():
+ for key in self._plot["SCATTER"].keys():
+ if "LABEL" in self._plot.keys():
try:
- label = self._plot['LABEL'][key]
- s = re.split('@', label)
+ label = self._plot["LABEL"][key]
+ s = re.split("@", label)
if len(s) >= 3:
label = s[0]
jj = 1
@@ -995,58 +1008,60 @@ def _make_scatter(self):
if jj % 2 == 0:
label += j
else:
- label += str(StrInterpreter(
- j,
- self._cat,
- make_compare=False,
- mask_dict=self._mask_dict,
- ).result)
+ label += str(
+ StrInterpreter(
+ j,
+ self._cat,
+ make_compare=False,
+ mask_dict=self._mask_dict,
+ ).result
+ )
jj += 1
except Exception:
label = None
else:
label = None
- if 'MARKER' in self._plot.keys():
+ if "MARKER" in self._plot.keys():
try:
- marker = self._plot['MARKER'][key]
+ marker = self._plot["MARKER"][key]
except Exception:
- marker = '+'
+ marker = "+"
else:
- marker = '+'
- if 'ALPHA' in self._plot.keys():
+ marker = "+"
+ if "ALPHA" in self._plot.keys():
try:
- alpha = self._plot['ALPHA'][key]
+ alpha = self._plot["ALPHA"][key]
except Exception:
alpha = None
else:
alpha = None
try:
- x = self._plot['X'][key]
+ x = self._plot["X"][key]
except Exception:
- if len(self._plot['X']) == 1:
- x = self._plot['X'][self._plot['X'].keys()[0]]
+ if len(self._plot["X"]) == 1:
+ x = self._plot["X"][self._plot["X"].keys()[0]]
else:
raise ValueError(
- 'You need to specify X for each SCATTER provided if '
- + 'they dont have the same'
+ "You need to specify X for each SCATTER provided if "
+ + "they dont have the same"
)
try:
- y = self._plot['Y'][key]
+ y = self._plot["Y"][key]
except Exception:
- if len(self._plot['Y']) == 1:
- y = self._plot['Y'][self._plot['Y'].keys()[0]]
+ if len(self._plot["Y"]) == 1:
+ y = self._plot["Y"][self._plot["Y"].keys()[0]]
else:
raise ValueError(
- 'You need to specify Y for each SCATTER provided if '
- + 'they dont have the same'
+ "You need to specify Y for each SCATTER provided if "
+ + "they dont have the same"
)
plt.scatter(
StrInterpreter(x, self._cat, mask_dict=self._mask_dict).result,
StrInterpreter(y, self._cat, mask_dict=self._mask_dict).result,
c=StrInterpreter(
- self._plot['SCATTER'][key],
+ self._plot["SCATTER"][key],
self._cat,
mask_dict=self._mask_dict,
).result,
@@ -1056,22 +1071,22 @@ def _make_scatter(self):
figure=self._fig,
)
- if 'LABEL' in self._plot.keys():
+ if "LABEL" in self._plot.keys():
plt.legend()
- if 'XLABEL' in self._plot.keys():
- plt.xlabel(self._plot['XLABEL']['0'])
- if 'YLABEL' in self._plot.keys():
- plt.ylabel(self._plot['YLABEL']['0'])
+ if "XLABEL" in self._plot.keys():
+ plt.xlabel(self._plot["XLABEL"]["0"])
+ if "YLABEL" in self._plot.keys():
+ plt.ylabel(self._plot["YLABEL"]["0"])
plt.colorbar()
- if 'FORMAT' in self._plot.keys():
- out_format = self._plot['FORMAT']['0']
+ if "FORMAT" in self._plot.keys():
+ out_format = self._plot["FORMAT"]["0"]
else:
- out_format = 'PNG'
+ out_format = "PNG"
self._fig.savefig(
- f'{self._output_path}.{out_format.lower()}',
+ f"{self._output_path}.{out_format.lower()}",
format=out_format,
)
plt.close()
@@ -1088,9 +1103,9 @@ def _make_hist(self):
"""
self._fig = plt.figure()
- if 'TITLE' in self._plot.keys():
- title = self._plot['TITLE']['0']
- s = re.split('@', title)
+ if "TITLE" in self._plot.keys():
+ title = self._plot["TITLE"]["0"]
+ s = re.split("@", title)
if len(s) >= 3:
title = s[0]
counter = 1
@@ -1098,35 +1113,37 @@ def _make_hist(self):
if counter % 2 == 0:
title += idx
else:
- title += str(StrInterpreter(
- idx,
- self._cat,
- make_compare=False,
- mask_dict=self._mask_dict,
- ).result)
+ title += str(
+ StrInterpreter(
+ idx,
+ self._cat,
+ make_compare=False,
+ mask_dict=self._mask_dict,
+ ).result
+ )
counter += 1
else:
- title = ''
+ title = ""
self._fig.suptitle(title)
- if 'HTYPE' in self._plot.keys():
- htype = self._plot['HTYPE']['0']
+ if "HTYPE" in self._plot.keys():
+ htype = self._plot["HTYPE"]["0"]
else:
- htype = 'bar'
- if 'LOG' in self._plot.keys():
- if self._plot['LOG']['0'] in ['True', 'true', '1']:
+ htype = "bar"
+ if "LOG" in self._plot.keys():
+ if self._plot["LOG"]["0"] in ["True", "true", "1"]:
log = True
else:
log = False
else:
log = False
- for key in self._plot['Y'].keys():
- if 'LABEL' in self._plot.keys():
+ for key in self._plot["Y"].keys():
+ if "LABEL" in self._plot.keys():
try:
- label = self._plot['LABEL'][key]
- s = re.split('@', label)
+ label = self._plot["LABEL"][key]
+ s = re.split("@", label)
if len(s) >= 3:
label = s[0]
jj = 1
@@ -1134,37 +1151,39 @@ def _make_hist(self):
if jj % 2 == 0:
label += j
else:
- label += str(StrInterpreter(
- j,
- self._cat,
- make_compare=False,
- mask_dict=self._mask_dict,
- ).result)
+ label += str(
+ StrInterpreter(
+ j,
+ self._cat,
+ make_compare=False,
+ mask_dict=self._mask_dict,
+ ).result
+ )
jj += 1
except Exception:
label = None
else:
label = None
- if 'COLOR' in self._plot.keys():
+ if "COLOR" in self._plot.keys():
try:
- color = self._plot['COLOR'][key]
+ color = self._plot["COLOR"][key]
except Exception:
color = None
else:
color = None
- if 'BIN' in self._plot.keys():
+ if "BIN" in self._plot.keys():
try:
- bins = int(self._plot['BIN'][key])
+ bins = int(self._plot["BIN"][key])
except Exception:
- if len(self._plot['BIN']) == 1:
+ if len(self._plot["BIN"]) == 1:
bins = int(
- self._plot['BIN'][self._plot['BIN'].keys()[0]]
+ self._plot["BIN"][self._plot["BIN"].keys()[0]]
)
else:
bins = 50
- if 'ALPHA' in self._plot.keys():
+ if "ALPHA" in self._plot.keys():
try:
- alpha = float(self._plot['ALPHA'][key])
+ alpha = float(self._plot["ALPHA"][key])
except Exception:
alpha = None
else:
@@ -1172,7 +1191,7 @@ def _make_hist(self):
plt.hist(
StrInterpreter(
- self._plot['Y'][key],
+ self._plot["Y"][key],
self._cat,
mask_dict=self._mask_dict,
).result,
@@ -1184,19 +1203,19 @@ def _make_hist(self):
log=log,
)
- if 'LABEL' in self._plot.keys():
+ if "LABEL" in self._plot.keys():
plt.legend()
- if 'XLABEL' in self._plot.keys():
- plt.xlabel(self._plot['XLABEL']['0'])
- if 'YLABEL' in self._plot.keys():
- plt.ylabel(self._plot['YLABEL']['0'])
- if 'FORMAT' in self._plot.keys():
- out_format = self._plot['FORMAT']['0']
+ if "XLABEL" in self._plot.keys():
+ plt.xlabel(self._plot["XLABEL"]["0"])
+ if "YLABEL" in self._plot.keys():
+ plt.ylabel(self._plot["YLABEL"]["0"])
+ if "FORMAT" in self._plot.keys():
+ out_format = self._plot["FORMAT"]["0"]
else:
- out_format = 'PNG'
+ out_format = "PNG"
self._fig.savefig(
- f'{self._output_path}.{out_format.lower()}',
+ f"{self._output_path}.{out_format.lower()}",
format=out_format,
)
plt.close()
diff --git a/shapepipe/modules/setools_runner.py b/shapepipe/modules/setools_runner.py
index a076bd08e..f68720de3 100644
--- a/shapepipe/modules/setools_runner.py
+++ b/shapepipe/modules/setools_runner.py
@@ -11,11 +11,11 @@
@module_runner(
- input_module='sextractor_runner',
- version='1.1',
- file_pattern=['sexcat'],
- file_ext=['.fits'],
- depends=['numpy', 'matplotlib'],
+ input_module="sextractor_runner",
+ version="1.1",
+ file_pattern=["sexcat"],
+ file_ext=[".fits"],
+ depends=["numpy", "matplotlib"],
)
def setools_runner(
input_file_list,
@@ -27,12 +27,12 @@ def setools_runner(
):
"""Define The SETools Runner."""
# Get path to setools configuration file
- config_file = config.getexpanded(module_config_sec, 'SETOOLS_CONFIG_PATH')
+ config_file = config.getexpanded(module_config_sec, "SETOOLS_CONFIG_PATH")
# Create instance of SETools
se_inst = SETools(
input_file_list[0],
- run_dirs['output'],
+ run_dirs["output"],
file_number_string,
config_file,
)
diff --git a/shapepipe/modules/sextractor_package/__init__.py b/shapepipe/modules/sextractor_package/__init__.py
index 658acf8ef..e3cd01188 100644
--- a/shapepipe/modules/sextractor_package/__init__.py
+++ b/shapepipe/modules/sextractor_package/__init__.py
@@ -67,4 +67,4 @@
"""
-__all__ = ['sextractor_script']
+__all__ = ["sextractor_script"]
diff --git a/shapepipe/modules/sextractor_package/sextractor_script.py b/shapepipe/modules/sextractor_package/sextractor_script.py
index 45f44cb49..2c0124eed 100644
--- a/shapepipe/modules/sextractor_package/sextractor_script.py
+++ b/shapepipe/modules/sextractor_package/sextractor_script.py
@@ -41,7 +41,7 @@ def get_header_value(image_path, key):
val = float(val)
except Exception:
raise ValueError(
- f'The key {key} does not return a float value. Got {val}'
+ f"The key {key} does not return a float value. Got {val}"
)
return val
@@ -77,7 +77,8 @@ def make_post_process(cat_path, f_wcs_path, pos_params, ccd_size):
"""
cat = file_io.FITSCatalogue(
- cat_path, SEx_catalogue=True,
+ cat_path,
+ SEx_catalogue=True,
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
)
cat.open()
@@ -85,31 +86,35 @@ def make_post_process(cat_path, f_wcs_path, pos_params, ccd_size):
f_wcs = SqliteDict(f_wcs_path)
key_list = list(f_wcs.keys())
if len(key_list) == 0:
- raise IOError(f'Could not read sql file \'{f_wcs_path}\'')
+ raise IOError(f"Could not read sql file '{f_wcs_path}'")
n_hdu = len(f_wcs[key_list[0]])
history = []
for idx in cat.get_data(1)[0][0]:
- if re.split('HISTORY', idx)[0] == '':
+ if re.split("HISTORY", idx)[0] == "":
history.append(idx)
exp_list = []
- pattern = r'([0-9]*)p\.(.*)'
+ pattern = r"([0-9]*)p\.(.*)"
for hist in history:
m = re.search(pattern, hist)
exp_list.append(m.group(1))
- obj_id = np.copy(cat.get_data()['NUMBER'])
+ obj_id = np.copy(cat.get_data()["NUMBER"])
- n_epoch = np.zeros(len(obj_id), dtype='int32')
+ n_epoch = np.zeros(len(obj_id), dtype="int32")
for idx, exp in enumerate(exp_list):
- pos_tmp = np.ones(len(obj_id), dtype='int32') * -1
+ pos_tmp = np.ones(len(obj_id), dtype="int32") * -1
for idx_j in range(n_hdu):
- w = f_wcs[exp][idx_j]['WCS']
+ if exp not in f_wcs:
+ raise KeyError(
+ f"Exposure {exp} used in image {cat_path} but not"
+ + f" found in header file {f_wcs_path}. Make sure this"
+ + " file is complete."
+ )
+ w = f_wcs[exp][idx_j]["WCS"]
pix_tmp = w.all_world2pix(
- cat.get_data()[pos_params[0]],
- cat.get_data()[pos_params[1]],
- 0
+ cat.get_data()[pos_params[0]], cat.get_data()[pos_params[1]], 0
)
ind = (
(pix_tmp[0] > int(ccd_size[0]))
@@ -126,22 +131,22 @@ def make_post_process(cat_path, f_wcs_path, pos_params, ccd_size):
for ii in range(len(exp_name))
],
dtype=[
- ('NUMBER', obj_id.dtype),
- ('EXP_NAME', exp_name.dtype),
- ('CCD_N', pos_tmp.dtype)
- ]
+ ("NUMBER", obj_id.dtype),
+ ("EXP_NAME", exp_name.dtype),
+ ("CCD_N", pos_tmp.dtype),
+ ],
)
- cat.save_as_fits(data=a, ext_name=f'EPOCH_{idx}')
+ cat.save_as_fits(data=a, ext_name=f"EPOCH_{idx}")
cat.open()
f_wcs.close()
- cat.add_col('N_EPOCH', n_epoch)
+ cat.add_col("N_EPOCH", n_epoch)
cat.close()
-class SExtractorCaller():
+class SExtractorCaller:
"""The SExtractor Caller.
This class constructs the command line to call SExtractor based on the
@@ -187,28 +192,28 @@ class SExtractorCaller():
"""
def __init__(
- self,
- path_input_files,
- path_output_dir,
- number_string,
- path_dot_sex,
- path_dot_param,
- path_dot_conv,
- use_weight,
- use_flag,
- use_psf,
- use_detection_image,
- use_detection_weight,
- use_zero_point,
- use_background,
- zero_point_key=None,
- background_key=None,
- check_image=None,
- output_prefix=None,
+ self,
+ path_input_files,
+ path_output_dir,
+ number_string,
+ path_dot_sex,
+ path_dot_param,
+ path_dot_conv,
+ use_weight,
+ use_flag,
+ use_psf,
+ use_detection_image,
+ use_detection_weight,
+ use_zero_point,
+ use_background,
+ zero_point_key=None,
+ background_key=None,
+ check_image=None,
+ output_prefix=None,
):
- self.cmd_line = ''
- self._cmd_line_extra = ''
+ self.cmd_line = ""
+ self._cmd_line_extra = ""
self._meas_img_path = path_input_files[0]
self._all_input_path = path_input_files
@@ -221,8 +226,13 @@ def __init__(
self._path_dot_param = path_dot_param
self._path_dot_conv = path_dot_conv
- self.set_input_files(use_weight, use_flag, use_psf,
- use_detection_image, use_detection_weight)
+ self.set_input_files(
+ use_weight,
+ use_flag,
+ use_psf,
+ use_detection_image,
+ use_detection_weight,
+ )
# Collect optional arguments for SExtractor
self.get_zero_point(use_zero_point, zero_point_key)
@@ -246,25 +256,25 @@ def get_output_name(self, output_prefix=None):
"""
if isinstance(output_prefix, type(None)):
- self.prefix = ''
+ self.prefix = ""
else:
- if (output_prefix.lower() is not None) & (output_prefix != ''):
- self.prefix = output_prefix + '_'
+ if (output_prefix.lower() is not None) & (output_prefix != ""):
+ self.prefix = output_prefix + "_"
else:
- self.prefix = ''
+ self.prefix = ""
- output_file_name = self.prefix + f'sexcat{self._num_str}.fits'
- output_file_path = f'{self._path_output_dir}/{output_file_name}'
+ output_file_name = self.prefix + f"sexcat{self._num_str}.fits"
+ output_file_path = f"{self._path_output_dir}/{output_file_name}"
return output_file_path
def set_input_files(
- self,
- use_weight,
- use_flag,
- use_psf,
- use_detect_img,
- use_detect_weight,
+ self,
+ use_weight,
+ use_flag,
+ use_psf,
+ use_detect_img,
+ use_detect_weight,
):
"""Set Input Files.
@@ -297,15 +307,13 @@ def set_input_files(
if use_flag:
self._cmd_line_extra += (
- ' -FLAG_IMAGE '
- + f'{self._all_input_path[extra]}'
+ " -FLAG_IMAGE " + f"{self._all_input_path[extra]}"
)
extra += 1
if use_psf:
self._cmd_line_extra += (
- ' -PSF_NAME '
- + f'{self._all_input_path[extra]}'
+ " -PSF_NAME " + f"{self._all_input_path[extra]}"
)
extra += 1
@@ -314,13 +322,12 @@ def set_input_files(
# First, consistency checks
if use_detect_weight and not use_detect_img:
raise ValueError(
- 'DETECTION_WEIGHT cannot be True '
- + 'if DETECTION_IMAGE is False'
+ "DETECTION_WEIGHT cannot be True "
+ + "if DETECTION_IMAGE is False"
)
if use_detect_weight and not use_weight:
raise ValueError(
- 'DETECTION_WEIGHT cannot be True '
- + 'if WEIGHT_FILE is False'
+ "DETECTION_WEIGHT cannot be True " + "if WEIGHT_FILE is False"
)
# Check for separate image file for detection and measurement
@@ -341,18 +348,17 @@ def set_input_files(
else:
detect_weight_path = weight_image
self._cmd_line_extra += (
- f' -WEIGHT_IMAGE {detect_weight_path}'
- + f',{weight_image}'
+ f" -WEIGHT_IMAGE {detect_weight_path}" + f",{weight_image}"
)
else:
- self._cmd_line_extra += ' -WEIGHT_TYPE None'
+ self._cmd_line_extra += " -WEIGHT_TYPE None"
if extra != len(self._all_input_path):
raise ValueError(
- 'Incoherence between input file number and keys '
- + f'related to extra files: 1 regular + {extra-1} extra '
- + 'files not compatible with total file list '
- + f'length of {len(self._all_input_path)}'
+ "Incoherence between input file number and keys "
+ + f"related to extra files: 1 regular + {extra-1} extra "
+ + "files not compatible with total file list "
+ + f"length of {len(self._all_input_path)}"
)
def get_zero_point(self, use_zp, zp_key=None):
@@ -370,7 +376,7 @@ def get_zero_point(self, use_zp, zp_key=None):
"""
if use_zp and not isinstance(zp_key, type(None)):
zp_value = get_header_value(self._meas_img_path, zp_key)
- self._cmd_line_extra += f' -MAG_ZEROPOINT {zp_value}'
+ self._cmd_line_extra += f" -MAG_ZEROPOINT {zp_value}"
def get_background(self, use_bkg, bkg_key=None):
"""Get Background.
@@ -388,7 +394,7 @@ def get_background(self, use_bkg, bkg_key=None):
if use_bkg and not isinstance(bkg_key, type(None)):
bkg_value = get_header_value(self._meas_img_path, bkg_key)
self._cmd_line_extra += (
- f' -BACK_TYPE MANUAL -BACK_VALUE {bkg_value}'
+ f" -BACK_TYPE MANUAL -BACK_VALUE {bkg_value}"
)
def get_check_image(self, check_image):
@@ -402,18 +408,21 @@ def get_check_image(self, check_image):
List of SExtractor keys corresponding to check images
"""
- if (len(check_image) == 1) & (check_image[0] == ''):
- check_type = ['NONE']
- check_name = ['none']
+ if (len(check_image) == 1) & (check_image[0] == ""):
+ check_type = ["NONE"]
+ check_name = ["none"]
else:
check_type = []
check_name = []
for key in check_image:
check_type.append(key.upper())
check_name.append(
- self._path_output_dir + '/' + self.prefix
+ self._path_output_dir
+ + "/"
+ + self.prefix
+ key.lower()
- + self._num_str + '.fits'
+ + self._num_str
+ + ".fits"
)
self._cmd_line_extra += (
@@ -439,14 +448,14 @@ def make_command_line(self, exec_path):
"""
# Base arguments for SExtractor
command_line_base = (
- f'{exec_path} {self._detect_img_path},{self._meas_img_path} '
- + f'-c {self._path_dot_sex} '
- + f'-PARAMETERS_NAME {self._path_dot_param} '
- + f'-FILTER_NAME {self._path_dot_conv} '
- + f'-CATALOG_NAME {self.path_output_file}'
+ f"{exec_path} {self._detect_img_path},{self._meas_img_path} "
+ + f"-c {self._path_dot_sex} "
+ + f"-PARAMETERS_NAME {self._path_dot_param} "
+ + f"-FILTER_NAME {self._path_dot_conv} "
+ + f"-CATALOG_NAME {self.path_output_file}"
)
- command_line = f'{command_line_base} {self._cmd_line_extra}'
+ command_line = f"{command_line_base} {self._cmd_line_extra}"
return command_line
@@ -470,11 +479,11 @@ def parse_errors(stderr, stdout):
Updated standard output and error
"""
- check_error = re.findall('error', stdout.lower())
- check_error2 = re.findall('all done', stdout.lower())
+ check_error = re.findall("error", stdout.lower())
+ check_error2 = re.findall("all done", stdout.lower())
if check_error == []:
- stderr2 = ''
+ stderr2 = ""
else:
stderr2 = stdout
diff --git a/shapepipe/modules/sextractor_runner.py b/shapepipe/modules/sextractor_runner.py
index 9e3bac7d3..869523441 100644
--- a/shapepipe/modules/sextractor_runner.py
+++ b/shapepipe/modules/sextractor_runner.py
@@ -2,7 +2,7 @@
Module runner for ``sextractor``.
-:Author: Axel Guinot
+:Author:s Axel Guinot, Martin Kilbinger
"""
@@ -14,12 +14,12 @@
@module_runner(
- version='1.0.1',
- input_module='mask_runner',
- file_pattern=['image', 'weight', 'flag'],
- file_ext=['.fits', '.fits', '.fits'],
- executes=['sex'],
- depends=['numpy'],
+ version="1.0.1",
+ input_module="mask_runner",
+ file_pattern=["image", "weight", "flag"],
+ file_ext=[".fits", ".fits", ".fits"],
+ executes=["sex"],
+ depends=["numpy"],
)
def sextractor_runner(
input_file_list,
@@ -31,47 +31,47 @@ def sextractor_runner(
):
"""Define The SExtractor Runner."""
# Set the SExtractor executable name
- if config.has_option(module_config_sec, 'EXEC_PATH'):
- exec_path = config.getexpanded(module_config_sec, 'EXEC_PATH')
+ if config.has_option(module_config_sec, "EXEC_PATH"):
+ exec_path = config.getexpanded(module_config_sec, "EXEC_PATH")
else:
- exec_path = 'sex'
+ exec_path = "sex"
# Get SExtractor config options
- dot_sex = config.getexpanded(module_config_sec, 'DOT_SEX_FILE')
- dot_param = config.getexpanded(module_config_sec, 'DOT_PARAM_FILE')
- dot_conv = config.getexpanded(module_config_sec, 'DOT_CONV_FILE')
- weight_file = config.getboolean(module_config_sec, 'WEIGHT_IMAGE')
- flag_file = config.getboolean(module_config_sec, 'FLAG_IMAGE')
- psf_file = config.getboolean(module_config_sec, 'PSF_FILE')
- detection_image = config.getboolean(module_config_sec, 'DETECTION_IMAGE')
- detection_weight = config.getboolean(module_config_sec, 'DETECTION_WEIGHT')
-
- zp_from_header = config.getboolean(module_config_sec, 'ZP_FROM_HEADER')
+ dot_sex = config.getexpanded(module_config_sec, "DOT_SEX_FILE")
+ dot_param = config.getexpanded(module_config_sec, "DOT_PARAM_FILE")
+ dot_conv = config.getexpanded(module_config_sec, "DOT_CONV_FILE")
+ weight_file = config.getboolean(module_config_sec, "WEIGHT_IMAGE")
+ flag_file = config.getboolean(module_config_sec, "FLAG_IMAGE")
+ psf_file = config.getboolean(module_config_sec, "PSF_FILE")
+ detection_image = config.getboolean(module_config_sec, "DETECTION_IMAGE")
+ detection_weight = config.getboolean(module_config_sec, "DETECTION_WEIGHT")
+
+ zp_from_header = config.getboolean(module_config_sec, "ZP_FROM_HEADER")
if zp_from_header:
- zp_key = config.get(module_config_sec, 'ZP_KEY')
+ zp_key = config.get(module_config_sec, "ZP_KEY")
else:
zp_key = None
- bkg_from_header = config.getboolean(module_config_sec, 'BKG_FROM_HEADER')
+ bkg_from_header = config.getboolean(module_config_sec, "BKG_FROM_HEADER")
if bkg_from_header:
- bkg_key = config.get(module_config_sec, 'BKG_KEY')
+ bkg_key = config.get(module_config_sec, "BKG_KEY")
else:
bkg_key = None
- if config.has_option(module_config_sec, 'CHECKIMAGE'):
- check_image = config.getlist(module_config_sec, 'CHECKIMAGE')
+ if config.has_option(module_config_sec, "CHECKIMAGE"):
+ check_image = config.getlist(module_config_sec, "CHECKIMAGE")
else:
- check_image = ['']
+ check_image = [""]
- if config.has_option(module_config_sec, 'PREFIX'):
- prefix = config.get(module_config_sec, 'PREFIX')
+ if config.has_option(module_config_sec, "PREFIX"):
+ prefix = config.get(module_config_sec, "PREFIX")
else:
prefix = None
# Create sextractor caller class instance
ss_inst = ss.SExtractorCaller(
input_file_list,
- run_dirs['output'],
+ run_dirs["output"],
file_number_string,
dot_sex,
dot_param,
@@ -91,7 +91,7 @@ def sextractor_runner(
# Generate sextractor command line
command_line = ss_inst.make_command_line(exec_path)
- w_log.info(f'Calling command: {command_line}')
+ w_log.info(f"Calling command: {command_line}")
# Execute command line
stderr, stdout = execute(command_line)
@@ -100,14 +100,12 @@ def sextractor_runner(
stdout, stderr = ss_inst.parse_errors(stderr, stdout)
# Run sextractor post processing
- if config.getboolean(module_config_sec, 'MAKE_POST_PROCESS'):
- f_wcs_path = config.getexpanded(module_config_sec, 'LOG_WCS')
- pos_params = config.getlist(module_config_sec, 'WORLD_POSITION')
- ccd_size = config.getlist(module_config_sec, 'CCD_SIZE')
+ if config.getboolean(module_config_sec, "MAKE_POST_PROCESS"):
+ f_wcs_path = config.getexpanded(module_config_sec, "LOG_WCS")
+ pos_params = config.getlist(module_config_sec, "WORLD_POSITION")
+ ccd_size = config.getlist(module_config_sec, "CCD_SIZE")
ss.make_post_process(
- ss_inst.path_output_file,
- f_wcs_path,
- pos_params, ccd_size
+ ss_inst.path_output_file, f_wcs_path, pos_params, ccd_size
)
# Return stdout and stderr
diff --git a/shapepipe/modules/split_exp_package/__init__.py b/shapepipe/modules/split_exp_package/__init__.py
index fb55a7f42..4cfb8a764 100644
--- a/shapepipe/modules/split_exp_package/__init__.py
+++ b/shapepipe/modules/split_exp_package/__init__.py
@@ -39,4 +39,4 @@
"""
-__all__ = ['split_exp.py']
+__all__ = ["split_exp.py"]
diff --git a/shapepipe/modules/split_exp_package/split_exp.py b/shapepipe/modules/split_exp_package/split_exp.py
index 2dd1a5875..c4b824389 100644
--- a/shapepipe/modules/split_exp_package/split_exp.py
+++ b/shapepipe/modules/split_exp_package/split_exp.py
@@ -42,7 +42,7 @@ def __init__(
output_dir,
file_number_string,
output_suffix,
- n_hdu
+ n_hdu,
):
self._input_file_list = input_file_list
@@ -58,29 +58,19 @@ def process(self):
"""
for exp_path, output_suffix in zip(
- self._input_file_list,
- self._output_suffix
+ self._input_file_list, self._output_suffix
):
- transf_int = 'flag' in output_suffix
- transf_coord = 'image' in output_suffix
- save_header = 'image' in output_suffix
+ transf_int = "flag" in output_suffix
+ transf_coord = "image" in output_suffix
+ save_header = "image" in output_suffix
self.create_hdus(
- exp_path,
- output_suffix,
- transf_coord,
- transf_int,
- save_header
+ exp_path, output_suffix, transf_coord, transf_int, save_header
)
def create_hdus(
- self,
- exp_path,
- output_suffix,
- transf_coord,
- transf_int,
- save_header
+ self, exp_path, output_suffix, transf_coord, transf_int, save_header
):
"""Create HDUs.
@@ -100,26 +90,43 @@ def create_hdus(
Save WCS information if ``True``
"""
- header_file = np.zeros(self._n_hdu, dtype='O')
+ header_file = np.zeros(self._n_hdu, dtype="O")
+
+ hdu_list = fits.open(exp_path)
+ if len(hdu_list) != self._n_hdu + 1:
+ raise ValueError(
+ f"Image {exp_path} has {len(hdu_list)} + 1 HDUs,"
+ + f" expected were {self._n_hdu} + 1"
+ )
for idx in range(1, self._n_hdu + 1):
- h = fits.getheader(exp_path, idx)
+ # h = fits.getheader(exp_path, idx)
+ h = hdu_list[idx].header
if transf_coord:
stp.pv_to_sip(h)
- d = fits.getdata(exp_path, idx)
+ # d = fits.getdata(exp_path, idx)
+ try:
+ d = hdu_list[idx].data
+ except TypeError as e:
+ msg = (
+ f"Error retrieving data of HDU #{idx} of image {exp_path}."
+ + f" Check if image file is complete."
+ )
+ print(msg, e)
+ raise
+
if transf_int:
d = d.astype(np.int16)
file_name = (
- f'{self._output_dir}/{output_suffix}'
- + f'{self._file_number_string}-{str(idx-1)}.fits'
+ f"{self._output_dir}/{output_suffix}"
+ + f"{self._file_number_string}-{str(idx-1)}.fits"
)
new_file = file_io.FITSCatalogue(
- file_name,
- open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
+ file_name, open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
)
new_file.save_as_fits(data=d, image=True, image_header=h)
@@ -127,12 +134,12 @@ def create_hdus(
try:
w = WCS(h)
except Exception:
- print(f'WCS error for file {exp_path}')
+ print(f"WCS error for file {exp_path}")
raise
- header_file[idx - 1] = {'WCS': w, 'header': h.tostring()}
+ header_file[idx - 1] = {"WCS": w, "header": h.tostring()}
if save_header:
file_name = (
- f'{self._output_dir}/headers{self._file_number_string}.npy'
+ f"{self._output_dir}/headers{self._file_number_string}.npy"
)
np.save(file_name, header_file)
diff --git a/shapepipe/modules/split_exp_runner.py b/shapepipe/modules/split_exp_runner.py
index 5ddae5328..77e6010d0 100644
--- a/shapepipe/modules/split_exp_runner.py
+++ b/shapepipe/modules/split_exp_runner.py
@@ -11,12 +11,12 @@
@module_runner(
- version='1.1',
- input_module='get_images_runner',
- file_pattern=['image', 'weight', 'flag'],
- file_ext=['.fz', '.fz', '.fz'],
- depends=['numpy', 'astropy', 'sip_tpv'],
- run_method='parallel',
+ version="1.1",
+ input_module="get_images_runner",
+ file_pattern=["image", "weight", "flag"],
+ file_ext=[".fz", ".fz", ".fz"],
+ depends=["numpy", "astropy", "sip_tpv"],
+ run_method="parallel",
)
def split_exp_runner(
input_file_list,
@@ -28,17 +28,17 @@ def split_exp_runner(
):
"""Define The Split Exposures Runner."""
# Get file suffix
- output_suffix = config.getlist(module_config_sec, 'OUTPUT_SUFFIX')
+ output_suffix = config.getlist(module_config_sec, "OUTPUT_SUFFIX")
# Get the number of HDUs
- n_hdu = config.getint(module_config_sec, 'N_HDU')
+ n_hdu = config.getint(module_config_sec, "N_HDU")
# Create split exposures class instance
split_inst = SplitExposures(
input_file_list,
- run_dirs['output'],
+ run_dirs["output"],
file_number_string,
output_suffix,
- n_hdu
+ n_hdu,
)
# Process splitting
diff --git a/shapepipe/modules/spread_model_package/__init__.py b/shapepipe/modules/spread_model_package/__init__.py
index 045e19977..336283e78 100644
--- a/shapepipe/modules/spread_model_package/__init__.py
+++ b/shapepipe/modules/spread_model_package/__init__.py
@@ -33,4 +33,4 @@
"""
-__all__ = ['spread_model']
+__all__ = ["spread_model"]
diff --git a/shapepipe/modules/spread_model_package/spread_model.py b/shapepipe/modules/spread_model_package/spread_model.py
index 9d4bd76ea..0ea9c51f9 100644
--- a/shapepipe/modules/spread_model_package/spread_model.py
+++ b/shapepipe/modules/spread_model_package/spread_model.py
@@ -61,7 +61,7 @@ def get_sm(obj_vign, psf_vign, model_vign, weight_vign):
tnt = np.sum(t_v * noise_v * t_v * w_v)
pnp = np.sum(psf_v * noise_v * psf_v * w_v)
tnp = np.sum(t_v * noise_v * psf_v * w_v)
- err = tnt * pg ** 2 + pnp * tg ** 2 - 2 * tnp * pg * tg
+ err = tnt * pg**2 + pnp * tg**2 - 2 * tnp * pg * tg
# Compute spread model
if pg > 0:
@@ -102,9 +102,7 @@ def get_model(sigma, flux, img_shape, pixel_scale=0.186):
"""
# Get scale radius
- scale_radius = (
- 1 / 16 * galaxy.sigma_to_fwhm(sigma, pixel_scale=pixel_scale)
- )
+ scale_radius = 1 / 16 * galaxy.sigma_to_fwhm(sigma, pixel_scale=pixel_scale)
# Get galaxy model
gal_obj = galsim.Exponential(scale_radius=scale_radius, flux=flux)
@@ -117,15 +115,11 @@ def get_model(sigma, flux, img_shape, pixel_scale=0.186):
# Draw galaxy and PSF on vignets
gal_vign = gal_obj.drawImage(
- nx=img_shape[0],
- ny=img_shape[1],
- scale=pixel_scale
+ nx=img_shape[0], ny=img_shape[1], scale=pixel_scale
).array
psf_vign = psf_obj.drawImage(
- nx=img_shape[0],
- ny=img_shape[1],
- scale=pixel_scale
+ nx=img_shape[0], ny=img_shape[1], scale=pixel_scale
).array
return gal_vign, psf_vign
@@ -167,7 +161,7 @@ def __init__(
weight_cat_path,
output_path,
pixel_scale,
- output_mode
+ output_mode,
):
self._sex_cat_path = sex_cat_path
@@ -186,11 +180,11 @@ def process(self):
# Get data
sex_cat = file_io.FITSCatalogue(self._sex_cat_path, SEx_catalogue=True)
sex_cat.open()
- obj_id = np.copy(sex_cat.get_data()['NUMBER'])
- obj_vign = np.copy(sex_cat.get_data()['VIGNET'])
+ obj_id = np.copy(sex_cat.get_data()["NUMBER"])
+ obj_vign = np.copy(sex_cat.get_data()["VIGNET"])
obj_mag = None
- if self._output_mode == 'new':
- obj_mag = np.copy(sex_cat.get_data()['MAG_AUTO'])
+ if self._output_mode == "new":
+ obj_mag = np.copy(sex_cat.get_data()["MAG_AUTO"])
sex_cat.close()
psf_cat = SqliteDict(self._psf_cat_path)
@@ -200,7 +194,7 @@ def process(self):
SEx_catalogue=True,
)
weight_cat.open()
- weigh_vign = weight_cat.get_data()['VIGNET']
+ weigh_vign = weight_cat.get_data()["VIGNET"]
weight_cat.close()
# Get spread model
@@ -210,7 +204,7 @@ def process(self):
for idx, id_tmp in enumerate(obj_id):
sigma_list = []
- if psf_cat[str(id_tmp)] == 'empty':
+ if psf_cat[str(id_tmp)] == "empty":
spread_model_final.append(-1)
spread_model_err_final.append(1)
continue
@@ -219,44 +213,40 @@ def process(self):
for expccd_name_tmp in psf_expccd_name:
psf_cat_id_ccd = psf_cat[str(id_tmp)][expccd_name_tmp]
- sigma_list.append(
- psf_cat_id_ccd['SHAPES']['SIGMA_PSF_HSM']
- )
+ sigma_list.append(psf_cat_id_ccd["SHAPES"]["SIGMA_PSF_HSM"])
- obj_vign_tmp = obj_vign[idx]
- obj_flux_tmp = 1.
obj_sigma_tmp = np.mean(sigma_list)
- obj_weight_tmp = weigh_vign[idx]
- obj_model_tmp, obj_psf_tmp = get_model(
- obj_sigma_tmp,
- obj_flux_tmp,
- obj_vign_tmp.shape,
- self._pixel_scale
- )
+ if obj_sigma_tmp > 0:
+ obj_vign_tmp = obj_vign[idx]
+ obj_flux_tmp = 1.0
+ obj_weight_tmp = weigh_vign[idx]
+ obj_model_tmp, obj_psf_tmp = get_model(
+ obj_sigma_tmp,
+ obj_flux_tmp,
+ obj_vign_tmp.shape,
+ self._pixel_scale,
+ )
- obj_sm, obj_sm_err = get_sm(
- obj_vign_tmp,
- obj_psf_tmp,
- obj_model_tmp,
- obj_weight_tmp
- )
+ obj_sm, obj_sm_err = get_sm(
+ obj_vign_tmp, obj_psf_tmp, obj_model_tmp, obj_weight_tmp
+ )
+ else:
+ # size < 0, something is not right with this object
+ obj_sm, obj_sm_err = -1.0, -1.0
spread_model_final.append(obj_sm)
spread_model_err_final.append(obj_sm_err)
- spread_model_final = np.array(spread_model_final, dtype='float64')
+ spread_model_final = np.array(spread_model_final, dtype="float64")
spread_model_err_final = np.array(
spread_model_err_final,
- dtype='float64',
+ dtype="float64",
)
psf_cat.close()
self.save_results(
- spread_model_final,
- spread_model_err_final,
- obj_mag,
- obj_id
+ spread_model_final, spread_model_err_final, obj_mag, obj_id
)
def save_results(self, sm, sm_err, mag, number):
@@ -281,23 +271,22 @@ def save_results(self, sm, sm_err, mag, number):
For incorrect output mode
"""
- if self._output_mode == 'new':
+ if self._output_mode == "new":
new_cat = file_io.FITSCatalogue(
self._output_path,
SEx_catalogue=True,
- open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
+ open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
)
dict_data = {
- 'NUMBER': number,
- 'MAG': mag,
- 'SPREAD_MODEL': sm,
- 'SPREADERR_MODEL': sm_err
+ "NUMBER": number,
+ "MAG": mag,
+ "SPREAD_MODEL": sm,
+ "SPREADERR_MODEL": sm_err,
}
new_cat.save_as_fits(
- data=dict_data,
- sex_cat_path=self._sex_cat_path
+ data=dict_data, sex_cat_path=self._sex_cat_path
)
- elif self._output_mode == 'add':
+ elif self._output_mode == "add":
ori_cat = file_io.FITSCatalogue(
self._sex_cat_path,
SEx_catalogue=True,
@@ -306,17 +295,14 @@ def save_results(self, sm, sm_err, mag, number):
new_cat = file_io.FITSCatalogue(
self._output_path,
SEx_catalogue=True,
- open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite
+ open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
)
ori_cat.add_col(
- 'SPREAD_MODEL',
- sm,
- new_cat=True,
- new_cat_inst=new_cat
+ "SPREAD_MODEL", sm, new_cat=True, new_cat_inst=new_cat
)
ori_cat.close()
new_cat.open()
- new_cat.add_col('SPREADERR_MODEL', sm_err)
+ new_cat.add_col("SPREADERR_MODEL", sm_err)
new_cat.close()
else:
- raise ValueError('Mode must be in [new, add].')
+ raise ValueError("Mode must be in [new, add].")
diff --git a/shapepipe/modules/spread_model_runner.py b/shapepipe/modules/spread_model_runner.py
index 59e1319be..16c9a2d3b 100644
--- a/shapepipe/modules/spread_model_runner.py
+++ b/shapepipe/modules/spread_model_runner.py
@@ -11,16 +11,16 @@
@module_runner(
- version='1.1',
+ version="1.1",
input_module=[
- 'sextractor_runner',
- 'psfex_interp_runner',
- 'vignetmaker_runner'
+ "sextractor_runner",
+ "psfex_interp_runner",
+ "vignetmaker_runner",
],
- file_pattern=['sexcat', 'galaxy_psf', 'weight_vign'],
- file_ext=['.fits', '.sqlite', '.fits'],
- depends=['numpy', 'galsim'],
- run_method='parallel',
+ file_pattern=["sexcat", "galaxy_psf", "weight_vign"],
+ file_ext=[".fits", ".sqlite", ".fits"],
+ depends=["numpy", "galsim"],
+ run_method="parallel",
)
def spread_model_runner(
input_file_list,
@@ -35,21 +35,21 @@ def spread_model_runner(
sex_cat_path, psf_cat_path, weight_cat_path = input_file_list
# Get file prefix (optional)
- if config.has_option(module_config_sec, 'PREFIX'):
- prefix = config.get(module_config_sec, 'PREFIX')
- if (prefix.lower() != 'none') & (prefix != ''):
- prefix = prefix + '_'
+ if config.has_option(module_config_sec, "PREFIX"):
+ prefix = config.get(module_config_sec, "PREFIX")
+ if (prefix.lower() != "none") & (prefix != ""):
+ prefix = prefix + "_"
else:
- prefix = ''
+ prefix = ""
else:
- prefix = ''
+ prefix = ""
# Get pixel scale and output mode
- pixel_scale = config.getfloat(module_config_sec, 'PIXEL_SCALE')
- output_mode = config.get(module_config_sec, 'OUTPUT_MODE')
+ pixel_scale = config.getfloat(module_config_sec, "PIXEL_SCALE")
+ output_mode = config.get(module_config_sec, "OUTPUT_MODE")
# Set output file path
- file_name = f'{prefix}sexcat_sm{file_number_string}.fits'
+ file_name = f"{prefix}sexcat_sm{file_number_string}.fits"
output_path = f'{run_dirs["output"]}/{file_name}'
# Create spread model class instance
diff --git a/shapepipe/modules/uncompress_fits_package/__init__.py b/shapepipe/modules/uncompress_fits_package/__init__.py
index 2630e1ab4..5f5cd26bc 100644
--- a/shapepipe/modules/uncompress_fits_package/__init__.py
+++ b/shapepipe/modules/uncompress_fits_package/__init__.py
@@ -29,4 +29,4 @@
"""
-__all__ = ['uncompress_fits']
+__all__ = ["uncompress_fits"]
diff --git a/shapepipe/modules/uncompress_fits_package/uncompress_fits.py b/shapepipe/modules/uncompress_fits_package/uncompress_fits.py
index f8eca921d..55f3d4d75 100644
--- a/shapepipe/modules/uncompress_fits_package/uncompress_fits.py
+++ b/shapepipe/modules/uncompress_fits_package/uncompress_fits.py
@@ -35,7 +35,7 @@ def __init__(
output_pattern_list,
output_dir,
file_number_string,
- data_hdu
+ data_hdu,
):
self._input_file_list = input_file_list
@@ -61,7 +61,7 @@ def process(self):
hdu = fits.PrimaryHDU(data, header)
hdul = fits.HDUList([hdu])
hdul.writeto(
- f'{self._output_dir}/'
- + f'{self._output_pattern_list[idx]}'
- + f'{self._file_number_string}.fits'
+ f"{self._output_dir}/"
+ + f"{self._output_pattern_list[idx]}"
+ + f"{self._file_number_string}.fits"
)
diff --git a/shapepipe/modules/uncompress_fits_runner.py b/shapepipe/modules/uncompress_fits_runner.py
index 3ff070233..39ee4186e 100644
--- a/shapepipe/modules/uncompress_fits_runner.py
+++ b/shapepipe/modules/uncompress_fits_runner.py
@@ -11,10 +11,10 @@
@module_runner(
- version='1.1',
- file_pattern=['image'],
- file_ext=['.fits'],
- numbering_scheme='_0',
+ version="1.1",
+ file_pattern=["image"],
+ file_ext=[".fits"],
+ numbering_scheme="_0",
)
def uncompress_fits_runner(
input_file_list,
@@ -26,27 +26,27 @@ def uncompress_fits_runner(
):
"""Define The Uncompress Fits Runner."""
# Get HDU number of input image data
- if config.has_option(module_config_sec, 'HDU_DATA'):
- data_hdu = config.getint(module_config_sec, 'HDU_DATA')
+ if config.has_option(module_config_sec, "HDU_DATA"):
+ data_hdu = config.getint(module_config_sec, "HDU_DATA")
else:
data_hdu = 0
# Get output patterns
- output_pattern_list = config.getlist(module_config_sec, 'OUTPUT_PATTERN')
+ output_pattern_list = config.getlist(module_config_sec, "OUTPUT_PATTERN")
# Check consistency of input and output list lengths
if len(input_file_list) != len(output_pattern_list):
raise ValueError(
- f'Lists INPUT_PATH ({len(input_file_list)})'
- + f' and OUTPUT_PATTERN ({len(output_pattern_list)})'
- + 'need to be of equal length.'
+ f"Lists INPUT_PATH ({len(input_file_list)})"
+ + f" and OUTPUT_PATTERN ({len(output_pattern_list)})"
+ + "need to be of equal length."
)
# Create instance of uncompress
uncompress_inst = uncompress_fits.Uncompress(
input_file_list,
output_pattern_list,
- run_dirs['output'],
+ run_dirs["output"],
file_number_string,
data_hdu,
)
diff --git a/shapepipe/modules/vignetmaker_package/__init__.py b/shapepipe/modules/vignetmaker_package/__init__.py
index a61e83c27..b24f8397e 100644
--- a/shapepipe/modules/vignetmaker_package/__init__.py
+++ b/shapepipe/modules/vignetmaker_package/__init__.py
@@ -47,4 +47,4 @@
"""
-__all__ = ['vignetmaker']
+__all__ = ["vignetmaker"]
diff --git a/shapepipe/modules/vignetmaker_package/vignetmaker.py b/shapepipe/modules/vignetmaker_package/vignetmaker.py
index 047de8a6b..de05a9f2b 100644
--- a/shapepipe/modules/vignetmaker_package/vignetmaker.py
+++ b/shapepipe/modules/vignetmaker_package/vignetmaker.py
@@ -7,6 +7,7 @@
"""
import re
+import os
import numpy as np
from astropy.wcs import WCS
@@ -68,17 +69,24 @@ def process(self, image_path_list, rad, prefix):
Prefix of the output file
"""
+ # Loop over input image files
for _prefix, img in zip(prefix, image_path_list):
image_path = img
- if self._pos_type == 'PIX':
+ # Set x and y positions according to input coordinate type
+ if self._pos_type == "PIX":
+ # Cartesian pixel coordinates: leave as is
pos = self._pos
- elif self._pos_type == 'SPHE':
+
+ elif self._pos_type == "SPHE":
+ # Spherical world coordinates: transform using image header WCS
pos = convert_pos(image_path)
+
else:
raise ValueError(
- 'Coordinates type must be in : PIX (pixel), '
- + 'SPHE (spherical).'
+ f"Invalid coordinates type {self._pos_type}; allowed are"
+ + " 'PIX' (Cartesian pixel coordinates) and "
+ + "'SPHE' (spherical world coordinates))"
)
vign = self._get_stamp(image_path, pos - 1, rad)
@@ -94,13 +102,14 @@ def process(self, image_path_list, rad, prefix):
def get_pos(self, pos_params):
"""Get Positions.
- Get the positions of the given parameters from SExtractor catalogue.
+ Get the positions according to the position parameter column names
+ from the SExtractor cinput atalogue.
Parameters
----------
pos_params : list
- List of string containing the SExtractor's parameters to use as
- positions
+ column names (SExtractor output parameters) to use as
+ positions for x and y (ra and dec); length has to be 2
Returns
-------
@@ -122,7 +131,8 @@ def get_pos(self, pos_params):
def convert_pos(self, image_path):
"""Convert Position.
- Convert positions from world coordinates to pixel coordinates.
+ Convert positions from world coordinates to pixel coordinates using
+ image header WCS.
Parameters
----------
@@ -135,18 +145,25 @@ def convert_pos(self, image_path):
New positions in pixel coordinates
"""
+ # Get image header
file = file_io.FITSCatalogue(image_path)
file.open()
head = file.get_header(0)
file.close()
+ # Get WCS transformation matrix
wcs = WCS(head)
+ # Create copy of input positions
pos_tmp = np.copy(self._pos)
+
+ # Exchange x and y
pos_tmp[:, [0, 1]] = pos_tmp[:, [1, 0]]
+ # Transform from world to pixel coordinates
new_pos = wcs.all_world2pix(pos_tmp, 1)
+ # Exchange x and y back to original
new_pos[:, [0, 1]] = new_pos[:, [1, 0]]
return new_pos
@@ -183,40 +200,39 @@ def _get_stamp(self, img_path, pos, rad):
return vign
- def _get_stamp_me(self, image_dir, image_pattern):
+ def _get_stamp_me(self, image_dirs, image_pattern):
"""Get Stamp Multi-Epoch.
Get stamps for multi-epoch data.
Parameters
----------
- image_dir : str
- Path to the directory where the images are
+ image_dirs : list
+ Path to directories to search for input images
image_pattern : str
Common part of the file names
Returns
-------
dict
- Directory containing object id and vignets for each epoch
+ Dictionary containing object id and vignets for each epoch
"""
cat = file_io.FITSCatalogue(self._galcat_path, SEx_catalogue=True)
cat.open()
- all_id = np.copy(cat.get_data()['NUMBER'])
- n_epoch = np.copy(cat.get_data()['N_EPOCH'])
+ all_id = np.copy(cat.get_data()["NUMBER"])
+ n_epoch = np.copy(cat.get_data()["N_EPOCH"])
list_ext_name = cat.get_ext_name()
hdu_ind = [
- i for i in range(len(list_ext_name))
- if 'EPOCH' in list_ext_name[i]
+ i for i in range(len(list_ext_name)) if "EPOCH" in list_ext_name[i]
]
final_list = []
for hdu_index in hdu_ind:
- exp_name = cat.get_data(hdu_index)['EXP_NAME'][0]
- ccd_list = list(set(cat.get_data(hdu_index)['CCD_N']))
+ exp_name = cat.get_data(hdu_index)["EXP_NAME"][0]
+ ccd_list = list(set(cat.get_data(hdu_index)["CCD_N"]))
array_vign = None
array_id = None
array_exp_name = None
@@ -226,19 +242,30 @@ def _get_stamp_me(self, image_dir, image_pattern):
if ccd == -1:
continue
- img_path = (
- image_dir + '/' + image_pattern + '-'
- + exp_name + '-' + str(ccd) + '.fits'
- )
- ind_obj = np.where(cat.get_data(hdu_index)['CCD_N'] == ccd)[0]
+ # Look for input image
+ found = False
+ image_name = f"{image_pattern}-{exp_name}-{ccd}.fits"
+ for image_dir in image_dirs:
+ img_path = f"{image_dir}/{image_name}"
+ if os.path.exists(img_path):
+ found = True
+ break
+ if not found:
+ raise FileNotFoundError(
+ f"Could not find image {image_name}"
+ )
+
+ ind_obj = np.where(cat.get_data(hdu_index)["CCD_N"] == ccd)[0]
obj_id = all_id[ind_obj]
- wcs_file = self._f_wcs_file[exp_name][ccd]['WCS']
- pos = np.array(wcs_file.all_world2pix(
- self._pos[:, 1][ind_obj],
- self._pos[:, 0][ind_obj],
- 1,
- )).T
+ wcs_file = self._f_wcs_file[exp_name][ccd]["WCS"]
+ pos = np.array(
+ wcs_file.all_world2pix(
+ self._pos[:, 1][ind_obj],
+ self._pos[:, 0][ind_obj],
+ 1,
+ )
+ ).T
pos[:, [0, 1]] = pos[:, [1, 0]]
tmp_vign = self._get_stamp(img_path, pos - 1, self._rad)
@@ -246,9 +273,7 @@ def _get_stamp_me(self, image_dir, image_pattern):
if array_vign is None:
array_vign = np.copy(tmp_vign)
else:
- array_vign = np.concatenate(
- (array_vign, np.copy(tmp_vign))
- )
+ array_vign = np.concatenate((array_vign, np.copy(tmp_vign)))
if array_id is None:
array_id = np.copy(obj_id)
@@ -256,7 +281,7 @@ def _get_stamp_me(self, image_dir, image_pattern):
array_id = np.concatenate((array_id, np.copy(obj_id)))
exp_name_tmp = np.array(
- [exp_name + '-' + str(ccd) for i in range(len(obj_id))]
+ [exp_name + "-" + str(ccd) for i in range(len(obj_id))]
)
if array_exp_name is None:
array_exp_name = exp_name_tmp
@@ -279,36 +304,36 @@ def _get_stamp_me(self, image_dir, image_pattern):
where_res = np.where(final_list[j][0] == id_tmp)[0]
- if (len(where_res) != 0):
+ if len(where_res) != 0:
index = final_list[j][2][where_res[0]]
output_dict[id_tmp][index] = {}
- output_dict[id_tmp][index]['VIGNET'] = (
- final_list[j][1][where_res[0]]
- )
+ output_dict[id_tmp][index]["VIGNET"] = final_list[j][1][
+ where_res[0]
+ ]
counter += 1
if counter == 0:
- output_dict[id_tmp] = 'empty'
+ output_dict[id_tmp] = "empty"
return output_dict
- def process_me(self, image_dir, image_pattern, f_wcs_path, rad):
+ def process_me(self, image_dirs, image_pattern, f_wcs_path, rad):
"""Process Multi-Epoch.
Main function to create the stamps in the multi-epoch case.
Parameters
----------
- image_dir : list
- List of directories where the image are; ff ``len(image_dir) == 1``
- -> all images are in the same directory, else ``len(image_dir)``
- must match ``len(image_pattern)``
+ image_dirs : list
+ Directories of image locations.
+ Each list item contains sublist in which images are searched.
+ Length of outer list has to match image_pattern, or be single item.
image_pattern : list
Common part of each kind of file names
f_wcs_path : str
Path to the log file containing the WCS for each CCDs
rad : int
- Radius of the stamp, must be odd
+ Radius of the stamp, must be an odd integer
"""
self._f_wcs_file = SqliteDict(f_wcs_path)
@@ -316,17 +341,15 @@ def process_me(self, image_dir, image_pattern, f_wcs_path, rad):
for idx in range(len(image_pattern)):
- if len(image_dir) != len(image_pattern):
- output_dict = self._get_stamp_me(
- image_dir[0],
- image_pattern[idx],
- )
-
+ if len(image_dirs) != len(image_pattern):
+ index = 0
else:
- output_dict = self._get_stamp_me(
- image_dir[idx],
- image_pattern[idx],
- )
+ index = idx
+
+ output_dict = self._get_stamp_me(
+ image_dirs[index],
+ image_pattern[idx],
+ )
self._save_vignet_me(output_dict, image_pattern[idx])
@@ -345,8 +368,8 @@ def _save_vignet_me(self, output_dict, prefix):
Prefix to use for the output file name
"""
- output_name = f'{self._output_dir}/{prefix}_vignet{self._image_num}'
- output_file = SqliteDict(output_name + '.sqlite')
+ output_name = f"{self._output_dir}/{prefix}_vignet{self._image_num}"
+ output_file = SqliteDict(output_name + ".sqlite")
for _index in output_dict.keys():
output_file[str(_index)] = output_dict[_index]
@@ -374,7 +397,7 @@ def get_original_vignet(galcat_path):
file = file_io.FITSCatalogue(galcat_path, SEx_catalogue=True)
file.open()
- vignet = file.get_data()['VIGNET']
+ vignet = file.get_data()["VIGNET"]
file.close()
@@ -425,7 +448,7 @@ def save_vignet(vignet, sexcat_path, output_dir, prefix, image_num):
Image numbering
"""
- output_name = f'{output_dir}/{prefix}_vignet{image_num}.fits'
+ output_name = f"{output_dir}/{prefix}_vignet{image_num}.fits"
file = file_io.FITSCatalogue(
output_name,
@@ -433,4 +456,4 @@ def save_vignet(vignet, sexcat_path, output_dir, prefix, image_num):
open_mode=file_io.BaseCatalogue.OpenMode.ReadWrite,
)
- file.save_as_fits(vignet, names=['VIGNET'], sex_cat_path=sexcat_path)
+ file.save_as_fits(vignet, names=["VIGNET"], sex_cat_path=sexcat_path)
diff --git a/shapepipe/modules/vignetmaker_runner.py b/shapepipe/modules/vignetmaker_runner.py
index 972e54e16..2448f9bbd 100644
--- a/shapepipe/modules/vignetmaker_runner.py
+++ b/shapepipe/modules/vignetmaker_runner.py
@@ -2,22 +2,22 @@
Module runner for ``vignetmaker``.
-:Author: Axel Guinot
+:Authors: Axel Guinot, Martin Kilbinger
"""
from shapepipe.modules.module_decorator import module_runner
from shapepipe.modules.vignetmaker_package import vignetmaker as vm
-from shapepipe.pipeline.run_log import get_last_dir
+from shapepipe.pipeline.run_log import get_last_dir, get_all_dirs
@module_runner(
- version='1.1',
- input_module='sextractor_runner',
- file_pattern=['galaxy_selection', 'image'],
- file_ext=['.fits', '.fits'],
- depends=['numpy', 'astropy', 'sf_tools', 'sqlitedict'],
+ version="1.1",
+ input_module="sextractor_runner",
+ file_pattern=["galaxy_selection", "image"],
+ file_ext=[".fits", ".fits"],
+ depends=["numpy", "astropy", "sf_tools", "sqlitedict"],
)
def vignetmaker_runner(
input_file_list,
@@ -31,84 +31,107 @@ def vignetmaker_runner(
# Get path to galaxy catalogue
galcat_path = input_file_list[0]
- # Check if masking should be performed
- # With masking
- if config.getboolean(module_config_sec, 'MASKING'):
- # Fetch the mask value
- mask_value = config.getfloat(module_config_sec, 'MASK_VALUE')
- # Make a mask
+ # Check whether mask is to be created
+ if config.getboolean(module_config_sec, "MASKING"):
+
+ # Get the mask value
+ mask_value = config.getfloat(module_config_sec, "MASK_VALUE")
+
+ # Create a mask postage stamp
vignet = vm.make_mask(galcat_path=galcat_path, mask_value=mask_value)
- # Save the vignet
+
+ # Save the mask postage stamp vignet
vm.save_vignet(
vignet=vignet,
sexcat_path=galcat_path,
- output_dir=run_dirs['output'],
- prefix='cat',
+ output_dir=run_dirs["output"],
+ prefix="cat",
image_num=file_number_string,
)
- # Without masking
else:
- # Fetch stamp size
- stamp_size = config.getint(module_config_sec, 'STAMP_SIZE') - 1
- # Check stamp size
+
+ # Get stamp size
+ stamp_size = config.getint(module_config_sec, "STAMP_SIZE") - 1
+
+ # Make sure stamp size is odd number
if stamp_size % 2 != 0:
- raise ValueError('The STAMP_SIZE must be odd')
+ raise ValueError(
+ f"Found even value {stamp_size} for postage stame size (STAMP"
+ + f"_SIZE entry in config file), must be odd"
+ )
+
# Set radius
radius = int(stamp_size / 2)
- # Fetch position type and values
- pos_type = config.get(module_config_sec, 'COORD')
- pos_params = config.getlist(module_config_sec, 'POSITION_PARAMS')
- # Fetch vignet run mode
- mode = config.get(module_config_sec, 'MODE')
+ # Get position type; allowed are "PIX" and "SPHE"
+ pos_type = config.get(module_config_sec, "COORD")
+
+ # Get position column names for x and y / ra and dec
+ pos_params = config.getlist(module_config_sec, "POSITION_PARAMS")
+
+ # Get vignet run mode; allowed are "CLASSIC", "MULTI-EPOCH"
+ mode = config.get(module_config_sec, "MODE")
# Create instance of VignetMaker
vm_inst = vm.VignetMaker(
galcat_path=galcat_path,
pos_type=pos_type,
pos_params=pos_params,
- output_dir=run_dirs['output'],
+ output_dir=run_dirs["output"],
image_num=file_number_string,
)
- # Run in CLASSIC mode
- if mode == 'CLASSIC':
- # Fetch prefix
- prefix = config.getlist(module_config_sec, 'PREFIX')
- # Check prefix
+ # Process module according to mode
+ if mode == "CLASSIC":
+ # Classsic mode = Single exposures
+
+ # Get file name prefix
+ prefix = config.getlist(module_config_sec, "PREFIX")
+
+ # Make sure number of prefixes match input files
if len(prefix) != len(input_file_list[1:]):
raise ValueError(
- f'The number of prefixes ({len(prefix)}) has to be '
- + 'equal to the number of input file types '
- + f'({len(input_file_list[1:])}).'
+ f"The number of prefixes ({len(prefix)}) has to be "
+ + "equal to the number of input file types "
+ + f"({len(input_file_list[1:])})."
)
# Process inputs
vm_inst.process(input_file_list[1:], radius, prefix)
- # Run in MULTI-EPOCH mode
- elif mode == 'MULTI-EPOCH':
- # Fetch image directory and patterns
- modules = config.getlist(module_config_sec, 'ME_IMAGE_DIR')
- image_dir = []
+ elif mode == "MULTI-EPOCH":
+ # Multi-epoch exposures
+
+ # Get input image directory and file patterns
+ modules = config.getlist(module_config_sec, "ME_IMAGE_DIR")
+ image_dirs = []
for module in modules:
- last_dir = get_last_dir(run_dirs['run_log'], module)
- image_dir.append(last_dir)
+ module_name = module.split(":")[-1]
+ if "last" in module:
+ dirs = [get_last_dir(run_dirs["run_log"], module_name)]
+ elif "all" in module:
+ dirs = get_all_dirs(run_dirs["run_log"], module_name)
+ else:
+ raise ValueError(
+ "Expected qualifier 'last:' or 'all' before module"
+ + f" '{module}' in config entry 'ME_IMAGE_DIR'"
+ )
+ image_dirs.append(dirs)
+
image_pattern = config.getlist(
module_config_sec,
- 'ME_IMAGE_PATTERN',
+ "ME_IMAGE_PATTERN",
)
- # Fetch WCS log path
- f_wcs_path = config.getexpanded(module_config_sec, 'ME_LOG_WCS')
+
+ # Get WCS log file path
+ f_wcs_path = config.getexpanded(module_config_sec, "ME_LOG_WCS")
# Process inputs
- vm_inst.process_me(image_dir, image_pattern, f_wcs_path, radius)
+ vm_inst.process_me(image_dirs, image_pattern, f_wcs_path, radius)
- # Invalid mode
else:
- # Raise error for invalid run mode
- raise ValueError(f'Invalid MODE=\'{mode}\'')
- # No return objects
+ raise ValueError(f"Invalid MODE='{mode}'")
+
return None, None
diff --git a/shapepipe/pipeline/__init__.py b/shapepipe/pipeline/__init__.py
index 588c375a5..3966563f6 100644
--- a/shapepipe/pipeline/__init__.py
+++ b/shapepipe/pipeline/__init__.py
@@ -7,17 +7,17 @@
"""
__all__ = [
- 'args',
- 'config',
- 'dependency_handler',
- 'execute',
- 'file_handler',
- 'file_io',
- 'job_handler',
- 'mpi_run',
- 'run_log',
- 'shared',
- 'str_handler',
- 'timeout',
- 'worker_handler',
+ "args",
+ "config",
+ "dependency_handler",
+ "execute",
+ "file_handler",
+ "file_io",
+ "job_handler",
+ "mpi_run",
+ "run_log",
+ "shared",
+ "str_handler",
+ "timeout",
+ "worker_handler",
]
diff --git a/shapepipe/pipeline/args.py b/shapepipe/pipeline/args.py
index e06e44ef9..70cb8c38b 100644
--- a/shapepipe/pipeline/args.py
+++ b/shapepipe/pipeline/args.py
@@ -42,16 +42,24 @@ def print_message(message):
Custom action class object
"""
+
class customAction(ap.Action):
- def __init__(self, option_strings, version=None, dest=ap.SUPPRESS,
- default=ap.SUPPRESS, help=help):
+ def __init__(
+ self,
+ option_strings,
+ version=None,
+ dest=ap.SUPPRESS,
+ default=ap.SUPPRESS,
+ help=help,
+ ):
super(customAction, self).__init__(
option_strings=option_strings,
dest=dest,
default=default,
nargs=0,
- help=help)
+ help=help,
+ )
def __call__(self, parser, args, values, option_string=None):
print(message)
@@ -71,10 +79,10 @@ def module_str():
Formatted string of module names
"""
- string = ''
+ string = ""
for module in __module_list__:
- string += f' - {module}\n'
+ string += f" - {module}\n"
return string
@@ -92,41 +100,44 @@ def create_arg_parser():
"""
# Create parser
parser = ap.ArgumentParser(
- add_help=False, description=shapepipe_logo(),
+ add_help=False,
+ description=shapepipe_logo(),
formatter_class=cutomFormatter,
)
- optional = parser.add_argument_group('Optional Arguments')
+ optional = parser.add_argument_group("Optional Arguments")
# Add arguments
optional.add_argument(
- '-h',
- '--help',
- action='help',
- help='show this help message and exit',
+ "-h",
+ "--help",
+ action="help",
+ help="show this help message and exit",
)
optional.add_argument(
- '-v',
- '--version',
- action='version',
- version=f'%(prog)s v{__version__}'
+ "-v", "--version", action="version", version=f"%(prog)s v{__version__}"
)
optional.add_argument(
- '-l',
- '--list_modules',
+ "-l",
+ "--list_modules",
action=print_message(
- f'ShapePipe modules currently available:\n{module_str()}'
+ f"ShapePipe modules currently available:\n{module_str()}"
),
- help='list modules currently available and exit',
+ help="list modules currently available and exit",
)
optional.add_argument(
- '-c',
- '--config',
- default='config.ini',
- help='configuration file name',
+ "-c",
+ "--config",
+ default="config.ini",
+ help="configuration file name",
)
+ optional.add_argument(
+ "-e",
+ "--exclusive",
+ help="exclusive input file number string",
+ )
# Return parser
return parser.parse_args()
diff --git a/shapepipe/pipeline/config.py b/shapepipe/pipeline/config.py
index 3db2a7b98..f43bf7345 100644
--- a/shapepipe/pipeline/config.py
+++ b/shapepipe/pipeline/config.py
@@ -37,7 +37,7 @@ def getexpanded(self, section, option):
"""
return self._get(section, os.path.expandvars, option)
- def getlist(self, section, option, delimiter=','):
+ def getlist(self, section, option, delimiter=","):
"""Get List.
This method retrieves a list of strings separated by a given
@@ -100,7 +100,7 @@ def file_name(self):
def file_name(self, value):
if not os.path.exists(value):
- raise IOError(f'Configuration file {value} does not exist.')
+ raise IOError(f"Configuration file {value} does not exist.")
self._file_name = value
@@ -110,14 +110,14 @@ def _set_defaults(self):
Set default configuration options.
"""
- if not self.config.has_option('DEFAULT', 'RUN_NAME'):
- self.config.set('DEFAULT', 'RUN_NAME', 'shapepipe_run')
+ if not self.config.has_option("DEFAULT", "RUN_NAME"):
+ self.config.set("DEFAULT", "RUN_NAME", "shapepipe_run")
- if not self.config.has_option('DEFAULT', 'RUN_DATETIME'):
- self.config.set('DEFAULT', 'RUN_DATETIME', 'True')
+ if not self.config.has_option("DEFAULT", "RUN_DATETIME"):
+ self.config.set("DEFAULT", "RUN_DATETIME", "True")
- if not self.config.has_option('DEFAULT', 'VERBOSE'):
- self.config.set('DEFAULT', 'VERBOSE', 'True')
+ if not self.config.has_option("DEFAULT", "VERBOSE"):
+ self.config.set("DEFAULT", "VERBOSE", "True")
def _set_execution_options(self):
"""Set Execution Options.
@@ -132,11 +132,11 @@ def _set_execution_options(self):
For non-existent module runner
"""
- if not self.config.has_option('EXECUTION', 'MODULE'):
- raise RuntimeError('No module(s) specified')
+ if not self.config.has_option("EXECUTION", "MODULE"):
+ raise RuntimeError("No module(s) specified")
- if not self.config.has_option('EXECUTION', 'MODE'):
- self.config.set('EXECUTION', 'MODE', 'smp')
+ if not self.config.has_option("EXECUTION", "MODE"):
+ self.config.set("EXECUTION", "MODE", "smp")
def _set_file_options(self):
"""Set File Options.
@@ -155,26 +155,26 @@ def _set_file_options(self):
For non-existent output directory
"""
- if not self.config.has_option('FILE', 'LOG_NAME'):
- self.config.set('FILE', 'LOG_NAME', 'shapepipe')
+ if not self.config.has_option("FILE", "LOG_NAME"):
+ self.config.set("FILE", "LOG_NAME", "shapepipe")
- if not self.config.has_option('FILE', 'RUN_LOG_NAME'):
- self.config.set('FILE', 'RUN_LOG_NAME', 'shapepipe_runs')
+ if not self.config.has_option("FILE", "RUN_LOG_NAME"):
+ self.config.set("FILE", "RUN_LOG_NAME", "shapepipe_runs")
- if not self.config.has_option('FILE', 'INPUT_DIR'):
- raise RuntimeError('Not input directory specified')
+ if not self.config.has_option("FILE", "INPUT_DIR"):
+ raise RuntimeError("Not input directory specified")
- if not self.config.has_option('FILE', 'OUTPUT_DIR'):
- raise RuntimeError('Not output directory specified')
+ if not self.config.has_option("FILE", "OUTPUT_DIR"):
+ raise RuntimeError("Not output directory specified")
- elif not os.path.isdir(self.config.getexpanded('FILE', 'OUTPUT_DIR')):
+ elif not os.path.isdir(self.config.getexpanded("FILE", "OUTPUT_DIR")):
raise OSError(
f'Directory {self.config.getexpanded("FILE", "OUTPUT_DIR")} '
- + 'not found.'
+ + "not found."
)
- if not self.config.has_option('FILE', 'CORRECT_FILE_PATTERN'):
- self.config.set('FILE', 'CORRECT_FILE_PATTERN', 'True')
+ if not self.config.has_option("FILE", "CORRECT_FILE_PATTERN"):
+ self.config.set("FILE", "CORRECT_FILE_PATTERN", "True")
def _set_worker_options(self):
"""Set Worker Options.
@@ -182,11 +182,11 @@ def _set_worker_options(self):
This module checks the worker options in the configuration file.
"""
- if not self.config.has_section('WORKER'):
- self.config.add_section('WORKER')
+ if not self.config.has_section("WORKER"):
+ self.config.add_section("WORKER")
- if not self.config.has_option('WORKER', 'PROCESS_PRINT_LIMIT'):
- self.config.set('WORKER', 'PROCESS_PRINT_LIMIT', '200')
+ if not self.config.has_option("WORKER", "PROCESS_PRINT_LIMIT"):
+ self.config.set("WORKER", "PROCESS_PRINT_LIMIT", "200")
def get_parser(self):
"""Get Parser.
diff --git a/shapepipe/pipeline/dependency_handler.py b/shapepipe/pipeline/dependency_handler.py
index 33b98f6f4..f4779e5ed 100644
--- a/shapepipe/pipeline/dependency_handler.py
+++ b/shapepipe/pipeline/dependency_handler.py
@@ -31,10 +31,10 @@ def __init__(self, dependencies=[], executables=[]):
self.depend = dependencies
self.execute = executables
- self._greq = '>='
- self._equal = '=='
- self._great = '>'
- self._less = '<'
+ self._greq = ">="
+ self._equal = "=="
+ self._great = ">"
+ self._less = "<"
self.dependency_list = []
self.executable_list = list(set(self.execute))
@@ -51,10 +51,10 @@ def depend(self):
def depend(self, value):
if not isinstance(value, list):
- raise TypeError('Input must be list type.')
+ raise TypeError("Input must be list type.")
if not all(isinstance(x, str) for x in value):
- raise ValueError('List elements must be strings.')
+ raise ValueError("List elements must be strings.")
self._depend = value
@@ -67,10 +67,10 @@ def execute(self):
def execute(self, value):
if not isinstance(value, list):
- raise TypeError('Input must be list type.')
+ raise TypeError("Input must be list type.")
if not all(isinstance(x, str) for x in value):
- raise ValueError('List elements must be strings.')
+ raise ValueError("List elements must be strings.")
self._execute = value
@@ -160,8 +160,7 @@ def _get_indices(array, value):
"""
return [
- index for index, element in enumerate(array)
- if element == value
+ index for index, element in enumerate(array) if element == value
]
@classmethod
@@ -210,7 +209,7 @@ def _check_executable(exe_name):
"""
if not isinstance(exe_name, str):
- raise TypeError('Executable name must be a string.')
+ raise TypeError("Executable name must be a string.")
def is_exe(fpath):
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
@@ -218,18 +217,20 @@ def is_exe(fpath):
fpath, fname = os.path.split(exe_name)
if not fpath:
- res = any([
- is_exe(os.path.join(path, exe_name))
- for path in os.environ['PATH'].split(os.pathsep)
- ])
+ res = any(
+ [
+ is_exe(os.path.join(path, exe_name))
+ for path in os.environ["PATH"].split(os.pathsep)
+ ]
+ )
else:
res = is_exe(exe_name)
if not res:
raise IOError(
- f'{exe_name} does not appear to be a valid executable on '
- + 'this system.'
+ f"{exe_name} does not appear to be a valid executable on "
+ + "this system."
)
def _split_string(self, string):
@@ -249,19 +250,19 @@ def _split_string(self, string):
"""
if self._greq in string:
- val = re.split(f'({self._greq})', string)
+ val = re.split(f"({self._greq})", string)
elif self._equal in string:
- val = re.split(f'({self._equal})', string)
+ val = re.split(f"({self._equal})", string)
elif self._great in string:
- val = re.split(f'({self._great})', string)
+ val = re.split(f"({self._great})", string)
elif self._less in string:
raise ValueError('"<" not permitted in package version string.')
else:
- val = [string, '', '']
+ val = [string, "", ""]
return val
@@ -271,10 +272,12 @@ def _split_strings(self):
This method splits the input dependency modules strings.
"""
- self._depend_arr = list(map(
- list,
- zip(*[self._split_string(string) for string in self.depend])
- ))
+ self._depend_arr = list(
+ map(
+ list,
+ zip(*[self._split_string(string) for string in self.depend]),
+ )
+ )
self._dependency_set = set(self._depend_arr[0])
def _unique_dependencies(self):
@@ -290,18 +293,18 @@ def _unique_dependencies(self):
if any(self._equal in element for element in subset):
subset = self._slice_col_val(subset, 1, self._equal)
- if any([ver != '' for ver in subset[2]]):
- subset = (self._slice_col_val(
+ if any([ver != "" for ver in subset[2]]):
+ subset = self._slice_col_val(
subset,
2,
- str(max(
- [self._convert_to_float(ver) for ver in subset[2]]
- ))
- ))
+ str(
+ max([self._convert_to_float(ver) for ver in subset[2]])
+ ),
+ )
subset = [element[0] for element in self._slice_2d(subset, [0])]
- self.dependency_list.append(''.join(subset))
+ self.dependency_list.append("".join(subset))
def check_dependencies(self):
"""Check Dependencies.
@@ -322,23 +325,23 @@ def check_dependencies(self):
package = importlib.import_module(dependency)
except Exception:
raise ImportError(
- f'Could not import pipeline dependency {dependency}'
+ f"Could not import pipeline dependency {dependency}"
)
- if hasattr(package, '__version__'):
+ if hasattr(package, "__version__"):
version = package.__version__
else:
- version = 'N/A'
+ version = "N/A"
- if hasattr(package, '__path__'):
+ if hasattr(package, "__path__"):
path = package.__path__[0]
- elif hasattr(package, '__file__'):
+ elif hasattr(package, "__file__"):
path = package.__file__
else:
- path = 'N/A'
+ path = "N/A"
dependency_status_list.append(
- f' - {package.__name__} {version} {path}'
+ f" - {package.__name__} {version} {path}"
)
return dependency_status_list
@@ -361,7 +364,7 @@ def check_executables(self):
self._check_executable(executable)
exe_path, err = subprocess.Popen(
- f'which {executable}',
+ f"which {executable}",
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
diff --git a/shapepipe/pipeline/execute.py b/shapepipe/pipeline/execute.py
index d9c63bcb1..0a69fae7f 100644
--- a/shapepipe/pipeline/execute.py
+++ b/shapepipe/pipeline/execute.py
@@ -32,7 +32,7 @@ def execute(command_line):
"""
if not isinstance(command_line, str):
- raise TypeError('Command line must be a string.')
+ raise TypeError("Command line must be a string.")
command = command_line.split()
check_executable(command[0])
@@ -40,7 +40,7 @@ def execute(command_line):
process = sp.Popen(command, stdout=sp.PIPE, stderr=sp.PIPE)
stdout, stderr = process.communicate()
- return stdout.decode('utf-8'), stderr.decode('utf-8')
+ return stdout.decode("utf-8"), stderr.decode("utf-8")
def check_executable(exe_name):
@@ -62,7 +62,7 @@ def check_executable(exe_name):
"""
if not isinstance(exe_name, str):
- raise TypeError('Executable name must be a string.')
+ raise TypeError("Executable name must be a string.")
def is_exe(fpath):
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
@@ -70,16 +70,18 @@ def is_exe(fpath):
fpath, fname = os.path.split(exe_name)
if not fpath:
- res = any([
- is_exe(os.path.join(path, exe_name))
- for path in os.environ['PATH'].split(os.pathsep)
- ])
+ res = any(
+ [
+ is_exe(os.path.join(path, exe_name))
+ for path in os.environ["PATH"].split(os.pathsep)
+ ]
+ )
else:
res = is_exe(exe_name)
if not res:
raise OSError(
- f'{exe_name} does not appear to be a valid executable on this '
- + 'system.'
+ f"{exe_name} does not appear to be a valid executable on this "
+ + "system."
)
diff --git a/shapepipe/pipeline/file_handler.py b/shapepipe/pipeline/file_handler.py
index b7479f6f3..e16ae99e8 100644
--- a/shapepipe/pipeline/file_handler.py
+++ b/shapepipe/pipeline/file_handler.py
@@ -32,52 +32,55 @@ class FileHandler(object):
List of modules to be run
config : CustomParser
Configuaration parser instance
+ exclusive : str, optional
+ Run this file number string exclusively if given, the default is None
verbose : bool, optional
Verbose setting, default is True
"""
- def __init__(self, run_name, modules, config, verbose=True):
+ def __init__(self, run_name, modules, config, exclusive=None, verbose=True):
self._run_name = run_name
self._module_list = modules
- if self._module_list[-1] == '':
- raise ValueError('Invalid module list, check for a trailing comma')
+ if self._module_list[-1] == "":
+ raise ValueError("Invalid module list, check for a trailing comma")
self._config = config
+ self._exclusive = exclusive
self._verbose = verbose
self.module_runners = get_module_runners(self._module_list)
- self._input_list = config.getlist('FILE', 'INPUT_DIR')
- self._output_dir = config.getexpanded('FILE', 'OUTPUT_DIR')
- self._log_name = config.get('FILE', 'LOG_NAME')
+ self._input_list = config.getlist("FILE", "INPUT_DIR")
+ self._output_dir = config.getexpanded("FILE", "OUTPUT_DIR")
+ self._log_name = config.get("FILE", "LOG_NAME")
self._correct_pattern = config.getboolean(
- 'FILE',
- 'CORRECT_FILE_PATTERN',
+ "FILE",
+ "CORRECT_FILE_PATTERN",
)
self._run_log_file = self.setpath(
self._output_dir,
- config.get('FILE', 'RUN_LOG_NAME'),
- '.txt',
+ config.get("FILE", "RUN_LOG_NAME"),
+ ".txt",
)
self._module_dict = {}
- if config.has_option('FILE', 'FILE_PATTERN'):
- self._file_pattern = config.getlist('FILE', 'FILE_PATTERN')
- if config.has_option('FILE', 'FILE_EXT'):
- self._file_ext = config.getlist('FILE', 'FILE_EXT')
- if config.has_option('FILE', 'NUMBERING_SCHEME'):
- self._numbering_scheme = config.get('FILE', 'NUMBERING_SCHEME')
+ if config.has_option("FILE", "FILE_PATTERN"):
+ self._file_pattern = config.getlist("FILE", "FILE_PATTERN")
+ if config.has_option("FILE", "FILE_EXT"):
+ self._file_ext = config.getlist("FILE", "FILE_EXT")
+ if config.has_option("FILE", "NUMBERING_SCHEME"):
+ self._numbering_scheme = config.get("FILE", "NUMBERING_SCHEME")
else:
- self._numbering_scheme = r'RE:\_\d+'
- if config.has_option('FILE', 'NUMBER_LIST'):
- if os.path.isfile(config.get('FILE', 'NUMBER_LIST')):
- self._number_list = (
- self.read_number_list(config.get('FILE', 'NUMBER_LIST'))
+ self._numbering_scheme = r"RE:\_\d+"
+ if config.has_option("FILE", "NUMBER_LIST"):
+ if os.path.isfile(config.get("FILE", "NUMBER_LIST")):
+ self._number_list = self.read_number_list(
+ config.get("FILE", "NUMBER_LIST")
)
else:
- self._number_list = config.getlist('FILE', 'NUMBER_LIST')
+ self._number_list = config.getlist("FILE", "NUMBER_LIST")
else:
self._number_list = None
@@ -93,7 +96,7 @@ def run_dir(self):
@run_dir.setter
def run_dir(self, value):
- self._run_dir = self.check_dir(value, check_exists=True)
+ self._run_dir = self.check_dir(value, check_exists=False)
@property
def _input_dir(self):
@@ -138,7 +141,7 @@ def read_number_list(file_name):
with open(file_name) as data_file:
number_list = data_file.readlines()
- return [value.rstrip('\n') for value in number_list]
+ return [value.rstrip("\n") for value in number_list]
@classmethod
def check_dir(cls, dir_name, check_exists=False):
@@ -158,7 +161,8 @@ def check_dir(cls, dir_name, check_exists=False):
"""
if check_exists and os.path.isdir(dir_name):
- raise OSError(f'Directory {dir_name} already exists.')
+ #raise OSError(f'Directory {dir_name} already exists.')
+ print(f'Warning: Directory {dir_name} already exists.')
return cls.strip_slash(dir_name)
@@ -188,11 +192,12 @@ def mkdir(cls, dir_name):
Directory name with full path
"""
- cls.check_dir(dir_name, check_exists=True)
- mkdir(dir_name)
+ cls.check_dir(dir_name, check_exists=False)
+ if not os.path.isdir(dir_name):
+ mkdir(dir_name)
@staticmethod
- def setpath(path, name, ext=''):
+ def setpath(path, name, ext=""):
"""Set Path Name.
This method appends the file/directory name to the input path.
@@ -212,7 +217,7 @@ def setpath(path, name, ext=''):
Formated path
"""
- return f'{path}/{name}{ext}'
+ return f"{path}/{name}{ext}"
@staticmethod
def strip_slash(path):
@@ -231,7 +236,7 @@ def strip_slash(path):
Updated path
"""
- return path.rstrip('/')
+ return path.rstrip("/")
@classmethod
def strip_slash_list(cls, path_list):
@@ -289,8 +294,8 @@ def _get_module_run_name(dir):
Module run name, module name, search string
"""
- string, module_run = dir.split(':')
- module = module_run.split('/')[0]
+ string, module_run = dir.split(":")
+ module = module_run.split("/")[0]
return module_run.lower(), module.lower(), string
@@ -318,30 +323,32 @@ def _check_input_dir_list(self, dir_list):
if os.path.isdir(dir):
input_dir.append(dir)
- elif 'last' in dir.lower():
+ elif "last" in dir.lower():
module_run, module, _ = self._get_module_run_name(dir)
runs = get_list(self._run_log_file)
last_module = get_last(runs, module)
input_dir.append(
self.setpath(
self.setpath(last_module, module_run),
- 'output',
+ "output",
)
)
- elif 'all' in dir.lower():
+ elif "all" in dir.lower():
module_run, module, _ = self._get_module_run_name(dir)
runs = get_list(self._run_log_file)
all_runs = get_all(runs, module)
- input_dir.extend([
- self.setpath(
- self.setpath(run.split(' ')[0], module_run),
- 'output'
- )
- for run in all_runs
- ])
+ input_dir.extend(
+ [
+ self.setpath(
+ self.setpath(run.split(" ")[0], module_run),
+ "output",
+ )
+ for run in all_runs
+ ]
+ )
- elif ':' in dir.lower():
+ elif ":" in dir.lower():
module_run, _, string = self._get_module_run_name(dir)
input_dir.append(
self.setpath(
@@ -349,15 +356,15 @@ def _check_input_dir_list(self, dir_list):
self._run_log.get_run(string),
module_run,
),
- 'output',
+ "output",
)
)
else:
raise ValueError(
- f'Invalid INPUT_DIR ({dir}). Make sure the paths '
- + 'provided are valid directories or use the '
- + 'allowed special keys.'
+ f"Invalid INPUT_DIR ({dir}). Make sure the paths "
+ + "provided are valid directories or use the "
+ + "allowed special keys."
)
return input_dir
@@ -377,8 +384,8 @@ def create_global_run_dirs(self):
"""
self.run_dir = self.setpath(self._output_dir, self._run_name)
- self._log_dir = self.setpath(self.run_dir, 'logs')
- self._tmp_dir = self.setpath(self.run_dir, 'tmp')
+ self._log_dir = self.setpath(self.run_dir, "logs")
+ self._tmp_dir = self.setpath(self.run_dir, "tmp")
self.log_name = self.setpath(self._log_dir, self._log_name)
self._run_log = RunLog(
self._run_log_file,
@@ -386,9 +393,12 @@ def create_global_run_dirs(self):
self.run_dir,
)
- self.mkdir(self.run_dir)
- self.mkdir(self._log_dir)
- self.mkdir(self._tmp_dir)
+ if not os.path.exists(self.run_dir):
+ self.mkdir(self.run_dir)
+ if not os.path.exists(self._log_dir):
+ self.mkdir(self._log_dir)
+ if not os.path.exists(self._tmp_dir):
+ self.mkdir(self._tmp_dir)
self._get_input_dir()
self._copy_config_to_log()
@@ -403,7 +413,7 @@ def _copy_config_to_log(self):
copyfile(
self._config.file_name,
- f'{self._log_dir}/{config_file_name}',
+ f"{self._log_dir}/{config_file_name}",
)
def get_module_current_run(self, module):
@@ -422,7 +432,7 @@ def get_module_current_run(self, module):
Module run count
"""
- return str(self._module_dict[module]['run_count'])
+ return str(self._module_dict[module]["run_count"])
def get_module_run_prop(self, module, property):
"""Get Module Run Property.
@@ -447,9 +457,9 @@ def get_module_run_prop(self, module, property):
For invalid module dictionary key
"""
- run_name = self._module_dict[module]['latest']
+ run_name = self._module_dict[module]["latest"]
- if property == 'run_name':
+ if property == "run_name":
value = run_name
elif property in self._module_dict[module].keys():
value = self._module_dict[module][property]
@@ -457,7 +467,7 @@ def get_module_run_prop(self, module, property):
value = self._module_dict[module][run_name][property]
else:
raise ValueError(
- f'Property {property} not found for module {module}.'
+ f"Property {property} not found for module {module}."
)
return value
@@ -478,7 +488,7 @@ def get_module_config_sec(self, module):
Configuration file section name
"""
- return self._module_dict[module]['latest'].upper()
+ return self._module_dict[module]["latest"].upper()
def get_add_module_property(self, run_name, property):
"""Get Additional Module Properties.
@@ -498,14 +508,14 @@ def get_add_module_property(self, run_name, property):
Additional module property values
"""
- if (self._config.has_option(
+ if self._config.has_option(
run_name.upper(),
- f'ADD_{property.upper()}',
- )):
+ f"ADD_{property.upper()}",
+ ):
return self._config.getlist(
run_name.upper(),
- f'ADD_{property.upper()}',
+ f"ADD_{property.upper()}",
)
def _set_module_property(self, module, run_name, property, get_type):
@@ -541,22 +551,22 @@ def _set_module_property(self, module, run_name, property, get_type):
"""
# 1) Check for parameter value in module section of config file
if self._config.has_option(run_name.upper(), property.upper()):
- if get_type == 'str':
+ if get_type == "str":
prop_val = self._config.get(
run_name.upper(),
property.upper(),
)
- elif get_type == 'list':
+ elif get_type == "list":
prop_val = self._config.getlist(
run_name.upper(),
property.upper(),
)
else:
- raise ValueError(f'{get_type} is not a valid get type')
+ raise ValueError(f"{get_type} is not a valid get type")
# 2) Check for default parameter values in file handler
- elif hasattr(self, f'_{property}'):
- prop_val = getattr(self, f'_{property}')
+ elif hasattr(self, f"_{property}"):
+ prop_val = getattr(self, f"_{property}")
# 3) Check for default parameter values in module runner
elif hasattr(self.module_runners[module], property):
@@ -564,13 +574,12 @@ def _set_module_property(self, module, run_name, property, get_type):
else:
raise ValueError(
- f'No value for {property} in {module} could be found.'
+ f"No value for {property} in {module} could be found."
)
# Look for additional module properties for list objects
- if (
- isinstance(prop_val, list)
- and self.get_add_module_property(run_name, property)
+ if isinstance(prop_val, list) and self.get_add_module_property(
+ run_name, property
):
prop_val += self.get_add_module_property(run_name, property)
@@ -588,37 +597,35 @@ def _set_module_properties(self, module, run_name):
"""
module_props = {
- 'numbering_scheme': 'str',
- 'run_method': 'str',
- 'input_module': 'list',
- 'file_pattern': 'list',
- 'file_ext': 'list',
- 'depends': 'list',
- 'executes': 'list'
+ "numbering_scheme": "str",
+ "run_method": "str",
+ "input_module": "list",
+ "file_pattern": "list",
+ "file_ext": "list",
+ "depends": "list",
+ "executes": "list",
}
for property, get_type in module_props.items():
self._set_module_property(module, run_name, property, get_type)
# Make sure the number of patterns and extensions match
- if (
- (len(self._module_dict[module][run_name]['file_ext']) == 1)
- and (len(self._module_dict[module][run_name]['file_pattern']) > 1)
+ if (len(self._module_dict[module][run_name]["file_ext"]) == 1) and (
+ len(self._module_dict[module][run_name]["file_pattern"]) > 1
):
- self._module_dict[module][run_name]['file_ext'] = [
- self._module_dict[module][run_name]['file_ext'][0]
- for i in self._module_dict[module][run_name]['file_pattern']
+ self._module_dict[module][run_name]["file_ext"] = [
+ self._module_dict[module][run_name]["file_ext"][0]
+ for i in self._module_dict[module][run_name]["file_pattern"]
]
- if (
- len(self._module_dict[module][run_name]['file_ext'])
- != len(self._module_dict[module][run_name]['file_pattern'])
+ if len(self._module_dict[module][run_name]["file_ext"]) != len(
+ self._module_dict[module][run_name]["file_pattern"]
):
- n_fext = len(self._module_dict[module][run_name]['file_ext'])
- n_fpat = len(self._module_dict[module][run_name]['file_pattern'])
+ n_fext = len(self._module_dict[module][run_name]["file_ext"])
+ n_fpat = len(self._module_dict[module][run_name]["file_pattern"])
raise ValueError(
- f'The number of file_ext values ({n_fext}) does not match the '
- + f'number of file_pattern values ({n_fpat}).'
+ f"The number of file_ext values ({n_fext}) does not match the "
+ + f"number of file_pattern values ({n_fpat})."
)
def _create_module_run_dirs(self, module, run_name):
@@ -632,34 +639,33 @@ def _create_module_run_dirs(self, module, run_name):
Module name
"""
- self._module_dict[module][run_name]['run_dir'] = (
- self.setpath(self._run_dir, run_name)
+ self._module_dict[module][run_name]["run_dir"] = self.setpath(
+ self._run_dir, run_name
)
- self._module_dict[module][run_name]['log_dir'] = (
- self.setpath(
- self._module_dict[module][run_name]['run_dir'],
- 'logs',
- )
+ self._module_dict[module][run_name]["log_dir"] = self.setpath(
+ self._module_dict[module][run_name]["run_dir"],
+ "logs",
)
- self._module_dict[module][run_name]['output_dir'] = (
- self.setpath(
- self._module_dict[module][run_name]['run_dir'],
- 'output',
- )
+ self._module_dict[module][run_name]["output_dir"] = self.setpath(
+ self._module_dict[module][run_name]["run_dir"],
+ "output",
)
- self.mkdir(self._module_dict[module][run_name]['run_dir'])
- self.mkdir(self._module_dict[module][run_name]['log_dir'])
- self.mkdir(self._module_dict[module][run_name]['output_dir'])
+ if not os.path.exists(self._module_dict[module][run_name]['run_dir']):
+ self.mkdir(self._module_dict[module][run_name]['run_dir'])
+ if not os.path.exists(self._module_dict[module][run_name]['log_dir']):
+ self.mkdir(self._module_dict[module][run_name]['log_dir'])
+ if not os.path.exists(self._module_dict[module][run_name]['output_dir']):
+ self.mkdir(self._module_dict[module][run_name]['output_dir'])
# Set current output directory to module output directory
- self.output_dir = self._module_dict[module][run_name]['output_dir']
+ self.output_dir = self._module_dict[module][run_name]["output_dir"]
self.module_run_dirs = {
- 'run': self.run_dir,
- 'log': self._log_dir,
- 'tmp': self._tmp_dir,
- 'output': self.output_dir,
- 'run_log': self._run_log_file
+ "run": self.run_dir,
+ "log": self._log_dir,
+ "tmp": self._tmp_dir,
+ "output": self.output_dir,
+ "run_log": self._run_log_file,
}
def _set_module_input_dir(self, module, run_name):
@@ -690,88 +696,82 @@ def _set_module_input_dir(self, module, run_name):
# run in the pipeline
if (
isinstance(
- self._module_dict[module][run_name]['input_module'],
+ self._module_dict[module][run_name]["input_module"],
type(None),
)
or len(self._module_dict) == 1
):
# If so, use the input directory/ies set in the [FILE] section
input_dir = self._input_dir
- dir_set_by = '[FILE]'
+ dir_set_by = "[FILE]"
# Check if input directory/ies has/have been set in the module config
# section
- if self._config.has_option(run_name.upper(), 'INPUT_DIR'):
+ if self._config.has_option(run_name.upper(), "INPUT_DIR"):
# If so set this/these as the input directory/ies, note that this
# overrides the value set in the [FILE] section
input_dir = self._check_input_dir_list(
- self._config.getlist(run_name.upper(), 'INPUT_DIR')
+ self._config.getlist(run_name.upper(), "INPUT_DIR")
)
- dir_set_by = f'[{run_name.upper()}]'
+ dir_set_by = f"[{run_name.upper()}]"
# Check if input directory/ies has/have has not been set and if input
# modules have been defined for the current module
- if (
- not input_dir
- and isinstance(
- self._module_dict[module][run_name]['input_module'],
- list
- )
+ if not input_dir and isinstance(
+ self._module_dict[module][run_name]["input_module"], list
):
- dir_set_by = f'{module}.py'
+ dir_set_by = f"{module}.py"
# If so, loop through all the input modules defined for the current
# module
- for input_module in (
- self._module_dict[module][run_name]['input_module']
- ):
+ for input_module in self._module_dict[module][run_name][
+ "input_module"
+ ]:
# Get the input module name and run
- input_module, in_mod_run = (
- shared.split_module_run(input_module)
- )
+ input_module, in_mod_run = shared.split_module_run(input_module)
# Check if the input module was part of the current pipeline
if input_module in self._module_dict:
# If so, check if the input module was a single run
if in_mod_run == input_module:
# If so, Set the input module run to the latest run
- in_mod_run = self._module_dict[input_module]['latest']
+ in_mod_run = self._module_dict[input_module]["latest"]
# Add the output directory of the input module to
# the list of input directories for the current module
input_dir.append(
self._module_dict[input_module][in_mod_run][
- 'output_dir'
+ "output_dir"
]
)
else:
# If not, add the last run of the input module to the
# list of input directories
- input_dir.append(f'{input_module}:last')
+ input_dir.append(f"{input_module}:last")
# Check if input directory/ies has/have been added in the module config
# section
- if self.get_add_module_property(run_name, 'input_dir'):
+ if self.get_add_module_property(run_name, "input_dir"):
# If so add this/these to the input directory/ies
- input_dir += self.get_add_module_property(run_name, 'input_dir')
- if not dir_set_by == f'[{module}]':
- dir_set_by = f'{dir_set_by} and [{run_name.upper()}]'
+ input_dir += self.get_add_module_property(run_name, "input_dir")
+ if not dir_set_by == f"[{module}]":
+ dir_set_by = f"{dir_set_by} and [{run_name.upper()}]"
# Check if no input directory has been set
if not input_dir:
# If so, raise an error
raise RuntimeError(
- 'Could not find appropriate input directory '
- + f'for module {run_name}.'
+ "Could not find appropriate input directory "
+ + f"for module {run_name}."
)
# Add the input directories for the current module to the module
# dictionary
- self._module_dict[module][run_name]['input_dir'] = (
- self.check_dirs(input_dir)
+ self._module_dict[module][run_name]["input_dir"] = self.check_dirs(
+ input_dir
)
- self._module_dict[module][run_name]['dir_set_by'] = dir_set_by
+ self._module_dict[module][run_name]["dir_set_by"] = dir_set_by
# Log the input directories and how they were set
- module_input_dir = f' -- Input directories: {input_dir}'
- module_dir_set_by = f' -- Inputs set by: {dir_set_by}'
+ module_input_dir = f" -- Input directories: {input_dir}"
+ module_dir_set_by = f" -- Inputs set by: {dir_set_by}"
self.log.info(module_input_dir)
self.log.info(module_dir_set_by)
@@ -803,18 +803,18 @@ def _generate_re_pattern(match_pattern):
"""
if not isinstance(match_pattern, str):
- TypeError('Match pattern must be a string.')
+ TypeError("Match pattern must be a string.")
chars = [char for char in match_pattern if not char.isalnum()]
- split_pattern = '|'.join(chars).replace('.', r'\.')
- chars = [f'\\{char}' for char in chars] + ['']
+ split_pattern = "|".join(chars).replace(".", r"\.")
+ chars = [f"\\{char}" for char in chars] + [""]
num_length = [
- f'\\d{{{len(digits)}}}'
+ f"\\d{{{len(digits)}}}"
for digits in re.split(split_pattern, match_pattern)
]
- re_pattern = r''.join(
+ re_pattern = r"".join(
[a for b in zip(num_length, chars) for a in b]
- ).replace('{1}', '+')
+ ).replace("{1}", "+")
return re.compile(re_pattern)
@@ -838,8 +838,9 @@ def _strip_dir_from_file(file_name, dir_list):
"""
return [
- file_name.replace(_dir + '/', '')
- for _dir in dir_list if _dir in file_name
+ file_name.replace(_dir + "/", "")
+ for _dir in dir_list
+ if _dir in file_name
][0]
@classmethod
@@ -866,13 +867,13 @@ def _get_re(cls, num_scheme):
"""
# Raise an error if num_scheme is None,
# but not if num_scheme==''
- if not num_scheme and num_scheme != '':
+ if not num_scheme and num_scheme != "":
- raise ValueError('No numbering scheme adapted')
+ raise ValueError("No numbering scheme adapted")
- elif num_scheme.startswith('RE:'):
+ elif num_scheme.startswith("RE:"):
- re_pattern = num_scheme.replace('RE:', '')
+ re_pattern = num_scheme.replace("RE:", "")
else:
@@ -881,12 +882,7 @@ def _get_re(cls, num_scheme):
return re_pattern
def _save_num_patterns(
- self,
- dir_list,
- re_pattern,
- pattern,
- ext,
- output_file
+ self, dir_list, re_pattern, pattern, ext, output_file
):
"""Save Number Patterns.
@@ -925,11 +921,11 @@ def _save_num_patterns(
if not true_file_list:
raise RuntimeError(
f'No files found matching "{pattern}" and "{ext}" in the '
- + f'directories {dir_list}.'
+ + f"directories {dir_list}."
)
# Correct the extension if necessary
- new_ext = '.' + ext if not ext.startswith('.') else ext
+ new_ext = "." + ext if not ext.startswith(".") else ext
if self._verbose and new_ext != ext:
print(f'Updating file extension from "{ext}" to "{new_ext}".')
@@ -957,7 +953,7 @@ def _save_num_patterns(
new_pattern = striped
for substring in (new_ext, file_name):
- new_pattern = new_pattern.replace(substring, '')
+ new_pattern = new_pattern.replace(substring, "")
if new_pattern != pattern:
print(
@@ -976,13 +972,13 @@ def _save_num_patterns(
)
elem = shared.check_duplicate(final_file_list)
- if elem != '':
+ if elem != "":
raise RuntimeError(
- 'Input file list contains at least one duplicate element, '
- + f'\'{elem}\' that matches '
- + 'file pattern and numbering scheme, leading to identical '
- + 'input files. Make sure that the correct input '
- + 'directory is used.'
+ "Input file list contains at least one duplicate element, "
+ + f"'{elem}' that matches "
+ + "file pattern and numbering scheme, leading to identical "
+ + "input files. Make sure that the correct input "
+ + "directory is used."
)
# Save file list
@@ -1006,14 +1002,13 @@ def _save_match_patterns(output_file, mmap_list):
List of memory maps
"""
- num_pattern_list = [np.load(mmap, mmap_mode='r') for mmap in mmap_list]
+ num_pattern_list = [np.load(mmap, mmap_mode="r") for mmap in mmap_list]
np.save(
output_file,
reduce(
- partial(np.intersect1d, assume_unique=True),
- num_pattern_list
- )
+ partial(np.intersect1d, assume_unique=True), num_pattern_list
+ ),
)
del num_pattern_list
@@ -1042,7 +1037,7 @@ def _get_file_name(path, pattern, number, ext):
File name
"""
- return f'{path}/{pattern}{number}{ext}'
+ return f"{path}/{pattern}{number}{ext}"
@staticmethod
def _remove_mmaps(mmap_list):
@@ -1096,7 +1091,7 @@ def _format_process_list(
pattern_list, ext_list, path_list = list(zip(*patterns))
if isinstance(self._number_list, type(None)):
- number_list = np.load(memory_map, mmap_mode='r')
+ number_list = np.load(memory_map, mmap_mode="r")
else:
number_list = self._number_list
@@ -1110,16 +1105,39 @@ def _format_process_list(
+ f'numbering scheme "{num_scheme}".'
)
- if run_method == 'serial':
+ # If "exclusive" options is set: discard all non-matching IDs
+ if self._exclusive is not None:
+ id_to_test = f"-{self._exclusive.replace('.', '-')}"
+ if number == id_to_test:
+ if self._verbose:
+ print(
+ f"-- Using exclusive number {self._exclusive} ({id_to_test})"
+ )
+ else:
+ if self._verbose:
+ # print(f"Skipping {number}, not equal to {self._exclusive} ({id_to_test})")
+ pass
+ continue
+
+ if run_method == "serial":
process_items = []
else:
process_items = [number]
- process_items.extend([
- self._get_file_name(path, fp, number, ext)
- for path, fp, ext in zip(path_list, pattern_list, ext_list)
- ])
+ process_items.extend(
+ [
+ self._get_file_name(path, fp, number, ext)
+ for path, fp, ext in zip(path_list, pattern_list, ext_list)
+ ]
+ )
process_list.append(process_items)
+ if len(process_list) == 0:
+ msg = "Empty process list"
+ if self._exclusive is not None:
+ if len(number_list) > 0:
+ msg = f"{msg}. No input file found matching exclusive ID"
+ raise ValueError(msg)
+
return process_list
def _save_process_list(
@@ -1147,24 +1165,19 @@ def _save_process_list(
"""
np_mmap_list = [
- self.setpath(self._tmp_dir, f'nums_{pattern}_{ext}.npy')
+ self.setpath(self._tmp_dir, f"nums_{pattern}_{ext}.npy")
for pattern, ext in zip(pattern_list, ext_list)
]
- match_mmap = self.setpath(self._tmp_dir, 'matching_num_patterns.npy')
- self.process_mmap = self.setpath(self._tmp_dir, 'process_list.npy')
+ match_mmap = self.setpath(self._tmp_dir, "matching_num_patterns.npy")
+ self.process_mmap = self.setpath(self._tmp_dir, "process_list.npy")
re_pattern = self._get_re(num_scheme)
temp = [
- self._save_num_patterns(
- dir_list,
- re_pattern,
- pattern,
- ext,
- np_mmap
+ self._save_num_patterns(dir_list, re_pattern, pattern, ext, np_mmap)
+ for pattern, ext, np_mmap in zip(
+ pattern_list, ext_list, np_mmap_list
)
- for pattern, ext, np_mmap in
- zip(pattern_list, ext_list, np_mmap_list)
]
self._save_match_patterns(match_mmap, np_mmap_list)
@@ -1180,7 +1193,7 @@ def _save_process_list(
np.save(self.process_mmap, np.array(process_list))
del process_list
- self.process_list = np.load(self.process_mmap, mmap_mode='r')
+ self.process_list = np.load(self.process_mmap, mmap_mode="r")
self.missed = []
@@ -1205,11 +1218,11 @@ def _get_module_input_files(self, module, run_name):
Module name
"""
- dir_list = self._module_dict[module][run_name]['input_dir']
- pattern_list = self._module_dict[module][run_name]['file_pattern']
- ext_list = self._module_dict[module][run_name]['file_ext']
- num_scheme = self._module_dict[module][run_name]['numbering_scheme']
- run_method = self._module_dict[module][run_name]['run_method']
+ dir_list = self._module_dict[module][run_name]["input_dir"]
+ pattern_list = self._module_dict[module][run_name]["file_pattern"]
+ ext_list = self._module_dict[module][run_name]["file_ext"]
+ num_scheme = self._module_dict[module][run_name]["numbering_scheme"]
+ run_method = self._module_dict[module][run_name]["run_method"]
self._save_process_list(
dir_list,
@@ -1233,19 +1246,19 @@ def set_up_module(self, module):
multi_call = self._module_list.count(module) > 1
if module in self._module_dict.keys():
- self._module_dict[module]['run_count'] += 1
+ self._module_dict[module]["run_count"] += 1
else:
self._module_dict[module] = {}
- self._module_dict[module]['run_count'] = 1
+ self._module_dict[module]["run_count"] = 1
if multi_call:
- call_num = self._module_dict[module]['run_count']
- run_name = f'{module}_run_{call_num}'
+ call_num = self._module_dict[module]["run_count"]
+ run_name = f"{module}_run_{call_num}"
else:
run_name = module
# Log run count
- module_prop_text = ' - Module properties'
+ module_prop_text = " - Module properties"
module_run_num = f' -- Run: {self._module_dict[module]["run_count"]}'
self.log.info(module_prop_text)
@@ -1255,7 +1268,7 @@ def set_up_module(self, module):
print(module_prop_text)
print(module_run_num)
- self._module_dict[module]['latest'] = run_name
+ self._module_dict[module]["latest"] = run_name
self._module_dict[module][run_name] = {}
self._set_module_properties(module, run_name)
@@ -1281,7 +1294,7 @@ def get_worker_log_name(self, module, file_number_string):
Worker log file name
"""
- run_name = self._module_dict[module]['latest']
- log_dir = self._module_dict[module][run_name]['log_dir']
+ run_name = self._module_dict[module]["latest"]
+ log_dir = self._module_dict[module][run_name]["log_dir"]
- return f'{log_dir}/process{file_number_string}'
+ return f"{log_dir}/process{file_number_string}"
diff --git a/shapepipe/pipeline/file_io.py b/shapepipe/pipeline/file_io.py
index 52e847147..ffe8bed82 100644
--- a/shapepipe/pipeline/file_io.py
+++ b/shapepipe/pipeline/file_io.py
@@ -87,7 +87,7 @@ def get_nb_rows(self):
Number of rows
"""
- raise BaseCatalogue.FeatureNotImplemented('get_nb_rows()')
+ raise BaseCatalogue.FeatureNotImplemented("get_nb_rows()")
def get_nb_cols(self):
"""Get Number of Columns.
@@ -111,7 +111,7 @@ def get_col_names(self):
list
list of column names
"""
- raise BaseCatalogue.FeatureNotImplemented('get_col_names()')
+ raise BaseCatalogue.FeatureNotImplemented("get_col_names()")
def get_col_formats(self):
"""Get Column Formats.
@@ -119,7 +119,7 @@ def get_col_formats(self):
Get the list of column formats in the order of columns
"""
- raise BaseCatalogue.FeatureNotImplemented('get_col_names()')
+ raise BaseCatalogue.FeatureNotImplemented("get_col_names()")
def add_col(
self,
@@ -144,7 +144,7 @@ def add_col(
Column data as a numpy array
"""
- raise BaseCatalogue.FeatureNotImplemented('add_col()')
+ raise BaseCatalogue.FeatureNotImplemented("add_col()")
def _file_exists(self, filepath):
"""File Exists.
@@ -174,9 +174,9 @@ class InputFormat:
class OpenMode:
"""Supported input catalogue open modes."""
- ReadOnly = 'readonly'
- ReadWrite = 'update'
- Append = 'append'
+ ReadOnly = "readonly"
+ ReadWrite = "update"
+ Append = "append"
class Column(object):
"""Column.
@@ -194,7 +194,7 @@ def name(self):
Get the name of the column
"""
- raise BaseCatalogue.FeatureNotImplemented('column.name')
+ raise BaseCatalogue.FeatureNotImplemented("column.name")
@property
def format(self):
@@ -203,7 +203,7 @@ def format(self):
Get the format of the column
"""
- raise BaseCatalogue.FeatureNotImplemented('column.format')
+ raise BaseCatalogue.FeatureNotImplemented("column.format")
@property
def data(self):
@@ -212,7 +212,7 @@ def data(self):
Get the data associated with the column
"""
- raise BaseCatalogue.FeatureNotImplemented('column.data')
+ raise BaseCatalogue.FeatureNotImplemented("column.data")
def get_nb_rows(self):
"""Get Number of Rows.
@@ -220,7 +220,7 @@ def get_nb_rows(self):
Retrieve the number of rows of the column.
"""
- raise BaseCatalogue.FeatureNotImplemented('get_nb_rows()')
+ raise BaseCatalogue.FeatureNotImplemented("get_nb_rows()")
def get_info(self):
"""Get Information.
@@ -228,7 +228,7 @@ def get_info(self):
Retrieve information about the column.
"""
- raise BaseCatalogue.FeatureNotImplemented('get_info()')
+ raise BaseCatalogue.FeatureNotImplemented("get_info()")
def get_type(self):
"""Get Type.
@@ -236,7 +236,7 @@ def get_type(self):
Get the data type of the column
"""
- raise BaseCatalogue.FeatureNotImplemented('get_type()')
+ raise BaseCatalogue.FeatureNotImplemented("get_type()")
class FeatureNotImplemented(NotImplementedError):
"""Feature Not Implemented.
@@ -253,8 +253,8 @@ def __init__(self, msg):
def __str__(self):
return (
- f'File IO *** ERROR ***: Feature: {self._msg} is not '
- + 'implemented in this class'
+ f"File IO *** ERROR ***: Feature: {self._msg} is not "
+ + "implemented in this class"
)
class catalogueNotOpen(Exception):
@@ -274,8 +274,8 @@ def __init__(self, filepath):
def __str__(self):
return (
- f'File IO *** ERROR ***: catalogue: {self._filepath} '
- + 'is not open'
+ f"File IO *** ERROR ***: catalogue: {self._filepath} "
+ + "is not open"
)
class DataNotFound(Exception):
@@ -298,8 +298,8 @@ def __init__(self, filepath, hdu):
def __str__(self):
return (
- f'File IO *** ERROR ***: File \'{self._filepath}\', '
- + f'hdu={self._hdu}: data not found'
+ f"File IO *** ERROR ***: File '{self._filepath}', "
+ + f"hdu={self._hdu}: data not found"
)
class catalogueFileNotFound(Exception):
@@ -319,7 +319,7 @@ def __init__(self, filepath):
def __str__(self):
"""Set string representation of the exception object."""
- return f'File IO *** ERROR ***: file {self._filepath} no found'
+ return f"File IO *** ERROR ***: file {self._filepath} no found"
class ColumnNotFound(Exception):
"""Column Not Found.
@@ -338,7 +338,7 @@ def __init__(self, col_name):
def __str__(self):
"""Set string representation of the exception object."""
- return f'File IO *** ERROR ***: column {self._col_name} no found'
+ return f"File IO *** ERROR ***: column {self._col_name} no found"
class catalogueNotCreated(Exception):
"""Catalogue Not Created.
@@ -357,8 +357,8 @@ def __init__(self, filepath):
def __str__(self):
return (
- f'File IO *** ERROR ***: catalogue: {self._filepath} could '
- + 'not be created'
+ f"File IO *** ERROR ***: catalogue: {self._filepath} could "
+ + "not be created"
)
class OpenModeNotSupported(Exception):
@@ -381,8 +381,8 @@ def __init__(self, filepath, open_mode):
def __str__(self):
return (
- f'File IO *** ERROR ***: catalogue: {self._filepath} '
- + 'Open Mode {self._open_mode} not supported'
+ f"File IO *** ERROR ***: catalogue: {self._filepath} "
+ + "Open Mode {self._open_mode} not supported"
)
class OpenModeConflict(Exception):
@@ -405,8 +405,8 @@ def __init__(self, open_mode, open_mode_needed):
def __str__(self):
return (
- 'File IO *** ERROR ***: catalogue has to be open as : '
- + f'{self._open_mode_needed} , Mode used : {self._open_mode}'
+ "File IO *** ERROR ***: catalogue has to be open as : "
+ + f"{self._open_mode_needed} , Mode used : {self._open_mode}"
)
@@ -419,14 +419,17 @@ class FITSCatalogue(BaseCatalogue):
----------
fullpath : str
Full path to file
- hdu_no : int
- HDU number
- open_mode : OpenMode
- File opening mode
- memmap : Bool
- Option to use memory mapping
- SEx_catalogue : bool
- Option to specify if the input is a SExtractor catalogue
+ hdu_no : int, optional
+ HDU number; default is ``None``, in which case
+ it will be set to 1 (2) if SEx_catalogue is ``False``
+ (``True``)
+ open_mode : OpenMode, optional
+ File opening mode, default is ``BaseCatalogue.OpenMode.ReadOnly``
+ memmap : bool, optional
+ Option to use memory mapping, default is ``False``
+ SEx_catalogue : bool, optional
+ Option to specify if the input is a SExtractor catalogue;
+ default is ``False``
"""
@@ -449,7 +452,7 @@ def __init__(
self._SEx_catalogue = SEx_catalogue
# HDU number of the underlying .FITS table
if hdu_no is None:
- # Default is 1 (or 2 if you are using )
+ # Set to default value if not given by user
if SEx_catalogue:
self._hdu_no = 2
else:
@@ -461,9 +464,9 @@ def __init__(
def __str__(self):
if self._cat_data is not None:
- info = f'{self.get_info()}'
+ info = f"{self.get_info()}"
else:
- info = 'No information'
+ info = "No information"
return info
@property
@@ -557,8 +560,8 @@ def create(self, ext_name=None, s_hdu=True, sex_cat_path=None):
raise BaseCatalogue.catalogueFileNotFound(sex_cat_path)
else:
raise ValueError(
- 'sex_cat_path needs to be provided to create a '
- + 'SEXtractor catalogue'
+ "sex_cat_path needs to be provided to create a "
+ + "SEXtractor catalogue"
)
elif s_hdu:
secondary_hdu = fits.BinTableHDU(
@@ -639,9 +642,9 @@ def apply_mask(
if fits_file._cat_data is None:
raise BaseCatalogue.catalogueNotOpen(fits_file.fullpath)
if mask is None:
- raise ValueError('Mask not provided')
+ raise ValueError("Mask not provided")
if type(mask) is not np.ndarray:
- raise TypeError('Mask need to be a numpy.ndarray')
+ raise TypeError("Mask need to be a numpy.ndarray")
if hdu_no is None:
hdu_no = fits_file.hdu_no
@@ -664,7 +667,7 @@ def apply_mask(
)
)
else:
- raise TypeError('Mask type must be of type int or bool')
+ raise TypeError("Mask type must be of type int or bool")
def save_as_fits(
self,
@@ -718,7 +721,7 @@ def save_as_fits(
)
if data is None:
- raise ValueError('Data not provided')
+ raise ValueError("Data not provided")
if not image:
if type(data) is dict:
@@ -758,7 +761,7 @@ def save_as_fits(
names = data.dtype.names
it = names
else:
- raise ValueError('Names not provided')
+ raise ValueError("Names not provided")
else:
it = range(len(names))
self._save_to_fits(
@@ -772,7 +775,7 @@ def save_as_fits(
elif type(data) is list:
if names is None:
- raise ValueError('Names not provided')
+ raise ValueError("Names not provided")
it = range(len(names))
data = np.asarray(data)
self._save_to_fits(
@@ -786,7 +789,7 @@ def save_as_fits(
elif type(data) is Table:
if names is None:
- raise ValueError('Names not provided')
+ raise ValueError("Names not provided")
it = names
self._save_to_fits(
data,
@@ -805,7 +808,7 @@ def save_as_fits(
overwrite=overwrite,
)
else:
- raise TypeError('Data need to be a numpy.ndarray')
+ raise TypeError("Data need to be a numpy.ndarray")
def create_from_numpy(
self,
@@ -848,7 +851,7 @@ def create_from_numpy(
fits_header = None
if header is not None:
fits_header = fits.Header()
- for (k, v) in header.items():
+ for k, v in header.items():
fits_header[k] = v
primary_hdu = fits.PrimaryHDU()
@@ -1178,16 +1181,16 @@ def get_header_value(self, request, hdu_no=None):
"""
if request is None:
- raise ValueError('request not provided')
+ raise ValueError("request not provided")
if type(request) is not str:
- raise TypeError('request has to be a string')
+ raise TypeError("request has to be a string")
if hdu_no is None:
hdu_no = self._hdu_no
header = self.get_header(hdu_no=hdu_no)
if header is None:
- raise ValueError(f'Empty header in the hdu : {hdu_no}')
+ raise ValueError(f"Empty header in the hdu : {hdu_no}")
return interpreter(string=request, catalogue=header).result
@@ -1222,7 +1225,7 @@ def add_header_card(self, key, value=None, comment=None, hdu_no=None):
card = []
if key is None:
- raise ValueError('key not provided')
+ raise ValueError("key not provided")
else:
card.append(key)
@@ -1230,7 +1233,7 @@ def add_header_card(self, key, value=None, comment=None, hdu_no=None):
card.append(value)
else:
if comment is not None:
- card.append('')
+ card.append("")
if comment is not None:
card.append(comment)
@@ -1305,12 +1308,12 @@ def get_col_comments(self, hdu_no=None):
if hdu_no is None:
hdu_no = self.hdu_no
hdr_col_types = [
- tt for tt in self._cat_data[hdu_no].header.keys()
- if 'TTYPE' in tt
+ tt
+ for tt in self._cat_data[hdu_no].header.keys()
+ if "TTYPE" in tt
]
return [
- self._cat_data[hdu_no].header.comments[c]
- for c in hdr_col_types
+ self._cat_data[hdu_no].header.comments[c] for c in hdr_col_types
]
else:
raise BaseCatalogue.catalogueNotOpen(self.fullpath)
@@ -1384,7 +1387,7 @@ def add_col(
)
if type(col_data) != np.ndarray:
- TypeError('col_data must be a numpy.ndarray')
+ TypeError("col_data must be a numpy.ndarray")
if hdu_no is None:
hdu_no = self.hdu_no
@@ -1410,31 +1413,43 @@ def add_col(
if len(data_shape) != 0:
for k in data_shape:
mem_size *= k
- data_format = f'{mem_size}{data_type}'
- new_col = fits.ColDefs([fits.Column(
- name=col_name,
- format=data_format,
- array=col_data,
- dim=dim,
- )])
+ data_format = f"{mem_size}{data_type}"
+ new_col = fits.ColDefs(
+ [
+ fits.Column(
+ name=col_name,
+ format=data_format,
+ array=col_data,
+ dim=dim,
+ )
+ ]
+ )
col_list += new_col
- elif data_type == 'A':
+ elif data_type == "A":
mem_size *= len(max(col_data, key=len))
- data_format = f'{mem_size}{data_type}'
- new_col = fits.ColDefs([fits.Column(
- name=col_name,
- format=data_format,
- array=col_data,
- dim=str((mem_size,)),
- )])
+ data_format = f"{mem_size}{data_type}"
+ new_col = fits.ColDefs(
+ [
+ fits.Column(
+ name=col_name,
+ format=data_format,
+ array=col_data,
+ dim=str((mem_size,)),
+ )
+ ]
+ )
col_list += new_col
else:
- data_format = f'{mem_size}{data_type}'
- new_col = fits.ColDefs([fits.Column(
- name=col_name,
- format=data_format,
- array=col_data,
- )])
+ data_format = f"{mem_size}{data_type}"
+ new_col = fits.ColDefs(
+ [
+ fits.Column(
+ name=col_name,
+ format=data_format,
+ array=col_data,
+ )
+ ]
+ )
col_list += new_col
new_fits.append(fits.BinTableHDU.from_columns(col_list, name=ext_name))
@@ -1463,7 +1478,7 @@ def remove_col(self, col_index):
Index of the column to delete
"""
- raise BaseCatalogue.FeatureNotImplemented('remove_col()')
+ raise BaseCatalogue.FeatureNotImplemented("remove_col()")
def remove_named_col(self, col_name):
"""Remove Named Column.
@@ -1508,11 +1523,15 @@ def _append_col(self, column, hdu_no=None):
orig_table = fits.open(self.fullpath)[hdu_no].data
orig_cols = orig_table.columns
- new_col = fits.ColDefs([fits.Column(
- name=column.name,
- format=column.format,
- array=np.zeros(len(orig_table)),
- )])
+ new_col = fits.ColDefs(
+ [
+ fits.Column(
+ name=column.name,
+ format=column.format,
+ array=np.zeros(len(orig_table)),
+ )
+ ]
+ )
col_list = orig_cols + new_col
hdu = fits.BinTableHDU.from_columns(col_list)
hdu.data[column.name] = column.data
@@ -1538,21 +1557,21 @@ def _get_fits_col_type(self, col_data):
"""
if col_data is None or len(col_data) == 0:
- col_type = 'D'
+ col_type = "D"
elif type(col_data[0]) in [np.int16]:
- col_type = 'I'
+ col_type = "I"
elif type(col_data[0]) in [np.int32]:
- col_type = 'J'
+ col_type = "J"
elif type(col_data[0]) in [int, np.int64]:
- col_type = 'K'
+ col_type = "K"
elif type(col_data[0]) in [float, np.float16, np.float32, np.float64]:
- col_type = 'D'
+ col_type = "D"
elif type(col_data[0]) is bool:
- col_type = 'L'
+ col_type = "L"
elif type(col_data[0]) in [str, np.str_, np.str0]:
- col_type = 'A'
+ col_type = "A"
else:
- col_type = 'D'
+ col_type = "D"
return col_type
@@ -1572,27 +1591,27 @@ def _get_python_col_type(self, col_type):
Column Python data type
"""
- if col_type in ['B', 'I', 'J', 'K']:
- pcol_type = '%d'
- elif col_type in ['D', 'E']:
- pcol_type = '%f'
- elif col_type in ['A', 'C', 'M']:
- pcol_type = '%s'
- elif col_type == 'L':
- pcol_type = '%s'
+ if col_type in ["B", "I", "J", "K"]:
+ pcol_type = "%d"
+ elif col_type in ["D", "E"]:
+ pcol_type = "%f"
+ elif col_type in ["A", "C", "M"]:
+ pcol_type = "%s"
+ elif col_type == "L":
+ pcol_type = "%s"
else:
- pcol_type = '%f'
+ pcol_type = "%f"
return pcol_type
def _save_to_fits(
- self,
- data,
- names,
- it,
- ext_name=None,
- sex_cat_path=None,
- overwrite=False,
+ self,
+ data,
+ names,
+ it,
+ ext_name=None,
+ sex_cat_path=None,
+ overwrite=False,
):
"""Save to FITS.
@@ -1615,24 +1634,24 @@ def _save_to_fits(
"""
if data is None:
- raise ValueError('Data not provided')
+ raise ValueError("Data not provided")
if self._file_exists(self.fullpath) and not overwrite:
if self._cat_data is None:
self.open()
if ext_name is None:
- ext_name = 'new'
+ ext_name = "new"
else:
if self._SEx_catalogue:
self.create(s_hdu=False, sex_cat_path=sex_cat_path)
self.open()
if ext_name is None:
- ext_name = 'LDAC_OBJECTS'
+ ext_name = "LDAC_OBJECTS"
else:
self.create(s_hdu=False)
self.open()
if ext_name is None:
- ext_name = 'new'
+ ext_name = "new"
if len(names) == 1:
data = np.array([data])
@@ -1646,29 +1665,35 @@ def _save_to_fits(
if len(data_shape) != 0:
for shape in data_shape:
mem_size *= shape
- data_format = f'{mem_size}{data_type}'
- col_list.append(fits.Column(
- name=name,
- format=data_format,
- array=data[idx],
- dim=dim,
- ))
- elif data_type == 'A':
+ data_format = f"{mem_size}{data_type}"
+ col_list.append(
+ fits.Column(
+ name=name,
+ format=data_format,
+ array=data[idx],
+ dim=dim,
+ )
+ )
+ elif data_type == "A":
mem_size *= len(max(data[idx], key=len))
- data_format = f'{mem_size}{data_type}'
- col_list.append(fits.Column(
- name=name,
- format=data_format,
- array=data[idx],
- dim=str((mem_size,)),
- ))
+ data_format = f"{mem_size}{data_type}"
+ col_list.append(
+ fits.Column(
+ name=name,
+ format=data_format,
+ array=data[idx],
+ dim=str((mem_size,)),
+ )
+ )
else:
- data_format = f'{mem_size}{data_type}'
- col_list.append(fits.Column(
- name=name,
- format=data_format,
- array=data[idx],
- ))
+ data_format = f"{mem_size}{data_type}"
+ col_list.append(
+ fits.Column(
+ name=name,
+ format=data_format,
+ array=data[idx],
+ )
+ )
self._cat_data.append(
fits.BinTableHDU.from_columns(col_list, name=ext_name)
@@ -1700,13 +1725,13 @@ def _save_from_recarray(
"""
if data is None:
- raise ValueError('Data not provided')
+ raise ValueError("Data not provided")
if self._file_exists(self.fullpath) and not overwrite:
if self._cat_data is None:
self.open()
if ext_name is None:
- ext_name = 'new'
+ ext_name = "new"
self._cat_data.append(fits.BinTableHDU(data, name=ext_name))
self.close()
else:
@@ -1714,14 +1739,14 @@ def _save_from_recarray(
self.create(s_hdu=False, sex_cat_path=sex_cat_path)
self.open()
if ext_name is None:
- ext_name = 'LDAC_OBJECTS'
+ ext_name = "LDAC_OBJECTS"
self._cat_data.append(fits.BinTableHDU(data, name=ext_name))
self.close()
else:
self.create(s_hdu=False)
self.open()
if ext_name is None:
- ext_name = 'new'
+ ext_name = "new"
self._cat_data.append(fits.BinTableHDU(data, name=ext_name))
self.close()
@@ -1740,13 +1765,13 @@ def _save_image(self, data=None, header=None, overwrite=False):
Option to overwrite an existing catalogue
"""
- if (data is not None):
+ if data is not None:
fits.PrimaryHDU(data, header).writeto(
self.fullpath,
overwrite=overwrite,
)
else:
- raise ValueError('Data or names not provided')
+ raise ValueError("Data or names not provided")
class Column(BaseCatalogue.Column):
"""Column.
@@ -1772,7 +1797,7 @@ def __init__(self, name, format=None, comment=None, data=None):
self._name = name
if format is None:
- format = 'D'
+ format = "D"
self._format = format
if comment is None:
@@ -1788,7 +1813,7 @@ def __init__(self, name, format=None, comment=None, data=None):
self._data = data
def __str__(self):
- info = f'{self._cat_col}'
+ info = f"{self._cat_col}"
return info
@property
@@ -1871,7 +1896,7 @@ def get_unit_from_fits_header(header, key):
idx = 1
idx_found = -1
while True:
- ttype_idx = f'TTYPE{idx}'
+ ttype_idx = f"TTYPE{idx}"
if ttype_idx not in header:
# Reached beyond last column
break
@@ -1883,14 +1908,13 @@ def get_unit_from_fits_header(header, key):
idx += 1
if idx_found == -1:
- raise IndexError(f'Column \'{key}\' not found in FITS header')
+ raise IndexError(f"Column '{key}' not found in FITS header")
# Extract coordinate unit string from header
- tcunit_idx = f'TCUNI{idx}'
+ tcunit_idx = f"TCUNI{idx}"
if tcunit_idx not in header:
raise IndexError(
- f'No coordinate unit found for column \'{key}\''
- ' in FITS header'
+ f"No coordinate unit found for column '{key}'" " in FITS header"
)
unit_str = header[tcunit_idx]
diff --git a/shapepipe/pipeline/job_handler.py b/shapepipe/pipeline/job_handler.py
index d6baebd89..9a6e01f1f 100644
--- a/shapepipe/pipeline/job_handler.py
+++ b/shapepipe/pipeline/job_handler.py
@@ -42,6 +42,8 @@ class JobHandler(object):
Joblib backend, the default is None (which corresponds to 'loky')
timeout : int, optional
Timeout limit for a given job in seconds, the default is None
+ exclusive : str, optional
+ Run this file number string exclusively if given, the default is None
verbose : bool, optional
Verbose setting, default is True
@@ -53,11 +55,12 @@ def __init__(
filehd,
config,
log,
- job_type='parallel',
- parallel_mode='smp',
+ job_type="parallel",
+ parallel_mode="smp",
batch_size=None,
backend=None,
timeout=None,
+ exclusive=None,
verbose=True,
):
@@ -72,6 +75,7 @@ def __init__(
self._module = module
self._module_runner = self.filehd.module_runners[self._module]
self.error_count = 0
+ self.exclusive = exclusive
self._verbose = verbose
# Add the job parameters to the log
@@ -105,7 +109,7 @@ def config(self, value):
if not isinstance(value, ConfigParser):
raise TypeError(
- 'config must be an instane of configparser.ConfigParser'
+ "config must be an instane of configparser.ConfigParser"
)
self._config = value
@@ -128,7 +132,7 @@ def log(self):
def log(self, value):
if not isinstance(value, Logger):
- raise TypeError('log must be an instance of logging.Logger.')
+ raise TypeError("log must be an instance of logging.Logger.")
self._log = value
@@ -149,8 +153,8 @@ def job_type(self):
@job_type.setter
def job_type(self, value):
- if value not in ('serial', 'parallel'):
- raise TypeError(f'{value} is not a valid job type.')
+ if value not in ("serial", "parallel"):
+ raise TypeError(f"{value} is not a valid job type.")
self._job_type = value
@@ -171,8 +175,8 @@ def parallel_mode(self):
@parallel_mode.setter
def parallel_mode(self, value):
- if value not in ('smp', 'mpi'):
- raise TypeError(f'{value} is not a valid parallel mode.')
+ if value not in ("smp", "mpi"):
+ raise TypeError(f"{value} is not a valid parallel mode.")
self._parallel_mode = value
@@ -193,20 +197,19 @@ def batch_size(self):
@batch_size.setter
def batch_size(self, value):
- if (
- isinstance(value, type(None))
- and self.config.has_option('JOB', 'SMP_BATCH_SIZE')
+ if isinstance(value, type(None)) and self.config.has_option(
+ "JOB", "SMP_BATCH_SIZE"
):
- value = self.config.getint('JOB', 'SMP_BATCH_SIZE')
+ value = self.config.getint("JOB", "SMP_BATCH_SIZE")
elif isinstance(value, type(None)):
value = 1
if not isinstance(value, int) or (value < 1):
- raise ValueError('Batch size must be an integer >= 1.')
+ raise ValueError("Batch size must be an integer >= 1.")
if value > cpu_count():
- warn('Batch size exeeds the number of available CPUs.')
+ warn("Batch size exeeds the number of available CPUs.")
self._batch_size = value
@@ -227,16 +230,15 @@ def backend(self):
@backend.setter
def backend(self, value):
- if (
- isinstance(value, type(None))
- and self.config.has_option('JOB', 'SMP_BACKEND')
+ if isinstance(value, type(None)) and self.config.has_option(
+ "JOB", "SMP_BACKEND"
):
- value = self.config.get('JOB', 'SMP_BACKEND').lower()
+ value = self.config.get("JOB", "SMP_BACKEND").lower()
elif isinstance(value, type(None)):
- value = 'loky'
+ value = "loky"
- if value not in ('loky', 'multiprocessing', 'threading'):
- raise ValueError(f'{value} is not a valid joblib backend.')
+ if value not in ("loky", "multiprocessing", "threading"):
+ raise ValueError(f"{value} is not a valid joblib backend.")
self._backend = value
@@ -259,15 +261,14 @@ def timeout(self):
@timeout.setter
def timeout(self, value):
- if (
- isinstance(value, type(None))
- and self.config.has_option('JOB', 'TIMEOUT')
+ if isinstance(value, type(None)) and self.config.has_option(
+ "JOB", "TIMEOUT"
):
- value = self.config.get('JOB', 'TIMEOUT')
- value = self.hms2sec(value) if ':' in value else int(value)
+ value = self.config.get("JOB", "TIMEOUT")
+ value = self.hms2sec(value) if ":" in value else int(value)
if not isinstance(value, (type(None), int)):
- raise TypeError('Timeout must be None or an integer.')
+ raise TypeError("Timeout must be None or an integer.")
self._timeout = value
@@ -279,12 +280,12 @@ def finish_up(self):
"""
self._check_for_errors()
self._check_missed_processes()
- self.log.info('All processes complete')
- self.log.info('')
+ self.log.info("All processes complete")
+ self.log.info("")
if self._verbose:
- print('All processes complete')
- print('')
+ print("All processes complete")
+ print("")
collect()
@@ -296,7 +297,7 @@ def submit_jobs(self):
Submit jobs in serial or parallel.
"""
- if self.job_type == 'serial':
+ if self.job_type == "serial":
self.submit_serial_job()
else:
self._distribute_smp_jobs()
@@ -324,7 +325,7 @@ def hms2sec(time_str):
Time strings should take the form 'HH:MM:SS'.
"""
- h, m, s = time_str.split(':')
+ h, m, s = time_str.split(":")
return int(h) * 3600 + int(m) * 60 + int(s)
@@ -334,15 +335,15 @@ def _log_job_parameters(self):
This method logs the job handler instance parameters.
"""
- text = 'Starting job handler with:'
- module_info = f' - Module: {self._module}'
- job_prop_text = ' - Job Properties:'
- job_type = f' -- Job Type: {self.job_type}'
- batch_info = f' -- Batch size: {self.batch_size}'
- time_info = f' -- Timeout Limit: {self.timeout}s'
+ text = "Starting job handler with:"
+ module_info = f" - Module: {self._module}"
+ job_prop_text = " - Job Properties:"
+ job_type = f" -- Job Type: {self.job_type}"
+ batch_info = f" -- Batch size: {self.batch_size}"
+ time_info = f" -- Timeout Limit: {self.timeout}s"
show_batch_into = (
- self.job_type == 'parallel' and self.parallel_mode == 'smp'
+ self.job_type == "parallel" and self.parallel_mode == "smp"
)
self.log.info(text)
@@ -368,7 +369,7 @@ def _log_num_processes(self):
This method logs the number of processes detected for a given module.
"""
- proc_info = f' -- Total number of processes: {self._n_procs}'
+ proc_info = f" -- Total number of processes: {self._n_procs}"
self.log.info(proc_info)
@@ -381,20 +382,18 @@ def _distribute_smp_jobs(self):
This method distributes the jobs to the workers using SMP.
"""
- result = (
- Parallel(n_jobs=self.batch_size, backend=self.backend)(
- delayed(WorkerHandler(verbose=self._verbose).worker)(
- process[1:],
- process[0],
- self.filehd.get_worker_log_name(self._module, process[0]),
- self.filehd.module_run_dirs,
- self.config,
- self.filehd.get_module_config_sec(self._module),
- self.timeout,
- self._module_runner
- )
- for process in self.filehd.process_list
+ result = Parallel(n_jobs=self.batch_size, backend=self.backend)(
+ delayed(WorkerHandler(verbose=self._verbose).worker)(
+ process[1:],
+ process[0],
+ self.filehd.get_worker_log_name(self._module, process[0]),
+ self.filehd.module_run_dirs,
+ self.config,
+ self.filehd.get_module_config_sec(self._module),
+ self.timeout,
+ self._module_runner,
)
+ for process in self.filehd.process_list
)
self.worker_dicts = result
@@ -410,9 +409,10 @@ def submit_serial_job(self):
result = wh.worker(
process,
- '',
- self.filehd.get_worker_log_name(self._module, '_serial'),
- self.filehd.module_run_dirs, self.config,
+ "",
+ self.filehd.get_worker_log_name(self._module, "_serial"),
+ self.filehd.module_run_dirs,
+ self.config,
self.filehd.get_module_config_sec(self._module),
self.timeout,
self._module_runner,
@@ -438,7 +438,7 @@ def _check_exception_status(self):
"""
for worker_dict in self.worker_dicts:
- if worker_dict['exception']:
+ if worker_dict["exception"]:
self.log.info(
f'ERROR: {worker_dict["exception"]} recorded '
+ f'in: {worker_dict["log"]}'
@@ -453,7 +453,7 @@ def _check_stderr_status(self):
"""
for worker_dict in self.worker_dicts:
- if worker_dict['stderr']:
+ if worker_dict["stderr"]:
self.log.info(
f'ERROR: stderr recorded in: {worker_dict["log"]}'
)
@@ -466,18 +466,16 @@ def _check_missed_processes(self):
submitted.
"""
- missed_txt = (
- ' - The following processes were not submitted to workers:'
- )
+ missed_txt = " - The following processes were not submitted to workers:"
if self.filehd.missed:
self.log.info(missed_txt)
- self.log.info(f' - {self.filehd.missed}')
+ self.log.info(f" - {self.filehd.missed}")
if self._verbose:
print(missed_txt)
- print(f' - {self.filehd.missed}')
+ print(f" - {self.filehd.missed}")
def clean_up(self):
"""Finish.
diff --git a/shapepipe/pipeline/mpi_run.py b/shapepipe/pipeline/mpi_run.py
index c92d943c8..5baf84227 100644
--- a/shapepipe/pipeline/mpi_run.py
+++ b/shapepipe/pipeline/mpi_run.py
@@ -36,6 +36,7 @@ def submit_mpi_jobs(
timeout,
run_dirs,
module_runner,
+ module_config_sec,
worker_log,
verbose,
):
@@ -57,6 +58,7 @@ def submit_mpi_jobs(
w_log_name,
run_dirs,
config,
+ module_config_sec,
timeout,
module_runner
))
diff --git a/shapepipe/pipeline/run_log.py b/shapepipe/pipeline/run_log.py
index 115e87de0..110378539 100644
--- a/shapepipe/pipeline/run_log.py
+++ b/shapepipe/pipeline/run_log.py
@@ -30,7 +30,7 @@ class RunLog(object):
def __init__(self, run_log_file, module_list, current_run):
self.run_log_file = run_log_file
- self._module_list = ','.join(module_list)
+ self._module_list = ",".join(module_list)
self.current_run = current_run
self._write()
self._runs = get_list(run_log_file)
@@ -41,8 +41,8 @@ def _write(self):
Write current run to the run log.
"""
- with open(self.run_log_file, 'a') as run_log:
- run_log.write(f'{self.current_run} {self._module_list}\n')
+ with open(self.run_log_file, "a") as run_log:
+ run_log.write(f"{self.current_run} {self._module_list}\n")
def get_run(self, search_string):
"""Get Run.
@@ -71,16 +71,16 @@ def get_run(self, search_string):
if len(runs) < 1:
raise RuntimeError(
- f'No runs found matching search string \'{search_string}\'.'
+ f"No runs found matching search string '{search_string}'."
)
elif len(runs) > 1:
raise RuntimeError(
- 'More than one run found matching search string '
- + f'\'{search_string}\''
+ "More than one run found matching search string "
+ + f"'{search_string}'"
)
- return runs[0].split(' ')[0]
+ return runs[0].split(" ")[0]
def get_list(run_log_file):
@@ -99,7 +99,7 @@ def get_list(run_log_file):
Run log file entries
"""
- with open(run_log_file, 'r') as run_log:
+ with open(run_log_file, "r") as run_log:
lines = run_log.readlines()
runs = [line.rstrip() for line in lines]
@@ -132,14 +132,9 @@ def get_all(runs, module):
"""
module_base, _ = split_module_run(module)
- all_runs = [
- run for run in runs
- if module_base in run.split()[1].split(',')
- ]
+ all_runs = [run for run in runs if module_base in run.split()[1].split(",")]
if len(all_runs) == 0:
- raise RuntimeError(
- f'No previous run of module \'{module_base}\' found'
- )
+ raise RuntimeError(f"No previous run of module '{module_base}' found")
all_runs = all_runs[::-1]
@@ -167,7 +162,36 @@ def get_last(runs, module):
all_runs = get_all(runs, module)
last_run = all_runs[0]
- return last_run.split(' ')[0]
+ return last_run.split(" ")[0]
+
+
+def get_all_dirs(run_log_file, module):
+ """Get All Dirs.
+
+ Return directory paths corresponding to all runs of given module.
+
+ Parameters
+ ----------
+ run_log_file : str
+ Run log file name
+ module : str
+ Module name
+
+ Returns
+ -------
+ list
+ Directory names of all module runs
+
+ """
+ runs = get_list(run_log_file)
+ all_runs = get_all(runs, module)
+
+ all_dirs = []
+ for run in all_runs:
+ dir_name = run.split(" ")[0]
+ all_dirs.append(f"{dir_name}/{module}/output")
+
+ return all_dirs
def get_last_dir(run_log_file, module):
@@ -188,9 +212,7 @@ def get_last_dir(run_log_file, module):
Directory name of last module run
"""
- runs = get_list(run_log_file)
- all_runs = get_all(runs, module)
- last_run = all_runs[0].split(' ')[0]
- last_dir = f'{last_run}/{module}/output'
+ all_dirs = get_all_dirs(run_log_file, module)
+ last_dir = all_dirs[0]
return last_dir
diff --git a/shapepipe/pipeline/shared.py b/shapepipe/pipeline/shared.py
index 75873251b..24984b34b 100644
--- a/shapepipe/pipeline/shared.py
+++ b/shapepipe/pipeline/shared.py
@@ -33,10 +33,10 @@ def check_duplicate(input_list):
else:
input_set.add(elem)
- return ''
+ return ""
-def find_files(path, pattern='*', ext='*'):
+def find_files(path, pattern="*", ext="*"):
"""Find Files.
This method recursively retrieves file names from a given path that
@@ -66,8 +66,8 @@ def find_files(path, pattern='*', ext='*'):
For invalid extension format
"""
- dot = '.'
- star = '*'
+ dot = "."
+ star = "*"
if pattern != star and star in pattern:
raise ValueError('Do not include "*" in pattern.')
@@ -81,7 +81,7 @@ def find_files(path, pattern='*', ext='*'):
if ext != star and not ext.startswith(dot):
ext = dot + ext
- search_string = f'{path}/**/*{pattern}*{ext}'
+ search_string = f"{path}/**/*{pattern}*{ext}"
return glob(search_string, recursive=True)
@@ -109,10 +109,10 @@ def split_module_run(module_str):
"""
if not isinstance(module_str, str):
raise TypeError(
- f'Input module_str must be a string not {type(module_str)}.'
+ f"Input module_str must be a string not {type(module_str)}."
)
- run_split = '_run_'
+ run_split = "_run_"
module_run = module_str
if run_split in module_str:
diff --git a/shapepipe/pipeline/str_handler.py b/shapepipe/pipeline/str_handler.py
index f64da49f0..e443e31f6 100644
--- a/shapepipe/pipeline/str_handler.py
+++ b/shapepipe/pipeline/str_handler.py
@@ -39,7 +39,7 @@ class StrInterpreter(object):
def __init__(self, string, catalogue, make_compare=False, mask_dict=None):
if type(string) is not str:
- raise ValueError('string has to be str type')
+ raise ValueError("string has to be str type")
else:
self._string = string
@@ -52,7 +52,7 @@ def __init__(self, string, catalogue, make_compare=False, mask_dict=None):
else:
self._cat = catalogue
else:
- raise ValueError('catalogue not provided')
+ raise ValueError("catalogue not provided")
self._make_compare = make_compare
@@ -61,12 +61,12 @@ def __init__(self, string, catalogue, make_compare=False, mask_dict=None):
self._init_stat_function()
self._comp_dict = {
- '<': operator.lt,
- '>': operator.gt,
- '<=': operator.le,
- '>=': operator.ge,
- '==': operator.eq,
- '!=': operator.ne,
+ "<": operator.lt,
+ ">": operator.gt,
+ "<=": operator.le,
+ ">=": operator.ge,
+ "==": operator.eq,
+ "!=": operator.ne,
}
self.result = self.interpret(self._string, self._make_compare)
@@ -107,7 +107,7 @@ def interpret(
result = self._compare(string)
else:
if make_operate:
- string_split = re.split(r'\*|\/|\-|\+\s*(?![^()]*\))', string)
+ string_split = re.split(r"\*|\/|\-|\+\s*(?![^()]*\))", string)
result = self._operate(string, string_split)
else:
if make_func:
@@ -128,14 +128,14 @@ def _compare(self, string):
strind containing the comparison.
"""
- comp = '<|>|<=|>=|==|!='
+ comp = "<|>|<=|>=|==|!="
if len(re.split(comp, string)) != 2:
raise Exception(
- 'Only one comparison in [<, >, <=, >=, ==, !=] per line'
+ "Only one comparison in [<, >, <=, >=, ==, !=] per line"
)
- for operator in ['<=', '>=', '<', '>', '==', '!=']:
+ for operator in ["<=", ">=", "<", ">", "==", "!="]:
terms = re.split(operator, string)
if len(terms) == 2:
self._make_compare = False
@@ -158,7 +158,7 @@ def _apply_func(self, string):
result of the function
"""
- str_split = re.split(r'\(|\)', string)
+ str_split = re.split(r"\(|\)", string)
if len(str_split) == 1:
return self.interpret(
@@ -168,7 +168,7 @@ def _apply_func(self, string):
make_operate=False,
)
elif len(str_split) == 3:
- str_split_2 = re.split(',', str_split[1])
+ str_split_2 = re.split(",", str_split[1])
if len(str_split_2) > 1:
param = [
self.interpret(
@@ -176,7 +176,8 @@ def _apply_func(self, string):
self._make_compare,
make_func=False,
make_operate=True,
- ) for char in str_split_2
+ )
+ for char in str_split_2
]
# Evaluate statistical function, raise error if failure
@@ -190,19 +191,21 @@ def _apply_func(self, string):
else:
if str_split[0] not in self._stat_func:
raise KeyError(
- f'Invalid function \'{str_split[0]}\' in expression '
- + f'\'{string}\''
+ f"Invalid function '{str_split[0]}' in expression "
+ + f"'{string}'"
+ )
+ return self._stat_func[str_split[0]](
+ self.interpret(
+ str_split[1],
+ self._make_compare,
+ make_func=False,
+ make_operate=True,
)
- return self._stat_func[str_split[0]](self.interpret(
- str_split[1],
- self._make_compare,
- make_func=False,
- make_operate=True,
- ))
+ )
else:
raise Exception(
- 'Only one function can be applied. Problem with the '
- + f'term: {string}'
+ "Only one function can be applied. Problem with the "
+ + f"term: {string}"
)
def _init_stat_function(self):
@@ -212,21 +215,21 @@ def _init_stat_function(self):
"""
self._stat_func = {}
- self._stat_func['mean'] = np.mean
- self._stat_func['median'] = np.median
- self._stat_func['mode'] = self._mode
- self._stat_func['sqrt'] = np.sqrt
- self._stat_func['pow'] = pow
- self._stat_func['log'] = np.log
- self._stat_func['log10'] = np.log10
- self._stat_func['exp'] = np.exp
- self._stat_func['std'] = np.std
- self._stat_func['var'] = np.var
- self._stat_func['sigma_mad'] = self._sigma_mad
- self._stat_func['len'] = len
- self._stat_func['min'] = min
- self._stat_func['max'] = max
- self._stat_func['homogen'] = self._test_homogeneity
+ self._stat_func["mean"] = np.mean
+ self._stat_func["median"] = np.median
+ self._stat_func["mode"] = self._mode
+ self._stat_func["sqrt"] = np.sqrt
+ self._stat_func["pow"] = pow
+ self._stat_func["log"] = np.log
+ self._stat_func["log10"] = np.log10
+ self._stat_func["exp"] = np.exp
+ self._stat_func["std"] = np.std
+ self._stat_func["var"] = np.var
+ self._stat_func["sigma_mad"] = self._sigma_mad
+ self._stat_func["len"] = len
+ self._stat_func["min"] = min
+ self._stat_func["max"] = max
+ self._stat_func["homogen"] = self._test_homogeneity
def _mean(self, input):
"""Get Mean.
@@ -303,7 +306,7 @@ def _mode(self, input, eps=0.001, iter_max=1000):
iteration += 1
if iteration == iter_max:
- raise ValueError('Mode computation failed')
+ raise ValueError("Mode computation failed")
else:
mode = (b_min + b_max) / 2.0
return mode
@@ -361,18 +364,18 @@ def _test_homogeneity(self, *args):
n_cells = args[2]
else:
raise ValueError(
- 'Inputs should be param_1, param_2 [optional], n_cells'
+ "Inputs should be param_1, param_2 [optional], n_cells"
)
if n_param == 2:
if len(param[0]) != len(param[1]):
raise ValueError(
- 'Both param_1 and param_2 must have the same '
- + f'length : {len(param[0])}, {len(param[1])}'
+ "Both param_1 and param_2 must have the same "
+ + f"length : {len(param[0])}, {len(param[1])}"
)
if np.sqrt(n_cells) % 1 != 0:
- raise ValueError('N_cells must be a square number')
+ raise ValueError("N_cells must be a square number")
n_tot = len(param[0])
homo_ratio = float(n_tot) / float(n_cells)
@@ -380,37 +383,52 @@ def _test_homogeneity(self, *args):
param_min = []
param_max = []
for idx in param:
- step = (
- (np.max(idx) - np.min(idx))
- / pow(n_cells, 1.0 / float(n_param))
+ step = (np.max(idx) - np.min(idx)) / pow(
+ n_cells, 1.0 / float(n_param)
)
param_min.append(
[val for val in np.arange(np.min(idx), np.max(idx), step)]
)
param_max.append(
[
- val for val in
- np.arange(np.min(idx) + step, np.max(idx) + step, step)
+ val
+ for val in np.arange(
+ np.min(idx) + step, np.max(idx) + step, step
+ )
]
)
if n_param == 1:
- n_obj = np.asarray([
- float(len(np.where(
- (param[0] >= param_min[0][idx])
- & (param[0] <= param_max[0][idx])
- )[0])) for idx in range(int(n_cells))
- ])
+ n_obj = np.asarray(
+ [
+ float(
+ len(
+ np.where(
+ (param[0] >= param_min[0][idx])
+ & (param[0] <= param_max[0][idx])
+ )[0]
+ )
+ )
+ for idx in range(int(n_cells))
+ ]
+ )
elif n_param == 2:
it = itertools.product(range(int(np.sqrt(n_cells))), repeat=2)
- n_obj = np.asarray([
- float(len(np.where(
- (param[0] >= param_min[0][idx_i])
- & (param[0] <= param_max[0][idx_i])
- & (param[1] >= param_min[1][idx_j])
- & (param[1] <= param_max[1][idx_j])
- )[0])) for idx_i, idx_j in it
- ])
+ n_obj = np.asarray(
+ [
+ float(
+ len(
+ np.where(
+ (param[0] >= param_min[0][idx_i])
+ & (param[0] <= param_max[0][idx_i])
+ & (param[1] >= param_min[1][idx_j])
+ & (param[1] <= param_max[1][idx_j])
+ )[0]
+ )
+ )
+ for idx_i, idx_j in it
+ ]
+ )
actual_std = np.std(n_obj / homo_ratio)
@@ -442,47 +460,47 @@ def _operate(self, string, string_split):
It's used as a recursive function
"""
- op = r'\*|\/|\-|\+\s*(?![^()]*\))'
+ op = r"\*|\/|\-|\+\s*(?![^()]*\))"
if string is None:
- raise ValueError('Parameter not specified')
+ raise ValueError("Parameter not specified")
if string_split is None:
- raise ValueError('Parameters splited not specified')
+ raise ValueError("Parameters splited not specified")
if len(re.split(op, string)) == 1:
return self.interpret(string, make_operate=False)
tmp = self._string_op_func(
- re.split(r'\+\s*(?![^()]*\))', string),
+ re.split(r"\+\s*(?![^()]*\))", string),
string_split,
operator.add,
0,
)
- if not np.isscalar(tmp) or tmp != 'pass':
+ if not np.isscalar(tmp) or tmp != "pass":
return tmp
else:
tmp = self._string_op_func(
- re.split(r'\-\s*(?![^()]*\))', string),
+ re.split(r"\-\s*(?![^()]*\))", string),
string_split,
operator.sub,
- 'init',
+ "init",
)
- if not np.isscalar(tmp) or tmp != 'pass':
+ if not np.isscalar(tmp) or tmp != "pass":
return tmp
else:
tmp = self._string_op_func(
- re.split(r'\*\s*(?![^()]*\))', string),
+ re.split(r"\*\s*(?![^()]*\))", string),
string_split,
operator.mul,
1,
)
- if not np.isscalar(tmp) or tmp != 'pass':
+ if not np.isscalar(tmp) or tmp != "pass":
return tmp
else:
return self._string_op_func(
- re.split(r'\/\s*(?![^()]*\))', string),
+ re.split(r"\/\s*(?![^()]*\))", string),
string_split,
operator.truediv,
- 'init',
+ "init",
)
def _string_op_func(self, string_op, string_split, op, tmp):
@@ -512,7 +530,7 @@ def _string_op_func(self, string_op, string_split, op, tmp):
"""
if len(string_op) > 2:
for operator in string_op:
- if tmp == 'init':
+ if tmp == "init":
tmp = self._operate(operator, string_split)
else:
tmp = op(tmp, self._operate(operator, string_split))
@@ -528,7 +546,7 @@ def _string_op_func(self, string_op, string_split, op, tmp):
second = self._operate(string_op[1], string_split)
return op(first, second)
else:
- return 'pass'
+ return "pass"
def _get_value(self, string):
"""Get Value.
@@ -558,28 +576,26 @@ def _get_value(self, string):
string_value = float(string)
return string_value
except Exception:
- str_split = re.split(r'\{|\}', string)
+ str_split = re.split(r"\{|\}", string)
if len(str_split) == 1:
try:
return self._cat[string]
except Exception:
raise ValueError(
- 'String has to be a float or a catalogue parameter. '
- + f'{string} not found'
+ "String has to be a float or a catalogue parameter. "
+ + f"{string} not found"
)
if len(str_split) == 3:
if str_split[1] in self._mask.keys():
try:
- return (
- self._cat[str_split[0]][self._mask[str_split[1]]]
- )
+ return self._cat[str_split[0]][self._mask[str_split[1]]]
except Exception:
raise ValueError(
- 'String has to be a catalogue parameter. '
- + f'{str_split[0]} not found'
+ "String has to be a catalogue parameter. "
+ + f"{str_split[0]} not found"
)
else:
raise ValueError(
- f'Mask has to be provided. {str_split[1]} not '
- + 'found in mask'
+ f"Mask has to be provided. {str_split[1]} not "
+ + "found in mask"
)
diff --git a/shapepipe/pipeline/timeout.py b/shapepipe/pipeline/timeout.py
index a27726b30..f37e1876e 100644
--- a/shapepipe/pipeline/timeout.py
+++ b/shapepipe/pipeline/timeout.py
@@ -28,9 +28,10 @@ def with_timeout(timeout, log_file):
For process exceeding timeout limit
"""
+
def handler(signum, frame):
raise TimeoutError(
- f'The process time exceeded {timeout}s in {log_file}'
+ f"The process time exceeded {timeout}s in {log_file}"
)
def decorator(decorated):
diff --git a/shapepipe/pipeline/worker_handler.py b/shapepipe/pipeline/worker_handler.py
index c8fb7cb2d..bdd8b037e 100644
--- a/shapepipe/pipeline/worker_handler.py
+++ b/shapepipe/pipeline/worker_handler.py
@@ -39,7 +39,7 @@ def worker(
config,
module_config_sec,
timeout,
- module_runner
+ module_runner,
):
"""Worker.
@@ -73,8 +73,7 @@ def worker(
self._config = config
self._module_config_sec = module_config_sec
self._module_runner = module_runner
- self._prepare_worker(process, job_name, timeout,
- module_runner.__name__)
+ self._prepare_worker(process, job_name, timeout, module_runner.__name__)
self._create_worker_log()
self._run_worker()
close_log(self.w_log, verbose=False)
@@ -98,7 +97,7 @@ def _set_job_name(num):
Job name
"""
- return f'process{num}'
+ return f"process{num}"
def _prepare_worker(self, process, job_name, timeout, module):
"""Prepare Worker.
@@ -117,18 +116,18 @@ def _prepare_worker(self, process, job_name, timeout, module):
Module runner name
"""
- self.worker_dict['pid'] = getpid()
- self.worker_dict['threads'] = active_count()
- self.worker_dict['node'] = platform.node()
- self.worker_dict['system'] = platform.system()
- self.worker_dict['machine'] = platform.machine()
- self.worker_dict['exception'] = False
- self.worker_dict['stderr'] = False
- self.worker_dict['process'] = list(process)
- self.worker_dict['file_number_string'] = job_name
- self.worker_dict['job_name'] = self._set_job_name(job_name)
- self.worker_dict['timeout'] = timeout
- self.worker_dict['module'] = module
+ self.worker_dict["pid"] = getpid()
+ self.worker_dict["threads"] = active_count()
+ self.worker_dict["node"] = platform.node()
+ self.worker_dict["system"] = platform.system()
+ self.worker_dict["machine"] = platform.machine()
+ self.worker_dict["exception"] = False
+ self.worker_dict["stderr"] = False
+ self.worker_dict["process"] = list(process)
+ self.worker_dict["file_number_string"] = job_name
+ self.worker_dict["job_name"] = self._set_job_name(job_name)
+ self.worker_dict["timeout"] = timeout
+ self.worker_dict["module"] = module
def _create_worker_log(self):
"""Create Worker Log.
@@ -137,18 +136,17 @@ def _create_worker_log(self):
worker parameters.
"""
- process_size = len(str(self.worker_dict['process']))
+ process_size = len(str(self.worker_dict["process"]))
if self._verbose:
- job_name = self.worker_dict['job_name']
- pid = self.worker_dict['pid']
+ job_name = self.worker_dict["job_name"]
+ pid = self.worker_dict["pid"]
- print(f' - {job_name} PID: {pid} ', end='')
+ print(f" - {job_name} PID: {pid} ", end="")
- if (
- process_size
- < self._config.getint('WORKER', 'PROCESS_PRINT_LIMIT')
+ if process_size < self._config.getint(
+ "WORKER", "PROCESS_PRINT_LIMIT"
):
print(
f'processing {self.worker_dict["file_number_string"]} '
@@ -158,8 +156,8 @@ def _create_worker_log(self):
print()
self.w_log = set_up_log(self._w_log_name, verbose=False)
- self.worker_dict['log'] = self.w_log.name
- self.w_log.info('Worker process running with:')
+ self.worker_dict["log"] = self.w_log.name
+ self.w_log.info("Worker process running with:")
self.w_log.info(f' - Job Name: {self.worker_dict["job_name"]}')
self.w_log.info(f' - PID: {self.worker_dict["pid"]}')
self.w_log.info(f' - Threads: {self.worker_dict["threads"]}')
@@ -177,13 +175,13 @@ def _run_worker(self):
"""
try:
- with_timeout(self.worker_dict['timeout'], self.w_log.name)(
+ with_timeout(self.worker_dict["timeout"], self.w_log.name)(
self._worker_execution
)()
except Exception as err:
catch_error(err, self.w_log)
- self.worker_dict['exception'] = type(err).__name__
+ self.worker_dict["exception"] = type(err).__name__
def _worker_execution(self):
"""Worker Execution.
@@ -205,12 +203,10 @@ def _run_module(self):
For non-existent module runner
"""
- self.w_log.info(
- f' - Running module: {self.worker_dict["module"]}'
- )
+ self.w_log.info(f' - Running module: {self.worker_dict["module"]}')
- file_number_string = self.worker_dict['file_number_string']
- input_file_list = self.worker_dict['process']
+ file_number_string = self.worker_dict["file_number_string"]
+ input_file_list = self.worker_dict["process"]
self._stdout, self._stderr = self._module_runner(
input_file_list,
@@ -228,11 +224,11 @@ def _log_stdout(self):
"""
self.w_log.info(
- f'Process produced the following output: {self._stdout}'
+ f"Process produced the following output: {self._stdout}"
)
if self._stderr:
self.w_log.info(
- f'Process produced the following error(s): {self._stderr}'
+ f"Process produced the following error(s): {self._stderr}"
)
- self.worker_dict['stderr'] = True
+ self.worker_dict["stderr"] = True
diff --git a/shapepipe/run.py b/shapepipe/run.py
index 2443eab50..52d772145 100644
--- a/shapepipe/run.py
+++ b/shapepipe/run.py
@@ -29,7 +29,7 @@
import_mpi = True
-class ShapePipe():
+class ShapePipe:
"""ShapePipe.
ShapePipe runner class.
@@ -49,14 +49,16 @@ def set_up(self):
self._args = create_arg_parser()
self.config = create_config_parser(self._args.config)
self._set_run_name()
- self.modules = self.config.getlist('EXECUTION', 'MODULE')
- self.mode = self.config.get('EXECUTION', 'MODE').lower()
- self.verbose = self.config.getboolean('DEFAULT', 'VERBOSE')
+ self.modules = self.config.getlist("EXECUTION", "MODULE")
+ self.mode = self.config.get("EXECUTION", "MODE").lower()
+ self.exclusive = self._args.exclusive
+ self.verbose = self.config.getboolean("DEFAULT", "VERBOSE")
self.filehd = FileHandler(
self._run_name,
self.modules,
self.config,
- self.verbose,
+ exclusive=self._args.exclusive,
+ verbose=self.verbose,
)
self.error_count = 0
self._prep_run()
@@ -67,10 +69,10 @@ def _set_run_name(self):
Set the name of the current pipeline run.
"""
- self._run_name = self.config.get('DEFAULT', 'RUN_NAME')
+ self._run_name = self.config.get("DEFAULT", "RUN_NAME")
- if self.config.getboolean('DEFAULT', 'RUN_DATETIME'):
- self._run_name += datetime.now().strftime('_%Y-%m-%d_%H-%M-%S')
+ if self.config.getboolean("DEFAULT", "RUN_DATETIME"):
+ self._run_name += datetime.now().strftime("_%Y-%m-%d_%H-%M-%S")
def _create_pipeline_log(self):
"""Create Pipeline Log.
@@ -80,16 +82,16 @@ def _create_pipeline_log(self):
"""
self.log = set_up_log(self.filehd.log_name, verbose=False)
- start_text = f'Starting ShapePipe Run: {self._run_name}'
+ start_text = f"Starting ShapePipe Run: {self._run_name}"
self.log.info(shapepipe_logo())
self.log.info(start_text)
- self.log.info('')
+ self.log.info("")
if self.verbose:
print(shapepipe_logo(colour=True))
print(start_text)
- print('')
+ print("")
# Temporary fix to give file handler access to the log. This should
# be improved at some point.
@@ -107,13 +109,13 @@ def close_pipeline_log(self):
"""
if self.error_count == 1:
- plur = ' was'
+ plur = " was"
else:
- plur = 's were'
+ plur = "s were"
final_error_count = (
- f'A total of {self.error_count} error{plur} recorded.'
+ f"A total of {self.error_count} error{plur} recorded."
)
- end_text = 'Finishing ShapePipe Run'
+ end_text = "Finishing ShapePipe Run"
self.log.info(final_error_count)
self.log.info(end_text)
@@ -172,15 +174,15 @@ def _check_dependencies(self):
Check that all pipeline dependencies have been installed.
"""
- module_dep = self._get_module_depends('depends') + __installs__
- module_exe = self._get_module_depends('executes')
+ module_dep = self._get_module_depends("depends") + __installs__
+ module_exe = self._get_module_depends("executes")
- module_dep += ['mpi4py'] if import_mpi else module_dep
+ module_dep += ["mpi4py"] if import_mpi else module_dep
dh = DependencyHandler(module_dep, module_exe)
- dep_text = 'Checking Python Dependencies:'
- exe_text = 'Checking System Executables:'
+ dep_text = "Checking Python Dependencies:"
+ exe_text = "Checking System Executables:"
self.log.info(dep_text)
if self.verbose:
@@ -193,9 +195,9 @@ def _check_dependencies(self):
if self.verbose:
print(dep)
- self.log.info('')
+ self.log.info("")
if self.verbose:
- print('')
+ print("")
self.log.info(exe_text)
if self.verbose:
@@ -208,9 +210,9 @@ def _check_dependencies(self):
if self.verbose:
print(exe)
- self.log.info('')
+ self.log.info("")
if self.verbose:
- print('')
+ print("")
def _check_module_versions(self):
"""Check Module Version.
@@ -218,7 +220,7 @@ def _check_module_versions(self):
Check versions of the modules.
"""
- ver_text = 'Checking Module Versions:'
+ ver_text = "Checking Module Versions:"
self.log.info(ver_text)
if self.verbose:
@@ -227,16 +229,16 @@ def _check_module_versions(self):
for module in set(self.modules):
module_txt = (
- f' - {module} {self.filehd.module_runners[module].version}'
+ f" - {module} {self.filehd.module_runners[module].version}"
)
self.log.info(module_txt)
if self.verbose:
print(module_txt)
- self.log.info('')
+ self.log.info("")
if self.verbose:
- print('')
+ print("")
def _check_system_setup(self):
"""Check System Set Up.
@@ -244,17 +246,17 @@ def _check_system_setup(self):
Check the set up of the machine on which the pipeline is running.
"""
- setup_text = 'Checking System Set Up:'
- cpu_info = f' - Number of available CPUs: {cpu_count()}'
+ setup_text = "Checking System Set Up:"
+ cpu_info = f" - Number of available CPUs: {cpu_count()}"
self.log.info(setup_text)
self.log.info(cpu_info)
- self.log.info('')
+ self.log.info("")
if self.verbose:
print(setup_text)
print(cpu_info)
- print('')
+ print("")
def _get_module_run_methods(self):
"""Get Module Run Method.
@@ -266,9 +268,9 @@ def _get_module_run_methods(self):
for module in self.modules:
- self.run_method[module] = (
- self.filehd.module_runners[module].run_method
- )
+ self.run_method[module] = self.filehd.module_runners[
+ module
+ ].run_method
def _prep_run(self):
"""Prepare Run.
@@ -300,13 +302,13 @@ def record_mode(self):
Log mode in which ShapePipe is running.
"""
- mode_text = f'Running ShapePipe using {self.mode}'
+ mode_text = f"Running ShapePipe using {self.mode}"
self.log.info(mode_text)
- self.log.info('')
+ self.log.info("")
if self.verbose:
print(mode_text)
- print('')
+ print("")
def run_smp(pipe):
@@ -330,6 +332,7 @@ def run_smp(pipe):
config=pipe.config,
log=pipe.log,
job_type=pipe.run_method[module],
+ exclusive=pipe.exclusive,
verbose=pipe.verbose,
)
@@ -387,7 +390,8 @@ def run_mpi(pipe, comm):
config=config,
log=pipe.log,
job_type=pipe.run_method[module],
- parallel_mode='mpi',
+ parallel_mode="mpi",
+ exclusive=pipe.exclusive,
verbose=verbose,
)
@@ -395,7 +399,7 @@ def run_mpi(pipe, comm):
job_type = jh.job_type
# Handle serial jobs
- if job_type == 'serial':
+ if job_type == "serial":
jh.submit_jobs()
# Handle parallel jobs
@@ -405,6 +409,7 @@ def run_mpi(pipe, comm):
# Get file handler objects
run_dirs = jh.filehd.module_run_dirs
module_runner = jh.filehd.module_runners[module]
+ module_config_sec = jh.filehd.get_module_config_sec(module)
worker_log = jh.filehd.get_worker_log_name
# Define process list
process_list = jh.filehd.process_list
@@ -412,18 +417,19 @@ def run_mpi(pipe, comm):
jobs = split_mpi_jobs(process_list, comm.size)
del process_list
else:
- job_type = module_runner = worker_log = timeout = \
- jobs = run_dirs = None
+ job_type = module_runner = module_config_sec = worker_log = \
+ timeout = jobs = run_dirs = None
# Broadcast job type to all nodes
job_type = comm.bcast(job_type, root=0)
- if job_type == 'parallel':
+ if job_type == "parallel":
# Broadcast objects to all nodes
run_dirs = comm.bcast(run_dirs, root=0)
module_runner = comm.bcast(module_runner, root=0)
+ module_config_sec = comm.bcast(module_config_sec, root=0)
worker_log = comm.bcast(worker_log, root=0)
timeout = comm.bcast(timeout, root=0)
jobs = comm.scatter(jobs, root=0)
@@ -436,14 +442,15 @@ def run_mpi(pipe, comm):
timeout,
run_dirs,
module_runner,
+ module_config_sec,
worker_log,
- verbose
+ verbose,
),
root=0,
)
# Delete broadcast objects
- del module_runner, worker_log, timeout, jobs
+ del module_runner, module_config_sec, worker_log, timeout, jobs
# Finish up parallel jobs
if master:
@@ -486,13 +493,13 @@ def run(*args):
pipe = None
mode = None
- mode = comm.bcast(mode, root=0) if import_mpi else 'smp'
+ mode = comm.bcast(mode, root=0) if import_mpi else "smp"
if master:
pipe.mode = mode
pipe.record_mode()
- if mode == 'mpi':
+ if mode == "mpi":
run_mpi(pipe, comm)
else:
run_smp(pipe)
diff --git a/shapepipe/tests/test_get_images.py b/shapepipe/tests/test_get_images.py
index ca492e9b6..860f37f97 100644
--- a/shapepipe/tests/test_get_images.py
+++ b/shapepipe/tests/test_get_images.py
@@ -19,8 +19,8 @@ class GetImagesTestCase(TestCase):
def setUp(self):
- self.number_tile = '123.456'
- self.number_exp = '2490092p'
+ self.number_tile = "123.456"
+ self.number_exp = "2490092p"
self.number_int = 123456
def tearDown(self):
@@ -32,13 +32,11 @@ def tearDown(self):
def test_in2out_pattern(self):
npt.assert_string_equal(
- get_images.in2out_pattern(self.number_tile),
- '123-456'
+ get_images.in2out_pattern(self.number_tile), "123-456"
)
npt.assert_string_equal(
- get_images.in2out_pattern(self.number_exp),
- '2490092'
+ get_images.in2out_pattern(self.number_exp), "2490092"
)
npt.assert_raises(
diff --git a/shapepipe/tests/test_pipeline.py b/shapepipe/tests/test_pipeline.py
index 24b9ce8ca..2a59a6c74 100644
--- a/shapepipe/tests/test_pipeline.py
+++ b/shapepipe/tests/test_pipeline.py
@@ -18,8 +18,8 @@ class ExecuteTestCase(TestCase):
def setUp(self):
- self.command_line = 'echo 1'
- self.output_tuple = ('1\n', '')
+ self.command_line = "echo 1"
+ self.output_tuple = ("1\n", "")
def tearDown(self):
@@ -34,5 +34,5 @@ def test_execute(self):
def test_check_executable(self):
npt.assert_raises(TypeError, execute.check_executable, 1)
- npt.assert_raises(OSError, execute.check_executable, '')
- self.assertIsNone(execute.check_executable('/bin/ls'))
+ npt.assert_raises(OSError, execute.check_executable, "")
+ self.assertIsNone(execute.check_executable("/bin/ls"))
diff --git a/shapepipe/tests/test_utilities.py b/shapepipe/tests/test_utilities.py
index d5c02233a..83d624108 100644
--- a/shapepipe/tests/test_utilities.py
+++ b/shapepipe/tests/test_utilities.py
@@ -45,22 +45,22 @@ def test_sigma_to_fwhm(self):
npt.assert_almost_equal(
galaxy.sigma_to_fwhm(self.sigma_float),
self.sigma_float_exp,
- err_msg='sigma_to_fwhm gave invalid result for float input',
+ err_msg="sigma_to_fwhm gave invalid result for float input",
)
npt.assert_almost_equal(
galaxy.sigma_to_fwhm(self.sigma_float, self.pixel_scale),
self.sigma_float_ps_exp,
err_msg=(
- 'sigma_to_fwhm gave invalid result for float input with '
- + 'non-default pixel scale'
+ "sigma_to_fwhm gave invalid result for float input with "
+ + "non-default pixel scale"
),
)
npt.assert_allclose(
galaxy.sigma_to_fwhm(self.sigma_array),
self.sigma_array_exp,
- err_msg='sigma_to_fwhm gave invalid result for array input',
+ err_msg="sigma_to_fwhm gave invalid result for array input",
)
npt.assert_raises(TypeError, galaxy.sigma_to_fwhm, self.sigma_int)
diff --git a/shapepipe/utilities/__init__.py b/shapepipe/utilities/__init__.py
index 63b425136..15e59739c 100644
--- a/shapepipe/utilities/__init__.py
+++ b/shapepipe/utilities/__init__.py
@@ -7,4 +7,4 @@
"""
-__all__ = ['file_system', 'cfis', 'galaxy']
+__all__ = ["file_system", "cfis", "galaxy"]
diff --git a/shapepipe/utilities/cfis.py b/shapepipe/utilities/cfis.py
index c8cdcb7a5..0d94b3be3 100644
--- a/shapepipe/utilities/cfis.py
+++ b/shapepipe/utilities/cfis.py
@@ -18,17 +18,17 @@
from shapepipe.utilities.file_system import mkdir
-unitdef = 'degree'
+unitdef = "degree"
# Maybe define class for these constants?
size = {}
-size['tile'] = 0.5
-size['weight'] = 0.5
-size['exposure'] = 1.0
+size["tile"] = 0.5
+size["weight"] = 0.5
+size["exposure"] = 1.0
# Cut criteria for exposures
exp_time_min = 95
-flag_valid = 'V'
+flag_valid = "V"
class param:
@@ -60,7 +60,7 @@ class CfisError(Exception):
pass
-class image():
+class image:
"""Image Class.
Class to store and create image information.
@@ -80,7 +80,7 @@ class image():
"""
- def __init__(self, name, ra, dec, exp_time=-1, valid='Unknown'):
+ def __init__(self, name, ra, dec, exp_time=-1, valid="Unknown"):
self.name = name
self.ra = ra
self.dec = dec
@@ -89,7 +89,7 @@ def __init__(self, name, ra, dec, exp_time=-1, valid='Unknown'):
else:
self.exp_time = exp_time
if valid is None:
- self.valid = 'Unknown'
+ self.valid = "Unknown"
else:
self.valid = valid
@@ -119,7 +119,7 @@ def cut(self, no_cuts=False):
return True
# Cut if validation flag is not valid (and not unknown)
- if self.valid != flag_valid and self.valid != 'Unknown':
+ if self.valid != flag_valid and self.valid != "Unknown":
return True
return False
@@ -140,18 +140,14 @@ def get_ID(self):
if name does not match to ID pattern
"""
- m = re.search(r'(\d{3}).{1}(\d{3})', self.name)
+ m = re.search(r"(\d{3}).{1}(\d{3})", self.name)
if m is None:
- raise ValueError(f'No ID match in file name {name}')
+ raise ValueError(f"No ID match in file name {name}")
else:
- return f'{m[1]}.{m[2]}'
+ return f"{m[1]}.{m[2]}"
def print(
- self,
- file=sys.stdout,
- base_name=False,
- name_only=True,
- ID_only=False
+ self, file=sys.stdout, base_name=False, name_only=True, ID_only=False
):
"""Print.
@@ -180,21 +176,21 @@ def print(
name = self.name
if ID_only:
- m = re.search(r'\d{3}.\d{3}', name)
+ m = re.search(r"\d{3}.\d{3}", name)
if m is None:
- raise ValueError(f'No ID match in file name {name}')
+ raise ValueError(f"No ID match in file name {name}")
else:
name = m[0]
- print(name, end='', file=file)
+ print(name, end="", file=file)
if not name_only:
if self.ra is not None:
ra_unit = getattr(self.ra, unitdef)
- print(f' {ra_unit:10.2f}', end='', file=file)
+ print(f" {ra_unit:10.2f}", end="", file=file)
if self.dec is not None:
dec_unit = getattr(self.dec, unitdef)
- print(f' {dec_unit:10.2f}', end='', file=file)
- print(f' {self.exp_time:5d} {self.valid:8s}', end='', file=file)
+ print(f" {dec_unit:10.2f}", end="", file=file)
+ print(f" {self.exp_time:5d} {self.valid:8s}", end="", file=file)
print(file=file)
def print_header(self, file=sys.stdout):
@@ -209,8 +205,8 @@ def print_header(self, file=sys.stdout):
"""
print(
- f'#Name ra[{unitdef}] dec[{unitdef}] exp_time[s] validation',
- file=file
+ f"#Name ra[{unitdef}] dec[{unitdef}] exp_time[s] validation",
+ file=file,
)
@@ -237,30 +233,30 @@ def log_command(argv, name=None, close_no_return=True):
"""
if name is None:
- name = 'log_' + os.path.basename(argv[0])
+ name = "log_" + os.path.basename(argv[0])
- if name == 'sys.stdout':
+ if name == "sys.stdout":
f = sys.stdout
- elif name == 'sys.stderr':
+ elif name == "sys.stderr":
f = sys.stderr
else:
- f = open(name, 'w')
+ f = open(name, "w")
for a in argv:
# Quote argument if special characters
- if ']' in a or ']' in a:
- a = f'\"{a}\"'
+ if "]" in a or "]" in a:
+ a = f'"{a}"'
- print(a, end='', file=f)
- print(' ', end='', file=f)
+ print(a, end="", file=f)
+ print(" ", end="", file=f)
- print('', file=f)
+ print("", file=f)
if not close_no_return:
return f
- if name != 'sys.stdout' and name != 'sys.stderr':
+ if name != "sys.stdout" and name != "sys.stderr":
f.close()
@@ -301,30 +297,30 @@ def my_string_split(string, num=-1, verbose=False, stop=False, sep=None):
return None
if sep is None:
- has_space = string.find(' ')
- has_underscore = string.find('_')
- has_dot = string.find('.')
+ has_space = string.find(" ")
+ has_underscore = string.find("_")
+ has_dot = string.find(".")
if has_space != -1:
- my_sep = ' '
+ my_sep = " "
elif has_underscore != -1:
- my_sep = '_'
+ my_sep = "_"
elif has_dot != -1:
- my_sep = '.'
+ my_sep = "."
else:
# no separator found, does string consist of only one element?
if num == -1 or num == 1:
my_sep = None
else:
raise Valueerror(
- 'No separator (\' \', \'_\', or \'.\') found in string'
- + f' \'{string}\', cannot split'
+ "No separator (' ', '_', or '.') found in string"
+ + f" '{string}', cannot split"
)
else:
if not string.find(sep):
raise ValueError(
- f'No separator \'{sep}\' found in string \'{string}\', '
- + 'cannot split'
+ f"No separator '{sep}' found in string '{string}', "
+ + "cannot split"
)
my_sep = sep
@@ -332,7 +328,7 @@ def my_string_split(string, num=-1, verbose=False, stop=False, sep=None):
if num != -1 and num != len(res) and stop:
raise CfisError(
- f'String \'{len(res)}\' has length {num}, required is {num}'
+ f"String '{len(res)}' has length {num}, required is {num}"
)
return res
@@ -364,46 +360,46 @@ def get_file_pattern(pattern, band, image_type, want_re=True, ext=True):
output pattern
"""
- if pattern == '':
+ if pattern == "":
if image_type in (
- 'exposure',
- 'exposure_flag',
- 'exposure_flag.fz',
- 'exposure_weight',
- 'exposure_weight.fz'
+ "exposure",
+ "exposure_flag",
+ "exposure_flag.fz",
+ "exposure_weight",
+ "exposure_weight.fz",
):
- pattern_base = r'\d{7}p'
+ pattern_base = r"\d{7}p"
else:
- pattern_base = rf'CFIS.*\.{band}'
+ pattern_base = rf"CFIS.*\.{band}"
else:
pattern_base = pattern
if ext:
- if image_type == 'exposure':
- pattern_out = rf'{pattern_base}\.fits\.fz'
- elif image_type == 'exposure_flag':
- pattern_out = rf'{pattern_base}\.flag\.fits'
- elif image_type == 'exposure_flag.fz':
- pattern_out = rf'{pattern_base}\.flag\.fits\.fz'
- elif image_type == 'exposure_weight':
- pattern_out = rf'{pattern_base}\.weight\.fits'
- elif image_type == 'exposure_weight.fz':
- pattern_out = rf'{pattern_base}\.weight\.fits\.fz'
- elif image_type == 'tile':
- pattern_out = rf'{pattern_base}\.fits'
- elif image_type == 'cat':
- pattern_out = rf'{pattern_base}\.cat'
- elif image_type == 'weight':
- pattern_out = rf'{pattern_base}\.weight\.fits'
- elif image_type == 'weight.fz':
- pattern_out = rf'{pattern_base}\.weight\.fits\.fz'
+ if image_type == "exposure":
+ pattern_out = rf"{pattern_base}\.fits\.fz"
+ elif image_type == "exposure_flag":
+ pattern_out = rf"{pattern_base}\.flag\.fits"
+ elif image_type == "exposure_flag.fz":
+ pattern_out = rf"{pattern_base}\.flag\.fits\.fz"
+ elif image_type == "exposure_weight":
+ pattern_out = rf"{pattern_base}\.weight\.fits"
+ elif image_type == "exposure_weight.fz":
+ pattern_out = rf"{pattern_base}\.weight\.fits\.fz"
+ elif image_type == "tile":
+ pattern_out = rf"{pattern_base}\.fits"
+ elif image_type == "cat":
+ pattern_out = rf"{pattern_base}\.cat"
+ elif image_type == "weight":
+ pattern_out = rf"{pattern_base}\.weight\.fits"
+ elif image_type == "weight.fz":
+ pattern_out = rf"{pattern_base}\.weight\.fits\.fz"
else:
- raise CfisError(f'Invalid type \'{image_type}\'')
+ raise CfisError(f"Invalid type '{image_type}'")
else:
pattern_out = pattern_base
if not want_re:
- pattern_out = pattern_out.replace('\\', '')
+ pattern_out = pattern_out.replace("\\", "")
return pattern_out
@@ -443,13 +439,13 @@ def get_tile_number_from_coord(ra, dec, return_type=str):
xi = 0
if return_type == str:
- nix = f'{xi:03d}'
- niy = f'{yi:03d}'
+ nix = f"{xi:03d}"
+ niy = f"{yi:03d}"
elif return_type == int:
nix = xi
niy = yi
else:
- raise CfisError(f'Invalid return type {return_type}')
+ raise CfisError(f"Invalid return type {return_type}")
return nix, niy
@@ -482,14 +478,14 @@ def get_tile_coord_from_nixy(nix, niy):
yi = int(niy)
d = yi / 2 - 90
- dec = coords.Angle(d, unit='deg')
+ dec = coords.Angle(d, unit="deg")
r = xi / 2 / np.cos(dec.radian)
- ra = coords.Angle(r, unit='deg')
+ ra = coords.Angle(r, unit="deg")
return ra, dec
-def get_tile_name(nix, niy, band, image_type='tile', input_format='full'):
+def get_tile_name(nix, niy, band, image_type="tile", input_format="full"):
"""Get Tile Name.
Return tile name for given tile numbers.
@@ -519,29 +515,29 @@ def get_tile_name(nix, niy, band, image_type='tile', input_format='full'):
"""
if type(nix) is int and type(niy) is int:
- if input_format == 'ID_only':
- tile_base = f'{nix:03d}.{niy:03d}'
+ if input_format == "ID_only":
+ tile_base = f"{nix:03d}.{niy:03d}"
else:
- tile_base = f'CFIS.{nix:03d}.{niy:03d}.{band}'
+ tile_base = f"CFIS.{nix:03d}.{niy:03d}.{band}"
elif type(nix) is str and type(niy) is str:
- if input_format == 'ID_only':
- tile_base = f'{nix}.{niy}'
+ if input_format == "ID_only":
+ tile_base = f"{nix}.{niy}"
else:
- tile_base = f'CFIS.{nix}.{niy}.{band}'
+ tile_base = f"CFIS.{nix}.{niy}.{band}"
else:
- raise CfisError(f'Invalid type for input tile numbers {nix}, {niy}')
+ raise CfisError(f"Invalid type for input tile numbers {nix}, {niy}")
- if input_format == 'ID_only':
+ if input_format == "ID_only":
tile_name = tile_base
else:
- if image_type == 'tile':
- tile_name = f'{tile_base}.fits'
- elif image_type == 'weight':
- tile_name = f'{tile_base}.weight.fits'
- elif image_type == 'weight.fz':
- tile_name = f'{tile_base}.weight.fits.fz'
+ if image_type == "tile":
+ tile_name = f"{tile_base}.fits"
+ elif image_type == "weight":
+ tile_name = f"{tile_base}.weight.fits"
+ elif image_type == "weight.fz":
+ tile_name = f"{tile_base}.weight.fits.fz"
else:
- raise CfisError(f'Invalid image type {image_type}')
+ raise CfisError(f"Invalid image type {image_type}")
return tile_name
@@ -567,10 +563,10 @@ def get_tile_number(tile_name):
tile number for x and tile number for y
"""
- m = re.search(r'(\d{3})[\.-](\d{3})', tile_name)
+ m = re.search(r"(\d{3})[\.-](\d{3})", tile_name)
if m is None or len(m.groups()) != 2:
raise CfisError(
- f'Image name \'{tile_name}\' does not match tile name syntax'
+ f"Image name '{tile_name}' does not match tile name syntax"
)
nix = m.groups()[0]
@@ -629,12 +625,12 @@ def get_log_file(path, verbose=False):
"""
if not os.path.isfile(path):
- raise CfisError(f'Log file \'{path}\' not found')
+ raise CfisError(f"Log file '{path}' not found")
- f_log = open(path, 'r')
+ f_log = open(path, "r")
log = f_log.readlines()
if verbose:
- print(f'Reading log file, {len(log)} lines found')
+ print(f"Reading log file, {len(log)} lines found")
f_log.close()
return log
@@ -663,7 +659,7 @@ def check_ra(ra):
"""
print(ra.deg)
if ra.deg < 0 or ra.deg > 360:
- raise CfisError('Invalid ra, valid range is 0 < ra < 360 deg')
+ raise CfisError("Invalid ra, valid range is 0 < ra < 360 deg")
return 1
return 0
@@ -691,7 +687,7 @@ def check_dec(dec):
"""
if dec.deg < -90 or dec.deg > 90:
- raise CfisError('Invalid dec, valid range is -90 < dec < 90 deg')
+ raise CfisError("Invalid dec, valid range is -90 < dec < 90 deg")
return 1
return 0
@@ -744,10 +740,7 @@ def get_Angle_arr(str_coord, num=-1, wrap=True, verbose=False):
"""
angles_mixed = my_string_split(
- str_coord,
- num=num,
- verbose=verbose,
- stop=True
+ str_coord, num=num, verbose=verbose, stop=True
)
n = len(angles_mixed)
n = int(n / 2)
@@ -784,12 +777,13 @@ def read_list(fname, col=None):
"""
if col is None:
- f = open(fname, 'rU', encoding='latin1')
+ f = open(fname, "rU", encoding="latin1")
file_list = [x.strip() for x in f.readlines()]
f.close()
else:
import pandas as pd
- dat = pd.read_csv(fname, sep=r'\s+', dtype='string', header=None)
+
+ dat = pd.read_csv(fname, sep=r"\s+", dtype="string", header=None)
if col not in dat:
col = int(col)
file_list = dat[col]
@@ -827,17 +821,17 @@ def create_image_list(fname, ra, dec, exp_time=[], valid=[]):
nr = len(ra)
nd = len(dec)
if nf == 0:
- raise CfisError('No entries in file name list')
+ raise CfisError("No entries in file name list")
if (nf != nr or nf != nd) and nr != 0 and nd != 0:
raise CfisError(
- f'Lists fname, ra, dec have not same length ({nf}, {nr}, {nd})'
+ f"Lists fname, ra, dec have not same length ({nf}, {nr}, {nd})"
)
images = []
for i in range(nf):
if nr > 0 and nd > 0:
- r = Angle(f'{ra[i]} {unitdef}')
- d = Angle(f'{dec[i]} {unitdef}')
+ r = Angle(f"{ra[i]} {unitdef}")
+ d = Angle(f"{dec[i]} {unitdef}")
else:
r = None
d = None
@@ -856,12 +850,7 @@ def create_image_list(fname, ra, dec, exp_time=[], valid=[]):
def get_image_list(
- inp,
- band,
- image_type,
- col=None,
- input_format='full',
- verbose=False
+ inp, band, image_type, col=None, input_format="full", verbose=False
):
"""Get Image List.
@@ -897,29 +886,29 @@ def get_image_list(
if os.path.isdir(inp):
if col is not None:
raise CfisError(
- 'Column name (-c option) only valid if input is file'
+ "Column name (-c option) only valid if input is file"
)
# Read file names from directory listing
- inp_type = 'dir'
- file_list = glob.glob(f'{os.path.abspath(inp)}/*')
+ inp_type = "dir"
+ file_list = glob.glob(f"{os.path.abspath(inp)}/*")
elif os.path.isfile(inp):
- if image_type in ('tile', 'weight', 'weight.fz'):
+ if image_type in ("tile", "weight", "weight.fz"):
# File names in single-column ascii file
- inp_type = 'file'
+ inp_type = "file"
file_list = read_list(inp, col=col)
- elif image_type == 'exposure':
+ elif image_type == "exposure":
# File names and coordinates in ascii file
- inp_type = 'file'
+ inp_type = "file"
dat = ascii.read(inp)
if len(dat.keys()) == 3:
# File is exposure + coord list
# (obtained from get_coord_CFIS_pointings.py)
- file_list = dat['Pointing']
- ra_list = dat['R.A.[degree]']
- dec_list = dat['Declination[degree]']
+ file_list = dat["Pointing"]
+ ra_list = dat["R.A.[degree]"]
+ dec_list = dat["Declination[degree]"]
elif len(dat.keys()) == 12:
# File is log file, e.g. from
# http://www.cfht.hawaii.edu/Science/CFIS-DATA
@@ -927,41 +916,35 @@ def get_image_list(
# Default file separator is '|'
for d in dat:
file_list.append(f'd{d["col1"]}p.fits.fz')
- ra = re.split(r'\s*', d['col4'])[0]
- dec = re.split(r'\s*', d['col4'])[1]
- ang = coords.Angle('{ra} hours')
+ ra = re.split(r"\s*", d["col4"])[0]
+ dec = re.split(r"\s*", d["col4"])[1]
+ ang = coords.Angle("{ra} hours")
ra_list.append(ang.degree)
dec_list.append(dec)
- exp_time = int(d['col5'])
+ exp_time = int(d["col5"])
exp_time_list.append(exp_time)
- valid = re.split(r'\s*', d['col11'])[2]
+ valid = re.split(r"\s*", d["col11"])[2]
valid_list.append(valid)
else:
raise CfisError(
- f'Wrong file format, #columns={len(dat.keys())},'
- + f' has to be 3 or 12'
+ f"Wrong file format, #columns={len(dat.keys())},"
+ + f" has to be 3 or 12"
)
else:
- raise CfisError(f'Image type \'{image_type}\' not supported')
+ raise CfisError(f"Image type '{image_type}' not supported")
# Create list of objects, coordinate lists can be empty
image_list = create_image_list(
- file_list,
- ra_list,
- dec_list,
- exp_time=exp_time_list,
- valid=valid_list
+ file_list, ra_list, dec_list, exp_time=exp_time_list, valid=valid_list
)
# Filter file list to match CFIS image pattern
img_list = []
- if input_format == 'ID_only':
- pattern = get_file_pattern(r'\d{3}.\d{3}', band, image_type, ext=False)
+ if input_format == "ID_only":
+ pattern = get_file_pattern(r"\d{3}.\d{3}", band, image_type, ext=False)
else:
pattern = get_file_pattern(
- rf'CFIS.\d{{3}}.\d{{3}}\.{band}',
- band,
- image_type
+ rf"CFIS.\d{{3}}.\d{{3}}\.{band}", band, image_type
)
for img in image_list:
@@ -979,9 +962,7 @@ def get_image_list(
img_list.append(img)
if verbose and len(img_list) > 0:
- print(
- f'{len(img_list)} image files found in input {inp_type} \'{inp}\''
- )
+ print(f"{len(img_list)} image files found in input {inp_type} '{inp}'")
return img_list
@@ -1013,8 +994,8 @@ def find_image_at_coord(
band,
image_type,
no_cuts=False,
- input_format='full',
- verbose=False
+ input_format="full",
+ verbose=False,
):
"""Find Image At Coordinates.
@@ -1055,16 +1036,12 @@ def find_image_at_coord(
ra, dec = get_Angle(coord)
if verbose:
- print(f'Looking for image at coordinates {ra}, {dec}')
+ print(f"Looking for image at coordinates {ra}, {dec}")
- if image_type in ('tile', 'weight', 'weight.fz'):
+ if image_type in ("tile", "weight", "weight.fz"):
nix, niy = get_tile_number_from_coord(ra, dec, return_type=int)
tile_name = get_tile_name(
- nix,
- niy,
- band,
- image_type,
- input_format=input_format
+ nix, niy, band, image_type, input_format=input_format
)
img_found = []
@@ -1074,9 +1051,9 @@ def find_image_at_coord(
ra_c, dec_c = get_tile_coord_from_nixy(nix, niy)
if img.ra is not None or img.dec is not None:
raise CfisError(
- 'Coordinates in image are already '
- + f'set to {img.ra}, {img.rec}, '
- + f'cannot update to {ra_c}, {ra_dec}'
+ "Coordinates in image are already "
+ + f"set to {img.ra}, {img.rec}, "
+ + f"cannot update to {ra_c}, {ra_dec}"
)
img.ra = ra_c
img.dec = dec_c
@@ -1086,12 +1063,12 @@ def find_image_at_coord(
pass
else:
if verbose:
- print(f'Tile with numbers ({nix}, {niy}) not found')
+ print(f"Tile with numbers ({nix}, {niy}) not found")
if len(img_found) > 1:
- raise CfisError(f'More than one tile ({img_found}) found')
+ raise CfisError(f"More than one tile ({img_found}) found")
- elif image_type == 'exposure':
+ elif image_type == "exposure":
sc_input = coords.SkyCoord(ra, dec)
img_found = []
@@ -1112,21 +1089,16 @@ def find_image_at_coord(
pass
else:
if verbose:
- print('No exposure image found')
+ print("No exposure image found")
else:
- raise CfisError('Only implemented for image_type=tile')
+ raise CfisError("Only implemented for image_type=tile")
return img_found
def find_images_in_area(
- images,
- angles,
- band,
- image_type,
- no_cuts=False,
- verbose=False
+ images, angles, band, image_type, no_cuts=False, verbose=False
):
"""Fine Images In Area.
@@ -1164,22 +1136,22 @@ def find_images_in_area(
if angles[1].ra > threesixty:
ra_bounds = [
[angles[0].ra, threesixty],
- [coords.Angle(0, unitdef), angles[1].ra - threesixty]
+ [coords.Angle(0, unitdef), angles[1].ra - threesixty],
]
else:
ra_bounds = [[angles[0].ra, angles[1].ra]]
if verbose:
print(
- 'Looking for all images within rectangle, '
- + f'dec=({angles[0].dec}, {angles[1].dec}), ',
- end=''
+ "Looking for all images within rectangle, "
+ + f"dec=({angles[0].dec}, {angles[1].dec}), ",
+ end="",
)
for ra_min_max in ra_bounds:
- print(f'ra=[({ra_min_max[0]}, {ra_min_max[1]}) ', end='')
+ print(f"ra=[({ra_min_max[0]}, {ra_min_max[1]}) ", end="")
print()
- if image_type in ('tile', 'weight', 'weight.fz'):
+ if image_type in ("tile", "weight", "weight.fz"):
for img in images:
nix, niy = get_tile_number(img.name)
ra, dec = get_tile_coord_from_nixy(nix, niy)
@@ -1188,7 +1160,7 @@ def find_images_in_area(
within = False
# Check whether image is in any of the ra bound pairs
- for (ra_min, ra_max) in ra_bounds:
+ for ra_min, ra_max in ra_bounds:
if ra.is_within_bounds(ra_min, ra_max):
within = True
break
@@ -1199,13 +1171,13 @@ def find_images_in_area(
found.append(img)
- elif image_type == 'exposure':
+ elif image_type == "exposure":
for img in images:
if img.dec.is_within_bounds(angles[0].dec, angles[1].dec):
within = False
# Check whether image is in any of the ra bound pairs
- for (ra_min, ra_max) in ra_bounds:
+ for ra_min, ra_max in ra_bounds:
if ra.is_within_bounds(ra_min, ra_max):
within = True
break
@@ -1214,10 +1186,10 @@ def find_images_in_area(
found.append(img)
else:
- raise CfisError(f'Image type \'{image_type}\' not implemented yet')
+ raise CfisError(f"Image type '{image_type}' not implemented yet")
if verbose:
- print(f'{len(found)} images found in area')
+ print(f"{len(found)} images found in area")
return found
@@ -1235,9 +1207,9 @@ def plot_init():
ax.yaxis.label.set_size(fs)
ax.xaxis.label.set_size(fs)
- plt.tick_params(axis='both', which='major', labelsize=fs)
+ plt.tick_params(axis="both", which="major", labelsize=fs)
- plt.rcParams.update({'figure.autolayout': True})
+ plt.rcParams.update({"figure.autolayout": True})
return ax
@@ -1255,7 +1227,7 @@ def plot_area(
ax=None,
lw=None,
save=True,
- dxy=0
+ dxy=0,
):
"""Plot Area.
@@ -1292,15 +1264,15 @@ def plot_area(
"""
if outbase is None:
- outname = 'plot.pdf'
+ outname = "plot.pdf"
else:
- outname = f'{outbase}.pdf'
+ outname = f"{outbase}.pdf"
if not lw:
my_lw = 0.1
else:
my_lw = lw
- color = {'tile': 'b', 'exposure': 'g', 'weight': 'r'}
+ color = {"tile": "b", "exposure": "g", "weight": "r"}
if not ax:
ax = plot_init()
@@ -1322,16 +1294,16 @@ def plot_area(
dy = abs(angles[0].dec - angles[1].dec)
dx = getattr(dx, unitdef)
dy = getattr(dy, unitdef)
- radius = (
- max(dx, dy) / 2 + (size['exposure'] + size['tile']) * np.sqrt(2)
+ radius = max(dx, dy) / 2 + (size["exposure"] + size["tile"]) * np.sqrt(
+ 2
)
circle = plt.Circle(
(ra_c.deg, dec_c.deg),
radius,
- color='r',
+ color="r",
fill=False,
)
- plt.plot(ra_c, dec_c, 'or', mfc='none', ms=3)
+ plt.plot(ra_c, dec_c, "or", mfc="none", ms=3)
ax.add_artist(circle)
else:
radius = 0
@@ -1349,24 +1321,24 @@ def plot_area(
plt.text(
x,
y,
- f'{nix}.{niy}',
+ f"{nix}.{niy}",
fontsize=3,
- horizontalalignment='center',
- verticalalignment='center'
+ horizontalalignment="center",
+ verticalalignment="center",
)
# Image boundary
dx = size[image_type] / 2 / cos_dec_c
dy = size[image_type] / 2
cx, cy = square_from_centre(x, y, dx, dy, dxy=dxy)
- ax.plot(cx, cy, '-', color=c, linewidth=my_lw)
+ ax.plot(cx, cy, "-", color=c, linewidth=my_lw)
if show_area_border:
cx, cy = square_from_corners(angles[0], angles[1])
- ax.plot(cx, cy, 'r-.', linewidth=my_lw)
+ ax.plot(cx, cy, "r-.", linewidth=my_lw)
- plt.xlabel('R.A. [degree]')
- plt.ylabel('Declination [degree]')
+ plt.xlabel("R.A. [degree]")
+ plt.ylabel("Declination [degree]")
if outbase is not None:
plt.title(outbase)
@@ -1385,7 +1357,7 @@ def plot_area(
plt.ylim(ym - lim / 2 - border, ym + lim / 2 + border)
if save:
- print(f'Saving plot to {outname}')
+ print(f"Saving plot to {outname}")
plt.savefig(outname)
if interactive:
diff --git a/shapepipe/utilities/file_system.py b/shapepipe/utilities/file_system.py
index 52f5fd906..b274a2aaf 100644
--- a/shapepipe/utilities/file_system.py
+++ b/shapepipe/utilities/file_system.py
@@ -37,7 +37,7 @@ def check_dir(dir_name):
"""
if not isinstance(dir_name, str):
raise TypeError(
- f'Directory name must be of type string, not {type(dir_name)}'
+ f"Directory name must be of type string, not {type(dir_name)}"
)
return os.path.isdir(dir_name)
@@ -67,9 +67,9 @@ def mkdir(dir_name, check_created=True, exist_ok=True):
If directory not properly created
"""
- os.makedirs(dir_name, exist_ok=exist_ok)
+ os.makedirs(dir_name, exist_ok=True)
if check_created and not check_dir(dir_name):
raise FileSystemError(
- f'Directory \"{dir_name}\" not found after mkdir command.'
+ f'Directory "{dir_name}" not found after mkdir command.'
)
diff --git a/shapepipe/utilities/galaxy.py b/shapepipe/utilities/galaxy.py
index eb05c4bc2..40948a8f1 100644
--- a/shapepipe/utilities/galaxy.py
+++ b/shapepipe/utilities/galaxy.py
@@ -61,32 +61,32 @@ def sigma_to_fwhm(sigma, pixel_scale=1.0):
"""
if not isinstance(sigma, (np.ndarray, float)):
raise TypeError(
- f'Sigma must be of type numpy array or float, not {type(sigma)}.'
+ f"Sigma must be of type numpy array or float, not {type(sigma)}."
)
elif isinstance(sigma, np.ndarray) and sigma.dtype != np.float64:
raise TypeError(
- f'Sigma array values must be of type float, not {sigma.dtype}.'
+ f"Sigma array values must be of type float, not {sigma.dtype}."
)
if not isinstance(pixel_scale, float):
raise TypeError(
- f'The pixel scale must of type float, not {type(pixel_scale)}.'
+ f"The pixel scale must of type float, not {type(pixel_scale)}."
)
if isinstance(sigma, np.ndarray) and np.any(sigma <= 0.0):
raise ValueError(
- f'Found {sigma[sigma <=0].size} invalid standard deviation array '
- + 'values, all elements must to be greater than 0.0.'
+ f"Found {sigma[sigma <=0].size} invalid standard deviation array "
+ + "values, all elements must to be greater than 0.0."
)
elif isinstance(sigma, float) and sigma <= 0.0:
raise ValueError(
- f'Invalid standard deviation {sigma}, needs to be greater than '
- + '0.0.'
+ f"Invalid standard deviation {sigma}, needs to be greater than "
+ + "0.0."
)
if pixel_scale <= 0.0:
raise ValueError(
- f'Invalid pixel scale {pixel_scale}, needs to be greater than 0.0.'
+ f"Invalid pixel scale {pixel_scale}, needs to be greater than 0.0."
)
cst = 2.35482004503
diff --git a/shapepipe/utilities/summary.py b/shapepipe/utilities/summary.py
new file mode 100755
index 000000000..201cbcd30
--- /dev/null
+++ b/shapepipe/utilities/summary.py
@@ -0,0 +1,788 @@
+"""SUMMARY
+
+Author: Martin Kilbinger
+
+"""
+
+import sys
+import os
+import re
+import fnmatch
+
+import logging
+
+from collections import Counter
+
+from tqdm import tqdm
+
+print("summaary v1.4")
+
+
+def init_par_runtime(list_tile_IDs):
+
+ # Numbers updated at runtime
+ par_runtime = {}
+
+ par_runtime["n_tile_IDs"] = len(list_tile_IDs)
+ par_runtime["list_tile_IDs"] = list_tile_IDs
+
+ return par_runtime
+
+
+def update_par_runtime_after_find_exp(par_runtime, all_exposures):
+
+ # Single-exposure images
+ par_runtime["n_exposures"] = len(all_exposures)
+ par_runtime["list_exposures"] = all_exposures
+
+ # Single-HDU single exposure images
+ n_CCD = 40
+ par_runtime["n_shdus"] = get_par_runtime(par_runtime, "exposures") * n_CCD
+ par_runtime["list_shdus"] = get_all_shdus(all_exposures, n_CCD)
+
+ return par_runtime
+
+
+def get_IDs_from_file(path):
+ """Get IDs From File.
+
+ Return IDs from text file. Removes letters and replaces
+ dots "." with dashes "-".
+
+ Parameters
+ ----------
+ path: str
+ input file path
+
+ Returns
+ --------
+ list
+ IDs
+
+ """
+ numbers = []
+ with open(path) as f_in:
+ for line in f_in:
+ entry = line.rstrip()
+ number = re.sub("[a-zA-Z]", "", entry)
+ numbers.append(number)
+
+ return numbers
+
+
+def get_all_exposures(exp_number_file_list, verbose=False):
+ """Get All Exposures.
+
+ Return all exposure names from a list of text files.
+
+ Parameters
+ ----------
+ exp_number_list: list
+ input file names
+
+ """
+ exposures = set()
+ for idx, path in enumerate(exp_number_file_list):
+ exps = get_IDs_from_file(path)
+ exposures.update(exps)
+
+ return list(exposures)
+
+
+def get_all_shdus(exposures, n_CCD):
+ """Get All SHDUs.
+
+ Return all single-exposure single-HDU (CCD) IDs.
+
+ Parameters
+ ----------
+ exposures: list
+ exposure names
+ n_CCD: int
+ number of CCDs per exposure
+
+ Returns
+ --------
+ list
+ single-exposure single-HDU IDs
+
+ """
+ shdus = []
+ for exposure in exposures:
+ for idx_CCD in range(n_CCD):
+ shdus.append(f"{exposure}-{idx_CCD}")
+
+ return shdus
+
+
+def set_as_list(item=None, n=None, default=1):
+ """Set As List.
+
+ Return input as list.
+
+ Parameters
+ -----------
+ item: str, int, or list, optional
+ input item(s); default is None, in which
+ case the return is [1] * n
+ n: int, optional
+ number of list items to return, default is None,
+ in which case the number will be set to 1. If item and
+ n are not None, n has to be equal to len(item)
+ default: int, optional
+ value to return if item is not given;
+ default is 1
+
+ Raises
+ -------
+ IndexError
+ if n != len(item)
+
+ Returns
+ -------
+ list
+ input item(s) as list
+ """
+ my_n = n or 1
+
+ if not item:
+ result = [default] * my_n
+ elif not isinstance(item, list):
+ result = [item] * my_n
+ else:
+ result = item
+ if len(item) != my_n:
+ raise IndexError(f"item has length {len(item)} != {n}")
+
+ return result
+
+
+def check_special_one(module, path):
+
+ with open(path) as f_in:
+ lines = f_in.readlines()
+ for line in lines:
+ entry = line.rstrip()
+
+ if module == "setools_runner":
+ m = re.search("Nb stars = (\S*)", line)
+ if m:
+ value = int(m[1])
+ if value < 2:
+ code = 0
+ msg = (
+ f"Not enough stars for random split:"
+ + f" #stars = {value}"
+ )
+ return msg, code
+ break
+ m = re.search("Mode computation failed", line)
+ if m:
+ code = 1
+ msg = "Mode computation of stellar locus failed"
+ return msg, code
+
+ if module == "psfex_interp_runner":
+ m = re.search("Key N_EPOCH not found", line)
+ if m:
+ code = 2
+ msg = "N_EPOCH not in SEx cat, rerun job 16"
+ return msg, code
+
+ m = re.search(
+ "ValueError: cannot reshape array of size 0 into shape",
+ line,
+ )
+ if m:
+ code = 3
+ msg = "found array of size 0"
+ return msg, code
+
+
+ return None, None
+
+
+class job_data(object):
+ """Job Data.
+
+ Class to handle a job.
+
+ Parameters
+ ----------
+ bit: int
+ bit-coded job number
+ run_dir: str or list
+ run directory(ies)
+ modules: list
+ module names
+ key_expected: int or str
+ number of expected output files; if str: will be updated
+ with runtime value
+ n_mult: int or list, optional
+ multiplicity of output files, default `None`, in which
+ case it is set to 1
+ pattern: list, optional
+ if not None, file pattern to match; defafult is `None`
+ path_main: str, optional
+ main (left-most) part of output directory, default is "."
+ path_left: str, optional
+ left (first) part of output directory, default is "./output"
+ output_subdirs: str, optional
+ output subdirectories if not `None`; default is `None`
+ path_right: str, optional
+ right (last) part of output subdir suffix if not `None`;
+ default is `None`
+ path_output: str, optional
+ module output path, default is "output"
+ output_path_missing_IDs: list, optional
+ output path of missing ID, if `None` (default) will be
+ given by job bit and module.
+ special: bool, optional
+ if True check output file content for special messages;
+ default is False
+ verbose: bool, optional
+ verbose output if True; default is False
+
+ """
+
+ def __init__(
+ self,
+ bit,
+ run_dir,
+ modules,
+ key_expected,
+ n_mult=None,
+ pattern=None,
+ path_main=".",
+ path_left="output",
+ output_subdirs=None,
+ path_right=None,
+ path_output="output",
+ output_path_missing_IDs=None,
+ special=False,
+ verbose=False,
+ ):
+ self._bit = bit
+ self._run_dir = set_as_list(item=run_dir, n=len(modules))
+ self._modules = modules
+ self._key_expected = set_as_list(item=key_expected, n=len(modules))
+ self._n_mult = set_as_list(item=n_mult, n=len(modules))
+ self._pattern = set_as_list(item=pattern, n=len(modules), default="")
+ self._path_main = path_main
+ self._path_left = path_left
+ self._output_subdirs = output_subdirs or [""]
+ self._path_right = set_as_list(
+ path_right,
+ len(modules),
+ default=".",
+ )
+ self._path_output = set_as_list(
+ path_output,
+ len(modules),
+ default="output",
+ )
+ self._output_path_missing_IDs=output_path_missing_IDs
+ self._special = set_as_list(
+ special,
+ len(modules),
+ default=False,
+ )
+ self._path_right = set_as_list(path_right, len(modules), default=".")
+ self._output_path_missing_IDs = output_path_missing_IDs
+ self._verbose = verbose
+
+ def print_intro(self):
+ """Print Intro.
+
+ Print header line for job statistics.
+
+ """
+ logging.info(f" # Job {self._bit}:")
+
+ @classmethod
+ def print_stats_header(self):
+ """Print Stats Header.
+
+ Print overall header information for stats output.
+
+ """
+ logging.info(
+ "module expected found"
+ + " missing uniq_miss fr_found"
+ )
+ logging.info("=" * 100)
+
+ def print_stats(
+ self,
+ module,
+ n_expected,
+ n_found,
+ n_special,
+ n_missing,
+ idx,
+ ):
+ """Print Stats.
+
+ Print output file statistics.
+
+ Parameters
+ ----------
+ module: str
+ module name
+ n_expected: int
+ number of expected files
+ n_found: int
+ number of found files
+ n_special: int
+ number of special cases
+ n_missing: int
+ number of missing files
+ idx: int
+ module index
+
+ """
+ module_str = module
+
+ if not self._special[idx]:
+ if n_expected > 0:
+ fraction_found = n_found / n_expected
+ else:
+ fraction_found = 1
+
+ n_missing_per_mult = n_missing / self._n_mult[idx]
+
+ else:
+ module_str = f"{module_str} (special)"
+ n_found = n_special
+ n_missing = -1
+ n_missing_per_mult = -1
+ fraction_found = n_found / n_expected
+ n_expected = -1
+
+ logging.info(
+ f"{module_str:30s} {n_expected:9d} {n_found:9d}"
+ + f" {n_missing:9d}"
+ + f" {n_missing_per_mult:9.1f} {fraction_found:9.1%}"
+ )
+
+ @classmethod
+ def is_ID_in_str(self, ID, path):
+ if ID in path:
+ return True
+
+ @classmethod
+ def is_not_in_any(self, ID, list_str):
+ return not any(ID in string for string in list_str)
+
+ @classmethod
+ def replace_dot_dash(self, numbers):
+
+ results = [re.sub("\.", "-", number) for number in numbers]
+
+ return results
+
+ @classmethod
+ def replace_dash_dot_if_tile(self, numbers):
+
+ pattern = re.compile(r"(\d{3})-(\d{3})")
+ results = [pattern.sub(r"\1.\2", number) for number in numbers]
+
+ return results
+
+ @classmethod
+ def get_unique(self, names):
+ n_all = len(names)
+ names_unique = list(set(names))
+ n_unique = len(names_unique)
+
+ if n_all != n_unique:
+ if True: # self._verbose:
+ logging.warning(
+ f"{n_all - n_unique} duplicates removed from {n_all} IDs"
+ )
+
+ return names_unique
+
+ @classmethod
+ def write_IDs_to_file(self, output_path, IDs):
+ """Write IDs to file.
+
+ Write list if image IDs to text file.
+
+ Parameters
+ ----------
+ output_path: str
+ output file path
+ IDs: list
+ image IDs
+
+ """
+ IDs_dot = self.replace_dash_dot_if_tile(IDs)
+ if len(IDs_dot) > 0:
+ # Write IDs to file
+ with open(output_path, "w") as f_out:
+ for ID in IDs_dot:
+ print(ID, file=f_out)
+ elif os.path.exists(output_path):
+ # Remove preivous obsolete ID file
+ os.unlink(output_path)
+
+ def check_special(self, module, idx):
+
+ messages = {}
+
+ if self._special[idx]:
+
+ # Loop over input file names and paths
+ for name, path in zip(self._names_in_dir[idx], self._paths_in_dir[idx]):
+
+ # Check if special case is found
+ msg, code = check_special_one(module, path)
+ if msg:
+ # First time occurance: create empty list for this code
+ if code not in messages:
+ messages[code] = [msg]
+ else:
+ # Append file name, message, and code
+ messages[code].append(f"{name} {code} {msg}")
+
+ if len(messages) > 0:
+ # Loop over codes = key in messages dict
+ for code in messages:
+ # Create output file for this code
+ output_path = (
+ f"{self._path_main}/summary/special_job_{self._bit}"
+ + f"_{module}_{code}.txt"
+ )
+ # Write all messages
+ with open(output_path, "w") as f_out:
+ for msg in messages[code]:
+ print(msg, file=f_out)
+
+ # Count all special cases = sum of cases over all codes
+ n_all = sum([len(messages[code]) for code in messages])
+ return n_all
+
+ def output_missing(
+ self,
+ module,
+ idx,
+ par_runtime=None,
+ ):
+ """Output Missing.
+
+ Writes IDs of missing images to disk.
+
+ """
+ key_expected = self._key_expected[idx]
+ names_in_dir = self._names_in_dir[idx]
+ paths_in_dir = self._paths_in_dir[idx]
+ n_mult = self._n_mult[idx]
+
+ list_expected = get_par_runtime(par_runtime, key_expected, kind="list")
+
+ # Count image IDs in names that were found earlier
+
+ # Get file name pattern
+ if module != "split_exp_runner":
+ pattern = re.compile(r"(?:\d{3}-\d{3}|\d{7}-\d+|\d{7})")
+ else:
+ # split_exp_runner: input is exp, output is shdu (images) and exp
+ # (header); ignore hdu number
+ pattern = re.compile(
+ r"(?:\d{3}-\d{3}|\d{7})"
+ )
+
+ ## Extract image IDs from names
+ IDs = []
+ for name, path in zip(names_in_dir, paths_in_dir):
+
+ match = pattern.search(name)
+ if match:
+ ID = match.group()
+ IDs.append(ID)
+ else:
+ msg = f"No ID found in {name}"
+ #raise ValueError(msg)
+ print(f"Warning: msg, continuing")
+
+
+ ## Count occurences
+ ID_counts = Counter(IDs)
+
+ ## Add to missing if ocurence less than n_mult
+ missing_IDs = []
+ for ID in list_expected:
+ if ID_counts[ID] < n_mult:
+ missing_IDs.append(ID)
+
+ n_all = len(missing_IDs)
+ missing_IDs_unique = self.get_unique(missing_IDs)
+
+ if not self._output_path_missing_IDs:
+ # Default name using bit and module
+ output_path = (
+ f"{self._path_main}/summary/missing_job_{self._bit}"
+ + f"_{module}.txt"
+ )
+ else:
+ # User-defined name (e.g. ngmix_runner_X)
+ output_path = self._output_path_missing_IDs[idx]
+ self.write_IDs_to_file(output_path, missing_IDs_unique)
+
+ return missing_IDs_unique
+
+ def output_missing_job(self):
+ output_path = (
+ f"{self._path_main}/summary/missing_job_{self._bit}_all.txt"
+ )
+
+ missing_IDs_all = set(self._missing_IDs_job)
+
+ self.write_IDs_to_file(output_path, missing_IDs_all)
+
+ @classmethod
+ def get_last_full_path(self, base_and_subdir, matches):
+ """Get Last Full Path
+
+ Return full path of last file in list.
+
+ """
+ # Sort according to creation time
+ matches_sorted = sorted(
+ matches,
+ key=lambda entry: entry.name,
+ )
+
+ # Get most recent one
+ last = matches_sorted[-1]
+
+ # Get full path
+ full_path = os.path.join(base_and_subdir, last.name)
+
+ return full_path
+
+ @classmethod
+ def get_module_output_dir(self, full_path, module, path_output):
+ """Get Module Output Dir.
+
+ Return output directory name for given module.
+
+ """
+ directory = f"{full_path}/{module}/{path_output}"
+
+ return directory
+
+ def get_matches_final(self, directory, idx):
+
+ # Loop over files
+ # os.path.whether exists is twice faster than try/except
+
+ if os.path.exists(directory):
+ pattern = f"{self._pattern[idx]}*"
+ for entry2 in os.scandir(directory):
+ if (
+ entry2.is_file()
+ and (fnmatch.fnmatch(entry2.name, pattern))
+ and entry2.stat().st_size > 0
+ ):
+ # Append matching files
+ self._names_in_dir[idx].append(entry2.name)
+ self._paths_in_dir[idx].append(
+ os.path.join(directory, entry2.name)
+ )
+
+ def get_names_in_dir(self, iterable, module, idx):
+
+ # Initialise output file names and paths
+ self._names_in_dir[idx] = []
+ self._paths_in_dir[idx] = []
+
+ # Loop over subdirs
+ for jdx, subdir in enumerate(iterable):
+ base_and_subdir = (
+ f"{self._path_main}/"
+ + f"{self._path_left}/{subdir}/"
+ + f"{self._path_right[idx]}"
+ )
+ if self._verbose:
+ print(f"**** base_and_subdir {base_and_subdir}")
+
+ if os.path.isdir(base_and_subdir):
+
+ matches = []
+
+ # Loop over entries (files and dirs)
+ with os.scandir(base_and_subdir) as entries:
+ for entry in entries:
+
+ # Append directory name if matches module
+ if entry.name.startswith(self._run_dir[idx]):
+ matches.append(entry)
+
+ # This entry does not match module -> next
+ if not matches:
+ continue
+
+ if self._verbose:
+ print("**** Matching entries: ", end="")
+ for match in matches:
+ print(match.name)
+
+ full_path = self.get_last_full_path(
+ base_and_subdir,
+ matches,
+ )
+
+ # Get module output directory
+ directory = self.get_module_output_dir(
+ full_path,
+ module,
+ self._path_output[idx],
+ )
+ if self._verbose:
+ print(f"**** Output dir = {directory}")
+
+ # Find matching file names and paths
+ self.get_matches_final(directory, idx)
+ else:
+ if self._verbose:
+ print(f"Directory {base_and_subdir} not found")
+
+ def update_subdirs(self, par_runtime):
+ """Update Subdirs.
+
+ Update subdir names with runtime information if required.
+
+ """
+ if not isinstance(self._output_subdirs, list):
+ self._output_subdirs = get_par_runtime(
+ par_runtime, self._output_subdirs, kind="list"
+ )
+
+ def check_numbers(self, par_runtime=None, indices=None):
+ """Check Numbers.
+
+ Check output file numbers and IDs.
+
+ Parameters
+ ----------
+ par_runtime : dict, optional
+ runtime parameter. default is None
+ indices: list, optional
+ if not None (default), only check modules corresponding
+ to indices
+
+ """
+ # Update subdirs if not already set as list
+ self.update_subdirs(par_runtime)
+
+ # Initialise variables
+ self._names_in_dir = {}
+ self._paths_in_dir = {}
+ self._missing_IDs_job = []
+ n_missing_job = 0
+
+ # Loop over modules
+ for idx, module in enumerate(self._modules):
+ if indices is not None and idx not in indices:
+ continue
+
+ if self._verbose:
+ print(f"** module {module}")
+
+ # Look over subdirs
+ iterable = self._output_subdirs
+ if len(iterable) > 1 and self._verbose:
+ iterable = tqdm(iterable, desc="subdirs", leave=False)
+
+ if self._verbose:
+ print(f"*** subdirs {self._output_subdirs}")
+
+ # Get output file names and paths
+ self.get_names_in_dir(
+ iterable,
+ module,
+ idx,
+ )
+
+ # If expected is string: Update parameter with runtime value
+ # and set as integer
+ if isinstance(self._key_expected[idx], str):
+ n_expected_base = get_par_runtime(
+ par_runtime, self._key_expected[idx], kind="n"
+ )
+ else:
+ n_expected_base = self._key_expected[idx]
+
+ # Get some numbers
+ n_found = len(self._names_in_dir[idx])
+ n_expected = n_expected_base * self._n_mult[idx]
+ n_missing = n_expected - n_found
+
+ n_special = self.check_special(
+ module,
+ idx,
+ )
+
+ # Print statistics
+ self.print_stats(
+ module,
+ n_expected,
+ n_found,
+ n_special,
+ n_missing,
+ idx,
+ )
+
+ # Write missing IDs for module to file
+ if n_missing > 0:
+ missing_IDs = self.output_missing(
+ module,
+ idx,
+ par_runtime=par_runtime,
+ )
+ n_missing_job += n_missing
+ self._missing_IDs_job.extend(missing_IDs)
+
+ # Empty line after job
+ logging.info("")
+
+ # Write missing IDs for entire job to file
+ # if n_missing_job > 0:
+ self.output_missing_job()
+
+
+def get_par_runtime(par_runtime, key, kind="n"):
+ """Get Par RunTime.
+
+ Return runtime parameter value.
+
+ Parameters
+ ----------
+ par_runtime: dict
+ runtime parameter
+ key: str
+ key
+
+ """
+ combined_key = f"{kind}_{key}"
+
+ return par_runtime[combined_key]
+
+
+def print_par_runtime(par_runtime, verbose=True):
+ # Print runtime parameter values
+ if True:
+ logging.info("")
+ logging.info("===========")
+ logging.info("par_runtime")
+ logging.info("-----------")
+ for key, value in par_runtime.items():
+ if not key.startswith("list"):
+ logging.info(f"{key:30s} {value:6d}")
+ else:
+ # logging.info(f"{key:30s} {len(value):6d} entries")
+ pass
+ logging.info("===========")
+ logging.info("")
diff --git a/xterm-start.sh b/xterm-start.sh
new file mode 100755
index 000000000..007a2516f
--- /dev/null
+++ b/xterm-start.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+xterm