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Is every function documented?

  • Does it follow the style guide? https://github.com/spacetelescope/style-guides/blob/master/guides/jupyter-notebooks.md

  • Do all code cells have corresponding narratives/comments?

    • +

  • Include information about runtime on fiducial Fornax server

    • +

  • Include information about which “image” the notebook uses when loggin into Fornax, ie., “Astrophysics default image”

  • Notebook execution, error handling, etc.:

    @@ -484,6 +486,8 @@

    Tech Review Checklist

    Have blocks of code that need to be re-used been turned into functions (rather than being duplicated)?

  • Have un-used libraries been removed from the requirements.txt file and the import statements?

  • Has un-used code been removed (e.g., unused functions and commented-out lines)?

    • +

  • Are comment lines wrapped so all fit within a max of 90 - 100 characters per line?

    • +

  • Are code lines reasonably short where possible? some code lines can’t easily be wrapped and that is ok

    • diff --git a/searchindex.js b/searchindex.js index eeb96f1b..a8787933 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"1) Loading data": [[9, "loading-data"]], "1. Define the Sample": [[19, "define-the-sample"]], "1. Define the sample": [[14, "define-the-sample"], [20, "define-the-sample"]], "1. Get an account on the Fornax Science Console": [[1, "get-an-account-on-the-fornax-science-console"]], "1. Read in a dataset of archival light curves": [[13, "read-in-a-dataset-of-archival-light-curves"]], "1. Retrieve Initial Catalog from IRSA": [[6, "retrieve-initial-catalog-from-irsa"]], "1.1 Build your own sample": [[14, "build-your-own-sample"]], "1.1) What is in this sample": [[9, "what-is-in-this-sample"]], "1.2 Write out your sample to disk": [[14, "write-out-your-sample-to-disk"], [20, "write-out-your-sample-to-disk"]], "1.3 Load the sample table from disk": [[14, "load-the-sample-table-from-disk"], [20, "load-the-sample-table-from-disk"]], "1.4 Initialize data structure to hold the light curves": [[14, "initialize-data-structure-to-hold-the-light-curves"]], "1.4 Initialize data structure to hold the spectra": [[20, "initialize-data-structure-to-hold-the-spectra"]], "1a. Filter Catalog": [[6, "a-filter-catalog"]], "2) Preprocess data for ML (ZTF bands)": [[9, "preprocess-data-for-ml-ztf-bands"]], "2. Data Prep": [[13, "data-prep"]], "2. Find light curves for these targets in NASA catalogs": [[14, "find-light-curves-for-these-targets-in-nasa-catalogs"]], "2. Find spectra for these targets in NASA and other ancillary catalogs": [[20, "find-spectra-for-these-targets-in-nasa-and-other-ancillary-catalogs"]], "2. Log into the Fornax Science Console": [[1, "log-into-the-fornax-science-console"]], "2. Query the Euclid catalog for the sample": [[19, "query-the-euclid-catalog-for-the-sample"]], "2. Retrieve Image Datasets from the Cloud": [[6, "retrieve-image-datasets-from-the-cloud"]], "2.1 HEASARC: FERMI & Beppo SAX": [[14, "heasarc-fermi-beppo-sax"]], "2.1 IRSA Archive": [[20, "irsa-archive"]], "2.1 Remove bands with not enough data": [[13, "remove-bands-with-not-enough-data"]], "2.2 Combine Labels for a Simpler Classification": [[13, "combine-labels-for-a-simpler-classification"]], "2.2 IRSA: ZTF": [[14, "irsa-ztf"]], "2.2 MAST Archive": [[20, "mast-archive"]], "2.3 Data Visualization": [[13, "data-visualization"]], "2.3 ESA Archive": [[20, "esa-archive"]], "2.3 IRSA: WISE": [[14, "irsa-wise"]], "2.4 Clean the dataset of unwanted data": [[13, "clean-the-dataset-of-unwanted-data"]], "2.4 MAST: Pan-STARRS": [[14, "mast-pan-starrs"]], "2.4 SDSS Archive": [[20, "sdss-archive"]], "2.5 DESI Archive": [[20, "desi-archive"]], "2.5 MAST: TESS, Kepler and K2": [[14, "mast-tess-kepler-and-k2"]], "2.5 Missing Data": [[13, "missing-data"]], "2.6 Make all objects and bands have identical time arrays (uniform length and spacing)": [[13, "make-all-objects-and-bands-have-identical-time-arrays-uniform-length-and-spacing"]], "2.6 MAST: Hubble Catalog of Variables (HCV)": [[14, "mast-hubble-catalog-of-variables-hcv"]], "2.7 Restructure dataframe": [[13, "restructure-dataframe"]], "2.8 Normalize": [[13, "normalize"]], "2.9 Cleanup": [[13, "cleanup"]], "3) Learn the Manifold": [[9, "learn-the-manifold"]], "3. Run Forced Photometry": [[6, "run-forced-photometry"]], "3. Find light curves for these targets in relevant, non-NASA catalogs": [[14, "find-light-curves-for-these-targets-in-relevant-non-nasa-catalogs"]], "3. Grab the images, 1D coadded spectrum, & individual spectra": [[19, "grab-the-images-1d-coadded-spectrum-individual-spectra"]], "3. Make plots of luminosity as a function of time": [[20, "make-plots-of-luminosity-as-a-function-of-time"]], "3. Prep for ML algorithms": [[13, "prep-for-ml-algorithms"]], "3. Start a new notebook.": [[1, "start-a-new-notebook"]], "3.1 Gaia": [[14, "gaia"]], "3.1 Train test split": [[13, "train-test-split"]], "3.1) Sample comparison on the UMAP": [[9, "sample-comparison-on-the-umap"]], "3.2) Reduced dimensions on a SOM grid": [[9, "reduced-dimensions-on-a-som-grid"]], "3.3 IceCube neutrinos": [[14, "icecube-neutrinos"]], "3a. Setup": [[6, "a-setup"]], "3b. Main Function to do the Forced Photometry": [[6, "b-main-function-to-do-the-forced-photometry"]], "3c. Calculate Forced Photometry with Straightforward but Slow Method": [[6, "c-calculate-forced-photometry-with-straightforward-but-slow-method"]], "3d. Calculate Forced Photometry - Parallelization": [[6, "d-calculate-forced-photometry-parallelization"]], "3e. Cleanup": [[6, "e-cleanup"]], "3f. Plot to Confirm our Photometry Results": [[6, "f-plot-to-confirm-our-photometry-results"]], "4) Repeating the above, this time with ZTF + WISE manifold": [[9, "repeating-the-above-this-time-with-ztf-wise-manifold"]], "4. Cross Match our New Photometry Catalog with an X-ray archival Catalog": [[6, "cross-match-our-new-photometry-catalog-with-an-x-ray-archival-catalog"]], "4. End your JupyterHub session.": [[1, "end-your-jupyterhub-session"]], "4. Parallel processing the archive calls": [[14, "parallel-processing-the-archive-calls"]], "4. Run sktime algorithms on the light curves": [[13, "run-sktime-algorithms-on-the-light-curves"]], "4. Visualize Euclid data": [[19, "visualize-euclid-data"]], "4.1 A single Classifier": [[13, "a-single-classifier"]], "4.1 Check that the data types are ok for sktime": [[13, "check-that-the-data-types-are-ok-for-sktime"]], "4.2 Loop over a bunch of classifiers": [[13, "loop-over-a-bunch-of-classifiers"]], "4a. Retrieve the HEASARC Catalog": [[6, "a-retrieve-the-heasarc-catalog"]], "4b. Run nway to do the Cross-Match": [[6, "b-run-nway-to-do-the-cross-match"]], "5) Wise bands alone": [[9, "wise-bands-alone"]], "5. Make plots of luminosity as a function of time": [[14, "make-plots-of-luminosity-as-a-function-of-time"]], "5. Plot Final Results": [[6, "plot-final-results"]], "5.0 Create a candidate list": [[13, "create-a-candidate-list"]], "6) UMAP with different metrics/distances on ZTF+WISE": [[9, "umap-with-different-metrics-distances-on-ztf-wise"]], "AGN Zoo: Comparison of AGN selected with different metrics": [[9, null]], "About this Notebook": [[9, "about-this-notebook"]], "About this notebook": [[16, "about-this-notebook"]], "Acknowledgements": [[13, "acknowledgements"]], "Acknowledgements:": [[6, "acknowledgements"], [14, "acknowledgements"], [20, "acknowledgements"]], "Additional Resources": [[1, "additional-resources"]], "Advice for the user": [[16, "advice-for-the-user"]], "Appendix: What to expect": [[16, "appendix-what-to-expect"]], "Authors": [[13, "authors"]], "Authors:": [[6, "authors"], [14, "authors"], [20, "authors"]], "Automated Multiband Forced Photometry on Large Datasets": [[6, null]], "Bash script flags": [[16, "bash-script-flags"]], "Can I install my own software on the Fornax Science Console?": [[1, "can-i-install-my-own-software-on-the-fornax-science-console"]], "Cancel": [[16, "cancel"]], "Challenges of large-scale runs": [[16, "challenges-of-large-scale-runs"]], "Citations": [[9, "citations"]], "Cloud": [[1, "cloud"]], "Code - 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Define the Sample": [[19, "define-the-sample"]], "1. Define the sample": [[14, "define-the-sample"], [20, "define-the-sample"]], "1. Get an account on the Fornax Science Console": [[1, "get-an-account-on-the-fornax-science-console"]], "1. Read in a dataset of archival light curves": [[13, "read-in-a-dataset-of-archival-light-curves"]], "1. Retrieve Initial Catalog from IRSA": [[6, "retrieve-initial-catalog-from-irsa"]], "1.1 Build your own sample": [[14, "build-your-own-sample"]], "1.1) What is in this sample": [[9, "what-is-in-this-sample"]], "1.2 Write out your sample to disk": [[14, "write-out-your-sample-to-disk"], [20, "write-out-your-sample-to-disk"]], "1.3 Load the sample table from disk": [[14, "load-the-sample-table-from-disk"], [20, "load-the-sample-table-from-disk"]], "1.4 Initialize data structure to hold the light curves": [[14, "initialize-data-structure-to-hold-the-light-curves"]], "1.4 Initialize data structure to hold the spectra": [[20, "initialize-data-structure-to-hold-the-spectra"]], "1a. Filter Catalog": [[6, "a-filter-catalog"]], "2) Preprocess data for ML (ZTF bands)": [[9, "preprocess-data-for-ml-ztf-bands"]], "2. Data Prep": [[13, "data-prep"]], "2. Find light curves for these targets in NASA catalogs": [[14, "find-light-curves-for-these-targets-in-nasa-catalogs"]], "2. Find spectra for these targets in NASA and other ancillary catalogs": [[20, "find-spectra-for-these-targets-in-nasa-and-other-ancillary-catalogs"]], "2. Log into the Fornax Science Console": [[1, "log-into-the-fornax-science-console"]], "2. Query the Euclid catalog for the sample": [[19, "query-the-euclid-catalog-for-the-sample"]], "2. Retrieve Image Datasets from the Cloud": [[6, "retrieve-image-datasets-from-the-cloud"]], "2.1 HEASARC: FERMI & Beppo SAX": [[14, "heasarc-fermi-beppo-sax"]], "2.1 IRSA Archive": [[20, "irsa-archive"]], "2.1 Remove bands with not enough data": [[13, "remove-bands-with-not-enough-data"]], "2.2 Combine Labels for a Simpler Classification": [[13, "combine-labels-for-a-simpler-classification"]], "2.2 IRSA: ZTF": [[14, "irsa-ztf"]], "2.2 MAST Archive": [[20, "mast-archive"]], "2.3 Data Visualization": [[13, "data-visualization"]], "2.3 ESA Archive": [[20, "esa-archive"]], "2.3 IRSA: WISE": [[14, "irsa-wise"]], "2.4 Clean the dataset of unwanted data": [[13, "clean-the-dataset-of-unwanted-data"]], "2.4 MAST: Pan-STARRS": [[14, "mast-pan-starrs"]], "2.4 SDSS Archive": [[20, "sdss-archive"]], "2.5 DESI Archive": [[20, "desi-archive"]], "2.5 MAST: TESS, Kepler and K2": [[14, "mast-tess-kepler-and-k2"]], "2.5 Missing Data": [[13, "missing-data"]], "2.6 Make all objects and bands have identical time arrays (uniform length and spacing)": [[13, "make-all-objects-and-bands-have-identical-time-arrays-uniform-length-and-spacing"]], "2.6 MAST: Hubble Catalog of Variables (HCV)": [[14, "mast-hubble-catalog-of-variables-hcv"]], "2.7 Restructure dataframe": [[13, "restructure-dataframe"]], "2.8 Normalize": [[13, "normalize"]], "2.9 Cleanup": [[13, "cleanup"]], "3) Learn the Manifold": [[9, "learn-the-manifold"]], "3. Run Forced Photometry": [[6, "run-forced-photometry"]], "3. Find light curves for these targets in relevant, non-NASA catalogs": [[14, "find-light-curves-for-these-targets-in-relevant-non-nasa-catalogs"]], "3. Grab the images, 1D coadded spectrum, & individual spectra": [[19, "grab-the-images-1d-coadded-spectrum-individual-spectra"]], "3. Make plots of luminosity as a function of time": [[20, "make-plots-of-luminosity-as-a-function-of-time"]], "3. Prep for ML algorithms": [[13, "prep-for-ml-algorithms"]], "3. Start a new notebook.": [[1, "start-a-new-notebook"]], "3.1 Gaia": [[14, "gaia"]], "3.1 Train test split": [[13, "train-test-split"]], "3.1) Sample comparison on the UMAP": [[9, "sample-comparison-on-the-umap"]], "3.2) Reduced dimensions on a SOM grid": [[9, "reduced-dimensions-on-a-som-grid"]], "3.3 IceCube neutrinos": [[14, "icecube-neutrinos"]], "3a. Setup": [[6, "a-setup"]], "3b. Main Function to do the Forced Photometry": [[6, "b-main-function-to-do-the-forced-photometry"]], "3c. Calculate Forced Photometry with Straightforward but Slow Method": [[6, "c-calculate-forced-photometry-with-straightforward-but-slow-method"]], "3d. Calculate Forced Photometry - Parallelization": [[6, "d-calculate-forced-photometry-parallelization"]], "3e. Cleanup": [[6, "e-cleanup"]], "3f. Plot to Confirm our Photometry Results": [[6, "f-plot-to-confirm-our-photometry-results"]], "4) Repeating the above, this time with ZTF + WISE manifold": [[9, "repeating-the-above-this-time-with-ztf-wise-manifold"]], "4. Cross Match our New Photometry Catalog with an X-ray archival Catalog": [[6, "cross-match-our-new-photometry-catalog-with-an-x-ray-archival-catalog"]], "4. End your JupyterHub session.": [[1, "end-your-jupyterhub-session"]], "4. Parallel processing the archive calls": [[14, "parallel-processing-the-archive-calls"]], "4. 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    2.2 MAST Archive

    2.3 ESA Archive#

    # Herschel PACS & SPIRE from ESA TAP using astroquery
-#This search is fully functional, but is commented out because it is very slow.
+#This search is fully functional, but is commented out because it takes ~4 hours to run to completion
 herschel_radius = 1.1  
 herschel_download_directory = 'data/herschel'