Final modifications for publication

.github/workflows/black.yml

@@ -0,0 +1,10 @@
+name: Black
+
+on: [workflow_call, push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable

.gitignore

@@ -1,6 +1,160 @@
-/.venv
-/__pycache__
-/build
-/build_old
-.gitignore
-README_absolete.md
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/

README.md

@@ -1,37 +1,54 @@
+[![Black](https://github.com/balciemrah/TME_Analyzer_20240320/actions/workflows/black.yml/badge.svg)](https://github.com/balciemrah/TME_Analyzer_20240320/actions/workflows/black.yml)
+
 # TME_Analyzer
 
 ## Introduction
-TME-Analyzer is a stand alone software for analysis of fluorescent and other high-dimensional images that have a nuclear marker for cell detection. It comes with integrated quantification of cellular and tissue phenotypes, their densities in defined compartments and their interspacing, as well as visualization and exportation of data. This repository contains the Python code, as described in the paper:
+[TME-Analyzer](https://tme-facility.com/technology/tme-analyzer) is a stand alone software developed in the [Laboratory of Tumor Immunology, Erasmus MC](https://www.erasmusmc.nl/en/cancer-institute/research/groups/medical-oncology-tumor-immunology) for analysis of fluorescent and other high-dimensional images that have a nuclear marker for cell detection. It comes with integrated quantification of cellular and tissue phenotypes, their densities in defined compartments and their interspacing, as well as visualization and exportation of data. This repository contains the Python code, as described in the paper:
 
 - Hayri E Balcioglu, Rebecca Wijers, Marcel Smid, Dora Hammerl, Anita M Trapman-Jansen, Astrid Oostvogels, Mieke Timmermans, John WM Martens and Reno Debets. 
 [*TME-Analyzer: a new interactive and dynamic image analysis tool that identified immune cell distances as predictors for survival of triple negative breast cancer patients*](https://doi.org/10.1038/s44303-024-00022-6).  
 npj Imaging.
 
+The stand alone software can be downloaded [*here*](https://drive.usercontent.google.com/download?id=1maGzQBfjvbCphI1srRWiicWShfaJLmWm&export=download&authuser=0).
+
 Please cite the paper if you are using TME-Analyzer or (parts of) this code in your research.
 
-## Getting started
+## Getting started 
+
+Follow one of the following installations approaches (pip, venv or conda)
+
+### pip
+
+The pip installation was created by [*Rolf Harkes*](https://github.com/rharkes).
+
+Get python version 3.11.9
+- Create a venv: `python.exe -m venv .venv`
+- Activate the environment `./.venv/Scripts/Activate.ps1`; 
+  - Maybe with an execution policy:  `powershell -ExecutionPolicy Bypass -File "./.venv/Scripts/Activate.ps1"`
+- Install tmeanalyzer in [editable](https://pip.pypa.io/en/stable/cli/pip_install/#options) format with pip: `pip install -e .`
+  - You can install in developer mode with: `pip install -e .[dev]`
+- Run TME-Analyzer: `tmeanalyzer`
 
 ### Venv
 
-Get python version 3.8.10
+Get python version 3.11.9
 - Create a venv: `python.exe -m venv .venv`
 - Activate the environment `./.venv/Scripts/Activate.ps1`; 
   - Maybe with an execution policy:  `powershell -ExecutionPolicy Bypass -File "./.venv/Scripts/Activate.ps1"`
 - install dependencies: `python.exe -m pip install -r requirements.txt`
-  - note that requirements.txt give the minimal packages, and this should get all the packages in the requirements_extended.txt file
 
-And run: `python.exe TME_analyzer.py`
+And run: `python ./src/tmeanalyzer/TME_analyzer.py`
 
 ### Conda
 
 Run: `mamba env create -f environment.yml`
 
-And run: `python.exe TME_analyzer.py`
+And run: `python ./src/tmeanalyzer/TME_analyzer.py`
 
-## Cx-Freeze
+## Freeze it with pyinstaller to create a single executable (available in developer mode, tested on Windows and Ubuntu 22.04)
 
-Pack the project into a single binary with: 
-```python setup.py build```
+  - Creat a `.spec` file with: `pyi-makespec --onefile --noconsole --paths=./src/tmeanalyzer ./src/tmeanalyzer/TME_analyzer.py --hidden-import='PIL._tkinter_finder'`
+  - Create an executable with: `pyinstaller TME_analyzer.spec`
 
 ## Image analysis tutorial
 
@@ -220,4 +237,4 @@ You should end up more or less with the same analysis you have performed above.
 - The analysis parameters through the `Data Analysis -> Display Log`, and pressing `Print params`. You would then have to change your analysis to the other (main window, dropdown at right bottom) and press `Print params` again.
 
 ## Final points
-Hope you made it here and are excited about TME-A. This tutorial does not cover all the aspects of the TME-A. So, feel free to explore and contact us with any questions, feedback, amendments you see necessary and bug reports. 
+Hope you made it here and are excited about TME-A. This tutorial does not cover all the aspects of the TME-A. So, feel free to explore and contact us with any questions, feedback, amendments you see necessary and bug reports.