Merge pull request #1 from AlphonsG/dev

Dev

.gitattributes

@@ -0,0 +1 @@
+*.pth filter=lfs diff=lfs merge=lfs -text

.github/workflows/codeql-analysis.yaml

@@ -0,0 +1,71 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ main ]
+  schedule:
+    - cron: '40 7 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/python-package.yaml

@@ -0,0 +1,45 @@
+name: Python package
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: windows-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ['3.10']
+
+    steps:
+    - name: Support longpaths
+      run: git config --system core.longpaths true
+    - uses: actions/checkout@v1
+      with:
+        lfs: 'true'
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -e .[test]
+    - name: Checkout submodule
+      run: |
+        git submodule sync
+        git submodule update --init --recursive
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest --cov=bimana --cov-report term-missing --cov-report lcov tests/
+    - name: Coveralls
+      uses: coverallsapp/github-action@master
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+        path-to-lcov: ./coverage.lcov

.gitignore

@@ -0,0 +1,6 @@
+
+.vscode/
+
+bimana.egg-info/
+
+*.pyc

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "third_party/DexiNed"]
+	path = third_party/DexiNed
+	url = https://github.com/AlphonsG/DexiNed

CONTRIBUTING.md

@@ -0,0 +1,34 @@
+# How to contribute to Bimana
+
+:+1::tada: First off, thanks for taking the time to contribute! :tada::+1:
+
+## Report issues or problems with the software
+
+* **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/AlphonsG/BIMANA/issues).
+
+* If you're unable to find an open issue addressing the problem, use the relevant bug report [template](https://github.com/AlphonsG/BIMANA/issues/new/choose) to create one.
+
+* If not possible, you can [open a blank issue](https://github.com/AlphonsG/BIMANA/issues/new). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample** or an **executable test case** demonstrating the expected behavior that is not occurring.
+
+## Submitting Changes
+
+* Open a new GitHub pull request with the change.
+
+* Ensure the PR description clearly describes the change. Include the relevant issue number if applicable.
+
+* At lease one reviewer should be added so that the code is looked over by someone else.
+
+Always write a clear log message for your commits, for example:
+
+    $ git commit -m "A brief summary of the commit
+    >
+    > A paragraph describing what changed and its impact."
+
+ ## Coding conventions
+
+ Please follow the [Google Python Style Guide](https://google.github.io/styleguide/pyguide.html) when contributing to the code.
+
+ ## Seek Support
+
+ Please feel free to send an email to the following address for other matters:
+ - [email protected]

README.md

@@ -1 +1,119 @@
-# BIMANA
+# Bimana
+
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![Python package](https://github.com/AlphonsG/BIMANA/actions/workflows/python-package.yaml/badge.svg?branch=dev)](https://github.com/AlphonsG/BIMANA/actions/workflows/python-package.yaml)
+[![Coverage
+Status](https://coveralls.io/repos/github/AlphonsG/BIMANA/badge.svg?branch=dev)](https://coveralls.io/github/AlphonsG/BIMANA?branch=dev)
+[![CodeFactor](https://www.codefactor.io/repository/github/alphonsg/bimana/badge/dev)](https://www.codefactor.io/repository/github/alphonsg/bimana/overview/dev)
+[![GitHub license](https://img.shields.io/github/license/AlphonsG/BIMANA)](https://github.com/AlphonsG/BIMANA/blob/main/LICENSE)
+
+![](misc/images/bimana.png?raw=true "Bimana Image Analysis")
+
+Package for performing automated bio-image analysis tasks.
+
+# Table of contents
+1. <a href="#installation">Installation</a>
+2. <a href="#usage">Usage</a>
+3. <a href="#license">License</a>
+4. <a href="#community-guidelines">Community Guidelines</a>
+5. <a href="#acknowledgements">Acknowledgements</a>
+## Installation <a id="installation"></a>
+
+Bimana can be installed on Linux, Windows (with 64 bit Python) & macOS and
+supports Python 3.10 and above. It is recommended to install and run Bimana
+within a [virtual environment](https://docs.python.org/3/tutorial/venv.html).
+
+1. Download and install [Python](https://www.python.org/downloads/) (Bimana was
+   tested using [Python version
+   3.10.6](https://www.python.org/downloads/release/python-3106/)),
+   [Git](https://git-scm.com/) and [Git LFS](https://git-lfs.github.com/).
+   Linux and macOS users must also install [libvips](https://www.libvips.org/install.html).
+
+2. Launch the terminal (*Linux* and *macOS* users) or command prompt (*Windows* users). The proceeding commands will be entered into the opened window<sup>1</sup>.
+
+3. Create and activate a virtual environment called 'bimana-env' in your desired directory:
+
+   ```pip install --upgrade pip```
+
+   ```python -m venv bimana-env```
+
+   ```. bimana-env/bin/activate``` (*Linux* and *macOS* users) or ```bimana-env\Scripts\activate.bat``` (*Windows* users)
+
+4. Install PyTorch by specifying your system configuration using the official [PyTorch get started tool](https://pytorch.org/get-started/locally/) and running the generated command:
+   <p style="text-align:center;">
+    <img src="misc/images/pytorch_get_started.png" width="750" alt="centered image" />
+    </p>
+   For example, according to the image above, Windows users without a GPU (i.e. CPU only) will run:
+
+   ```pip3 install torch torchvision torchaudio```
+
+
+5. Clone this repository into your desired directory:
+
+   ```
+   git lfs install
+   git clone https://github.com/AlphonsG/BIMANA.git
+   ```
+
+6. Navigate into the cloned directory:
+
+    ```cd BIMANA```
+
+7. Install Bimana:
+
+   ```
+   git submodule update --init --recursive
+   pip install -e .
+   ```
+
+Notes:
+  - <sup>1</sup>Confirm that the correct python version for Bimana has been installed using the `python -V` command in the terminal. If this command does not report the correct python version, try using the `python3 -v` command instead. If the second command produces the expected result, replace all `python` and `pip` commands in this guide with `python3` and `pip3`, respectively.
+
+  - The virtual environment can be deactivated using:
+
+      ```deactivate```
+
+## Usage <a id="usage"></a>
+
+Enter `bimana -h` or `bimana --help` within the `bimana-env` environment after installation for details on how to use Bimana.
+
+Example commands that can be used to test Bimana using input data provided in
+each folder [here](misc/examples) are given below. After
+processing is finished for a given folder containing input images, multiple subfolders
+containing generated outputs (e.g. images,  CSV files, etc) are created. Examples of these are also provided.
+
+Example commands (first run `cd misc` from the cloned repository folder):
+
+- Histological Section Analysis
+   ```
+   bimana histological-section-analysis --staining-amount-in-tissue-area  --cilia-amount-above-tissue-area
+   ```
+
+- Tight junction analysis
+   ```
+   bimana tight-junction-analysis misc/examples/tight_junctions  --analyse-tight-junctions --analyse-cells
+   ```
+- Live cell imaging metrics analysis
+   ```
+   bimana live-cell-imaging metrics-file-processing misc/examples/live_cell_imaging
+   ```
+
+## License <a id="license"></a>
+
+[MIT License](LICENSE)
+
+
+## Community guidelines <a id="community-guidelines"></a>
+
+ Guidelines for third-parties wishing to:
+
+- Contribute to the software
+- Report issues or problems with the software
+- Seek support
+
+can be found [here](CONTRIBUTING.md).
+
+## Acknowledgements <a id="acknowledgements"></a>
+
+- https://github.com/xavysp/DexiNed
+- https://github.com/DevonsMo/IJOQ

bimana/__main__.py

@@ -0,0 +1,11 @@
+from bimana.cli import cli
+
+
+def main() -> int:
+    cli()
+
+    return 0
+
+
+if __name__ == '__main__':
+    main()

bimana/cli.py

@@ -0,0 +1,21 @@
+import click
+
+from bimana.histological_section.commands import histological_section_analysis
+from bimana.tight_junctions.commands import tight_junction_analysis
+from bimana.live_cell_imaging.commands import live_cell_imaging
+
+CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'])
+
+
+@click.group(context_settings=CONTEXT_SETTINGS)
+def cli() -> None:
+    """ Simple command line utility called `bimana`.
+
+    The cli is composed of commands for performing automated bio-image
+    analysis tasks.
+    """
+
+
+cli.add_command(histological_section_analysis)
+cli.add_command(tight_junction_analysis)
+cli.add_command(live_cell_imaging)