AxonDeepSeg 5.4.0__tar.gz

axondeepseg-5.4.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us fix a software bug
+title: ''
+labels: category:BUG
+assignees: ''
+
+---
+<!-- Use this form to report software defects (inaccurate/erratic behavior, crashes, etc.).
+If you have questions about using the software or are encountering difficulties with installation, please create a topic in the forum (see the "Discussions" tab at the top of this page). -->
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+Feel free to add screenshots to illustrate the problem!
+
+**To Reproduce**
+<!--
+Please try to reproduce your issue using "./AxonDeepSeg/data_test" as inputs, and to provide a sequence of commands that can reproduce it.
+If this is not possible, try to isolate a minimal input on which the issue happens (e.g. one file among a dataset) and provide this file publicly. If the data can't be shared publicly, please coordinate with @jcohenadad in private.
+-->
+Steps to reproduce the behavior:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See "Error 1955: Out of Time"
+
+**Platform (please complete the following information):**
+ - OS: [e.g. Mac OS "Flaming Flamingo", Fedora 99, Ubuntu 48.04]
+ - AxonDeepSeg version number [e.g. 3.2.0, git master, etc.]

axondeepseg-5.4.0/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: Questions and Answers
+    url: https://github.com/neuropoly/axondeepseg/discussions
+    about: Please ask (and/or answer) installation and usage questions in our discussions forum

axondeepseg-5.4.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Describe a well-defined idea of a how a new functionality should work
+title: ''
+labels: category:FEATURE
+assignees: ''
+
+---
+<!-- 
+Use this form to describe a well-defined new feature that should be added to the software.
+If your idea is not fully fleshed out yet, consider brainstorming with us by creating a topic in the forum (see the "Discussions" tab at the top of this page) before making a formal feature request here.
+-->
+**Describe the problem**
+If possible, provide references to any discussions or theoretical work to help the reader better understand the feature.
+Feel free to add screenshots and mockups to illustrate the problem!
+
+**Proposed solution**
+A clear and concise description of what you want to happen, ideally as a result of an existing discussion or design work.
+
+Provide a "usage scenario", imagining how the feature would be used in practice (ideally inputs, a sequence of commands, and the desired outcome).

axondeepseg-5.4.0/.github/pull_request_template.md

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+## Checklist
+
+- [ ] I've given this PR a concise, self-descriptive, and meaningful title
+- [ ] I've linked relevant issues in the PR body
+- [ ] I've applied [the relevant labels](https://intranet.neuro.polymtl.ca/geek-tips/contributing#pr-labels-a-href-pr-labels-id-pr-labels-a) to this PR
+- [ ] I've added relevant tests for my contribution
+- [ ] I've updated the documentation and/or added correct docstrings
+- [ ] I've assigned a reviewer
+- [ ] I've consulted [ADS's internal developer documentation](https://github.com/neuropoly/axondeepseg/wiki/Guidelines-for-contribution) to ensure my contribution is in line with any relevant design decisions
+
+
+<!--- For the title, please observe the following rules:
+	- Provide a concise and self-descriptive title
+	- Do not include the applicable issue number in the title, do it in the PR body
+	- If the PR is not ready for review, convert it to a draft.
+-->
+
+## Description
+<!-- describe what the PR is about. Explain the approach and possible drawbacks.It's ok to repeat some text from the related issue. -->
+
+## Linked issues
+<!-- If the PR fixes any issues, indicate it here with issue-closing keywords: e.g. Resolves #XX, Fixes #XX, Addresses #XX. Note that if you want multiple issues to be autoclosed on PR merge, you must use the issue-closing verb before each relevant issue: e.g. Resolves #1, Resolves #2 -->

axondeepseg-5.4.0/.github/workflows/pipy_install_tests.yaml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+# Official DOc on GitHub Workflow Syntax: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions
+
+# Conda based env testing: https://github.com/conda-incubator/setup-miniconda
+name: Run tests on pypi install
+
+on:
+
+  # Trigger the workflow on push but only for the master branch
+  push:
+    branches:
+      - master
+      - 'release/**'
+
+  # Trigger current workflow on PR from ANY branch
+  pull_request:
+    types: [opened, reopened, synchronize]
+    branches:
+      - 'release/**'
+
+  # Cron based trigger
+  schedule:
+    # https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-syntax-for-github-actions#onschedule
+    # i.e. this runs every day at 4:33AM for the master branch.
+    - cron: '33 4 * * *'
+
+env:
+  # Even when given -y, apt will still sometimes hang at a prompt if a package
+  # has clarifications to ask; DEBIAN_FRONTEND=noninteractive prevents that,
+  # This will be defined for non-debian platforms below too, but there's no harm in that.
+  # (TravisCI quietly defined this on all their platforms, but we have to give it manually on GithubCI.)
+  DEBIAN_FRONTEND: 'noninteractive'
+
+jobs:
+  pypi_package_tests:
+    name: PyPi Package test for Python ${{ matrix.python-version }} on ${{ matrix.os }}
+
+    # Matrix driven OS
+    runs-on: ${{ matrix.os }}
+
+    # Defining matrix for OS and Python
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ "ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version:  [ "3.11", "3.12"]
+
+    # Main steps for the test to be reproduced across OS x Python
+    steps:
+      # Step 1: Checkout code.
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v5 
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Step 2: Install environment.
+      - name: Install Latest pypi version of AxonDeepSeg
+        run: |
+          pip install --upgrade pip
+          pip install axondeepseg==5.4.0 --no-cache-dir
+
+
+      # Step 2a: Modify MKL_THREADING_LAYER (Ubuntu only)
+      # See https://github.com/pytorch/pytorch/issues/37377#issuecomment-629530272
+      - name: Set MKL_THREADING_LAYER
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          echo "MKL_THREADING_LAYER=GNU" >> $GITHUB_ENV
+
+      # Step 3: Full PyTest
+      - name: Test with pytest (Unix)
+        if: ${{ (matrix.os == 'ubuntu-latest') || (matrix.os == 'macos-latest' && matrix.python-version == '3.11') }}
+        run: |
+
+          git pull --all
+          
+          git checkout $( git tag | tail -1)
+
+          rm -rf ./AxonDeepSeg/
+
+          python -c "import AxonDeepSeg.download_tests as download_tests; download_tests.main()"
+          python -c "import AxonDeepSeg.download_tests as download_tests; download_tests.main(['-d', './test/'])"
+          python -c "import AxonDeepSeg.download_model as download_model; download_model.main()"
+          python -c "import AxonDeepSeg.download_model as download_model; download_model.main(['-d', './AxonDeepSeg/models'])"
+
+          pytest ./ -v
+          echo "All done!"
+          exit 0 
+          
+    
+
+      - name: Test with pytest (Windows)
+        if: runner.os == 'Windows'
+        shell: cmd
+        run: |
+
+          for /f %%i in ('git tag') do set LATEST_TAG=%%i
+          git checkout %LATEST_TAG%
+
+          rmdir ./AxonDeepSeg/
+
+          python -c "import AxonDeepSeg.download_tests as download_tests; download_tests.main()"
+          python -c "import AxonDeepSeg.download_tests as download_tests; download_tests.main(['-d', './test/'])"
+          python -c "import AxonDeepSeg.download_model as download_model; download_model.main()"
+          python -c "import AxonDeepSeg.download_model as download_model; download_model.main(['-d', './AxonDeepSeg/models'])"
+
+          pytest.exe ./ -v
+
+
+  # This step is MANDATORY and used to indicate matrix completion to coveralls.io
+  # See here: https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support
+  finish:
+    needs: [pypi_package_tests]
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+      - name: Pypi install test finished
+        run: echo "Tests comlete!"
+

axondeepseg-5.4.0/.github/workflows/run_tests.yaml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+# Official DOc on GitHub Workflow Syntax: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions
+
+# Conda based env testing: https://github.com/conda-incubator/setup-miniconda
+name: Run tests
+
+on:
+
+  # Trigger the workflow on push but only for the master branch
+  push:
+    branches:
+      - master
+
+  # Trigger current workflow on PR from ANY branch
+  pull_request:
+    branches:
+      - '**'
+
+  # Cron based trigger
+  schedule:
+    # https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-syntax-for-github-actions#onschedule
+    # i.e. this runs every day at 4:33AM for the master branch.
+    - cron: '33 4 * * *'
+
+env:
+  # Even when given -y, apt will still sometimes hang at a prompt if a package
+  # has clarifications to ask; DEBIAN_FRONTEND=noninteractive prevents that,
+  # This will be defined for non-debian platforms below too, but there's no harm in that.
+  # (TravisCI quietly defined this on all their platforms, but we have to give it manually on GithubCI.)
+  DEBIAN_FRONTEND: 'noninteractive'
+  VISPY_GL_BACKEND: 'osmesa'
+
+jobs:
+  ultra_matrix_test:
+    name: Matrix Test of Python ${{ matrix.python-version }} on ${{ matrix.os }}
+
+    # Matrix driven OS
+    runs-on: ${{ matrix.os }}
+
+    # Default shell for ALL subsequent steps.
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    # Defining matrix for OS and Python
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ "ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: [ ">=3.11" ]
+
+    # Main steps for the test to be reproduced across OS x Python
+    steps:
+      # Step 0: Checkout code.
+      - uses: actions/checkout@v2
+
+      # Step 1: List main repo by time modified, and print path
+      - name: List all current repository files and modification date
+        # Parameters.
+        run: |
+          ls -lasth
+          pwd
+
+      # Step 2: Install environment.
+      - name: Install ADS from release branch (Unix)
+        if: runner.os != 'Windows'
+        run: ./install_ads -y
+      - name: Install ADS from release branch (Windows)
+        if: runner.os == 'Windows'
+        shell: cmd
+        run: install_ads.bat
+
+      # Step 2a: Modify MKL_THREADING_LAYER (Ubuntu only)
+      # See https://github.com/pytorch/pytorch/issues/37377#issuecomment-629530272
+      - name: Set MKL_THREADING_LAYER
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          echo "MKL_THREADING_LAYER=GNU" >> $GITHUB_ENV
+
+      # Step 2b: Add ADS to the PATH
+      - name: Update environment variables
+        # NB: I'm not sure what GHA's syntax is for cmd.exe, so we use bash just for this one change
+        # In a user install, the user would perform this step using the Windows PATH-changing GUI.
+        run: |
+          if [ "$RUNNER_OS" == "Windows" ]; then
+            echo "${GITHUB_WORKSPACE}" >> $ADS_DIR
+            echo "${GITHUB_WORKSPACE}\bin" >> $GITHUB_PATH
+          else
+            # NB: install_ads edits ~/.bashrc, but those environment changes don't get passed to subsequent steps in GH Actions.
+            # So, we filter through the .bashrc and pass the values to $GITHUB_ENV and $GITHUB_PATH.
+            # Relevant documentation: https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#environment-files
+            cat ~/.bashrc | grep "export ADS_DIR" | cut -d " " -f 2 >> $GITHUB_ENV
+            cat ~/.bashrc | grep "export PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH
+          fi
+
+      # Step 3: Full PyTest
+      - name: Test with pytest (Unix)
+        if: runner.os != 'Windows'
+        run: |
+          source ads_conda/bin/activate ads_conda/envs/venv_ads
+          pytest ./test/ -v --cov AxonDeepSeg/ --cov-report=lcov
+      - name: Test with pytest (Windows)
+        if: runner.os == 'Windows'
+        shell: cmd
+        run: |
+          CALL ads_conda\Scripts\activate.bat ads_conda\envs\venv_ads
+          pytest.exe ./test/ -v --cov AxonDeepSeg/ --cov-report=lcov
+      # Step 4: Submnit to coveralls
+      - name: Submit to coveralls
+        uses: coverallsapp/github-action@v2
+        with:
+          flag-name: ${{ matrix.os }}
+          parallel: true
+
+  # This step is MANDATORY and used to indicate matrix completion to coveralls.io
+  # See here: https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support
+  finish:
+    needs: [ultra_matrix_test]
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@v2
+      with:
+        github-token: ${{ secrets.github_token }}
+        parallel-finished: true

axondeepseg-5.4.0/.gitignore

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+# Can ignore ADS specific files/folders
+AxonDeepSeg\.egg-info/
+
+AxonDeepSeg/.adsconfig
+
+build/
+
+dist/
+
+config/
+
+\.idea/
+
+*.pyc
+
+*.png
+
+data/
+
+guidelines/.ipynb_checkpoints/
+
+summaries/
+
+trainingset/
+
+guidelines/test_weights\.ipynb
+
+notebooks/\.ipynb_checkpoints/
+
+notebooks/test_weights\.ipynb
+
+AxonDeepSeg/models
+
+models/
+
+test/__test_files__
+
+tmp/
+
+*.log
+
+# Files generated by the new SCT-based install script
+/bin
+/ads_conda
+/install_ads_log.txt
+
+# Generated image files
+AxonDeepSeg/data_test/AxonDeepSeg*
+
+# Python-related temp files
+.coverage
+.pytest_cache/
+.ipynb_checkpoints/
+
+# OS-related files/folders
+__MACOSX/
+.DS_Store
+.vscode/
+
+axondeepseg.log
+
+Pipfile
+
+*.egg-info/
+qa_test/
+
+docs/source/_generated_models.rst

axondeepseg-5.4.0/.readthedocs.yml

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+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+      python: "3.12"
+
+# Install Sphinx/RTD requirements
+python:
+  install:
+    - requirements: docs/source/requirements.txt
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: true
+

axondeepseg-5.4.0/AxonDeepSeg/__init__.py

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+import os
+import sys
+
+__name__ = "AxonDeepSeg"
+
+version_file = os.path.abspath(os.path.join(__file__, os.pardir, "version.txt"))
+with open(version_file, 'r') as f:
+    __version__ = f.read().rstrip()
+
+# make sure repo directory (two directories up) is on path (to access config.py)
+__repo_dir__ = os.path.abspath(os.path.join(__file__, os.pardir, os.pardir))
+sys.path.append(__repo_dir__)
+
+# verify that the repo was downloaded with `git clone`
+if os.path.exists(os.path.join(__repo_dir__, ".git")):
+    import subprocess
+    __git_sha1__ = subprocess.check_output(["git", "-C", __repo_dir__, "rev-parse", "HEAD"]).decode("utf-8").rstrip()
+else:
+    __git_sha1__ = "unknown commit"    
+__version_string__ = f"AxonDeepSeg v{__version__} - {__git_sha1__}"

axondeepseg-5.4.0/AxonDeepSeg/ads_napari/Settings_menu_ui.ui

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+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>Settings_menu_ui</class>
+ <widget class="QWidget" name="Settings_menu_ui">
+  <property name="windowModality">
+   <enum>Qt::WindowModal</enum>
+  </property>
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>399</width>
+    <height>209</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Settings menu</string>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout">
+   <item>
+    <layout class="QHBoxLayout" name="horizontalLayout_6">
+     <item>
+      <widget class="QLabel" name="label_5">
+       <property name="text">
+        <string>GPU ID</string>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <widget class="QSpinBox" name="gpu_id_spinBox"/>
+     </item>
+    </layout>
+   </item>
+   <item>
+    <layout class="QHBoxLayout" name="horizontalLayout_4">
+     <item>
+      <widget class="QLabel" name="label_4">
+       <property name="text">
+        <string>Axon Shape</string>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <widget class="QComboBox" name="axon_shape_comboBox">
+       <item>
+        <property name="text">
+         <string>circle</string>
+        </property>
+       </item>
+       <item>
+        <property name="text">
+         <string>ellipse</string>
+        </property>
+       </item>
+      </widget>
+     </item>
+    </layout>
+   </item>
+   <item>
+    <widget class="QPushButton" name="done_button">
+     <property name="text">
+      <string>Done</string>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <spacer name="verticalSpacer">
+     <property name="orientation">
+      <enum>Qt::Vertical</enum>
+     </property>
+     <property name="sizeHint" stdset="0">
+      <size>
+       <width>20</width>
+       <height>40</height>
+      </size>
+     </property>
+    </spacer>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>

axondeepseg-5.4.0/AxonDeepSeg/ads_napari/__init__.py

@@ -0,0 +1,5 @@
+from ._widget import ADSplugin
+
+__all__ = (
+    "ADSplugin"
+)