junifer 0.0.7.dev332__py3-none-any.whl → 0.0.8__py3-none-any.whl

junifer/external/BrainPrint/.github/workflows/build.yml

@@ -0,0 +1,53 @@
+name: build
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  pull_request:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  build:
+    timeout-minutes: 10
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu, macos, windows]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
+    name: ${{ matrix.os }} - py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off .[build]
+      - name: Test package install
+        run: brainprint-sys_info
+      - name: Remove package install
+        run: python -m pip uninstall -yq brainprint
+      - name: Build package
+        run: python -m build
+      - name: Install sdist
+        run: pip install ./dist/*.tar.gz
+      - name: Test sdist install
+        run: brainprint-sys_info
+      - name: Remove sdist install
+        run: python -m pip uninstall -yq brainprint
+      - name: Install wheel
+        run: pip install ./dist/*.whl
+      - name: Test wheel install
+        run: brainprint-sys_info
+      - name: Remove wheel install
+        run: python -m pip uninstall -yq brainprint

junifer/external/BrainPrint/.github/workflows/code-style.yml

@@ -0,0 +1,44 @@
+name: code-style
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  pull_request:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  style:
+    timeout-minutes: 10
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off .[style]
+      - name: Run Ruff
+        run: ruff check .
+      - name: Run isort
+        uses: isort/isort-action@master
+      - name: Run black
+        uses: psf/black@stable
+        with:
+          options: "--check --verbose"
+          version: "23.10.1"
+      - name: Run codespell
+        uses: codespell-project/actions-codespell@master
+        with:
+          check_filenames: true
+          check_hidden: true
+          skip: './.git,./build,./.mypy_cache,./.pytest_cache'
+          ignore_words_file: ./.codespellignore
+      # - name: Run pydocstyle
+      #   run: pydocstyle .

junifer/external/BrainPrint/.github/workflows/doc.yml

@@ -0,0 +1,65 @@
+name: doc
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  pull_request:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  build:
+    timeout-minutes: 10
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          path: ./main
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+          architecture: 'x64'
+      - name: Install package
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off main/.[doc]
+      - name: Display system information
+        run: brainprint-sys_info --developer
+      - name: Build doc
+        run: sphinx-build ./main/doc ./doc-build/dev -W --keep-going
+      - name: Upload documentation
+        uses: actions/upload-artifact@v4
+        with:
+          name: doc-dev
+          path: ./doc-build/dev
+
+  deploy:
+    if: github.event_name == 'push'
+    needs: build
+    timeout-minutes: 10
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Download documentation
+        uses: actions/download-artifact@v4
+        with:
+          name: doc-dev
+          path: ./doc-dev
+      - name: Deploy dev documentation
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc-dev
+          destination_dir: ./dev
+          user_name: 'github-actions[bot]'
+          user_email: 'github-actions[bot]@users.noreply.github.com'

junifer/external/BrainPrint/.github/workflows/publish.yml

@@ -0,0 +1,31 @@
+name: publish
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+
+jobs:
+  pypi:
+    timeout-minutes: 10
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off .[build]
+      - name: Display system information
+        run: brainprint-sys_info --developer
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN  }}
+        run: |
+          python -m build
+          twine upload dist/*

junifer/external/BrainPrint/.github/workflows/pytest.yml

@@ -0,0 +1,54 @@
+name: pytest
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  pull_request:
+    paths:
+      - '**.py'
+  push:
+    branches: [main]
+    paths:
+      - '**.py'
+  workflow_dispatch:
+
+jobs:
+  pytest:
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu, macos, windows]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
+    name: ${{ matrix.os }} - py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: 'x64'
+      - name: Install package
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off .[test]
+      - name: Display system information
+        run: brainprint-sys_info --developer
+      - name: Run pytest
+        run: pytest brainprint --cov=brainprint --cov-report=xml --cov-config=pyproject.toml
+      - name: Upload to codecov
+        if: ${{ matrix.os == 'ubuntu' && matrix.python-version == 3.9 }}
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          flags: unittests # optional
+          name: codecov-umbrella # optional
+          fail_ci_if_error: true # optional (default = false)
+          verbose: true # optional (default = false)
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: deep-mi/BrainPrint

junifer/external/BrainPrint/.gitignore

@@ -0,0 +1,123 @@
+# macOS
+.DS_Store
+
+# 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/
+*.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
+.hypothesis/
+.pytest_cache/
+junit-results.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+doc/_build/
+doc/generated/
+doc/api/generated/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# 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/
+
+# PyCharm
+**/.idea/

junifer/external/BrainPrint/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2019 Image Analysis, DZNE e.V.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

junifer/external/BrainPrint/README.md

@@ -0,0 +1,108 @@
+[![PyPI version](https://badge.fury.io/py/brainprint.svg)](https://pypi.org/project/brainprint/)
+# BrainPrint
+
+This is the `brainprint` python package, a derivative of the original
+[BrainPrint-legacy](https://github.com/Deep-MI/BrainPrint-legacy) scripts,
+with the primary goal to provide a Python-only version, to integrate the
+[LaPy](https://github.com/Deep-MI/LaPy) package, and to remove dependencies
+on third-party software (shapeDNA-* binaries, gmsh, meshfix). As a result,
+some functionality of the original BrainPrint-legacy scripts is no longer
+maintained (currently no support of tetrahedral meshes and no support of
+cortical parcellations or label files).
+
+## Installation
+
+Use the following code to install the latest release of LaPy into your local
+Python package directory:
+
+`python3 -m pip install brainprint`
+
+This will also install the necessary dependencies, e.g. the [LaPy](https://github.com/Deep-MI/LaPy)
+package. You may need to add your local Python package directory to your $PATH
+in order to run the scripts.
+
+## Usage
+### Command Line Interface (CLI)
+
+Once installed, the package provides a `brainprint` executable which can be run from the command line.
+
+The `brainprint` CLI enables per-subject computation of the individual brainprint descriptors. Its usage and options are summarized below;
+detailed info is available by calling the script without any arguments from the command line.
+
+```sh
+brainprint --sdir <directory> --sid <SubjectID>  [--num <num>] [--evec] [--skipcortex] [--norm <surface|volume|geometry|none> ] [--reweight] [--asymmetry] [--outdir <directory>] [--help] [--more-help]
+
+Options:
+  --help           Show this help message and exit
+  --more-help      Show extensive help message and exit
+
+Required options:
+  --sid <SubjectID>
+                   Subject ID (FreeSurfer-processed directory inside the
+                   subjects directory)
+  --sdir <directory>
+                   FreeSurfer subjects directory
+
+Processing directives:
+  --num <num>      Number of eigenvalues/vectors to compute (default: 50)
+  --evec           Switch on eigenvector computation (default: off)
+  --skipcortex     Skip cortical surfaces (default: off)
+  --norm <surface|volume|geometry|none>
+                   Switch on eigenvalue normalization; will be either surface,
+                   volume, or determined by the geometry of the object. Use
+                   "none" or leave out entirely to skip normalization.
+  --reweight       Switch on eigenvalue reweighting (default: off)
+  --asymmetry      Perform left-right asymmetry calculation (default: off)
+  --cholmod        Switch on use of (faster) Cholesky decomposition instead
+                   of (slower) LU decomposition (default: off). May require 
+                   manual install of scikit-sparse package. 
+
+Output parameters:
+  --outdir=OUTDIR  Output directory (default: <sdir>/<sid>/brainprint)
+  --keep-temp      Whether to keep the temporary files directory or not
+                   by default False
+```
+
+### Python Package
+
+`brainprint` can also be run within a pure Python environment, i.e. installed and imported as a Python package. E.g.:
+
+```python
+>>> from brainprint import Brainprint
+
+>>> subjects_dir = "/path/to/freesurfer/subjects_dir/"
+>>> subject_id = "42"
+
+>>> bp = Brainprint(subjects_dir=subjects_dir, asymmetry=True, keep_eigenvectors=True)
+>>> results = bp.run(subject_id=subject_id)
+>>> results
+{"eigenvalues": PosixPath("/path/to/freesurfer/subjects_dir/subject_id/brainprint/subject_id.brainprint.csv"), "eigenvectors": PosixPath("/path/to/freesurfer/subjects_dir/subject_id/brainprint/eigenvectors"), "distances": PosixPath("/path/to/freesurfer/subjects_dir/subject_id/brainprint/subject_id.brainprint.asymmetry.csv")}
+```
+
+## Output
+
+The script will create an output directory that contains a CSV table with
+values (in that order) for the area, volume, and first n eigenvalues per each
+FreeSurfer structure. An additional output file will be created if the
+asymmetry calculation is performed and/or for the eigenvectors (CLI `--evecs` flag or `keep_eigenvectors` on class initialization).
+
+## Changes
+
+There are some changes in functionality in comparison to the original [BrainPrint](https://github.com/Deep-MI/BrainPrint-legacy)
+scripts:
+
+- currently no support for tetrahedral meshes
+- currently no support for analyses of cortical parcellation or label files
+- no more Python 2.x compatibility
+
+## API Documentation
+
+The API Documentation can be found at https://deep-mi.org/BrainPrint .
+
+## References
+
+If you use this software for a publication please cite:
+
+[1] BrainPrint: a discriminative characterization of brain morphology. Wachinger C, Golland P, Kremen W, Fischl B, Reuter M. Neuroimage. 2015;109:232-48. http://dx.doi.org/10.1016/j.neuroimage.2015.01.032 http://www.ncbi.nlm.nih.gov/pubmed/25613439
+
+[2] Laplace-Beltrami spectra as 'Shape-DNA' of surfaces and solids. Reuter M, Wolter F-E, Peinecke N Computer-Aided Design. 2006;38:342-366. http://dx.doi.org/10.1016/j.cad.2005.10.011

junifer/external/BrainPrint/brainprint/cli/__init__.py

@@ -0,0 +1,11 @@
+"""
+BrainPrint analysis CLI.
+"""
+from ..brainprint import run_brainprint
+from .parser import parse_options
+
+
+def main():
+    options = parse_options()
+    if options is not None:
+        return run_brainprint(**options)

junifer/external/BrainPrint/brainprint/cli/help_text.py

@@ -0,0 +1,169 @@
+"""
+Help text strings for the :mod:`brainprint.cli` module.
+"""
+CLI_DESCRIPTION: str = (
+    "This program conducts a brainprint analysis of FreeSurfer output."
+)
+
+
+SUBJECT_ID: str = (
+    "Subject ID (FreeSurfer processed directory inside the subjects directory)"
+)
+SUBJECTS_DIR: str = "FreeSurfer subjects directory"
+OUTPUT_DIRECTORY: str = "Output directory (default: <sdir>/<sid>/brainprint)"
+NUM: str = "Number of eigenvalues/vectors to compute (default: 50)"
+EVEC: str = "Switch on eigenvector computation (default: off)"
+SKIP_CORTEX: str = "Skip cortical surfaces (default: off)"
+NORM: str = "Eigenvalues normalization method (default: none)"
+REWEIGHT: str = "Switch on eigenvalue reweighting (default: off)"
+ASYM: str = "Switch on additional asymmetry calculation (default: off)"
+ASYM_DISTANCE: str = (
+    "Distance measurement to use for asymmetry calculation (default: euc)"
+)
+CHOLMOD: str = "Use cholesky decomposition (faster) instead of LU decomposition (slower). May require manual install of scikit-sparse library. Default is LU decomposition."
+KEEP_TEMP: str = (
+    "Whether to keep the temporary files directory or not, by default False"
+)
+HELP: str = "Display this help message and exit"
+MORE_HELP: str = "Display extensive help message and exit"
+
+HELPTEXT: str = """
+brainprint.py
+Author: Martin Reuter, 2015
+
+=======
+SUMMARY
+=======
+
+Computes the BrainPrint for a FreeSurfer subject.
+
+The BrainPrint consists of the shape descriptors (Shape-DNA) [1]
+of a selection of both cortical and subcortical structures [2].
+
+Here is a list of structures and FreeSurfer aseg label ids:
+
+CorpusCallosum                  [251, 252, 253, 254, 255]
+Cerebellum                      [7, 8, 16, 46, 47]
+Ventricles                      [4, 5, 14, 24, 31, 43, 44, 63]
+3rd-Ventricle                   [14, 24]
+4th-Ventricle                   15
+Brain-Stem                      16
+Left-Striatum                   [11, 12, 26]
+Left-Lateral-Ventricle          [4, 5, 31]
+Left-Cerebellum-White-Matter    7
+Left-Cerebellum-Cortex          8
+Left-Thalamus-Proper            10
+Left-Caudate                    11
+Left-Putamen                    12
+Left-Pallidum                   13
+Left-Hippocampus                17
+Left-Amygdala                   18
+Left-Accumbens-area             26
+Left-VentralDC                  28
+Right-Striatum                  [50, 51, 58]
+Right-Lateral-Ventricle         [43, 44, 63]
+Right-Cerebellum-White-Matter   46
+Right-Cerebellum-Cortex         47
+Right-Thalamus-Proper           49
+Right-Caudate                   50
+Right-Putamen                   51
+Right-Pallidum                  52
+Right-Hippocampus               53
+Right-Amygdala                  54
+Right-Accumbens-area            58
+Right-VentralDC                 60
+
+And the following cortical structures:
+
+lh-white-2d    (left white matter surface triangles)
+lh-pial-2d     (left pial surface triangles)
+rh-white-2d    (same for right hemisphere ...)
+rh-pial-2d
+
+Processing of the cortical structures can be skipped (--skipcortex).
+
+Implicit Inputs:
+The mri/aseg.mgz and mri/norm.mgz should be available.
+Also surf/?h.pial and surf/?h.white need to be
+available unless --skipcortex is passed. norm.mgz is not
+absolutely necessary but highly recommended to fix the labels
+and obtain improved meshes.
+
+Output:
+The brainprint CSV table containing column headers for the
+structures, a row of areas, a row of volumes and N rows of
+the first N eigenvalues for each structure. An additional
+output file will be created if the asymmetry calculation is
+performed.
+
+==================
+COMMAND-LINE USAGE
+==================
+
+python3 brainprint.py --sdir <directory> --sid <SubjectID>  [--num <num>]
+                    [--evec] [--skipcortex] [--norm <surface|volume|geometry|none> ]
+                    [--reweight] [--asymmetry] [--cholmod] [--outdir <directory>] 
+                    [--help] [--more-help]
+
+Options:
+    --help           Show this help message and exit
+    --more-help      Show extensive help message and exit
+
+Required options:
+    --sid <SubjectID>
+                    Subject ID (FreeSurfer-processed directory inside the
+                    subjects directory)
+    --sdir <directory>
+                    FreeSurfer subjects directory
+
+Processing directives:
+    --num <num>      Number of eigenvalues/vectors to compute (default: 50)
+    --evec           Switch on eigenvector computation (default: off)
+    --skipcortex     Skip cortical surfaces (default: off)
+    --norm <surface|volume|geometry|none>
+                     Switch on eigenvalue normalization; will be either surface,
+                     volume, or determined by the geometry of the object. Use
+                     "none" or leave out entirely to skip normalization.
+    --reweight       Switch on eigenvalue reweighting (default: off)
+    --asymmetry      Perform left-right asymmetry calculation (default: off)
+    --cholmod        Use cholesky decomposition (faster) instead of LU 
+                     decomposition (slower). May require manual install of the
+                     scikit-sparse library. Default is LU decomposition.
+
+Output parameters:
+    --outdir=OUTDIR  Output directory (default: <sdir>/<sid>/brainprint)
+
+============
+PYTHON USAGE
+============
+
+As an alternative to the command-line usage described above, individual
+functions can also be called within a Python environment as follows:
+
+import lapy
+from brainprint import brainprint
+brainprint.run_brainprint(subjects_dir="/my/subjects/directory", subject_id="my_subject_id")
+
+Additional options are num=<int>, evec=<bool>, skipcortex=<bool>,
+norm=<"surface"|"volume"|"geometry"|"none">, reweight=<bool>, and outdir=<string>.
+
+==========
+REFERENCES
+==========
+
+If used for a publication, please cite both [1] for the shape
+descriptor method and [2] for the application to brain MRI and
+definition of the BrainPrint.
+
+[1] M. Reuter, F.-E. Wolter and N. Peinecke.
+Laplace-Beltrami spectra as "Shape-DNA" of surfaces and solids.
+Computer-Aided Design 38 (4), pp.342-366, 2006.
+http://dx.doi.org/10.1016/j.cad.2005.10.011
+
+[2] C. Wachinger, P. Golland, W. Kremen, B. Fischl, M. Reuter.
+BrainPrint: A discriminative characterization of brain morphology.
+NeuroImage Volume 109, pp.232-248, 2015.
+http://dx.doi.org/10.1016/j.neuroimage.2015.01.032
+"""
+
+# flake8: noqa: E501