PyNutil 0.5.4__tar.gz → 0.6.1__tar.gz

pynutil-0.6.1/.gitattributes

@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto

pynutil-0.6.1/.github/workflows/benchmark.yml

@@ -0,0 +1,35 @@
+name: Benchmark
+
+on: [push, pull_request]
+
+jobs:
+  benchmark:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+
+    - name: Run benchmark
+      run: python benchmarks/benchmark.py 2>&1
+
+    - name: Write job summary
+      run: cat benchmarks/results.md >> "$GITHUB_STEP_SUMMARY"
+
+    - name: Upload benchmark results
+      uses: actions/upload-artifact@v4
+      with:
+        name: benchmark-results
+        path: |
+          benchmarks/results.md
+          benchmarks/results.json

pynutil-0.6.1/.github/workflows/build.yml

@@ -0,0 +1,110 @@
+name: Build Application
+
+on:
+  release:
+    types: [published]  # Only trigger on published releases
+  workflow_dispatch:  # Allow manual triggering
+
+# Add global permissions
+permissions:
+  contents: write
+  
+jobs:
+  build-windows:
+    runs-on: windows-latest
+    steps:
+    - uses: actions/checkout@v3
+    
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+        
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pyinstaller
+        pip install ".[gui]"
+    - name: Build with PyInstaller
+      run: |
+        pyinstaller --windowed --icon=gui/Logo_PyNutil.ico --name PyNutil gui/PyNutilGUI.py
+        
+    - name: Create Windows ZIP archive
+      run: |
+        cd dist
+        powershell Compress-Archive -Path PyNutil -DestinationPath PyNutil-Windows.zip
+        
+    - name: Upload Windows artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: PyNutil-Windows
+        path: dist/PyNutil-Windows.zip
+        retention-days: 5
+
+  build-macos:
+    runs-on: macos-latest
+    steps:
+    - uses: actions/checkout@v3
+    
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+        
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pyinstaller
+        pip install dmgbuild
+        pip install ".[gui]"
+    - name: Build with PyInstaller
+      run: |
+        # Build without specifying an icon for macOS to avoid format issues
+        pyinstaller --windowed --osx-bundle-identifier com.pynutil.app --name PyNutil gui/PyNutilGUI.py
+        
+    - name: Create DMG
+      run: |
+        pip install dmgbuild
+        cat > dmg_settings.py << EOF
+        app = 'dist/PyNutil.app'
+        appname = 'PyNutil'
+        format = 'UDBZ'
+        size = '500M'
+        files = [app]
+        symlinks = {'Applications': '/Applications'}
+        # Remove badge_icon to avoid icon format issues
+        icon_locations = {
+            appname + '.app': (140, 120),
+            'Applications': (360, 120)
+        }
+        background = 'builtin-arrow'
+        EOF
+        dmgbuild -s dmg_settings.py "PyNutil" "dist/PyNutil-macOS.dmg" || true
+        
+    - name: Upload DMG artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: PyNutil-macOS
+        path: dist/PyNutil-macOS.dmg
+        retention-days: 5
+
+  create-release:
+    needs: [build-windows, build-macos]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+        
+      - name: List downloaded artifacts
+        run: |
+          find . -type f | sort
+        
+      - name: Attach Artifacts to Release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: |
+            PyNutil-Windows/PyNutil-Windows.zip
+            PyNutil-macOS/PyNutil-macOS.dmg
+          token: ${{ github.token }}

pynutil-0.6.1/.github/workflows/main.yml

@@ -0,0 +1,21 @@
+name: Mirror to Ebrains
+
+on:
+  push:
+    branches: [ main ]
+
+
+jobs:
+  # set the job name
+  to_ebrains:
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: syncmain
+        uses: wei/git-sync@v3
+
+        with:
+          source_repo: "Neural-Systems-at-UIO/PyNutil"
+          source_branch: "main"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/polarbean/PyNutil.git"
+          destination_branch: "main"

pynutil-0.6.1/.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,30 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write  # Required for trusted publisher authentication
+      contents: read   # Required for checkout
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        verbose: true

pynutil-0.6.1/.github/workflows/tests.yml

@@ -0,0 +1,33 @@
+name: Run Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'  # Specify your Python version
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .
+
+    - name: Download atlas
+      run: |
+        brainglobe install -a allen_mouse_25um
+        
+    - name: Run tests
+      run: |
+        python -m unittest discover -s tests -v

pynutil-0.6.1/.gitignore

@@ -0,0 +1,177 @@
+dmg.py
+# dev environment
+.vscode
+.claude
+.complexipy_cache
+.# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+demo_data/*
+# C extensions
+*.so
+# WSL zone identifiers
+*:Zone.Identifier*
+*:encryptable*
+# 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/
+
+
+#inputs
+
+#outputs
+test_result/
+
+# Benchmark generated data
+benchmarks/results.json
+benchmarks/results.md

pynutil-0.6.1/MANIFEST.in

@@ -0,0 +1 @@
+prune tests

{pynutil-0.5.4 → pynutil-0.6.1}/PKG-INFO

@@ -1,9 +1,17 @@
 Metadata-Version: 2.4
 Name: PyNutil
-Version: 0.5.4
+Version: 0.6.1
 Summary: a package to quantify atlas registered brain data
-Home-page: https://github.com/Neural-Systems-at-UIO/PyNutil
-License: MIT
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/Neural-Systems-at-UIO/PyNutil
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
@@ -16,13 +24,10 @@ Requires-Dist: scipy
 Requires-Dist: nibabel
 Requires-Dist: orjson
 Requires-Dist: tqdm
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: license
+Requires-Dist: tifffile
+Provides-Extra: gui
+Requires-Dist: PyQt6; extra == "gui"
 Dynamic: license-file
-Dynamic: requires-dist
-Dynamic: summary
 
 # PyNutil
 
@@ -151,9 +156,6 @@ PyNutil is developed at the Neural Systems Laboratory at the Institute of Basic
 # Contributors
 Harry Carey, Sharon C Yates, Gergely Csucs, Arda Balkir, Ingvild Bjerke, Rembrandt Bakker, Nicolaas Groeneboom, Maja A Puchades, Jan G Bjaalie.
 
-# Licence
-GNU General Public License v3
-
 # Related articles
 Yates SC, Groeneboom NE, Coello C, et al. & Bjaalie JG (2019) QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front. Neuroinform. 13:75. https://doi.org/10.3389/fninf.2019.00075
 

{pynutil-0.5.4 → pynutil-0.6.1}/PyNutil/__init__.py

@@ -1,8 +1,11 @@
-from .results import AtlasData, ExtractionResult, PointSetResult
+from .results import AtlasData, ExtractionResult, PointSetResult, VolumeResult
 from .processing.adapters.base import RegistrationData
 from .processing.adapters import read_alignment
-from .io.atlas_loader import load_atlas_data, load_custom_atlas
+from .io.atlas_loader import load_custom_atlas
+from .image_series import Section, ImageSeries
 from .processing.pipeline.batch_processor import (
+    read_segmentation_dir,
+    read_image_dir,
     seg_to_coords,
     image_to_coords,
     xy_to_coords,
@@ -10,7 +13,7 @@ from .processing.pipeline.batch_processor import (
 from .processing.analysis.data_analysis import quantify_coords
 from .io.file_operations import save_analysis
 from .processing.section_volume import interpolate_volume
-from .io.volume_nifti import save_volume_niftis
+from .io.volume_nifti import save_volumes
 
 __all__ = [
     "AtlasData",
@@ -18,13 +21,17 @@ __all__ = [
     "PointSetResult",
     "RegistrationData",
     "read_alignment",
-    "load_atlas_data",
     "load_custom_atlas",
+    "Section",
+    "ImageSeries",
+    "read_segmentation_dir",
+    "read_image_dir",
     "seg_to_coords",
     "image_to_coords",
     "xy_to_coords",
     "quantify_coords",
     "save_analysis",
+    "VolumeResult",
     "interpolate_volume",
-    "save_volume_niftis",
+    "save_volumes",
 ]

{pynutil-0.5.4 → pynutil-0.6.1}/PyNutil/context.py

@@ -7,13 +7,15 @@ processing layers.
 from __future__ import annotations
 
 from dataclasses import dataclass
-from typing import List, Optional, Union
+from typing import TYPE_CHECKING, Optional
 
 import numpy as np
 import pandas as pd
 
 from .processing.adapters.base import SliceInfo
-from .processing.adapters.segmentation import SegmentationAdapter
+
+if TYPE_CHECKING:
+    from .processing.adapters.segmentation import SegmentationAdapter
 
 
 @dataclass(frozen=True)
@@ -30,16 +32,10 @@ class PipelineContext:
         3-D hemisphere mask (same shape as *atlas_volume*).
     segmentation_adapter : SegmentationAdapter
         Pre-resolved adapter for the current segmentation format.
-    non_linear : bool
-        Whether to apply non-linear deformation.
     object_cutoff : int
         Minimum connected-component area (binary pipeline).
-    use_flat : bool
-        If True, load flat-file atlas maps instead of slicing the volume.
     pixel_id : object
         Pixel colour to match, or ``"auto"`` for auto-detection.
-    apply_damage_mask : bool
-        Apply the damage / exclusion mask when available.
     intensity_channel : str or None
         Channel name for the intensity pipeline (``None`` in binary mode).
     min_intensity : int or None
@@ -52,12 +48,8 @@ class PipelineContext:
     atlas_volume: Optional[np.ndarray]
     hemi_map: Optional[np.ndarray]
     segmentation_adapter: SegmentationAdapter
-    non_linear: bool
     object_cutoff: int
-    use_flat: bool
     pixel_id: object
-    apply_damage_mask: bool
-    flat_label_path: Optional[str] = None
     intensity_channel: Optional[str] = None
     min_intensity: Optional[int] = None
     max_intensity: Optional[int] = None
@@ -70,12 +62,8 @@ class PipelineContext:
         atlas_labels,
         atlas_volume,
         hemi_map,
-        non_linear: bool,
         object_cutoff: int,
-        use_flat: bool,
         pixel_id,
-        apply_damage_mask: bool,
-        flat_label_path=None,
         intensity_channel=None,
         min_intensity=None,
         max_intensity=None,
@@ -88,12 +76,8 @@ class PipelineContext:
             atlas_volume=atlas_volume,
             hemi_map=hemi_map,
             segmentation_adapter=SegmentationAdapterRegistry.get(segmentation_format),
-            non_linear=non_linear,
             object_cutoff=object_cutoff,
-            use_flat=use_flat,
             pixel_id=pixel_id,
-            apply_damage_mask=apply_damage_mask,
-            flat_label_path=flat_label_path,
             intensity_channel=intensity_channel,
             min_intensity=min_intensity,
             max_intensity=max_intensity,
@@ -110,13 +94,13 @@ class SectionContext:
         Numeric section identifier matching the alignment JSON.
     slice_info : SliceInfo
         Registration data for this section (anchoring, deformation, damage …).
-    segmentation_path : str
-        Path to the segmentation / image file on disk.
-    flat_file_path : str or None
-        Path to the corresponding flat-file atlas, if any.
+    image : np.ndarray
+        Pre-loaded image array for this section.
+    filename : str
+        Source filename, used for output tracking (empty string if unknown).
     """
 
     section_number: int
     slice_info: SliceInfo
-    segmentation_path: str
-    flat_file_path: Optional[str] = None
+    image: np.ndarray
+    filename: str = ""

pynutil-0.6.1/PyNutil/image_series.py

@@ -0,0 +1,91 @@
+"""Image series and section data containers.
+
+These classes represent a series of sections (images or segmentations) to be
+processed through the PyNutil pipeline.  Users with custom segmentation types
+can construct :class:`Section` and :class:`ImageSeries` objects directly,
+providing their own ``numpy`` arrays instead of reading from disk.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Dict, List, Optional
+
+import numpy as np
+
+
+@dataclass
+class Section:
+    """A single section, identified by number and backed by an image.
+
+    Either *image* or *path* must be provided.  When only *path* is given the
+    image is loaded lazily the first time it is needed by the pipeline.
+
+    Parameters
+    ----------
+    section_number:
+        Numeric identifier that must match a section in the alignment JSON.
+    filename:
+        Display name used in :attr:`~PyNutil.ExtractionResult.section_filenames`.
+        Defaults to *path* when not set explicitly.
+    image:
+        Pre-loaded image array (2-D or 3-D ``numpy`` array).  Provide this
+        when you have already loaded or generated the image data yourself.
+    path:
+        Path to the image file on disk.  The image is loaded on demand by the
+        configured segmentation adapter when the section is processed.
+    """
+
+    section_number: int
+    filename: str = ""
+    image: Optional[np.ndarray] = field(default=None, repr=False)
+    path: Optional[str] = None
+
+    def get_image(self, adapter) -> np.ndarray:
+        """Return the image array, loading from *path* if not pre-loaded.
+
+        Parameters
+        ----------
+        adapter:
+            A :class:`~PyNutil.processing.adapters.segmentation.SegmentationAdapter`
+            used to load the file when *image* is ``None``.
+        """
+        if self.image is not None:
+            return self.image
+        if self.path is not None:
+            return adapter.load(self.path)
+        raise ValueError(
+            f"Section {self.section_number} has neither image data nor a file path."
+        )
+
+
+@dataclass
+class ImageSeries:
+    """An ordered collection of :class:`Section` objects.
+
+    Construct this directly when you want to supply custom image data, or use
+    :func:`~PyNutil.read_segmentation_dir` / :func:`~PyNutil.read_image_dir`
+    to build one from a folder of image files.
+
+    Parameters
+    ----------
+    sections:
+        Dictionary mapping ``section_number`` to :class:`Section` objects.
+    pixel_id:
+        RGB value (or label) identifying the segmented class of interest.
+        Set by :func:`~PyNutil.read_segmentation_dir` and consumed by
+        :func:`~PyNutil.seg_to_coords`.
+    segmentation_format:
+        Name of the segmentation adapter to use (e.g. ``"binary"`` or
+        ``"cellpose"``).  Set by :func:`~PyNutil.read_segmentation_dir` and
+        consumed by :func:`~PyNutil.seg_to_coords`.
+    """
+
+    sections: Dict[int, Section] = field(default_factory=dict)
+    pixel_id: object = field(default_factory=lambda: [0, 0, 0])
+    segmentation_format: str = "binary"
+
+    @property
+    def filenames(self) -> List[str]:
+        """Display filenames for all sections."""
+        return [s.filename for s in self.sections.values()]