PyNutil 0.5.3__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-0.5.3 → pynutil-0.6.1}/PKG-INFO

@@ -1,9 +1,17 @@
 Metadata-Version: 2.4
 Name: PyNutil
-Version: 0.5.3
+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
@@ -16,17 +24,16 @@ 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
 
-## PyNutil is still under development and the API is subject to change 
+> [!WARNING]  
+> PyNutil is still under development and the API is subject to change.
+
 
 PyNutil is a Python library for brain-wide quantification and spatial analysis of features in serial section images from the brain. It aims to replicate the Quantifier feature of the Nutil software (RRID: SCR_017183). 
 
@@ -71,37 +78,31 @@ As input, PyNutil requires:
 3. A segmentation file for each brain section with the features to be quantified displayed with a unique RGB colour code (it currently accepts many image formats: png, jpg, jpeg, etc).
 
 ```python
-from PyNutil import PyNutil
-
-"""
-Here we define a quantifier object
-The segmentations should be images which come out of ilastik, segmenting objects-of-interest
-The alignment json should be from DeepSlice, QuickNII, or VisuAlign, it defines the sections position in an atlas
-The colour says which colour is the object you want to quantify in your segmentation. It is defined in RGB
-Finally the atlas name is the relevant atlas from brainglobe_atlasapi or a custom atlas in nrrd format.
-
-basic_example.py (brainglobe_atlasapi)
-basic_example_custom_atlas.py (custom atlas)
-
-"""
-pnt = PyNutil(
-    segmentation_folder='../tests/test_data/non_linear_allen_mouse/segmentations/',
-    alignment_json='../tests/test_data/non_linear_allen_mouse/alignment.json',
-    colour=[0, 0, 0],
-    atlas_name='allen_mouse_25um'
-    #If you would like to use cellpose segmentations add:
-    #segmentation_format = 'cellpose'
+from brainglobe_atlasapi import BrainGlobeAtlas
+import PyNutil as pnt
+
+# Load an atlas (BrainGlobe) and alignment
+atlas = BrainGlobeAtlas("allen_mouse_25um")
+alignment = pnt.read_alignment("path/to/alignment.json")
+
+# Extract coordinates from segmentations
+coords = pnt.seg_to_coords(
+    "path/to/segmentations/",
+    alignment,
+    atlas,
+    pixel_id=[0, 0, 0],
+    # For cellpose segmentations: segmentation_format="cellpose"
 )
 
-#optionally, if you want to generate a 3D heatmap
-pnt.interpolate_volume()
-
-pnt.get_coordinates(object_cutoff=0)
-
-pnt.quantify_coordinates()
+# Quantify by atlas region
+label_df = pnt.quantify_coords(coords, atlas)
 
-pnt.save_analysis("PyNutil/test_result/myResults")
+# Save results
+pnt.save_analysis("path/to/output", coords, atlas, label_df=label_df)
 ```
+
+For custom atlases (not from BrainGlobe), use `pnt.load_custom_atlas()` instead.
+See `demos/basic_example.py` and `demos/basic_example_custom_atlas.py` for complete examples.
 PyNutil generates a series of reports in the folder which you specify.
 
 ## Per-Hemisphere Quantification
@@ -155,9 +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-0.6.1/PyNutil/__init__.py

@@ -0,0 +1,37 @@
+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_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,
+)
+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_volumes
+
+__all__ = [
+    "AtlasData",
+    "ExtractionResult",
+    "PointSetResult",
+    "RegistrationData",
+    "read_alignment",
+    "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_volumes",
+]

{pynutil-0.5.3 → pynutil-0.6.1}/PyNutil/config.py

@@ -1,9 +1,10 @@
 from __future__ import annotations
 
-import json
 from dataclasses import dataclass
 from typing import Any, Dict, Optional
 
+from .io.loaders import load_json_file
+
 
 @dataclass
 class PyNutilConfig:
@@ -25,8 +26,7 @@ class PyNutilConfig:
 
     @classmethod
     def from_settings_file(cls, settings_file: str) -> "PyNutilConfig":
-        with open(settings_file, "r") as f:
-            settings = json.load(f)
+        settings = load_json_file(settings_file)
         return cls.from_settings_dict(settings)
 
     @classmethod

{pynutil-0.5.3 → 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
@@ -52,16 +48,41 @@ 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
 
+    @classmethod
+    def from_format(
+        cls,
+        *,
+        segmentation_format: str,
+        atlas_labels,
+        atlas_volume,
+        hemi_map,
+        object_cutoff: int,
+        pixel_id,
+        intensity_channel=None,
+        min_intensity=None,
+        max_intensity=None,
+    ) -> "PipelineContext":
+        """Construct a PipelineContext, resolving *segmentation_format* to an adapter."""
+        from .processing.adapters.segmentation import SegmentationAdapterRegistry
+
+        return cls(
+            atlas_labels=atlas_labels,
+            atlas_volume=atlas_volume,
+            hemi_map=hemi_map,
+            segmentation_adapter=SegmentationAdapterRegistry.get(segmentation_format),
+            object_cutoff=object_cutoff,
+            pixel_id=pixel_id,
+            intensity_channel=intensity_channel,
+            min_intensity=min_intensity,
+            max_intensity=max_intensity,
+        )
+
 
 @dataclass(frozen=True)
 class SectionContext:
@@ -73,13 +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 = ""