wsi-toolbox 0.1.0__py3-none-any.whl

wsi_toolbox-0.1.0.dist-info/METADATA

@@ -0,0 +1,269 @@
+Metadata-Version: 2.4
+Name: wsi-toolbox
+Version: 0.1.0
+Summary: A comprehensive toolkit for Whole Slide Image processing, feature extraction, and clustering analysis
+Project-URL: Homepage, https://github.com/endaaman/wsi-toolbox
+Project-URL: Repository, https://github.com/endaaman/wsi-toolbox
+Project-URL: Documentation, https://github.com/endaaman/wsi-toolbox/blob/master/README.md
+Author-email: Ken Enda <ken@endaaman.com>
+License: MIT License
+        
+        Copyright (c) 2025 Ken Enda
+        
+        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.
+License-File: LICENSE
+Keywords: clustering,deep-learning,histopathology,pathology,wsi
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.11
+Requires-Dist: h5py>=3.13.0
+Requires-Dist: hdbscan>=0.8.40
+Requires-Dist: imagecodecs>=2024.12.30
+Requires-Dist: joblib>=1.4.2
+Requires-Dist: leidenalg>=0.10.2
+Requires-Dist: matplotlib>=3.9.4
+Requires-Dist: networkx>=3.3
+Requires-Dist: numpy<2
+Requires-Dist: opencv-python-headless>=4.11.0.86
+Requires-Dist: openpyxl>=3.1.5
+Requires-Dist: openslide-python>=1.4.1
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: pillow>=11.0.0
+Requires-Dist: pydantic-autocli>=0.1.4
+Requires-Dist: pydantic>=2.10.6
+Requires-Dist: pyqt6>=6.8.1
+Requires-Dist: python-igraph>=0.11.8
+Requires-Dist: rich>=14.0.0
+Requires-Dist: scikit-learn>=1.6.1
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: streamlit-aggrid>=0.3.4.post3
+Requires-Dist: streamlit-antd-components>=0.3.2
+Requires-Dist: streamlit>=1.43.2
+Requires-Dist: taskipy>=1.14.1
+Requires-Dist: tifffile>=2025.2.18
+Requires-Dist: timm>=0.9.16
+Requires-Dist: torch>=2.5.1
+Requires-Dist: torchvision>=0.20.1
+Requires-Dist: umap-learn>=0.5.7
+Requires-Dist: zarr>=3
+Provides-Extra: build
+Requires-Dist: packaging; extra == 'build'
+Requires-Dist: setuptools; extra == 'build'
+Requires-Dist: torch; extra == 'build'
+Requires-Dist: wheel; extra == 'build'
+Provides-Extra: compile
+Requires-Dist: flash-attn; extra == 'compile'
+Description-Content-Type: text/markdown
+
+# WSI Toolbox
+
+A comprehensive toolkit for Whole Slide Image (WSI) processing, feature extraction, and clustering analysis.
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install wsi-toolbox
+```
+
+### For development
+
+```bash
+# Clone repository
+git clone https://github.com/endaaman/WSI-toolbox.git
+cd WSI-toolbox
+
+# Install dependencies
+uv sync
+```
+
+**Note**: For gigapath slide-level encoder (CLI only), install manually:
+```bash
+pip install git+https://github.com/prov-gigapath/prov-gigapath.git@5d77be0
+pip install flash-attn einops fairscale
+```
+
+## Quick Start
+
+### As a Python Library
+
+```python
+import wsi_toolbox as wt
+
+# Basic workflow
+wt.set_default_model('uni')
+cmd = wt.Wsi2HDF5Command(patch_size=256)
+result = cmd('input.ndpi', 'output.h5')
+```
+
+**See [README_API.md](README_API.md) for comprehensive API documentation** (detailed examples, command patterns, utilities, etc.)
+
+### As a CLI Tool
+
+```bash
+# Convert WSI to HDF5
+wsi-toolbox wsi2h5 --in input.ndpi --out output.h5 --patch-size 256
+
+# Extract features
+wsi-toolbox embed --in output.h5 --model uni
+
+# Clustering
+wsi-toolbox cluster --in output.h5 --resolution 1.0
+
+# For all commands
+wsi-toolbox --help
+```
+
+### Streamlit Web Application
+
+```bash
+uv run task app
+```
+
+## HDF5 File Structure
+
+WSI-toolbox stores all data in a single HDF5 file:
+
+```python
+# Core data
+'patches'                      # Patch images: [N, H, W, 3], e.g., [3237, 256, 256, 3]
+'coordinates'                  # Patch pixel coordinates: [N, 2]
+
+# Metadata
+'metadata/original_mpp'        # Original microns per pixel
+'metadata/original_width'      # Original image width (level=0)
+'metadata/original_height'     # Original image height (level=0)
+'metadata/image_level'         # Image level used (typically 0)
+'metadata/mpp'                 # Output patch MPP
+'metadata/scale'               # Scale factor
+'metadata/patch_size'          # Patch size (e.g., 256)
+'metadata/patch_count'         # Total patch count
+'metadata/cols'                # Grid columns
+'metadata/rows'                # Grid rows
+
+# Model features (per model: uni, gigapath, virchow2)
+'{model}/features'             # Patch features: [N, D]
+                               #   uni: [N, 1024]
+                               #   gigapath: [N, 1536]
+                               #   virchow2: [N, 2560]
+'{model}/latent_features'      # Latent features (optional): [N, K, K, D]
+'{model}/clusters'             # Cluster labels: [N]
+
+# Gigapath slide-level (CLI only)
+'gigapath/slide_feature'       # Slide-level features: [768]
+```
+
+## Features
+
+- WSI processing (.ndpi, .svs, .tiff → HDF5)
+- Feature extraction (UNI, Gigapath, Virchow2)
+- Leiden clustering with UMAP visualization
+- Preview generation (cluster overlays, latent PCA)
+- Type-safe command pattern with Pydantic results
+- CLI, Python API, and Streamlit GUI
+
+## Documentation
+
+- [API Guide](README_API.md) - Comprehensive Python API documentation (日本語)
+- [CLAUDE.md](CLAUDE.md) - Development guidelines
+
+## Development
+
+### Setup Development Environment
+
+```bash
+# Clone repository
+git clone https://github.com/endaaman/wsi-toolbox.git
+cd wsi-toolbox
+
+# Install all dependencies
+uv sync
+
+# Install with optional gigapath support
+uv sync --extra gigapath
+
+# Install build tools
+uv sync --group build
+```
+
+### Run Tests and Development Tools
+
+```bash
+# Run CLI
+uv run wsi-toolbox --help
+
+# Run Streamlit app
+uv run task app
+
+# Run watcher
+uv run task watcher
+```
+
+### Build and Deploy
+
+#### Build Package
+
+```bash
+# Clean previous builds
+uv run task clean
+
+# Build package
+uv run task build
+# or
+python -m build
+
+# Check package integrity
+uv run task check
+# or
+python -m twine check dist/*
+```
+
+#### Deploy to PyPI
+
+**Prerequisites**: Install build tools first
+```bash
+uv sync --group build
+```
+
+**Deploy**:
+```bash
+# Using deploy script (recommended)
+./deploy.sh
+
+# Or manually
+python -m build
+python -m twine check dist/*
+python -m twine upload dist/*
+```
+
+**Note**: Configure your PyPI credentials before deploying:
+```bash
+# Create ~/.pypirc with your API token
+# Or use environment variables
+export TWINE_USERNAME=__token__
+export TWINE_PASSWORD=<your-pypi-token>
+```
+
+## License
+
+MIT

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wsi_toolbox-0.1.0.dist-info/WHEEL

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+Generator: hatchling 1.27.0
+Root-Is-Purelib: true
+Tag: py3-none-any

wsi_toolbox-0.1.0.dist-info/entry_points.txt

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+[console_scripts]
+wsi-toolbox = wsi_toolbox.cli:main

wsi_toolbox-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Ken Enda
+
+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.