wsi-toolbox 0.2.0__py3-none-any.whl

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Files changed (30) hide show
  1. wsi_toolbox/__init__.py +122 -0
  2. wsi_toolbox/app.py +874 -0
  3. wsi_toolbox/cli.py +599 -0
  4. wsi_toolbox/commands/__init__.py +66 -0
  5. wsi_toolbox/commands/clustering.py +198 -0
  6. wsi_toolbox/commands/data_loader.py +219 -0
  7. wsi_toolbox/commands/dzi.py +160 -0
  8. wsi_toolbox/commands/patch_embedding.py +196 -0
  9. wsi_toolbox/commands/pca.py +206 -0
  10. wsi_toolbox/commands/preview.py +394 -0
  11. wsi_toolbox/commands/show.py +171 -0
  12. wsi_toolbox/commands/umap_embedding.py +174 -0
  13. wsi_toolbox/commands/wsi.py +223 -0
  14. wsi_toolbox/common.py +148 -0
  15. wsi_toolbox/models.py +30 -0
  16. wsi_toolbox/utils/__init__.py +109 -0
  17. wsi_toolbox/utils/analysis.py +174 -0
  18. wsi_toolbox/utils/hdf5_paths.py +232 -0
  19. wsi_toolbox/utils/plot.py +227 -0
  20. wsi_toolbox/utils/progress.py +207 -0
  21. wsi_toolbox/utils/seed.py +26 -0
  22. wsi_toolbox/utils/st.py +55 -0
  23. wsi_toolbox/utils/white.py +121 -0
  24. wsi_toolbox/watcher.py +256 -0
  25. wsi_toolbox/wsi_files.py +619 -0
  26. wsi_toolbox-0.2.0.dist-info/METADATA +253 -0
  27. wsi_toolbox-0.2.0.dist-info/RECORD +30 -0
  28. wsi_toolbox-0.2.0.dist-info/WHEEL +4 -0
  29. wsi_toolbox-0.2.0.dist-info/entry_points.txt +3 -0
  30. wsi_toolbox-0.2.0.dist-info/licenses/LICENSE +21 -0
wsi_toolbox/__init__.py ADDED
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+ """
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+ WSI-toolbox: Whole Slide Image analysis toolkit
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+
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+ A comprehensive toolkit for WSI processing, feature extraction, and clustering.
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+
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+ Basic Usage:
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+ >>> import wsi_toolbox as wt
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+ >>>
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+ >>> # Convert WSI to HDF5
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+ >>> cmd = wt.Wsi2HDF5Command(patch_size=256)
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+ >>> result = cmd('input.ndpi', 'output.h5')
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+ >>>
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+ >>> # Extract features with preset model
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+ >>> wt.set_default_model_preset('uni')
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+ >>> wt.set_default_device('cuda')
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+ >>> emb_cmd = wt.PatchEmbeddingCommand(batch_size=256)
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+ >>> emb_result = emb_cmd('output.h5')
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+ >>>
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+ >>> # Clustering
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+ >>> cluster_cmd = wt.ClusteringCommand(resolution=1.0)
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+ >>> cluster_result = cluster_cmd(['output.h5'])
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+ >>>
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+ >>> # UMAP
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+ >>> umap_cmd = wt.UmapCommand()
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+ >>> umap_result = umap_cmd('output.h5')
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+ """
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+
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+ # Version info
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+ __version__ = "0.1.0"
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+
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+ # Configuration
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+ # Commands
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+ from .commands import (
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+ ClusteringCommand,
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+ DziCommand,
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+ PatchEmbeddingCommand,
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+ PreviewClustersCommand,
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+ PreviewLatentClusterCommand,
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+ PreviewLatentPCACommand,
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+ PreviewScoresCommand,
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+ ShowCommand,
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+ Wsi2HDF5Command,
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+ )
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+ from .commands.clustering import ClusteringResult
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+ from .commands.patch_embedding import PatchEmbeddingResult
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+ from .commands.pca import PCACommand
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+ from .commands.umap_embedding import UmapCommand
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+
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+ # Command result types
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+ from .commands.wsi import Wsi2HDF5Result
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+ from .common import (
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+ create_default_model,
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+ get_config,
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+ set_default_device,
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+ set_default_model,
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+ set_default_model_preset,
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+ set_default_progress,
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+ set_verbose,
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+ )
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+
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+ # Models
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+ from .models import (
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+ MODEL_NAMES,
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+ create_foundation_model,
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+ )
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+
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+ # Utility functions
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+ from .utils.analysis import leiden_cluster, reorder_clusters_by_pca
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+
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+ # WSI file classes
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+ from .wsi_files import (
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+ NativeLevel,
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+ OpenSlideFile,
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+ PyramidalTiffFile,
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+ PyramidalWSIFile,
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+ StandardImage,
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+ WSIFile,
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+ create_wsi_file,
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+ )
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+
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+ __all__ = [
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+ # Version
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+ "__version__",
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+ # Configuration functions
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+ "get_config",
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+ "set_default_progress",
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+ "set_default_model",
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+ "set_default_model_preset",
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+ "create_default_model",
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+ "set_default_device",
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+ "set_verbose",
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+ # Commands
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+ "Wsi2HDF5Command",
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+ "PatchEmbeddingCommand",
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+ "ClusteringCommand",
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+ "UmapCommand",
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+ "PCACommand",
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+ "PreviewClustersCommand",
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+ "PreviewScoresCommand",
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+ "PreviewLatentPCACommand",
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+ "PreviewLatentClusterCommand",
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+ "ShowCommand",
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+ "DziCommand",
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+ # Result types
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+ "Wsi2HDF5Result",
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+ "PatchEmbeddingResult",
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+ "ClusteringResult",
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+ # WSI files
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+ "WSIFile",
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+ "PyramidalWSIFile",
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+ "NativeLevel",
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+ "OpenSlideFile",
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+ "PyramidalTiffFile",
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+ "StandardImage",
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+ "create_wsi_file",
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+ # Models
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+ "MODEL_NAMES",
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+ "create_foundation_model",
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+ # Utilities
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+ "leiden_cluster",
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+ "reorder_clusters_by_pca",
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+ ]