wsi-toolbox 0.1.0__py3-none-any.whl

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Files changed (25) hide show
  1. wsi_toolbox/__init__.py +119 -0
  2. wsi_toolbox/app.py +753 -0
  3. wsi_toolbox/cli.py +485 -0
  4. wsi_toolbox/commands/__init__.py +92 -0
  5. wsi_toolbox/commands/clustering.py +214 -0
  6. wsi_toolbox/commands/dzi_export.py +202 -0
  7. wsi_toolbox/commands/patch_embedding.py +199 -0
  8. wsi_toolbox/commands/preview.py +335 -0
  9. wsi_toolbox/commands/wsi.py +196 -0
  10. wsi_toolbox/exp.py +466 -0
  11. wsi_toolbox/models.py +38 -0
  12. wsi_toolbox/utils/__init__.py +153 -0
  13. wsi_toolbox/utils/analysis.py +127 -0
  14. wsi_toolbox/utils/cli.py +25 -0
  15. wsi_toolbox/utils/helpers.py +57 -0
  16. wsi_toolbox/utils/progress.py +206 -0
  17. wsi_toolbox/utils/seed.py +21 -0
  18. wsi_toolbox/utils/st.py +53 -0
  19. wsi_toolbox/watcher.py +261 -0
  20. wsi_toolbox/wsi_files.py +187 -0
  21. wsi_toolbox-0.1.0.dist-info/METADATA +269 -0
  22. wsi_toolbox-0.1.0.dist-info/RECORD +25 -0
  23. wsi_toolbox-0.1.0.dist-info/WHEEL +4 -0
  24. wsi_toolbox-0.1.0.dist-info/entry_points.txt +2 -0
  25. wsi_toolbox-0.1.0.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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+ >>> wt.set_default_progress('tqdm')
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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
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+ >>> wt.set_default_model('gigapath')
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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, use_umap=True)
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+ >>> cluster_result = cluster_cmd(['output.h5'])
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+ >>>
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+ >>> # Plot UMAP
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+ >>> umap_embs = cluster_cmd.get_umap_embeddings()
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+ >>> fig = wt.plot_umap(umap_embs, cluster_cmd.total_clusters)
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+ >>> fig.savefig('umap.png')
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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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+ # Commands
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+ from .commands import (
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+ # Configuration
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+ set_default_progress,
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+ set_default_model,
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+ set_default_device,
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+ set_verbose,
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+
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+ # Main commands
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+ Wsi2HDF5Command,
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+ PatchEmbeddingCommand,
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+ ClusteringCommand,
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+
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+ # Preview commands
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+ PreviewClustersCommand,
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+ PreviewScoresCommand,
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+ PreviewLatentPCACommand,
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+ PreviewLatentClusterCommand,
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+
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+ # Export commands
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+ DziExportCommand,
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+ )
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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 .commands.patch_embedding import PatchEmbeddingResult
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+ from .commands.clustering import ClusteringResult
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+
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+ # WSI file classes
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+ from .wsi_files import (
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+ WSIFile,
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+ OpenSlideFile,
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+ TiffFile,
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+ StandardImage,
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+ create_wsi_file,
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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_LABELS,
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+ create_model,
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+ )
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+
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+ # Utility functions
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+ from .utils import plot_umap
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+ from .utils.analysis import leiden_cluster
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+
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+ __all__ = [
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+ # Version
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+ '__version__',
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+
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+ # Configuration functions
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+ 'set_default_progress',
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+ 'set_default_model',
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+ 'set_default_device',
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+ 'set_verbose',
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+
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+ # Commands
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+ 'Wsi2HDF5Command',
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+ 'PatchEmbeddingCommand',
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+ 'ClusteringCommand',
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+ 'PreviewClustersCommand',
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+ 'PreviewScoresCommand',
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+ 'PreviewLatentPCACommand',
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+ 'PreviewLatentClusterCommand',
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+ 'DziExportCommand',
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+
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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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+
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+ # WSI files
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+ 'WSIFile',
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+ 'OpenSlideFile',
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+ 'TiffFile',
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+ 'StandardImage',
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+ 'create_wsi_file',
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+
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+ # Models
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+ 'MODEL_LABELS',
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+ 'create_model',
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+
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+ # Utilities
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+ 'plot_umap',
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+ 'leiden_cluster',
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+ ]