📝 Update 05-patch-prediction notebook for the New API
#977
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## dev-define-engines-abc #977 +/- ##
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- Coverage 95.18% 95.15% -0.03%
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Files 77 77
Lines 9689 9699 +10
Branches 1255 1255
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+ Hits 9222 9229 +7
- Misses 431 434 +3
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…es model attributes regardless of DataParallel wrapping
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shaneahmed
changed the title
05-patch-prediction notebook to Make it Compatible with the New Engines API
shaneahmed
changed the title
05-patch-prediction notebook to Make it Compatible with the New Engines API05-patch-prediction notebook for the New API
| """Return a model attribute, unwrapping DataParallel if required.""" | ||
| try: | ||
| return getattr(self.model, attr_name) | ||
| except AttributeError: |
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| except AttributeError: | |
| except AttributeError: # pragma: no cover |
| """ | ||
| for path in files: | ||
| notebook = json.loads(path.read_text()) | ||
| with Path.open(path, encoding="utf-8", errors="ignore") as f: |
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| with Path.open(path, encoding="utf-8", errors="ignore") as f: | |
| notebook = json.loads(path.read_text()) |
| for path in files: | ||
| notebook = json.loads(path.read_text()) | ||
| with Path.open(path, encoding="utf-8", errors="ignore") as f: | ||
| notebook = json.load(f) |
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| notebook = json.load(f) |
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View / edit / reply to this conversation on ReviewNB shaneahmed commented on 2025-12-19T11:40:55Z zarr_output = zarr.open("path/to/zarr", mode="r")
predictions = {}
for key in zarr_output: predictions[key]=da.from_zarr(zarr_output[key})
_ = predictor.save_predictions(predictions, output_type="annotation_store") |
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View / edit / reply to this conversation on ReviewNB shaneahmed commented on 2025-12-19T11:40:55Z Line #2. tiatoolbox visualize --slides ./tmp/slides --overlays ./tmp/wsi_predictions_annotationstore/ |
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View / edit / reply to this conversation on ReviewNB shaneahmed commented on 2025-12-19T11:45:19Z Add class_dict for visualization |
Updates examples/05-patch-prediction.ipynb to match the new PatchPredictor engine, and adds a new “Visualize in TIAViz” section so readers can inspect results directly using TIAViz.
Fixes the EngineABC's model-attribute retrieval bug, so it unwraps DataParallel models when needed (using "_get_model_attr()"); this removes the previous multi-GPU crashes caused by attributes living on the wrapped module.