📝 Update 05-patch-prediction notebook for the New API#977
📝 Update 05-patch-prediction notebook for the New API#977shaneahmed merged 21 commits intodev-define-engines-abcfrom
05-patch-prediction notebook for the New API#977Conversation
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## dev-define-engines-abc #977 +/- ##
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Coverage 95.30% 95.30%
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Lines 9945 9955 +10
Branches 1280 1280
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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
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| 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 |
# Conflicts: # tiatoolbox/models/engine/patch_predictor.py
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Summary
This PR updates the patch‑prediction example to align with the new
PatchPredictorengine and fixes a long‑standing issue inEngineABCrelated to model‑attribute retrieval when usingDataParallel.What’s Changed
🔧 Example Notebook Updates
examples/05-patch-prediction.ipynbto use the newPatchPredictorengine API.🐛 EngineABC Bug Fix
EngineABCwhere model attributes were incorrectly retrieved from aDataParallelwrapper._get_model_attr()to safely unwrap the underlying model when needed.Why This Matters
Testing