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PatchWSIDataset#1835

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bhashemian merged 27 commits intoProject-MONAI:masterfrom
bhashemian:behrooz_patch_wsi_dataset
Mar 25, 2021
Merged

PatchWSIDataset#1835
bhashemian merged 27 commits intoProject-MONAI:masterfrom
bhashemian:behrooz_patch_wsi_dataset

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@bhashemian bhashemian commented Mar 24, 2021 •
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Description

It adds two datasets for pathology use cases: PatchWSIDataset and SmartCachePatchWSIDataset. They extract patches on a grid from whole slide images and associate them with their corresponding labels.

Status

Ready

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

bhashemian added 12 commits March 22, 2021 23:51
@bhashemian
Implement PatchWSIDataset and SmartCachePathWSIDataset
f929e98 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Remove label preprocessing and adopt new type of inputs
ea0b515 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update type hints
1d7ec17 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add init file
9065fe0 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Change grid_size to grid_shape
ce4150d 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add a unittest for PatchWSIDataset
f2c8306 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add more unittests
3506740 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update docstrings and make minor changes
d81ef16 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Convert labels to numpy to match the change in dataset
472c421 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update location from center to corner
79c35b5 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update unittests locations from center to corner
c8542bd 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update docs for pathology datasets
854ceb5 
Signed-off-by: Behrooz <[email protected]>
@bhashemian bhashemian requested review from Nic-Ma and wyli March 24, 2021 02:43
@bhashemian bhashemian removed request for Nic-Ma and wyli March 24, 2021 03:20
bhashemian
bhashemian commented Mar 24, 2021
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bhashemian commented Mar 24, 2021 •
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@wyli @Nic-Ma , do you know what the problem is here? https://github.com/Project-MONAI/MONAI/pull/1835/checks?check_run_id=2188219644#step:7:217

/home/runner/work/MONAI/MONAI/monai/apps/pathology/datasets.py:docstring of monai.apps.pathology.datasets.SmartCachePatchWSIDataset:37: WARNING: Unexpected indentation.
/home/runner/work/MONAI/MONAI/monai/apps/pathology/datasets.py:docstring of monai.apps.pathology.datasets.SmartCachePatchWSIDataset:38: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/MONAI/MONAI/monai/apps/pathology/datasets.py:docstring of monai.apps.pathology.datasets.SmartCachePatchWSIDataset:44: WARNING: Definition list ends without a blank line; unexpected unindent.

It seems that it is somehow related to SmartCacheDataset in class SmartCachePatchWSIDataset(SmartCacheDataset) because if I change it to class SmartCachePatchWSIDataset(Dataset), the doc compilation warning goes away!

@bhashemian bhashemian requested review from Nic-Ma and wyli March 24, 2021 22:07
wyli
wyli reviewed Mar 24, 2021
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thanks! I put some minor comments inline. I couldn't figure out the docstring errors... any idea? @Nic-Ma @rijobro @ericspod

https://github.com/Project-MONAI/MONAI/pull/1835/checks?check_run_id=2188647158

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bhashemian commented Mar 25, 2021

@wyli @Nic-Ma , do you know what the problem is here? https://github.com/Project-MONAI/MONAI/pull/1835/checks?check_run_id=2188219644#step:7:217

/home/runner/work/MONAI/MONAI/monai/apps/pathology/datasets.py:docstring of monai.apps.pathology.datasets.SmartCachePatchWSIDataset:37: WARNING: Unexpected indentation.
/home/runner/work/MONAI/MONAI/monai/apps/pathology/datasets.py:docstring of monai.apps.pathology.datasets.SmartCachePatchWSIDataset:38: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/MONAI/MONAI/monai/apps/pathology/datasets.py:docstring of monai.apps.pathology.datasets.SmartCachePatchWSIDataset:44: WARNING: Definition list ends without a blank line; unexpected unindent.

It seems that it is somehow related to SmartCacheDataset in class SmartCachePatchWSIDataset(SmartCacheDataset) because if I change it to class SmartCachePatchWSIDataset(Dataset), the doc compilation warning goes away!

@Nic-Ma @rijobro @ericspod Any thought on this?

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rijobro commented Mar 25, 2021 •
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I've created a PR to your branch @behxyz (didn't have push privilege). Think there was a problem in the docstring of the constructor of the inherited class. Solved the problem by moving that docstring inside the classes main docstring.

PR: bhashemian#3.

@bhashemian
Merge pull request #3 from rijobro/behrooz_patch_wsi_dataset
59f6ff4 
move init docstring to class docstring
Nic-Ma
Nic-Ma approved these changes Mar 25, 2021
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Looks good to me.
Thanks.

@wyli wyli enabled auto-merge (squash) March 25, 2021 14:49
@bhashemian bhashemian disabled auto-merge March 25, 2021 16:21
@bhashemian bhashemian enabled auto-merge (squash) March 25, 2021 16:22
@bhashemian bhashemian merged commit 7e7cd94 into Project-MONAI:master Mar 25, 2021
@bhashemian bhashemian deleted the behrooz_patch_wsi_dataset branch March 25, 2021 18:04
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