PatchWSIDataset by bhashemian · Pull Request #1835 · Project-MONAI/MONAI

bhashemian · 2021-03-24T02:40:56Z

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.

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

bhashemian · 2021-03-24T21:33:25Z

@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!

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

wyli

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

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

bhashemian · 2021-03-25T04:19:05Z

@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?

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

rijobro · 2021-03-25T08:43:12Z

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.

move init docstring to class docstring

Nic-Ma

Looks good to me.
Thanks.

bhashemian added 12 commits March 22, 2021 23:51

Implement PatchWSIDataset and SmartCachePathWSIDataset

f929e98

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Remove label preprocessing and adopt new type of inputs

ea0b515

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Update type hints

1d7ec17

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Add init file

9065fe0

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Change grid_size to grid_shape

ce4150d

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Add a unittest for PatchWSIDataset

f2c8306

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Add more unittests

3506740

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Update docstrings and make minor changes

d81ef16

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Convert labels to numpy to match the change in dataset

472c421

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Update location from center to corner

79c35b5

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Update unittests locations from center to corner

c8542bd

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Update docs for pathology datasets

854ceb5

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

bhashemian requested review from Nic-Ma and wyli March 24, 2021 02:43

Merge branch 'master' into behrooz_patch_wsi_dataset

f4285ae

bhashemian removed request for Nic-Ma and wyli March 24, 2021 03:20

Update type hint and doc

c9ffa44

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

bhashemian commented Mar 24, 2021

View reviewed changes

Comment thread monai/apps/pathology/datasets.py Outdated

Nic-Ma reviewed Mar 24, 2021

View reviewed changes

Comment thread docs/source/apps.rst Outdated

Comment thread monai/apps/pathology/datasets.py Outdated

bhashemian added 3 commits March 24, 2021 14:26

Merge branch 'behrooz_patch_wsi_dataset' into behrooz_patch_wsi_dataset

0910e21

Update docstrings

96b6df5

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Format docstring

2d56c98

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

bhashemian requested review from Nic-Ma and wyli March 24, 2021 22:07

bhashemian added 2 commits March 24, 2021 22:34

Update length of the smartcache dataset

de3b67b

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Add unittest for SmartCachePatchWSIDataset

ef8daf9

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

wyli reviewed Mar 24, 2021

View reviewed changes

Minor changes and fixes

3f130f0

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

bhashemian added 4 commits March 24, 2021 20:18

Add unnittest for OpenSlide option

9c4e158

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Add new line

27aac0c

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Merge branch 'master' into behrooz_patch_wsi_dataset

eae7b3c

Remove SmartCachePatchWSIDataset test to fix it

11210d4

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

move init docstring to class docstring

7ec1e50

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Merge pull request #3 from rijobro/behrooz_patch_wsi_dataset

59f6ff4

move init docstring to class docstring

Nic-Ma approved these changes Mar 25, 2021

View reviewed changes

Merge branch 'master' into behrooz_patch_wsi_dataset

d99d41b

wyli enabled auto-merge (squash) March 25, 2021 14:49

bhashemian disabled auto-merge March 25, 2021 16:21

bhashemian enabled auto-merge (squash) March 25, 2021 16:22

bhashemian merged commit 7e7cd94 into Project-MONAI:master Mar 25, 2021

bhashemian deleted the behrooz_patch_wsi_dataset branch March 25, 2021 18:04

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PatchWSIDataset#1835

PatchWSIDataset#1835
bhashemian merged 27 commits into
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bhashemian:behrooz_patch_wsi_dataset

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