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Update SmartCachePatchWSIDataset and add unittests#1853

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bhashemian merged 6 commits intoProject-MONAI:masterfrom
bhashemian:smartcache_wsi_dataset_unittests
Mar 27, 2021
Merged

Update SmartCachePatchWSIDataset and add unittests#1853
bhashemian merged 6 commits intoProject-MONAI:masterfrom
bhashemian:smartcache_wsi_dataset_unittests

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Description

Turn shuffling off for SmartCachePatchWSIDataset, since PatchWSIDataset object does not support item assignment, and added unittests for SmartCachePatchWSIDataset.

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 bhashemian requested review from Nic-Ma and wyli March 26, 2021 00:52
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@Nic-Ma Nic-Ma left a comment

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Thanks for your quick update.
Looks good to me.
Could you please also add a test case to run your SmartCachePatchWSIDataset with SmartCacheHandler to make sure it can work well with our workflows?

Thanks.

@bhashemian bhashemian enabled auto-merge (squash) March 26, 2021 13:36
@bhashemian bhashemian disabled auto-merge March 26, 2021 13:48
@bhashemian
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Thanks for your quick update.
Looks good to me.
Could you please also add a test case to run your SmartCachePatchWSIDataset with SmartCacheHandler to make sure it can work well with our workflows?

Thanks.

Thanks @Nic-Ma ,
Using SmartCacheHandler requires to use a MONAI engine like SupervisedTraining, right? Is there any simpler way to test it?
I have already tested it with pathology MMAR and it worked.

@Nic-Ma
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Nic-Ma commented Mar 26, 2021

Thanks for your quick update.
Looks good to me.
Could you please also add a test case to run your SmartCachePatchWSIDataset with SmartCacheHandler to make sure it can work well with our workflows?
Thanks.

Thanks @Nic-Ma ,
Using SmartCacheHandler requires to use a MONAI engine like SupervisedTraining, right? Is there any simpler way to test it?
I have already tested it with pathology MMAR and it worked.

Hi @behxyz ,

You can refer to this test program: https://github.com/Project-MONAI/MONAI/blob/master/tests/test_handler_smartcache.py

Thanks.

@bhashemian
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Thanks for your quick update.
Looks good to me.
Could you please also add a test case to run your SmartCachePatchWSIDataset with SmartCacheHandler to make sure it can work well with our workflows?
Thanks.

Thanks @Nic-Ma ,
Using SmartCacheHandler requires to use a MONAI engine like SupervisedTraining, right? Is there any simpler way to test it?
I have already tested it with pathology MMAR and it worked.

Hi @behxyz ,

You can refer to this test program: https://github.com/Project-MONAI/MONAI/blob/master/tests/test_handler_smartcache.py

Thanks.

@Nic-Ma, I need to finish all the other pathology components by the end of week and I've got a lot on my plate. I'll go back to it after that if you don't mind.

@Nic-Ma
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Nic-Ma commented Mar 26, 2021

Thanks for your quick update.
Looks good to me.
Could you please also add a test case to run your SmartCachePatchWSIDataset with SmartCacheHandler to make sure it can work well with our workflows?
Thanks.

Thanks @Nic-Ma ,
Using SmartCacheHandler requires to use a MONAI engine like SupervisedTraining, right? Is there any simpler way to test it?
I have already tested it with pathology MMAR and it worked.

Hi @behxyz ,
You can refer to this test program: https://github.com/Project-MONAI/MONAI/blob/master/tests/test_handler_smartcache.py
Thanks.

@Nic-Ma, I need to finish all the other pathology components by the end of week and I've got a lot on my plate. I'll go back to it after that if you don't mind.

Sure, sounds good.
Thanks.

@bhashemian bhashemian enabled auto-merge (squash) March 26, 2021 15:00
@bhashemian bhashemian disabled auto-merge March 26, 2021 21:13
@bhashemian bhashemian enabled auto-merge (squash) March 26, 2021 21:13
wyli
wyli previously requested changes Mar 26, 2021
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@bhashemian
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could you please address https://github.com/Project-MONAI/MONAI/pull/1853/files#r602317744 in this PR?

@wyli, I'll do it later in another PR since it affects almost all the pathology related unittests. It's on my to-do list.

@wyli wyli dismissed their stale review March 27, 2021 02:10

will be addressed in a follow up

@bhashemian bhashemian merged commit c157fb8 into Project-MONAI:master Mar 27, 2021
@bhashemian bhashemian deleted the smartcache_wsi_dataset_unittests branch March 27, 2021 03:02
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3 participants