WSIReader read by power and mpp #6244

drbeh · 2023-03-27T14:32:08Z

Description

This PR enable WSIReader to be provided with objective power and resolution (micron per pixel) to decide which WSI level to load. It also set absolute and relative tolerances for power and mpp.

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
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 --disttests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

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

monai/data/wsi_reader.py

tests/test_wsireader.py

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

…-mpp

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

for more information, see https://pre-commit.ci

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

…-mpp

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

monai/data/wsi_reader.py

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

drbeh · 2023-04-04T00:49:51Z

@Nic-Ma @wyli please let me know if you have any other comments. Otherwise, this PR is ready to be merged. Thanks

monai/data/wsi_reader.py

wyli · 2023-04-04T10:13:49Z

this missing piece is an option for handling the resampling e.g. when the requested exact mpp is not available. could you please add this?

@wyli that's correct! We have discussed about it in the pathology working group few weeks ago and we decided not to include resampling in this PR and leave it as a feature request for the future since it requires some decision on how and when exactly to do resampling.

so in that case this PR wouldn't close #4980 as the description suggested?

drbeh · 2023-04-04T14:15:01Z

this missing piece is an option for handling the resampling e.g. when the requested exact mpp is not available. could you please add this?

@wyli that's correct! We have discussed about it in the pathology working group few weeks ago and we decided not to include resampling in this PR and leave it as a feature request for the future since it requires some decision on how and when exactly to do resampling.

so in that case this PR wouldn't close #4980 as the description suggested?

Fair enough! I'll make it clear in a separate issue.

wyli

thanks, it looks good to me now

sorry I thought it was updated

wyli · 2023-04-04T17:41:52Z

cc @cooperlab @gigony @manthey @shaneahmed from the original feature request in case they are interested in sharing some comments

drbeh · 2023-04-04T18:03:57Z

cc @cooperlab @gigony @manthey @shaneahmed from the original feature request in case they are interested in sharing some comments

@wyli as I said we all have already discussed about this in our pathology WG so please be respectful of people's time and do not solicit their comments if not necessary.

wyli · 2023-04-04T18:28:03Z

@wyli as I said we all have already discussed about this in our pathology WG so please be respectful of people's time and do not solicit their comments if not necessary.

thanks, I couldn't find any documentation/discussion about the proposed interfaces as recommended in rapidsai/cucim#389

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

…-mpp

drbeh · 2023-04-04T18:54:14Z

@wyli as I said we all have already discussed about this in our pathology WG so please be respectful of people's time and do not solicit their comments if not necessary.

thanks, I couldn't find any documentation/discussion about the proposed interfaces as recommended in rapidsai/cucim#389

I believe what you are referring to is not related to this PR. As you correctly spotted, this PR is not addressing #4980, which is related to that cucim feature request. This PR is now closing this feature request #6289. Please let me know if you have any question.

wyli · 2023-04-04T21:34:04Z

@wyli as I said we all have already discussed about this in our pathology WG so please be respectful of people's time and do not solicit their comments if not necessary.

thanks, I couldn't find any documentation/discussion about the proposed interfaces as recommended in rapidsai/cucim#389

I believe what you are referring to is not related to this PR. As you correctly spotted, this PR is not addressing #4980, which is related to that cucim feature request. This PR is now closing this feature request #6289. Please let me know if you have any question.

I saw that you have edited ticket #6289 to have the opposite meaning, I kind of agree more with the previous edit...

drbeh · 2023-04-05T13:35:24Z

I saw that you have edited ticket #6289 to have the opposite meaning, I kind of agree more with the previous edit...

@wyli I have reverted the update to the issue. Please take another look and let me know if all is good with you for this PR to me merged. Thanks

drbeh · 2023-04-06T16:41:12Z

@wyli @Nic-Ma if there is not any other comments, we should be able to merge this PR. Thanks

Nic-Ma · 2023-04-06T23:55:28Z

@wyli @Nic-Ma if there is not any other comments, we should be able to merge this PR. Thanks

I already approved the PR before, @wyli Do you have any other comments?

Thanks.

wyli · 2023-04-11T11:51:23Z

/build

drbeh added 11 commits February 9, 2023 10:09

Implement read by magnification power and mpp

008ed39

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

update defaults and comments

622b19a

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

merge dev

10c39af

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

update defaults and add test cases

01e7687

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

update error msg:

1814396

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

Merge branch 'dev' of github.com:Project-MONAI/MONAI into wsireader-mpp

8a3d66f

formatting

67ce0cb

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

arrange params

c5bf655

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

micor docstring update

82da62e

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

update docstring

008f9dc

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

add defaults

cfd20e1

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

drbeh marked this pull request as ready for review March 27, 2023 23:03

drbeh requested review from wyli, KumoLiu and Nic-Ma March 27, 2023 23:04

Merge branch 'dev' into wsireader-mpp

d2595ef

atbenmurray mentioned this pull request Mar 28, 2023

update docstring and eval with overrides #6241

Closed

7 tasks

KumoLiu reviewed Mar 28, 2023

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drbeh and others added 8 commits March 29, 2023 10:06

update mpp, power and add several unittests to cover them

b4c2dd1

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

Merge branch 'wsireader-mpp' of github.com:drbeh/MONAI into wsireader…

8894dbd

…-mpp

remove redundant check

3d2ad49

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

[pre-commit.ci] auto fixes from pre-commit.com hooks

45145aa

for more information, see https://pre-commit.ci

update unit tests with new wsi key

91da7d7

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

Merge branch 'wsireader-mpp' of github.com:drbeh/MONAI into wsireader…

93ae205

…-mpp

update docsting and mmp for cucim

db809dc

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

update docstring

20180dc

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drbeh requested a review from KumoLiu March 29, 2023 20:10

Merge branch 'dev' into wsireader-mpp

ac1e7d6

KumoLiu reviewed Mar 30, 2023

View reviewed changes

address comments

d757ee8

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

correct removed files

0a46908

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

Merge branch 'dev' into wsireader-mpp

1a1757e

drbeh mentioned this pull request Apr 4, 2023

Fix redundancy in test WSI image #5878

Closed

1 task

wyli reviewed Apr 4, 2023

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Merge branch 'dev' into wsireader-mpp

ad20310

drbeh linked an issue Apr 4, 2023 that may be closed by this pull request

WSIReader support for reading by existing power and mpp #6289

Closed

wyli previously approved these changes Apr 4, 2023

View reviewed changes

drbeh added 2 commits April 4, 2023 14:43

simplify find closest level

ce8c49a

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

Merge branch 'wsireader-mpp' of github.com:drbeh/MONAI into wsireader…

8094e03

…-mpp

Merge branch 'dev' into wsireader-mpp

9529e98

drbeh enabled auto-merge (squash) April 5, 2023 18:29

drbeh disabled auto-merge April 5, 2023 18:29

drbeh enabled auto-merge (squash) April 5, 2023 18:30

Merge branch 'dev' into wsireader-mpp

3779bff

Merge branch 'dev' into wsireader-mpp

d7e61ae

drbeh merged commit 0a29bc1 into Project-MONAI:dev Apr 11, 2023

drbeh deleted the wsireader-mpp branch April 11, 2023 13:17

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WSIReader read by power and mpp #6244

WSIReader read by power and mpp #6244

drbeh commented Mar 27, 2023 •

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wyli commented Apr 11, 2023

WSIReader read by power and mpp #6244

WSIReader read by power and mpp #6244

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drbeh commented Mar 27, 2023 • edited Loading

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