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Fixes #4154

Description

This PR implement OpenSlideWSIReader, which read patches from whole slide images using openslide library in the back.

Status

Ready

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>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian requested a review from Nic-Ma April 20, 2022 20:12
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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@Nic-Ma Nic-Ma left a comment

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Looks good to me except for some minor comments inline.

Thanks.

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian self-assigned this Apr 21, 2022
@bhashemian bhashemian linked an issue Apr 21, 2022 that may be closed by this pull request
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@bhashemian bhashemian enabled auto-merge (squash) April 21, 2022 21:54
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@Nic-Ma can you /build here? Thanks

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Nic-Ma commented Apr 22, 2022

/build

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Nic-Ma commented Apr 22, 2022

/build

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Nic-Ma commented Apr 22, 2022

/build

@pxLi
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pxLi commented Apr 22, 2022

/build

@bhashemian bhashemian merged commit ed70e11 into Project-MONAI:dev Apr 22, 2022
@bhashemian bhashemian deleted the openslide-new branch April 25, 2022 14:58
Can-Zhao pushed a commit to Can-Zhao/MONAI that referenced this pull request May 10, 2022
* Implement WSIReader with OpenSlide backend .

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

* Add unittest for openslide

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

* Add docs

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

* formatting

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

* Update imports and few fixes

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

* Fix x,y in docstrings

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

* Address comments

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

* Remove x and y

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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Successfully merging this pull request may close these issues.

Docstrings in wsi_reader.py are not consistent Add OpenSlide support for new WSIReader

3 participants