Split transform #4153
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Split transform #4153
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* Redesign BaseWSIReader, WSIReader, CuCIMWSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add image mode for output validation Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update references to new WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove legacy WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update unittests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * sort imports Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Clean up imports Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs and docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix a typo Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove redundant checking Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update read and other methods Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update wsireader to support multi image and update docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Make workaround for CuImage objects Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for multi image reading Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update a note about cucim Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update type hints and docstrings 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>
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>
Nic-Ma
reviewed
Apr 21, 2022
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>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Member
Author
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Any other comments, @Nic-Ma? Thanks |
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Member
Author
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Thank you @Nic-Ma! It just need a /build! |
Contributor
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/build |
1 similar comment
Contributor
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/build |
Contributor
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Hi @drbeh , The Blossom CI failed due to these cuCIM / tifffile errors: Could you please help take a look? Thanks. |
Contributor
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BTW, I saw you added new test files as "XXX_new.py", would you rename the file name later to remove the "_new" postfix? Thanks. |
Contributor
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Hi @drbeh , Above CI tests error is because Thanks. |
Contributor
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/build |
wyli
added a commit
that referenced
this pull request
Apr 26, 2022
* 4095 Add bundle download (#4114) * draft download Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update bundle download Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add url and load Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename args and remove a few places Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix flake8 issue Signed-off-by: Yiheng Wang <vennw@nvidia.com> * enhance with reviews Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add instantiate for load Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix black error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add unittest Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add load to docs Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add skip Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add schemaerror Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix partial places Signed-off-by: Yiheng Wang <vennw@nvidia.com> * download zip bundle Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [DLMED] restore Exception for test Signed-off-by: Nic Ma <nma@nvidia.com> * update ts features Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add config_files test case Signed-off-by: Yiheng Wang <vennw@nvidia.com> * enhance docstring example for args_file Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> * Disable pylint error and fix CI tests of new tifffile (#4162) * workaround Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix tifffile issue Signed-off-by: Nic Ma <nma@nvidia.com> * Fixed an error in DiNTS model implementation and enabled act and norm layer options (#4157) * fixed a bug Signed-off-by: dongy <dongy@nvidia.com> * autofix Signed-off-by: dongy <dongy@nvidia.com> * update test case Signed-off-by: dongy <dongy@nvidia.com> Co-authored-by: dongy <dongy@nvidia.com> * Split transform (#4153) * Redesign whole slide image reading (#4107) * Redesign BaseWSIReader, WSIReader, CuCIMWSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add image mode for output validation Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update references to new WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove legacy WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update unittests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * sort imports Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Clean up imports Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs and docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix a typo Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove redundant checking Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update read and other methods Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update wsireader to support multi image and update docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Make workaround for CuImage objects Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for multi image reading Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update a note about cucim Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update type hints and docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Implement Split transform Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update formatting Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Implement SplitDict Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for SplitDict Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove images from docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Address all comments Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add example and size check Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Revert references to new wsireader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add missing comma Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * fix bundle download test issue (#4169) Signed-off-by: Yiheng Wang <vennw@nvidia.com> * 4094 Enhance `ckpt_export` to save config files (#4159) * [DLMED] enhance checkpoint export Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * Move RGB/RGBA checks to base class (#4171) Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> * [CICD] To support temp dgx runner (#4175) * Support new temp dgx runner Signed-off-by: Peixin Li <pxli@nyu.edu> * atol 1e-5 Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> * Test fix for AMP kwargs (#4178) Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: dongyang0122 <don.yang.mech@gmail.com> Co-authored-by: dongy <dongy@nvidia.com> Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Peixin <pxli@nyu.edu> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Can-Zhao
pushed a commit
to Can-Zhao/MONAI
that referenced
this pull request
May 10, 2022
* Redesign whole slide image reading (Project-MONAI#4107) * Redesign BaseWSIReader, WSIReader, CuCIMWSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add image mode for output validation Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update references to new WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove legacy WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update unittests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * sort imports Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Clean up imports Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs and docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix a typo Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove redundant checking Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update read and other methods Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update wsireader to support multi image and update docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Make workaround for CuImage objects Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for multi image reading Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update a note about cucim Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update type hints and docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Implement Split transform Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update formatting Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Implement SplitDict Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for SplitDict Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove images from docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Address all comments Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add example and size check Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Revert references to new wsireader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add missing comma Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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Fixes #4013
Description
Implement
Splittransform that splits an image based on a grid. This transform is particularly useful in pathology pipelines.Status
Ready/Work in progress/Hold
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.