Update cucim dependency for cucim transforms #2987
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wyli
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looks like there are some changes in the API? https://github.com/Project-MONAI/MONAI/pull/2987/checks?check_run_id=3663775638#step:7:14689
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@wyli I've been looking into this and it does not happen on my local with the same version of cucim. I re-ran the test to see if it persists. I'll further look into it once the tests are done. |
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I can confirm that there is no API changes. There is not any issue with our tests on actual TIF files. The issue is when we are using simple uncompressed TIF files that are crated using PIL. I'm contacting cucim development team to find a way out for our cucim tests. |
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@wyli as you mentioned there are two issues here:
The first one should be resolved by the new commits here. I had a meeting with cuCIM team and it seems the second issue is related to CUDA version, where cuCIM works with CUDA>11.0, thus #2999. |
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Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
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closing this in favor of #3006 |
auto-merge was automatically disabled
September 22, 2021 16:37
Pull request was closed
This was referenced Sep 28, 2021
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) - Add `cucim.is_available()` method Users can query if a specific module is available or not. For example, if cucim.clara module which requires C shared library is not available: ``` >>> import cucim >>> cucim.is_available() False >>> cucim.is_available("skimage") True >>> cucim.is_available("core") True >>> cucim.is_available("clara") False ``` Resolves #104 Supports Project-MONAI/MONAI#2987 Authors: - Gigon Bae (https://github.com/gigony) Approvers: - Gregory R. Lee (https://github.com/grlee77) - https://github.com/jakirkham URL: #107
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Due to #17 ([BUG] Compression scheme 33003 tile decoding is not implemented), #19 (Check compression method used in the image) was merged so cuCIM has been handling only particular formats (only jpeg/deflate-compressed image). If the input TIFF image has no-compressed RAW tile image, cuCIM showed the following error message: > RuntimeError: This format (compression: 1, sample_per_pixel: 1, planar_config: 1, photometric: 1) is not supported yet!. https://github.com/Project-MONAI/MONAI/pull/2987/checks?check_run_id=3667530814#step:7:15641 This patch is to support raw RGB tiled TIFF with fast-path, re-allowing non-compressed image with slow-path (in case the input is not tiled RGB image). This supports Project-MONAI/MONAI#2987. Authors: - Gigon Bae (https://github.com/gigony) Approvers: - Gregory R. Lee (https://github.com/grlee77) - https://github.com/jakirkham URL: #108
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Description
This PR updates the cucim dependency to support cuCIM Transforms.
Status
Ready
Types of changes