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Address a removed monai function, fix CUDA 11 runtime lib, and resurrect option to omit or not DICOM SEG empty frame #471

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merged 4 commits into from
Nov 17, 2023

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@MMelQin MMelQin commented Nov 16, 2023

This PR expanded from its initial scope to include addition changes required.

  • first is to update the code where the MONAI Core transforms function AddChannel is imported and used, namely in the MedNIST and Nuance PIN integration example applications. MONAI Core 1.3 was release in mid Oct, 2003, and the aforementioned function was removed, and EnsureChannelFirst function is to be used. Most examples had already been updated to make use the new function, except the aforementioned ones.
  • second is that the in PR triggered Github CI actions, pytype check failed due to failure to find libcudart.so.11.0 when importing holoscan. Limiting torch to v2.0.1 to piggyback on ii to find CUDA runtime lib did not work, and had to explicitly export LD_LIBRARY_PATH pointing to the Python version specific site-packages folder.
  • third is that the DICOM Seg Writer in App SDK v0.6 somehow omitted the option of include empty frame. Added it back in, but since it is an built-in operator in the App SDK package, won't be effective until the next release of the SDK.

@MMelQin MMelQin force-pushed the mqin/update_mednist_app branch from 456aacd to 88b1e73 Compare November 17, 2023 01:55
@MMelQin MMelQin force-pushed the mqin/update_mednist_app branch from 88b1e73 to c59a088 Compare November 17, 2023 01:59
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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
7.7% 7.7% Duplication

@MMelQin MMelQin changed the title Updated the code where a deprecated monai core function is used. Address a removed monai function, fix CUDA 11 runtime lib, and resurrect option to omit or not DICOM SEG empty frame Nov 17, 2023
@MMelQin MMelQin linked an issue Nov 17, 2023 that may be closed by this pull request
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MMelQin commented Nov 17, 2023

Did the final changes and review with @gigony together, so a separate review in not needed.

@MMelQin MMelQin merged commit d159cb5 into main Nov 17, 2023
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Error with monai.transforms AddChannel
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