GridPatch with both count and threshold filtering

[drbeh]

Fixes #6049

Description

This PR add support to GridPatch for both filtering by count and threshold. When filtering by threshold, the num_patches will be treated as maximum number of patches.

UPDATE: It also removes the deprecated argument of skimage.measure.regionprops, 'coordinates', which was causing some test to fail.

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.

[drbeh]

@kenza-bouzid @KumoLiu could you please let me know if you have any other comment? Otherwise, we can merge this PR. @wyli @Nic-Ma

[wyli]

/build

[kenza-bouzid]

LGTM!

[wyli]

thanks, I'm merging this for now, please follow up if you have any concerns @Nic-Ma @KumoLiu

[kenza-bouzid]

@drbeh what is the timeline for this feature to be released?

[drbeh]

@drbeh what is the timeline for this feature to be released?

Hi @kenza-bouzid, it is merged and is the dev branch of MONAI (and the next weekly release) but it will be released in v1.2 which is due in about a month.

[kenza-bouzid]

Hi @drbeh I am trying to install a version of MONAI that includes this fix
microsoft/hi-ml#834
But my Docker image build fails with the following error:

  Running command git clone -q https://github.com/Project-MONAI/MONAI.git /tmp/pip-req-build-injno4yb
  Running command git checkout -q 958aac78ab8130517638a47175571e081ae03aee
  ERROR: Command errored out with exit status 1:
   command: /azureml-envs/azureml_6f4ca4ccd5cfecbee0a7e6231b99b5fc/bin/python /azureml-envs/azureml_6f4ca4ccd5cfecbee0a7e6231b99b5fc/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /tmp/tmpq3ubf06k
       cwd: /tmp/pip-req-build-injno4yb
  Complete output (36 lines):
  Please set environment variable `BUILD_MONAI=1` to enable Cpp/CUDA extension build.
  BUILD_MONAI_CPP=False, BUILD_MONAI_CUDA=False, TORCH_VERSION=0.
  Traceback (most recent call last):
    File "/tmp/pip-build-env-axzysf86/overlay/lib/python3.9/site-packages/torch/__init__.py", line 172, in _load_global_deps
      ctypes.CDLL(lib_path, mode=ctypes.RTLD_GLOBAL)
    File "/azureml-envs/azureml_6f4ca4ccd5cfecbee0a7e6231b99b5fc/lib/python3.9/ctypes/__init__.py", line 382, in __init__
      self._handle = _dlopen(self._name, mode)
  OSError: /tmp/pip-build-env-axzysf86/overlay/lib/python3.9/site-packages/torch/lib/../../nvidia/cublas/lib/libcublas.so.11: undefined symbol: cublasLtGetStatusString, version libcublasLt.so.11

Any idea how to fix this? I am relying on AzureML environment build so I can't easily set extra environment variables.

The latest available release is 1.1.0 https://pypi.org/project/monai/#history you mentioned a weekly release, is it a different dev package?

[drbeh]

Hi @kenza-bouzid,
I am not sure what's the source of the error that you get but maybe a weekly pypi build would be an easier option for the meantime. You can find the monai-weekly here: https://pypi.org/project/monai-weekly/, which is built every Saturday.
The latest version monai-weekly==1.2.dev2310 (built on March 4) should include the changes that you need. Please let me know if you encounter any problem.

[kenza-bouzid]

@drbeh, the weekly pipy build is working fine. Thank you!