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@KumoLiu KumoLiu commented Apr 25, 2025

remove deprecated functionality

Part of #8421

Description

Removed Functionality:

  • metrics: Removed compute_percent_hausdorff_distance. Use compute_hausdorff_distance with the percentile argument instead.
  • bundle: Removed net_name, net_kwargs, and return_state_dict arguments from load(). Use the model argument for network instantiation.
  • bundle: Removed workflow argument from BundleWorkflow and ConfigWorkflow. Use workflow_type instead.
  • networks: Removed img_size argument from SwinUNETR. Input size checks are now performed during forward().

Default Value Changes:

  • GeneralizedDiceScore: Changed default reduction from MEAN_BATCH to MEAN.
  • CropForeground / CropForegroundd: Changed default allow_smaller from True to False.
  • get_mask_edges: Changed default always_return_as_numpy from True to False.
  • generate_spatial_bounding_box: Changed default allow_smaller from True to False.

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • 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.

KumoLiu and others added 5 commits April 25, 2025 21:55
remove deprecated functionality

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
@KumoLiu KumoLiu requested a review from ericspod April 27, 2025 09:13
KumoLiu added 2 commits April 27, 2025 17:15
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
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KumoLiu commented May 8, 2025

/build

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KumoLiu commented May 9, 2025

Error log:

[2025-05-08T08:11:12.365Z] ======================================================================
[2025-05-08T08:11:12.365Z] ERROR: test_get_history (tests.integration.test_auto3dseg_hpo.TestHPO)
[2025-05-08T08:11:12.365Z] ----------------------------------------------------------------------
[2025-05-08T08:11:12.365Z] Traceback (most recent call last):
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/integration/test_auto3dseg_hpo.py", line 180, in test_get_history
[2025-05-08T08:11:12.365Z]     NNIGen().run_algo(obj_filename, self.work_dir)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/auto3dseg/hpo_gen.py", line 233, in run_algo
[2025-05-08T08:11:12.365Z]     self.algo.train(self.params)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/auto3dseg/bundle_gen.py", line 300, in train
[2025-05-08T08:11:12.365Z]     return self._run_cmd(cmd)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/auto3dseg/bundle_gen.py", line 277, in _run_cmd
[2025-05-08T08:11:12.365Z]     return run_cmd(cmd.split(), run_cmd_verbose=True, env=ps_environ, check=True)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/utils/misc.py", line 892, in run_cmd
[2025-05-08T08:11:12.365Z]     return subprocess.run(cmd_list, **kwargs)
[2025-05-08T08:11:12.365Z]   File "/usr/lib/python3.10/subprocess.py", line 526, in run
[2025-05-08T08:11:12.365Z]     raise CalledProcessError(retcode, process.args,
[2025-05-08T08:11:12.365Z] subprocess.CalledProcessError: Command '['python', '/tmp/tmpz6gujw0_/workdir/swinunetr_0_override_None/scripts/train.py', 'run', "--config_file='/tmp/tmpz6gujw0_/workdir/swinunetr_0_override_None/configs/hyper_parameters.yaml,/tmp/tmpz6gujw0_/workdir/swinunetr_0_override_None/configs/network.yaml,/tmp/tmpz6gujw0_/workdir/swinunetr_0_override_None/configs/transforms_infer.yaml,/tmp/tmpz6gujw0_/workdir/swinunetr_0_override_None/configs/transforms_train.yaml,/tmp/tmpz6gujw0_/workdir/swinunetr_0_override_None/configs/transforms_validate.yaml'"]' returned non-zero exit status 1.
[2025-05-08T08:11:12.365Z] 
[2025-05-08T08:11:12.365Z] ======================================================================
[2025-05-08T08:11:12.365Z] ERROR: test_run_algo (tests.integration.test_auto3dseg_hpo.TestHPO)
[2025-05-08T08:11:12.365Z] ----------------------------------------------------------------------
[2025-05-08T08:11:12.365Z] Traceback (most recent call last):
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/integration/test_auto3dseg_hpo.py", line 148, in test_run_algo
[2025-05-08T08:11:12.365Z]     NNIGen().run_algo(obj_filename, self.work_dir)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/auto3dseg/hpo_gen.py", line 233, in run_algo
[2025-05-08T08:11:12.365Z]     self.algo.train(self.params)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/auto3dseg/bundle_gen.py", line 300, in train
[2025-05-08T08:11:12.365Z]     return self._run_cmd(cmd)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/auto3dseg/bundle_gen.py", line 277, in _run_cmd
[2025-05-08T08:11:12.365Z]     return run_cmd(cmd.split(), run_cmd_verbose=True, env=ps_environ, check=True)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/utils/misc.py", line 892, in run_cmd
[2025-05-08T08:11:12.365Z]     return subprocess.run(cmd_list, **kwargs)
[2025-05-08T08:11:12.365Z]   File "/usr/lib/python3.10/subprocess.py", line 526, in run
[2025-05-08T08:11:12.365Z]     raise CalledProcessError(retcode, process.args,
[2025-05-08T08:11:12.365Z] subprocess.CalledProcessError: Command '['python', '/tmp/tmpg8livo0_/workdir/swinunetr_0_override_None/scripts/train.py', 'run', "--config_file='/tmp/tmpg8livo0_/workdir/swinunetr_0_override_None/configs/hyper_parameters.yaml,/tmp/tmpg8livo0_/workdir/swinunetr_0_override_None/configs/network.yaml,/tmp/tmpg8livo0_/workdir/swinunetr_0_override_None/configs/transforms_infer.yaml,/tmp/tmpg8livo0_/workdir/swinunetr_0_override_None/configs/transforms_train.yaml,/tmp/tmpg8livo0_/workdir/swinunetr_0_override_None/configs/transforms_validate.yaml'"]' returned non-zero exit status 1.
[2025-05-08T08:11:12.365Z] 
[2025-05-08T08:11:12.365Z] ======================================================================
[2025-05-08T08:11:12.365Z] ERROR: test_run_optuna (tests.integration.test_auto3dseg_hpo.TestHPO)
[2025-05-08T08:11:12.365Z] ----------------------------------------------------------------------
[2025-05-08T08:11:12.365Z] Traceback (most recent call last):
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/integration/test_auto3dseg_hpo.py", line 163, in test_run_optuna
[2025-05-08T08:11:12.365Z]     study.optimize(
[2025-05-08T08:11:12.365Z]   File "/usr/local/lib/python3.10/dist-packages/optuna/study/study.py", line 475, in optimize
[2025-05-08T08:11:12.365Z]     _optimize(
[2025-05-08T08:11:12.365Z]   File "/usr/local/lib/python3.10/dist-packages/optuna/study/_optimize.py", line 63, in _optimize
[2025-05-08T08:11:12.365Z]     _optimize_sequential(
[2025-05-08T08:11:12.365Z]   File "/usr/local/lib/python3.10/dist-packages/optuna/study/_optimize.py", line 160, in _optimize_sequential
[2025-05-08T08:11:12.365Z]     frozen_trial = _run_trial(study, func, catch)
[2025-05-08T08:11:12.365Z]   File "/usr/local/lib/python3.10/dist-packages/optuna/study/_optimize.py", line 248, in _run_trial
[2025-05-08T08:11:12.365Z]     raise func_err
[2025-05-08T08:11:12.365Z]   File "/usr/local/lib/python3.10/dist-packages/optuna/study/_optimize.py", line 197, in _run_trial
[2025-05-08T08:11:12.365Z]     value_or_values = func(trial)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/auto3dseg/hpo_gen.py", line 338, in __call__
[2025-05-08T08:11:12.365Z]     self.run_algo(obj_filename, output_folder, template_path)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/auto3dseg/hpo_gen.py", line 396, in run_algo
[2025-05-08T08:11:12.365Z]     self.algo.train(self.params)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/auto3dseg/bundle_gen.py", line 300, in train
[2025-05-08T08:11:12.365Z]     return self._run_cmd(cmd)
[2025-05-08T08:11:12.365Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/auto3dseg/bundle_gen.py", line 277, in _run_cmd
[2025-05-08T08:11:12.365Z]     return run_cmd(cmd.split(), run_cmd_verbose=True, env=ps_environ, check=True)
[2025-05-08T08:11:12.366Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/utils/misc.py", line 892, in run_cmd
[2025-05-08T08:11:12.366Z]     return subprocess.run(cmd_list, **kwargs)
[2025-05-08T08:11:12.366Z]   File "/usr/lib/python3.10/subprocess.py", line 526, in run
[2025-05-08T08:11:12.366Z]     raise CalledProcessError(retcode, process.args,
[2025-05-08T08:11:12.366Z] subprocess.CalledProcessError: Command '['python', '/tmp/tmpjt2los39/optuna_test/swinunetr_0_override_learning_rate_0.01/scripts/train.py', 'run', "--config_file='/tmp/tmpjt2los39/optuna_test/swinunetr_0_override_learning_rate_0.01/configs/hyper_parameters.yaml,/tmp/tmpjt2los39/optuna_test/swinunetr_0_override_learning_rate_0.01/configs/network.yaml,/tmp/tmpjt2los39/optuna_test/swinunetr_0_override_learning_rate_0.01/configs/transforms_infer.yaml,/tmp/tmpjt2los39/optuna_test/swinunetr_0_override_learning_rate_0.01/configs/transforms_train.yaml,/tmp/tmpjt2los39/optuna_test/swinunetr_0_override_learning_rate_0.01/configs/transforms_validate.yaml'", '--learning_rate=0.01']' returned non-zero exit status 1.

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ericspod commented May 9, 2025

Hi @KumoLiu can you set MONAI_DEBUG=1 in the blossom script? This should cause the commands that are failing to save their outputs, this statement is causing the output to be discarded.

KumoLiu added a commit to Project-MONAI/research-contributions that referenced this pull request May 9, 2025
Remove deprecated `img_size` args in `SwinUNETR`
Add `allow_smaller=True` in CropForeground / CropForegroundd since
default value has been changed

Project-MONAI/MONAI#8430

---------

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
@KumoLiu
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KumoLiu commented May 9, 2025

Hi @KumoLiu can you set MONAI_DEBUG=1 in the blossom script? This should cause the commands that are failing to save their outputs, this statement is causing the output to be discarded.

Hi @ericspod, it should be fixed by this PR: Project-MONAI/research-contributions#416.
If not, I will try to add MONAI_DEBUG=1.

KumoLiu and others added 2 commits May 9, 2025 10:42
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KumoLiu commented May 9, 2025

/build

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KumoLiu commented May 9, 2025

Identify the issue: There’s a dependency between this one and #8443. They must be merged simultaneously. If the changes to core aren’t merged, the algo adjustments won’t function properly.

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ericspod commented May 9, 2025

Identify the issue: There’s a dependency between this one and #8443. They must be merged simultaneously. If the changes to core aren’t merged, the algo adjustments won’t function properly.

OK it's fine to just copy the change from #8443 here then.

@KumoLiu KumoLiu enabled auto-merge (squash) May 9, 2025 15:40
@KumoLiu KumoLiu merged commit f97a0e9 into Project-MONAI:dev May 9, 2025
25 checks passed
@KumoLiu KumoLiu deleted the remove-deprecated branch June 12, 2025 09:24
nishanthta pushed a commit to nishanthta/monai-dae that referenced this pull request Sep 9, 2025
Remove deprecated `img_size` args in `SwinUNETR`
Add `allow_smaller=True` in CropForeground / CropForegroundd since
default value has been changed

Project-MONAI/MONAI#8430

---------

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
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4 participants