Remove deprecated functionality for v1.5 #8430

KumoLiu · 2025-04-25T13:58:17Z

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.

remove deprecated functionality Signed-off-by: YunLiu <[email protected]>

for more information, see https://pre-commit.ci

Signed-off-by: YunLiu <[email protected]>

…recated

Signed-off-by: YunLiu <[email protected]>

KumoLiu · 2025-05-08T07:29:35Z

/build

KumoLiu · 2025-05-09T01:09:20Z

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.

ericspod · 2025-05-09T10:40:29Z

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.

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 <[email protected]>

KumoLiu · 2025-05-09T10:42:39Z

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 5 commits April 25, 2025 21:55

part of Project-MONAI#8421

0c98432

remove deprecated functionality Signed-off-by: YunLiu <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

a106e72

for more information, see https://pre-commit.ci

fix ci and format

815c500

Signed-off-by: YunLiu <[email protected]>

Merge remote-tracking branch 'yliu/remove-deprecated' into remove-dep…

29476b3

…recated

fix isort

a176ae1

Signed-off-by: YunLiu <[email protected]>

KumoLiu requested a review from ericspod April 27, 2025 09:13

KumoLiu added 2 commits April 27, 2025 17:15

fix format

617a019

Signed-off-by: YunLiu <[email protected]>

fix mypy

e6064f9

Signed-off-by: YunLiu <[email protected]>

Jose1654 approved these changes Apr 29, 2025

View reviewed changes

ericspod approved these changes Apr 29, 2025

View reviewed changes

Merge remote-tracking branch 'origin/dev' into remove-deprecated

9ca41c6

Signed-off-by: YunLiu <[email protected]>

KumoLiu mentioned this pull request May 9, 2025

Remove deprecated img_size args in SwinUNETR Project-MONAI/research-contributions#416

Merged

Merge branch 'dev' into remove-deprecated

1d21296

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Remove deprecated functionality for v1.5 #8430

Remove deprecated functionality for v1.5 #8430

KumoLiu commented Apr 25, 2025 •

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KumoLiu commented May 8, 2025

KumoLiu commented May 9, 2025

ericspod commented May 9, 2025

KumoLiu commented May 9, 2025

Remove deprecated functionality for v1.5 #8430

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Remove deprecated functionality for v1.5 #8430

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KumoLiu commented Apr 25, 2025 • edited Loading

Description

Types of changes

KumoLiu commented May 8, 2025

KumoLiu commented May 9, 2025

ericspod commented May 9, 2025

KumoLiu commented May 9, 2025

KumoLiu commented Apr 25, 2025 •

edited

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