Lazy functionality 1 2 #6537

atbenmurray · 2023-05-22T07:45:34Z

Reduced lazy resampling functionality for MONAI 1.2

Description

This PR is a subset of #6257 intended for MONAI 1.2. It contains the basic resampling strategy that has been approved for the 1.2 release during MONAI core dev meeting of 19th May, 2023.

Draft status:

still to do
- doc strings
- topic page
- resolve compose reference doc issue

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.

Signed-off-by: Ben Murray <ben.murray@gmail.com>

…arameter, refactoring spatial arrays to support lazy_evaluation call time parameter, refactoring _apply_transform to pass call time lazy_evaluation flag Signed-off-by: Ben Murray <ben.murray@gmail.com>

… transforms Signed-off-by: Ben Murray <ben.murray@gmail.com>

lazy_evaluation initing / calls Signed-off-by: Ben Murray <ben.murray@gmail.com>

Signed-off-by: Ben Murray <ben.murray@gmail.com>

croppad/array Signed-off-by: Ben Murray <ben.murray@gmail.com>

Signed-off-by: Ben Murray <ben.murray@gmail.com>

meaningful . Adding ApplyPending and ApplyPendingd transforms Signed-off-by: Ben Murray <ben.murray@gmail.com>

respectively Signed-off-by: Ben Murray <ben.murray@gmail.com>

Filter for metatensors in ApplyPending / ApplyPendingd classes Signed-off-by: Ben Murray <ben.murray@gmail.com>

Signed-off-by: Ben Murray <ben.murray@gmail.com>

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

Signed-off-by: Ben Murray <ben.murray@gmail.com>

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

Signed-off-by: Ben Murray <ben.murray@gmail.com>

…o lazy_eval_refactor

Signed-off-by: Ben Murray <ben.murray@gmail.com>

…pply_pending. Fixing various tests by moving to use of 'overrides' on apply_pending Signed-off-by: Ben Murray <ben.murray@gmail.com>

Signed-off-by: Ben Murray <ben.murray@gmail.com>

**kwargs parameter from apply_pending Signed-off-by: Ben Murray <ben.murray@gmail.com>

Signed-off-by: Ben Murray <ben.murray@gmail.com>

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monai/transforms/lazy/functional.py

ericspod

I'm good with it now, we need to rerun tests with the current dev merged in. @Nic-Ma? Thanks!

Nic-Ma

Thanks for the quick update, put some comments inline, others look good to me now.

monai/apps/auto3dseg/data_analyzer.py

monai/transforms/compose.py

monai/transforms/lazy/functional.py

monai/transforms/utils.py

monai/transforms/compose.py

monai/transforms/utils.py

tests/test_integration_lazy_samples.py

Nic-Ma · 2023-05-30T14:03:18Z

Hi @KumoLiu ,

The functionality of this PR is ready, just some minor comments left.
Could you please help quickly run the benchmark tutorials with this PR to verify the performance for MONAI 1.2 release?

Thanks in advance.

Nic-Ma · 2023-05-30T14:07:04Z

Hi @mingxin-zheng , @dongyang0122 , @wyli ,

I see some Auto3D failures in the CI results of this PR, could you please help confirm whether they are related to this PR?
@atbenmurray Can you run these tests locally to verify?

======================================================================
ERROR: test_get_history (tests.test_auto3dseg_hpo.TestHPO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/__w/MONAI/MONAI/tests/test_auto3dseg_hpo.py", line 180, in test_get_history
    NNIGen().run_algo(obj_filename, self.work_dir)
  File "/__w/MONAI/MONAI/monai/apps/auto3dseg/hpo_gen.py", line 231, in run_algo
    self.algo.train(self.params)
  File "/__w/MONAI/MONAI/monai/apps/auto3dseg/bundle_gen.py", line 269, in train
    return self._run_cmd(cmd)
  File "/__w/MONAI/MONAI/monai/apps/auto3dseg/bundle_gen.py", line 246, in _run_cmd
    return subprocess.run(cmd_list, env=ps_environ, check=True)
  File "/opt/conda/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['torchrun', '--nnodes=1', '--nproc_per_node=2', '/tmp/tmp51lklfjx/workdir/swinunetr_0_override_None/scripts/train.py', 'run', "--config_file='/tmp/tmp51lklfjx/workdir/swinunetr_0_override_None/configs/hyper_parameters.yaml','/tmp/tmp51lklfjx/workdir/swinunetr_0_override_None/configs/network.yaml','/tmp/tmp51lklfjx/workdir/swinunetr_0_override_None/configs/transforms_infer.yaml','/tmp/tmp51lklfjx/workdir/swinunetr_0_override_None/configs/transforms_train.yaml','/tmp/tmp51lklfjx/workdir/swinunetr_0_override_None/configs/transforms_validate.yaml'"]' returned non-zero exit status 1.

======================================================================
ERROR: test_run_algo (tests.test_auto3dseg_hpo.TestHPO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/__w/MONAI/MONAI/tests/test_auto3dseg_hpo.py", line 148, in test_run_algo
    NNIGen().run_algo(obj_filename, self.work_dir)
  File "/__w/MONAI/MONAI/monai/apps/auto3dseg/hpo_gen.py", line 231, in run_algo
    self.algo.train(self.params)
  File "/__w/MONAI/MONAI/monai/apps/auto3dseg/bundle_gen.py", line 269, in train
    return self._run_cmd(cmd)
  File "/__w/MONAI/MONAI/monai/apps/auto3dseg/bundle_gen.py", line 246, in _run_cmd
    return subprocess.run(cmd_list, env=ps_environ, check=True)
  File "/opt/conda/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['torchrun', '--nnodes=1', '--nproc_per_node=2', '/tmp/tmpe1a9xrrd/workdir/swinunetr_0_override_None/scripts/train.py', 'run', "--config_file='/tmp/tmpe1a9xrrd/workdir/swinunetr_0_override_None/configs/hyper_parameters.yaml','/tmp/tmpe1a9xrrd/workdir/swinunetr_0_override_None/configs/network.yaml','/tmp/tmpe1a9xrrd/workdir/swinunetr_0_override_None/configs/transforms_infer.yaml','/tmp/tmpe1a9xrrd/workdir/swinunetr_0_override_None/configs/transforms_train.yaml','/tmp/tmpe1a9xrrd/workdir/swinunetr_0_override_None/configs/transforms_validate.yaml'"]' returned non-zero exit status 1.

======================================================================
ERROR: test_run_optuna (tests.test_auto3dseg_hpo.TestHPO)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/__w/MONAI/MONAI/tests/test_auto3dseg_hpo.py", line 163, in test_run_optuna
    study.optimize(
  File "/opt/conda/lib/python3.8/site-packages/optuna/study/study.py", line 443, in optimize
    _optimize(
  File "/opt/conda/lib/python3.8/site-packages/optuna/study/_optimize.py", line 66, in _optimize
    _optimize_sequential(
  File "/opt/conda/lib/python3.8/site-packages/optuna/study/_optimize.py", line 163, in _optimize_sequential
    frozen_trial = _run_trial(study, func, catch)
  File "/opt/conda/lib/python3.8/site-packages/optuna/study/_optimize.py", line 251, in _run_trial
    raise func_err
  File "/opt/conda/lib/python3.8/site-packages/optuna/study/_optimize.py", line 200, in _run_trial
    value_or_values = func(trial)
  File "/__w/MONAI/MONAI/monai/apps/auto3dseg/hpo_gen.py", line 336, in __call__
    self.run_algo(obj_filename, output_folder, template_path)
  File "/__w/MONAI/MONAI/monai/apps/auto3dseg/hpo_gen.py", line 394, in run_algo
    self.algo.train(self.params)
  File "/__w/MONAI/MONAI/monai/apps/auto3dseg/bundle_gen.py", line 269, in train
    return self._run_cmd(cmd)
  File "/__w/MONAI/MONAI/monai/apps/auto3dseg/bundle_gen.py", line 246, in _run_cmd
    return subprocess.run(cmd_list, env=ps_environ, check=True)
  File "/opt/conda/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['torchrun', '--nnodes=1', '--nproc_per_node=2', '/tmp/tmpx65fltgg/optuna_test/swinunetr_0_override_learning_rate_0.01/scripts/train.py', 'run', "--config_file='/tmp/tmpx65fltgg/optuna_test/swinunetr_0_override_learning_rate_0.01/configs/hyper_parameters.yaml','/tmp/tmpx65fltgg/optuna_test/swinunetr_0_override_learning_rate_0.01/configs/network.yaml','/tmp/tmpx65fltgg/optuna_test/swinunetr_0_override_learning_rate_0.01/configs/transforms_infer.yaml','/tmp/tmpx65fltgg/optuna_test/swinunetr_0_override_learning_rate_0.01/configs/transforms_train.yaml','/tmp/tmpx65fltgg/optuna_test/swinunetr_0_override_learning_rate_0.01/configs/transforms_validate.yaml'", '--learning_rate=0.01']' returned non-zero exit status 1.

----------------------------------------------------------------------
Ran 13507 tests in 1115.695s

FAILED (errors=3, skipped=911)

Thanks in advance.

mingxin-zheng · 2023-05-31T03:41:30Z

Hi @Nic-Ma @atbenmurray , looks like the error is generated by this PR. I ran it on my local machine and the error log indicates the causes are auto3dseg templates use lazy_evaluation:

TypeError: __init__() got an unexpected keyword argument 'lazy_evaluation'

https://github.com/Project-MONAI/research-contributions/blob/fddf97ac09a176d9df4c4369cd07fe176b1c4eb4/auto3dseg/algorithm_templates/swinunetr/configs/transforms_train.yaml#L5

I think it is an expected failure and can be addressed in another PR.

Nic-Ma · 2023-05-31T05:43:56Z

Hi @dongyang0122 ,

Could you please help update the Auto3DSeg templates accordingly to avoid any lazy resampling logic?

Thanks in advance.

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Nic-Ma · 2023-06-01T01:24:43Z

/black

Nic-Ma · 2023-06-01T01:24:52Z

/build

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

Nic-Ma · 2023-06-01T07:47:26Z

/build

atbenmurray · 2023-06-01T09:17:40Z

@ericspod @Nic-Ma @wyli Are we ready to merge then?

Signed-off-by: Ben Murray <ben.murray@gmail.com>

… into lazy_functionality_1_2

Nic-Ma · 2023-06-01T09:33:19Z

/black

Nic-Ma · 2023-06-01T09:34:08Z

/build

ericspod · 2023-06-01T09:50:12Z

I'm good to go!

…

On Thu., Jun. 1, 2023, 10:17 a.m. Ben Murray, ***@***.***> wrote: @ericspod <https://github.com/ericspod> @Nic-Ma <https://github.com/Nic-Ma> @wyli <https://github.com/wyli> Are we ready to merge then? — Reply to this email directly, view it on GitHub <#6537 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHHUWWM2FYRZSMGOHFMOMTXJBM4DANCNFSM6AAAAAAYKBEHWU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

atbenmurray and others added 30 commits March 27, 2023 22:43

Initial commit

06d5842

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Refactors and simplification of api / calls

2507a0b

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Refactoring functional spatial transform to support lazy_evaluation p…

56b618e

…arameter, refactoring spatial arrays to support lazy_evaluation call time parameter, refactoring _apply_transform to pass call time lazy_evaluation flag Signed-off-by: Ben Murray <ben.murray@gmail.com>

Making lazy_evaluation parameter consistent across spatial array lazy…

315e5b7

… transforms Signed-off-by: Ben Murray <ben.murray@gmail.com>

Updating apply and dictionary spatial transforms to support

4e69313

lazy_evaluation initing / calls Signed-off-by: Ben Murray <ben.murray@gmail.com>

Missing changes to spatial dictionary

99fa35b

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Enable call-time overriding of lazy_evaluation in croppad/functional and

a798e0e

croppad/array Signed-off-by: Ben Murray <ben.murray@gmail.com>

Updating croppad dictionary and croppad array for call-time laziness

114b8cc

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Fix for push_transform; updating the lazy integration test

5df4261

Signed-off-by: Ben Murray <ben.murray@gmail.com>

removing issue.txt

84d65f7

Signed-off-by: Ben Murray <ben.murray@gmail.com>

. Renaming apply_transform to apply_pending as it is more semantically

7ec442f

meaningful . Adding ApplyPending and ApplyPendingd transforms Signed-off-by: Ben Murray <ben.murray@gmail.com>

Tweaked array ApplyPending and ApplyPendingd for array and dict data

8f62776

respectively Signed-off-by: Ben Murray <ben.murray@gmail.com>

Added missing license text.

2492223

Filter for metatensors in ApplyPending / ApplyPendingd classes Signed-off-by: Ben Murray <ben.murray@gmail.com>

Missing import for apply_pending

0064326

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Merge branch 'dev' into lazy_eval_refactor

0646602

Signed-off-by: Ben Murray <ben.murray@gmail.com>

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

05eb3f9

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Fixing syntax error created by merge of dev to PR

788cd74

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Fixing issues with pad_func post merge

4bd22f8

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

1e0510c

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Fixing issues in crop while running unit tests

c36b69f

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Merge branch 'lazy_eval_refactor' of github.com:atbenmurray/monai int…

8a4f310

…o lazy_eval_refactor

Fixing issues with OneOf/SomeOf/RandomOrder after dev merge

3c69776

Signed-off-by: Ben Murray <ben.murray@gmail.com>

More croppad fixes post dev merge

6b94aa1

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Fixing test_nvtx_decorator after def merge

bf1c01a

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Removed use of **kwargs parameter in tests as it isn't supported by a…

19745f9

…pply_pending. Fixing various tests by moving to use of 'overrides' on apply_pending Signed-off-by: Ben Murray <ben.murray@gmail.com>

Setting use of lazy_evaluation to False for Rand2D/Rand3DElastic

b219f13

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Fixed test_spatial_pad

6af8f24

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Renaming lazy_evaluation to lazy

173c161

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Fixed all outstanding usages of apply_pending in tests. Removed the

2262ba9

**kwargs parameter from apply_pending Signed-off-by: Ben Murray <ben.murray@gmail.com>

Merge branch 'dev' into lazy_eval_refactor

aaaea13

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atbenmurray and others added 2 commits May 30, 2023 10:20

Missing images for lazy resampling

21c9f84

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ericspod reviewed May 30, 2023

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monai/transforms/lazy/functional.py Show resolved Hide resolved

Merge branch 'dev' into lazy_functionality_1_2

7495c07

ericspod self-requested a review May 30, 2023 11:37

ericspod approved these changes May 30, 2023

View reviewed changes

Nic-Ma approved these changes May 30, 2023

View reviewed changes

atbenmurray and others added 5 commits May 31, 2023 10:02

Updating docs for has_status_key, removing dead import statement

cd65152

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autofix

2e5f23d

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Removing erroneous arg from docstring

5a754c8

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Renaming _raise_if_tensor_is_not_invertible

c3b8c1f

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Merge branch 'dev' into lazy_functionality_1_2

ff73762

[MONAI] code formatting

0d4143c

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

atbenmurray added 2 commits June 1, 2023 10:25

Removing type: ignore from auto3dseg/data_analyser.py

e766652

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Merge branch 'lazy_functionality_1_2' of github.com:atbenmurray/monai…

1320aea

… into lazy_functionality_1_2

Nic-Ma enabled auto-merge (squash) June 1, 2023 09:54

Nic-Ma merged commit e597994 into Project-MONAI:dev Jun 1, 2023

This was referenced Jun 9, 2023

Meta_dict and lazy resampling in apply transform #6595

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Lazy functionality 1 2 #6537

Lazy functionality 1 2 #6537

atbenmurray commented May 22, 2023 •

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Lazy functionality 1 2 #6537

Lazy functionality 1 2 #6537

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