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test_integration_nnunetv2_runner error #7478

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KumoLiu opened this issue Feb 20, 2024 · 0 comments
Closed

test_integration_nnunetv2_runner error #7478

KumoLiu opened this issue Feb 20, 2024 · 0 comments
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KumoLiu commented Feb 20, 2024 •
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test nnunetv2runner is broken after the recent update MIC-DKFZ/nnUNet#1967 (comment)

[2024-02-19T23:30:47.247Z] ERROR: test_nnunetv2runner (__main__.TestnnUNetV2Runner)
[2024-02-19T23:30:47.247Z] ----------------------------------------------------------------------
[2024-02-19T23:30:47.247Z] Traceback (most recent call last):
[2024-02-19T23:30:47.247Z]   File "/home/jenkins/agent/workspace/Monai-notebooks/MONAI/tests/test_integration_nnunetv2_runner.py", line 87, in test_nnunetv2runner
[2024-02-19T23:30:47.247Z]     runner.run(run_train=False, run_find_best_configuration=False, run_predict_ensemble_postprocessing=False)
[2024-02-19T23:30:47.247Z]   File "/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/nnunet/nnunetv2_runner.py", line 954, in run
[2024-02-19T23:30:47.247Z]     self.plan_and_process()
[2024-02-19T23:30:47.247Z]   File "/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/nnunet/nnunetv2_runner.py", line 481, in plan_and_process
[2024-02-19T23:30:47.247Z]     self.extract_fingerprints(fpe, npfp, verify_dataset_integrity, clean, verbose)
[2024-02-19T23:30:47.247Z]   File "/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/nnunet/nnunetv2_runner.py", line 320, in extract_fingerprints
[2024-02-19T23:30:47.247Z]     from nnunetv2.experiment_planning.plan_and_preprocess_api import extract_fingerprints
[2024-02-19T23:30:47.247Z]   File "/usr/local/lib/python3.10/dist-packages/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 8, in <module>
[2024-02-19T23:30:47.247Z]     from nnunetv2.experiment_planning.experiment_planners.default_experiment_planner import ExperimentPlanner
[2024-02-19T23:30:47.247Z]   File "/usr/local/lib/python3.10/dist-packages/nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py", line 8, in <module>
[2024-02-19T23:30:47.247Z]     from dynamic_network_architectures.architectures.unet import PlainConvUNet, ResidualEncoderUNet
[2024-02-19T23:30:47.247Z] ImportError: cannot import name 'ResidualEncoderUNet' from 'dynamic_network_architectures.architectures.unet' (/usr/local/lib/python3.10/dist-packages/dynamic_network_architectures/architectures/unet.py)
@KumoLiu KumoLiu added bug Something isn't working Contribution wanted labels Feb 20, 2024
@KumoLiu KumoLiu changed the title test_nnunetv2runner error test_integration_nnunetv2_runner error Feb 20, 2024
@KumoLiu KumoLiu closed this as completed Feb 21, 2024
@KumoLiu KumoLiu reopened this Feb 21, 2024
@KumoLiu KumoLiu mentioned this issue Feb 21, 2024
Merged
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KumoLiu added a commit that referenced this issue Feb 22, 2024
@KumoLiu
Update test_nnunetv2runner (#7483)
f4103c5 
Fixes #7013 #7478

### Description
replace `predict_from_raw_data` with `nnUNetPredictor` in
test_nnunetv2runner

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com>
@KumoLiu KumoLiu closed this as completed Feb 22, 2024
juampatronics pushed a commit to juampatronics/MONAI that referenced this issue Mar 25, 2024
@KumoLiu @juampatronics
Update test_nnunetv2runner (Project-MONAI#7483)
ff19822 
Fixes Project-MONAI#7013 Project-MONAI#7478

### Description
replace `predict_from_raw_data` with `nnUNetPredictor` in
test_nnunetv2runner

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>
Yu0610 pushed a commit to Yu0610/MONAI that referenced this issue Apr 11, 2024
@KumoLiu @Yu0610
Update test_nnunetv2runner (Project-MONAI#7483)
9092e5d 
Fixes Project-MONAI#7013 Project-MONAI#7478

### Description
replace `predict_from_raw_data` with `nnUNetPredictor` in
test_nnunetv2runner

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: Yu0610 <612410030@alum.ccu.edu.tw>
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