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test_nnunetv2runner #7013

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wyli opened this issue Sep 20, 2023 · 0 comments · Fixed by #7483 · May be fixed by #7069
Closed

test_nnunetv2runner #7013

wyli opened this issue Sep 20, 2023 · 0 comments · Fixed by #7483 · May be fixed by #7069
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bug Something isn't working Contribution wanted

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@wyli
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wyli commented Sep 20, 2023

test nnunetv2runner is broken after the recent update https://pypi.org/project/nnunetv2/#history

[2023-09-19T22:32:39.490Z] ======================================================================
[2023-09-19T22:32:39.490Z] ERROR: test_nnunetv2runner (__main__.TestnnUNetV2Runner)
[2023-09-19T22:32:39.490Z] ----------------------------------------------------------------------
[2023-09-19T22:32:39.490Z] Traceback (most recent call last):
[2023-09-19T22:32:39.490Z]   File "/home/jenkins/agent/workspace/Monai-notebooks/MONAI/tests/test_integration_nnunetv2_runner.py", line 89, in test_nnunetv2runner
[2023-09-19T22:32:39.490Z]     runner.predict_ensemble_postprocessing()
[2023-09-19T22:32:39.490Z]   File "/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/nnunet/nnunetv2_runner.py", line 900, in predict_ensemble_postprocessing
[2023-09-19T22:32:39.490Z]     self.predict(
[2023-09-19T22:32:39.490Z]   File "/home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/nnunet/nnunetv2_runner.py", line 827, in predict
[2023-09-19T22:32:39.490Z]     from nnunetv2.inference.predict_from_raw_data import predict_from_raw_data
[2023-09-19T22:32:39.490Z] ImportError: cannot import name 'predict_from_raw_data' from 'nnunetv2.inference.predict_from_raw_data' (/usr/local/lib/python3.10/dist-packages/nnunetv2/inference/predict_from_raw_data.py)
[2023-09-19T22:32:39.490Z] 
[2023-09-19T22:32:39.490Z] ----------------------------------------------------------------------
@wyli wyli added bug Something isn't working Contribution wanted labels Sep 20, 2023
@JupiLogy JupiLogy mentioned this issue Sep 30, 2023
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@KumoLiu KumoLiu mentioned this issue Jan 9, 2024
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KumoLiu added a commit to KumoLiu/MONAI that referenced this issue Feb 21, 2024
@KumoLiu
fix Project-MONAI#7013
004c7a3 
Signed-off-by: YunLiu <[email protected]>
@KumoLiu KumoLiu mentioned this issue Feb 21, 2024
Merged
7 tasks
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 <[email protected]>
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 <[email protected]>
Signed-off-by: Juan Pablo de la Cruz Gutiérrez <[email protected]>
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 <[email protected]>
Signed-off-by: Yu0610 <[email protected]>
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Update test_nnunetv2runner KumoLiu/MONAI
Reworking nnunetv2 predictor JupiLogy/MONAI
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@wyli