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Update test_nnunetv2runner (Project-MONAI#7483)
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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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KumoLiu authored and Yu0610 committed Apr 11, 2024
1 parent 3376abd commit 9092e5d
Showing 1 changed file with 12 additions and 10 deletions.
22 changes: 12 additions & 10 deletions monai/apps/nnunet/nnunetv2_runner.py
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ class nnUNetV2Runner: # noqa: N801
"""
``nnUNetV2Runner`` provides an interface in MONAI to use `nnU-Net` V2 library to analyze, train, and evaluate
neural networks for medical image segmentation tasks.
A version of nnunetv2 higher than 2.2 is needed for this class.
``nnUNetV2Runner`` can be used in two ways:
Expand Down Expand Up @@ -770,7 +771,7 @@ def find_best_configuration(
def predict(
self,
list_of_lists_or_source_folder: str | list[list[str]],
output_folder: str,
output_folder: str | None | list[str],
model_training_output_dir: str,
use_folds: tuple[int, ...] | str | None = None,
tile_step_size: float = 0.5,
Expand Down Expand Up @@ -824,28 +825,29 @@ def predict(
"""
os.environ["CUDA_VISIBLE_DEVICES"] = f"{gpu_id}"

from nnunetv2.inference.predict_from_raw_data import predict_from_raw_data
from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor

n_processes_preprocessing = (
self.default_num_processes if num_processes_preprocessing < 0 else num_processes_preprocessing
)
n_processes_segmentation_export = (
self.default_num_processes if num_processes_segmentation_export < 0 else num_processes_segmentation_export
)

predict_from_raw_data(
list_of_lists_or_source_folder=list_of_lists_or_source_folder,
output_folder=output_folder,
model_training_output_dir=model_training_output_dir,
use_folds=use_folds,
predictor = nnUNetPredictor(
tile_step_size=tile_step_size,
use_gaussian=use_gaussian,
use_mirroring=use_mirroring,
perform_everything_on_gpu=perform_everything_on_gpu,
perform_everything_on_device=perform_everything_on_gpu,
verbose=verbose,
)
predictor.initialize_from_trained_model_folder(
model_training_output_dir=model_training_output_dir, use_folds=use_folds, checkpoint_name=checkpoint_name
)
predictor.predict_from_files(
list_of_lists_or_source_folder=list_of_lists_or_source_folder,
output_folder_or_list_of_truncated_output_files=output_folder,
save_probabilities=save_probabilities,
overwrite=overwrite,
checkpoint_name=checkpoint_name,
num_processes_preprocessing=n_processes_preprocessing,
num_processes_segmentation_export=n_processes_segmentation_export,
folder_with_segs_from_prev_stage=folder_with_segs_from_prev_stage,
Expand Down

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