From 11648f411054831fb5211bd643bce3063c5c7442 Mon Sep 17 00:00:00 2001 From: Jupilogy Date: Sat, 30 Sep 2023 13:51:16 +0100 Subject: [PATCH 1/4] Reworking nnunetv2 predictor Signed-off-by: Jupilogy --- monai/apps/nnunet/nnunetv2_runner.py | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/monai/apps/nnunet/nnunetv2_runner.py b/monai/apps/nnunet/nnunetv2_runner.py index a3357cd9b3..9c17983975 100644 --- a/monai/apps/nnunet/nnunetv2_runner.py +++ b/monai/apps/nnunet/nnunetv2_runner.py @@ -824,7 +824,7 @@ 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 @@ -833,19 +833,22 @@ def predict( 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, - tile_step_size=tile_step_size, + predictor = nnUNetPredictor( use_gaussian=use_gaussian, use_mirroring=use_mirroring, perform_everything_on_gpu=perform_everything_on_gpu, verbose=verbose, - save_probabilities=save_probabilities, - overwrite=overwrite, + ) + predictor.initialise_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=output_folder, + save_probabilities=saved_probabilities, + overwrite=overwrite, 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, From ffcf5e3490011ff2a1269c5ef9de1cb04934cca4 Mon Sep 17 00:00:00 2001 From: Jupy Date: Sat, 30 Sep 2023 15:18:50 +0100 Subject: [PATCH 2/4] typo and formatting Signed-off-by: Jupilogy --- monai/apps/nnunet/nnunetv2_runner.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/monai/apps/nnunet/nnunetv2_runner.py b/monai/apps/nnunet/nnunetv2_runner.py index 9c17983975..fb864be3ba 100644 --- a/monai/apps/nnunet/nnunetv2_runner.py +++ b/monai/apps/nnunet/nnunetv2_runner.py @@ -840,14 +840,12 @@ def predict( verbose=verbose, ) predictor.initialise_from_trained_model_folder( - model_training_output_dir=model_training_output_dir, - use_folds=use_folds, - checkpoint_name=checkpoint_name, + 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=output_folder, - save_probabilities=saved_probabilities, + save_probabilities=save_probabilities, overwrite=overwrite, num_processes_preprocessing=n_processes_preprocessing, num_processes_segmentation_export=n_processes_segmentation_export, From e3b4022bedf4b70b4edcb43514475e6117886c1b Mon Sep 17 00:00:00 2001 From: Jupilogy Date: Mon, 2 Oct 2023 08:46:01 +0100 Subject: [PATCH 3/4] typo --- monai/apps/nnunet/nnunetv2_runner.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/monai/apps/nnunet/nnunetv2_runner.py b/monai/apps/nnunet/nnunetv2_runner.py index fb864be3ba..b009ad1b51 100644 --- a/monai/apps/nnunet/nnunetv2_runner.py +++ b/monai/apps/nnunet/nnunetv2_runner.py @@ -839,7 +839,7 @@ def predict( perform_everything_on_gpu=perform_everything_on_gpu, verbose=verbose, ) - predictor.initialise_from_trained_model_folder( + 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( From f59a7f18f574bcb5575b57a261c9db17225cb749 Mon Sep 17 00:00:00 2001 From: COJD Date: Mon, 2 Oct 2023 11:43:20 +0100 Subject: [PATCH 4/4] changing folder names Signed-off-by: jupilogy --- monai/apps/nnunet/nnunetv2_runner.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/monai/apps/nnunet/nnunetv2_runner.py b/monai/apps/nnunet/nnunetv2_runner.py index b009ad1b51..b6bbac2e07 100644 --- a/monai/apps/nnunet/nnunetv2_runner.py +++ b/monai/apps/nnunet/nnunetv2_runner.py @@ -167,12 +167,12 @@ def __init__( else: raise ValueError(f"{input_config} is not a valid file or dict") - self.nnunet_raw = self.input_info.pop("nnunet_raw", os.path.join(".", self.work_dir, "nnUNet_raw_data_base")) + self.nnunet_raw = self.input_info.pop("nnunet_raw", os.path.join(".", self.work_dir, "nnUNetv2_raw_data_base")) self.nnunet_preprocessed = self.input_info.pop( - "nnunet_preprocessed", os.path.join(".", self.work_dir, "nnUNet_preprocessed") + "nnunet_preprocessed", os.path.join(".", self.work_dir, "nnUNetv2_preprocessed") ) self.nnunet_results = self.input_info.pop( - "nnunet_results", os.path.join(".", self.work_dir, "nnUNet_trained_models") + "nnunet_results", os.path.join(".", self.work_dir, "nnUNetv2_trained_models") ) if not os.path.exists(self.nnunet_raw):