From 6dc7a289dbd7f46fe749ef1b7d1c95f5a7be9da4 Mon Sep 17 00:00:00 2001 From: Rahul Soni Date: Tue, 18 Jun 2024 17:47:10 +0530 Subject: [PATCH] fix rois --- .../bamf_nnunet_mr_breast/utils/BreastPostProcessor.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/models/bamf_nnunet_mr_breast/utils/BreastPostProcessor.py b/models/bamf_nnunet_mr_breast/utils/BreastPostProcessor.py index ad15a8f9..cdf0a3a8 100644 --- a/models/bamf_nnunet_mr_breast/utils/BreastPostProcessor.py +++ b/models/bamf_nnunet_mr_breast/utils/BreastPostProcessor.py @@ -64,10 +64,10 @@ def merge_segmentations(self, breast_and_fgt_seg:sitk.Image, tumor_seg:sitk.Imag return seg_img @IO.Instance() - @IO.Input('in_breast_and_fgt_data', 'nifti:mod=seg:nnunet_task=Dataset009_Breast', the='input data from breast and fgt segmentation') - @IO.Input('in_breast_tumor_data', 'nifti:mod=seg:nnunet_task=Dataset011_Breast', the='input data from breast tumor segmentation') + @IO.Input('in_breast_and_fgt_data', 'nifti:mod=seg:nnunet_dataset=Dataset009_Breast', the='input data from breast and fgt segmentation') + @IO.Input('in_breast_tumor_data', 'nifti:mod=seg:nnunet_dataset=Dataset011_Breast', the='input data from breast tumor segmentation') @IO.Input('in_mr_data', 'nifti:mod=mr', the='input mr data') - @IO.Output('out_data', 'bamf_processed.nii.gz', 'nifti:mod=seg:processor=bamf:roi=BREAST,BREAST+FGT,BREAST_TUMOR', + @IO.Output('out_data', 'bamf_processed.nii.gz', 'nifti:mod=seg:processor=bamf:roi=BREAST,FGT,BREAST+TUMOR', the="get breast_fgt and breast segmentation file") def task(self, instance: Instance, in_breast_and_fgt_data: InstanceData, in_breast_tumor_data: InstanceData, in_mr_data: InstanceData, out_data: InstanceData): @@ -86,8 +86,8 @@ def task(self, instance: Instance, in_breast_and_fgt_data: InstanceData, in_brea # Merged segmentation masks output_seg = self.merge_segmentations( - breast_and_fgt = np.copy(breast_and_fgt_seg), - breast_tumor = np.copy(tumor_seg), + breast_and_fgt_seg = np.copy(breast_and_fgt_seg), + tumor_seg = np.copy(tumor_seg), mr_path = in_mr_data.abspath ) process_dir = self.config.data.requestTempDir(label="nnunet-breast-processor")