[Feature] Add msd crop code

PaddleCV-SIG / MedicalSeg

MedicalSeg is an easy-to-use 3D medical image segmentation toolkit that supports the whole segmentation process. Specially, We provide data preprocessing acceleration, high precision model on COVID-19 CT scans dataset and MRISpineSeg spine dataset, and a 3D visualization demo based on itkwidgets.

Apache License 2.0

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[Feature] Add msd crop code #54

Closed justld closed 2 years ago

justld commented 2 years ago

msd数据crop，已与官方repo生成的crop数据对比验证dataset_property.pkl, .pkl, .npz, **.nii.gz。

from preprocess_utils import crop
crop("\xx_decalthon\Task004_Hippocampus",   # decalthon数据目录
         "\xx_cropped\Task004_Hippocampus",    # crop保存数据目录
          override=True, 
          data_json="dataset.json", 
          train_images_dir="imagesTr", 
          train_labels_dir="labelsTr",
          num_threads=8)