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import os |
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import pydicom |
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import pydicom_seg |
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import dicom2nifti |
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import pandas as pd |
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import SimpleITK as sitk |
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from tqdm import tqdm |
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data = pd.read_csv('NSCLC-Radiomics/metadata.csv') |
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patient_ids = data['Subject ID'].unique() |
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for pid in tqdm(patient_ids): |
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row = data[data['Subject ID'] == pid] |
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out_fn = f'NSCLC-Radiomics-NIFTI/{pid}' |
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os.makedirs(out_fn) |
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inp_fn_img = row[row['SOP Class Name'] == 'CT Image Storage']['File Location'].values[0] |
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dicom2nifti.convert_directory(inp_fn_img, out_fn) |
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if pid == 'LUNG1-128': continue |
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inp_fn_seg = row[row['SOP Class Name'] == 'Segmentation Storage']['File Location'].values[0] + '/1-1.dcm' |
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dcm = pydicom.dcmread(inp_fn_seg) |
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reader = pydicom_seg.SegmentReader() |
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result = reader.read(dcm) |
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for segment_number in result.available_segments: |
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image = result.segment_image(segment_number) |
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sitk.WriteImage(image, os.path.join(out_fn, f'seg-{result.segment_infos[segment_number].SegmentDescription}.nii.gz'), True) |
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