Commit
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5809257
1
Parent(s):
11a4b70
Update convert.py
Browse files- convert.py +15 -19
convert.py
CHANGED
@@ -3,12 +3,15 @@ import os
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import pydicom
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import pydicom_seg
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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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patient_ids = data['Subject ID'].unique()
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for pid in tqdm(patient_ids):
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@@ -17,23 +20,16 @@ for pid in tqdm(patient_ids):
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out_fn = f'NSCLC-Radiomics-NIFTI/{pid}'
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os.makedirs(out_fn)
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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) # lazy construction
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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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except:
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print(f'Segmentation {inp_fn_seg} failed to convert')
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pass
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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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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 # LUNG1-128 missing segmentation
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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) # lazy construction
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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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