convert_segm.py

import os

import pydicom
import pydicom_seg

import pandas as pd
import SimpleITK as sitk

from tqdm import tqdm


patient_ids = data['Subject ID'].unique()

for pid in tqdm(patient_ids):

    row = data[data['Subject ID'] == pid]
    out_fn = f'NSCLC-Radiomics-NIFTI3/{pid}'
    os.makedirs(out_fn)

    try:
        inp_fn_img = row[row['Number of Images'] > 1]['File Location'].values[0]
        dicom2nifti.convert_directory(inp_fn_img, out_fn)
    except:
        print(f'Image {inp_fn_img} failed to convert')
        pass

    try:
        inp_fn_seg = row[row['File Location'].str.contains('Segmentation')]['File Location'].values[0] + '/1-1.dcm'
        dcm = pydicom.dcmread(inp_fn_seg)
        reader = pydicom_seg.SegmentReader()
        result = reader.read(dcm)

        for segment_number in result.available_segments:
            image = result.segment_image(segment_number)  # lazy construction
            sitk.WriteImage(image, os.path.join(out_fn, f'seg-{result.segment_infos[segment_number].SegmentDescription}.nii.gz'), True)
    except:
        print(f'Segmentation {inp_fn_seg} failed to convert')
        pass