dicom-segmentation.py

import pydicom
import os

def split_multiframe_dicom(input_file):
  ds = pydicom.dcmread(input_file)
  number_of_frames = int(ds.NumberOfFrames)
  pixelArray = ds.pixel_array.squeeze()

  for idx in range(number_of_frames):
    file_meta = pydicom.dataset.FileMetaDataset()
    file_meta.MediaStorageSOPClassUID = pydicom.uid.SecondaryCaptureImageStorage
    file_meta.MediaStorageSOPInstanceUID = pydicom.uid.generate_uid()
    file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian

    tmp_ds = pydicom.dataset.Dataset()
    tmp_ds.file_meta = file_meta
    tmp_ds.is_little_endian = tmp_ds.file_meta.TransferSyntaxUID.is_little_endian
    tmp_ds.is_implicit_VR = tmp_ds.file_meta.TransferSyntaxUID.is_implicit_VR

    essential_group_list = [0x0020, 0x0028]
    for group in essential_group_list:
        for key, value in ds.group_dataset(group).items():
            tmp_ds[key] = value

    del tmp_ds.NumberOfFrames
    tmp_ds.InstanceNumber = idx + 1
    tmp_ds.PixelData = pixelArray[idx, :].squeeze().tobytes()

    output_path = os.path.join("build", f"slice_{idx + 1}.dcm")
    tmp_ds.save_as(output_path, write_like_original=False)

split_multiframe_dicom("<file>.dcm")