convert dicom files into mhd file

convert_dcm_to_mhd.py

'''
-----------------------------------------------
File Name: convert_dcm_to_mhd$
Description: convert dicom files into mhd file
Author: Jing$
Date: 16/11/2022$
-----------------------------------------------
'''

import os
import SimpleITK as sitk
import pydicom
import numpy as np
import glob

def convert(input_path,output_path):
    '''
    Procedure:
    # To get first image as refenece image, supposed all images have same dimensions
    # To get Dimensions, 3D spacing, image origin
    # To make numpy array
    # loop through all the DICOM files
        # To read the dicom file
        # store the raw image data

    :param input_path: the path of dicom files
    :param output_path: the output path of mhd files
    :return: null
    '''

    DICOM_directory = glob.glob(input_path)
    Image = pydicom.read_file(DICOM_directory[0])
    Dimension = (int(Image.Rows), int(Image.Columns), len(DICOM_directory))
    Spacing = (float(Image.PixelSpacing[0]), float(Image.PixelSpacing[1]), float(Image.SliceThickness))
    Origin = Image.ImagePositionPatient
    NpArrDc = np.zeros(Dimension, dtype=Image.pixel_array.dtype)
    for filename in DICOM_directory:
        df = pydicom.read_file(filename)
        NpArrDc[:, :, DICOM_directory.index(filename)] = df.pixel_array

    NpArrDc = np.transpose(NpArrDc, (2, 0, 1))  # axis transpose
    sitk_img = sitk.GetImageFromArray(NpArrDc, isVector=False)
    sitk_img.SetSpacing(Spacing)
    sitk_img.SetOrigin(Origin)
    sitk.WriteImage(sitk_img, os.path.join(output_path + ".mhd"))
    return

convert(input_path="dicoms/*.dcm",output_path="samples/sample")

Reference https://github.com/hfarhidzadeh/DicomToMhd