nifti2dicom.py

import nibabel
import numpy as np
import pydicom
import os
from tqdm import tqdm


def convertNsave(arr,file_dir, index=0):
    """
    `arr`: parameter will take a numpy array that represents only one slice.
    `file_dir`: parameter will take the path to save the slices
    `index`: parameter will represent the index of the slice, so this parameter will be used to put 
    the name of each slice while using a for loop to convert all the slices
    """
    
    dicom_file = pydicom.dcmread('images/dcmimage.dcm')
    arr = arr.astype('uint16')
    dicom_file.Rows = arr.shape[0]
    dicom_file.Columns = arr.shape[1]
    dicom_file.PhotometricInterpretation = "MONOCHROME2"
    dicom_file.SamplesPerPixel = 1
    dicom_file.BitsStored = 16
    dicom_file.BitsAllocated = 16
    dicom_file.HighBit = 15
    dicom_file.PixelRepresentation = 1
    dicom_file.PixelData = arr.tobytes()
    dicom_file.save_as(os.path.join(file_dir, f'slice{index}.dcm'))


def nifti2dicom_1file(nifti_dir, out_dir):
    """
    This function is to convert only one nifti file into dicom series

    `nifti_dir`: the path to the one nifti file
    `out_dir`: the path to output
    """

    nifti_file = nibabel.load(nifti_dir)
    nifti_array = nifti_file.get_fdata()
    number_slices = nifti_array.shape[2]

    for slice_ in tqdm(range(number_slices)):
        convertNsave(nifti_array[:,:,slice_], out_dir, slice_)


def nifti2dicom_mfiles(nifti_dir, out_dir=''):
    """
    This function is to convert multiple nifti files into dicom files

    `nifti_dir`: You enter the global path to all of the nifti files here.
    `out_dir`: Put the path to where you want to save all the dicoms here.

    PS: Each nifti file's folders will be created automatically, so you do not need to create an empty folder for each patient.
    """

    files = os.listdir(nifti_dir)
    for file in files:
        in_path = os.path.join(nifti_dir, file)
        out_path = os.path.join(out_dir, file)
        os.mkdir(out_path)
        nifti2dicom_1file(in_path, out_path)
            
if __name__ == '__main__':
    nifti_dir="E:\\bigorgs\\cardiovascular\\workspace\\Medical_tools\\nifti\\"
    out_dir="E:\\bigorgs\\cardiovascular\\workspace\\Medical_tools\\out\\"
    nifti2dicom_mfiles(nifti_dir,out_dir)