Dicom Resample and Save as nii

"""
convert dcm 2 nii
1. read dicom series
2. clarify and sort series
3. skip scout series
4. convert series to 3d
5. resample and save as nii## usage ##
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-- parent(root)|-- Folder1(subdir)|    ||    -- DICOMS/  -- 4d-dicom file-- Folder2|-- DICOMS
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input: root
output: subdir, include several nii files determined by seriesdependencies:
python 3.9.2 (used for log)
SimpleITK
numpylogging:
support output to console and file"""import SimpleITK as sitk
import numpy as np
import logging
from pathlib import Pathdef set_logger(mylogger, file):mylogger.setLevel(logging.DEBUG)# create file handler which logs even debug messagesfh = logging.FileHandler(file)fh.setLevel(logging.DEBUG)# create console handler with a higher log levelch = logging.StreamHandler()ch.setLevel(logging.DEBUG)# create formatter and add it to the handlersformatter = logging.Formatter('%(asctime)s [%(name)s] [%(levelname)s] %(message)s')ch.setFormatter(formatter)fh.setFormatter(formatter)# add the handlers to loggermylogger.addHandler(ch)mylogger.addHandler(fh)# resample image using new spacing
def resample_image(itk_image, out_spacing):original_spacing = itk_image.GetSpacing()original_size = itk_image.GetSize()# image size according to new spacingout_size = [int(np.round(original_size[0] * original_spacing[0] / out_spacing[0])),int(np.round(original_size[1] * original_spacing[1] / out_spacing[1])),int(np.round(original_size[2] * original_spacing[2] / out_spacing[2]))]resample = sitk.ResampleImageFilter()resample.SetOutputSpacing(out_spacing)resample.SetSize(out_size)resample.SetOutputDirection(itk_image.GetDirection())resample.SetOutputOrigin(itk_image.GetOrigin())resample.SetTransform(sitk.Transform())resample.SetDefaultPixelValue(itk_image.GetPixelIDValue())resample.SetInterpolator(sitk.sitkBSpline)# print(resample)return resample.Execute(itk_image)# read and save nii file
# def resample_nii(input_path, out_file):
#     original_img = sitk.ReadImage(input_path)
#     resample_nii_image(original_img, out_file)def resample_nii_image(nii_img, out_file):pix_spacing = nii_img.GetSpacing()logger.info('Original image Spacing：')logger.info(pix_spacing)logger.info('Original image Size：')logger.info(nii_img.GetSize())new_pix_spacing = [pix_spacing[0], pix_spacing[0], pix_spacing[0]]resample_img = resample_image(nii_img, new_pix_spacing)logger.info('Resampled image Spacing：')logger.info(resample_img.GetSpacing())logger.info('Resampled image Size：')logger.info(resample_img.GetSize())sitk.WriteImage(resample_img, out_file)def convert_dcm2nii_resample(directory_path):reader = sitk.ImageSeriesReader()reader.MetaDataDictionaryArrayUpdateOn()reader.LoadPrivateTagsOn()series_ids = sitk.ImageSeriesReader.GetGDCMSeriesIDs(directory_path)arr_index = 0for series_ID in series_ids:arr_index += 1logger.info("series id: " + series_ID)dicom_names = reader.GetGDCMSeriesFileNames(directory_path, series_ID)# if 3 == arr_index:#     dicom_names = dicom_names[1409:2152]# else:#     print("skip series number: ", str(arr_index))#     continuereader.SetFileNames(dicom_names)image3d = reader.Execute()series_number = reader.GetMetaData(0, '0020|0011')# series_description = reader.GetMetaData(0, '0008|103e')# if series_number == '3 ':#     dicom_names = dicom_names[1409:2152]#     reader.SetFileNames(dicom_names)#     image3d = reader.Execute()# else:#     print("skip series number: ", str(series_number))#     continue# determine if it is scout protocolslice_number = 0# slice_keys = reader.GetMetaDataKeys(slice_number)# reader.HasMetaDataKey(slice_number, '0008|0008')# image typeimage_type = reader.GetMetaData(slice_number, '0008|0008')scout_flag = "LOCALIZER"if scout_flag in image_type:logger.info("skip scout")continue# saved pathsave_path = Path(directory_path).parent.as_posix()# save_path = save_path + "//" + str(series_number)+ "_" + str(series_description) + ".nii.gz"save_path = save_path + "//" + str(series_number) + "_" + ".nii.gz"# save_path = re.sub(r"[\n\t\s]*", "", save_path)# save_path1 = save_path.strip()# resampleresample_nii_image(image3d, save_path)logger.info("saved file: ")logger.info(save_path)def get_paths(input_path, out_paths):path = Path(input_path)for subdir in path.iterdir():if subdir.is_dir():get_paths(subdir, out_paths)else:if "nii.gz" in subdir.name:continueelse:out_paths.append(subdir.parent)breakdef main():path = Path(r"C:\Data\mydata\SID221153")logger.info("--------------------task begin-----------------------")input_dir = []get_paths(path, input_dir)logger.info("folder size: " + str(len(input_dir)))logger.info(input_dir)for convert_dir in input_dir:logger.info("---begin dir---")logger.info(convert_dir)convert_dcm2nii_resample(Path(convert_dir).as_posix())logger.info("---finish dir---")logger.info("--------------------task finish-----------------------")logger = logging.getLogger('dcm2nii')
set_logger(logger, "log/convert_test.log")if __name__ == '__main__':main()