def convert_ima(input_dir, output_dir):
import dicom2nifti
import dicom2nifti.settings as settings
settings.disable_validate_orthogonal()
settings.enable_resampling()
settings.set_resample_spline_interpolation_order(1)
settings.set_resample_padding(-1000)
dicom2nifti.convert_directory(input_dir, output_dir)
def test_convert_directory(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.enable_resampling()
settings.set_resample_spline_interpolation_order(1)
settings.set_resample_padding(-1000)
settings.disable_validate_slice_increment()
settings.disable_validate_orthogonal()
convert_directory.convert_directory("/Users/abrys/Downloads/dicom_CT_UNKNOWN_3",
"/Users/abrys/Downloads")
finally:
shutil.rmtree(tmp_output_dir)
def test_convert_directory(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.enable_resampling()
settings.set_resample_spline_interpolation_order(1)
settings.set_resample_padding(-1000)
settings.disable_validate_slice_increment()
settings.disable_validate_orthogonal()
convert_directory.convert_directory("/Users/abrys/Downloads/test",
"/Users/abrys/Downloads")
finally:
shutil.rmtree(tmp_output_dir)
def generate_inconsistent_slice_incement():
settings.disable_validate_orthogonal()
settings.disable_validate_slice_increment()
settings.enable_resampling()
settings.set_resample_padding(0)
settings.set_resample_spline_interpolation_order(1)
dicom_directory = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'tests',
'data', 'failing', 'sliceincrement', '002')
output_file = dicom_directory + '_ground_truth.nii.gz'
reoriented_file = dicom_directory + '_ground_truth_reoriented.nii.gz'
generate_ground_truth(dicom_directory, output_file, reoriented_file)
settings.disable_resampling()
settings.enable_validate_slice_increment()
settings.enable_validate_orientation()
def test_inconsistent_slice_increment_resampling(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.disable_validate_orthogonal()
settings.disable_validate_slice_increment()
settings.enable_resampling()
settings.set_resample_padding(0)
settings.set_resample_spline_interpolation_order(1)
results = convert_generic.dicom_to_nifti(read_dicom_directory(test_data.FAILING_SLICEINCREMENT_2),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.FAILING_SLICEINCREMENT_2)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
finally:
settings.disable_resampling()
settings.enable_validate_slice_increment()
settings.enable_validate_orientation()
shutil.rmtree(tmp_output_dir)
def generate_inconsistent_slice_incement():
settings.disable_validate_orthogonal()
settings.disable_validate_slice_increment()
settings.enable_resampling()
settings.set_resample_padding(0)
settings.set_resample_spline_interpolation_order(1)
dicom_directory = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
'tests',
'data',
'failing',
'sliceincrement',
'002')
output_file = dicom_directory + '_ground_truth.nii.gz'
reoriented_file = dicom_directory + '_ground_truth_reoriented.nii.gz'
generate_ground_truth(dicom_directory, output_file, reoriented_file)
settings.disable_resampling()
settings.enable_validate_slice_increment()
settings.enable_validate_orientation()
def test_inconsistent_slice_increment_resampling(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.disable_validate_orthogonal()
settings.disable_validate_slice_increment()
settings.enable_resampling()
settings.set_resample_padding(0)
settings.set_resample_spline_interpolation_order(1)
results = convert_generic.dicom_to_nifti(
read_dicom_directory(test_data.FAILING_SLICEINCREMENT_2),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.FAILING_SLICEINCREMENT_2)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
finally:
settings.disable_resampling()
settings.enable_validate_slice_increment()
settings.enable_validate_orientation()
shutil.rmtree(tmp_output_dir)
def setUp(self):
settings.disable_validate_orthogonal()
settings.enable_resampling()
settings.set_resample_padding(-1000)
settings.set_resample_spline_interpolation_order(1)
# Import necessary dcm2niix python wrapper
import dicom2nifti
import dicom2nifti.settings as settings
# Set settings for conversion
settings.enable_resampling()
settings.set_resample_spline_interpolation_order(1)
settings.set_resample_padding(-3024)
dicom2nifti.settings.disable_validate_orthogonal()
# Get directory of .dcm folder
import os
import shutil
dirs = os.listdir("D:\MDRP/train/")
# I'm going to output the file to a temporary folder because I can't rename the file
# The script names the file as the modality instead of original folder name and I can't find how to change it in the python wrapper
temp_folder = 'D:\MDRP/preprocessing/temp/'
# This is the main output folder where we want our correctly named files
output_folder = 'D:\MDRP/preprocessing/nifti_output/'
for file in dirs:
try:
original_file = file
# First we list the directories
dicom_directory = 'D:\MDRP/train/' + (original_file)
# Converting a file in the dcm directory to the temp folder
# [email protected], [email protected], [email protected] import os, argparse, dicom2nifti, dicom2nifti.settings as settings from tqdm import tqdm if __name__ == '__main__': parser = argparse.ArgumentParser('Dicom2Nifti') parser.add_argument('--dicom', type=str, default=None, help='Directory for DICOM Image Series/Directories') parser.add_argument('--output', type=str, default=None, help='Output NIFTI Filename/Directory') parser.add_argument('--batch', action='store_true', default=False, help='Batch Generation') settings.disable_validate_slice_increment() settings.enable_resampling() settings.set_resample_spline_interpolation_order(1) settings.set_resample_padding(-1000) '''Ref: https://dicom2nifti.readthedocs.io/en/latest/_modules/dicom2nifti/convert_dicom.html#dicom_series_to_nifti''' '''Ref: https://dicom2nifti.readthedocs.io/en/latest/readme.html#from-python''' args = parser.parse_args() if args.batch: os.mkdir(args.output) if not os.path.exists(args.output) else None for dir_ in tqdm(os.listdir(args.dicom)): # dicom2nifti.convert_directory(args.dicom, args.output) intputd = os.path.join(args.dicom, dir_) outputf = os.path.join(args.output, dir_) dicom2nifti.convert_dicom.dicom_series_to_nifti(intputd, outputf) else: dicom2nifti.convert_dicom.dicom_series_to_nifti(args.dicom, args.output)