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_not_a_volume(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.disable_validate_orthogonal()
with self.assertRaises(ConversionError) as exception:
convert_generic.dicom_to_nifti(
read_dicom_directory(test_data.FAILING_NOTAVOLUME),
os.path.join(tmp_output_dir, 'test.nii.gz'))
self.assertEqual(str(exception.exception), 'NOT_A_VOLUME')
finally:
settings.enable_validate_orthogonal()
shutil.rmtree(tmp_output_dir)
def test_not_a_volume(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.disable_validate_orthogonal()
with self.assertRaises(ConversionError) as exception:
convert_generic.dicom_to_nifti(read_dicom_directory(test_data.FAILING_NOTAVOLUME),
os.path.join(tmp_output_dir, 'test.nii.gz'))
self.assertEqual(str(exception.exception),
'NOT_A_VOLUME')
finally:
settings.enable_validate_orthogonal()
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/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)
def convertDicom2Nifti( inputFiles,outputDirectory ):
mapOfFileNames = {}
settings.disable_validate_orientation()
settings.disable_validate_orthogonal()
settings.disable_validate_slice_increment()
import asyncio
from pydicom import dcmread
from pydicom.tag import Tag
import dicom2nifti
import os
import pathlib
from pydcmq import *
import dicom2nifti.settings as settings
settings.disable_validate_orthogonal()
settings.disable_validate_slice_increment()
settings.enable_resampling()
settings.set_resample_spline_interpolation_order(1)
settings.set_resample_padding(-1024)
async def dcmhandler(channel, ds, uri, routing_key):
print(f"dcm2niix: converting {uri} ({ds.SeriesDescription})")
outdir = f"{os.environ['HOME']}/.dcmq/nii/{ds.StudyInstanceUID}"
pathlib.Path(outdir).mkdir(parents=True, exist_ok=True)
count = 0
with os.scandir(uri) as it:
for series in it:
if series.is_dir():
with os.scandir(series) as it2:
for instance in it2:
if instance.is_file():
dcmfilename = instance.name
break
refds = dcmread(os.path.join(uri, series.name, dcmfilename))
try: