def assert_compare_nifti(nifti_file_1, nifti_file_2):
logging.info("%s %s" % (nifti_file_1, nifti_file_2))
work_dir = tempfile.mkdtemp()
try:
tmp_nifti_file_1 = os.path.join(work_dir,
os.path.basename(nifti_file_1))
tmp_nifti_file_2 = os.path.join(work_dir,
os.path.basename(nifti_file_2))
image_reorientation.reorient_image(nifti_file_1, tmp_nifti_file_1)
image_reorientation.reorient_image(nifti_file_2, tmp_nifti_file_2)
nifti_1 = nibabel.load(tmp_nifti_file_1)
nifti_2 = nibabel.load(tmp_nifti_file_2)
# check the affine
if not numpy.allclose(nifti_1.affine, nifti_2.affine):
raise Exception('affine mismatch')
# check the data
if nifti_1.get_data_dtype() != nifti_2.get_data_dtype():
raise Exception('dtype mismatch')
if not numpy.allclose(nifti_1.get_data(), nifti_2.get_data()):
raise Exception('data mismatch')
except:
shutil.rmtree(work_dir)
def compare_nifti(nifti_file_1, nifti_file_2):
result = True
logging.info("%s %s" % (nifti_file_1, nifti_file_2))
work_dir = tempfile.mkdtemp()
try:
tmp_nifti_file_1 = os.path.join(work_dir,
os.path.basename(nifti_file_1))
tmp_nifti_file_2 = os.path.join(work_dir,
os.path.basename(nifti_file_2))
image_reorientation.reorient_image(nifti_file_1, tmp_nifti_file_1)
image_reorientation.reorient_image(nifti_file_2, tmp_nifti_file_2)
nifti_1 = nibabel.load(tmp_nifti_file_1)
nifti_2 = nibabel.load(tmp_nifti_file_2)
# check the affine
if not numpy.allclose(nifti_1.affine, nifti_2.affine):
logging.warning('affine mismatch')
result = False
# check the data
if nifti_1.get_data_dtype() != nifti_2.get_data_dtype():
logging.warning('dtype mismatch')
result = False
if not (nifti_1.get_data() == nifti_2.get_data()).all():
logging.warning('data mismatch')
result = False
except:
shutil.rmtree(work_dir)
return result
def dicom_array_to_nifti(dicom_list, output_file, reorient_nifti=True):
""" Converts dicom single series (see pydicom) to nifty, mimicking SPM
Examples: See unit test
will return a dictionary containing
- the NIFTI under key 'NIFTI'
- the NIFTI file path under 'NII_FILE'
- the BVAL file path under 'BVAL_FILE' (only for dti)
- the BVEC file path under 'BVEC_FILE' (only for dti)
IMPORTANT:
If no specific sequence type can be found it will default to anatomical and try to convert.
You should check that the data you are trying to convert is supported by this code
Inspired by http://nipy.sourceforge.net/nibabel/dicom/spm_dicom.html
Inspired by http://code.google.com/p/pydicom/source/browse/source/dicom/contrib/pydicom_series.py
:param reorient_nifti: if True the nifti affine and data will be updated so the data is stored LAS oriented
:param output_file: file path to write to
:param dicom_list: list with uncompressed dicom objects as read by pydicom
"""
# copy files so we can can modify without altering the original
if not are_imaging_dicoms(dicom_list):
raise ConversionValidationError('NON_IMAGING_DICOM_FILES')
vendor = _get_vendor(dicom_list)
if vendor == Vendor.GENERIC:
results = convert_generic.dicom_to_nifti(dicom_list, output_file)
elif vendor == Vendor.SIEMENS:
results = convert_siemens.dicom_to_nifti(dicom_list, output_file)
elif vendor == Vendor.GE:
results = convert_ge.dicom_to_nifti(dicom_list, output_file)
elif vendor == Vendor.PHILIPS:
results = convert_philips.dicom_to_nifti(dicom_list, output_file)
elif vendor == Vendor.HITACHI:
results = convert_hitachi.dicom_to_nifti(dicom_list, output_file)
else:
raise ConversionValidationError("UNSUPPORTED_DATA")
# do image reorientation if needed
if reorient_nifti or settings.resample:
image_reorientation.reorient_image(results['NII_FILE'],
results['NII_FILE'])
# resampling needs to be after reorientation
if settings.resample:
if not common.is_orthogonal_nifti(results['NII_FILE']):
resample.resample_single_nifti(results['NII_FILE'])
return results
def dicom_array_to_nifti(dicom_list, output_file, reorient_nifti=True):
""" Converts dicom single series (see pydicom) to nifty, mimicking SPM
Examples: See unit test
will return a dictionary containing
- the NIFTI under key 'NIFTI'
- the NIFTI file path under 'NII_FILE'
- the BVAL file path under 'BVAL_FILE' (only for dti)
- the BVEC file path under 'BVEC_FILE' (only for dti)
IMPORTANT:
If no specific sequence type can be found it will default to anatomical and try to convert.
You should check that the data you are trying to convert is supported by this code
Inspired by http://nipy.sourceforge.net/nibabel/dicom/spm_dicom.html
Inspired by http://code.google.com/p/pydicom/source/browse/source/dicom/contrib/pydicom_series.py
:param reorient_nifti: if True the nifti affine and data will be updated so the data is stored LAS oriented
:param output_file: file path to write to
:param dicom_list: list with uncompressed dicom objects as read by pydicom
"""
# copy files so we can can modify without altering the original
if not are_imaging_dicoms(dicom_list):
raise ConversionValidationError('NON_IMAGING_DICOM_FILES')
vendor = _get_vendor(dicom_list)
if vendor == Vendor.GENERIC:
results = convert_generic.dicom_to_nifti(dicom_list, output_file)
elif vendor == Vendor.SIEMENS:
results = convert_siemens.dicom_to_nifti(dicom_list, output_file)
elif vendor == Vendor.GE:
results = convert_ge.dicom_to_nifti(dicom_list, output_file)
elif vendor == Vendor.PHILIPS:
results = convert_philips.dicom_to_nifti(dicom_list, output_file)
elif vendor == Vendor.HITACHI:
results = convert_hitachi.dicom_to_nifti(dicom_list, output_file)
else:
raise ConversionValidationError("UNSUPPORTED_DATA")
# do image reorientation if needed
if reorient_nifti or settings.resample:
image_reorientation.reorient_image(results['NII_FILE'], results['NII_FILE'])
# resampling needs to be after reorientation
if settings.resample:
if not common.is_orthogonal_nifti(results['NII_FILE']):
resample.resample_single_nifti(results['NII_FILE'])
return results
def main():
for root, dir_names, _ in os.walk(os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
'dicom2nifti',
'tests',
'data')):
settings.disable_validate_multiframe_implicit()
# New directory
for dir_name in dir_names:
dir_path = os.path.join(root, dir_name)
if subdir_count(dir_path) > 0:
continue # not processing because not lowest level of directory
print(dir_path)
output_file = dir_path + '_ground_truth.nii.gz'
reoriented_file = dir_path + '_ground_truth_reoriented.nii.gz'
# noinspection PyBroadException
try:
dicom2nifti.dicom_series_to_nifti(dir_path, output_file, False)
image_reorientation.reorient_image(output_file, reoriented_file)
except: # explicitly capturing everything here
pass
def assert_compare_nifti(nifti_file_1, nifti_file_2):
logging.info("%s %s" % (nifti_file_1, nifti_file_2))
work_dir = tempfile.mkdtemp()
try:
tmp_nifti_file_1 = os.path.join(work_dir, os.path.basename(nifti_file_1))
tmp_nifti_file_2 = os.path.join(work_dir, os.path.basename(nifti_file_2))
image_reorientation.reorient_image(nifti_file_1, tmp_nifti_file_1)
image_reorientation.reorient_image(nifti_file_2, tmp_nifti_file_2)
nifti_1 = nibabel.load(tmp_nifti_file_1)
nifti_2 = nibabel.load(tmp_nifti_file_2)
# check the affine
if not numpy.allclose(nifti_1.affine, nifti_2.affine):
raise Exception('affine mismatch')
# check the data
if nifti_1.get_data_dtype() != nifti_2.get_data_dtype():
raise Exception('dtype mismatch')
if not numpy.allclose(nifti_1.get_data(), nifti_2.get_data()):
raise Exception('data mismatch')
except:
shutil.rmtree(work_dir)
raise
def generate_ground_truth(dicom_directory, output_file, reoriented_file):
if not os.path.isfile(output_file):
dicom2nifti.dicom_series_to_nifti(dicom_directory, output_file, False)
image_reorientation.reorient_image(output_file, reoriented_file)
def generate_ground_truth(dicom_directory, output_file, reoriented_file):
if not os.path.isfile(output_file):
dicom2nifti.dicom_series_to_nifti(dicom_directory, output_file, False)
image_reorientation.reorient_image(output_file, reoriented_file)
