def test_4d(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_siemens.dicom_to_nifti(
read_dicom_directory(test_data.SIEMENS_FMRI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_FMRI)[0]) is True
results = convert_siemens.dicom_to_nifti(
read_dicom_directory(test_data.SIEMENS_FMRI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_FMRI_IMPLICIT)[0]) is True
results = convert_siemens.dicom_to_nifti(
read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_CLASSIC_FMRI)[0]) is True
results = convert_siemens.dicom_to_nifti(
read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT)[0]) is True
finally:
shutil.rmtree(tmp_output_dir)
def test_4d(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI),
None)
self.assertTrue(results.get('NII_FILE') is None)
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_FMRI)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_FMRI_IMPLICIT)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_CLASSIC_FMRI)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
finally:
shutil.rmtree(tmp_output_dir)
def test_4d(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI),
None)
self.assertTrue(results.get('NII_FILE') is None)
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_FMRI)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_FMRI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_FMRI_IMPLICIT)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_CLASSIC_FMRI)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_siemens.dicom_to_nifti(read_dicom_directory(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_CLASSIC_FMRI_IMPLICIT)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
finally:
shutil.rmtree(tmp_output_dir)
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:
results['NII'] = image_reorientation.reorient_image(
results['NII'], results['NII_FILE'])
# resampling needs to be after reorientation
if settings.resample:
if not common.is_orthogonal_nifti(results['NII']):
results['NII'] = resample.resample_single_nifti(
results['NII'], 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 test_diffusion_imaging(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_siemens.dicom_to_nifti(
read_dicom_directory(test_data.SIEMENS_DTI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_DTI)[0]) == True
assert compare_bval(
results['BVAL_FILE'],
ground_thruth_filenames(test_data.SIEMENS_DTI)[2]) == True
assert compare_bvec(
results['BVEC_FILE'],
ground_thruth_filenames(test_data.SIEMENS_DTI)[3]) == True
results = convert_siemens.dicom_to_nifti(
read_dicom_directory(test_data.SIEMENS_DTI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_DTI_IMPLICIT)[0]) == True
assert compare_bval(
results['BVAL_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_DTI_IMPLICIT)[2]) == True
assert compare_bvec(
results['BVEC_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_DTI_IMPLICIT)[3]) == True
results = convert_siemens.dicom_to_nifti(
read_dicom_directory(test_data.SIEMENS_CLASSIC_DTI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_CLASSIC_DTI)[0]) == True
assert compare_bval(
results['BVAL_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_CLASSIC_DTI)[2]) == True
assert compare_bvec(
results['BVEC_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_CLASSIC_DTI)[3]) == True
results = convert_siemens.dicom_to_nifti(
read_dicom_directory(test_data.SIEMENS_CLASSIC_DTI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_CLASSIC_DTI_IMPLICIT)[0]) == True
assert compare_bval(
results['BVAL_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_CLASSIC_DTI_IMPLICIT)[2]) == True
assert compare_bvec(
results['BVEC_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_CLASSIC_DTI_IMPLICIT)[3]) == True
finally:
shutil.rmtree(tmp_output_dir)
