def test_anatomical(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_ge.dicom_to_nifti(
read_dicom_directory(test_data.GE_ANATOMICAL), None)
self.assertTrue(results.get('NII_FILE') is None)
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_ge.dicom_to_nifti(
read_dicom_directory(test_data.GE_ANATOMICAL),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GE_ANATOMICAL)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_ge.dicom_to_nifti(
read_dicom_directory(test_data.GE_ANATOMICAL_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GE_ANATOMICAL_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 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_anatomical(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_ANATOMICAL),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_ANATOMICAL)[0]) is True
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_ANATOMICAL_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_ANATOMICAL_IMPLICIT)[0]) is True
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_ENHANCED_ANATOMICAL),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_ENHANCED_ANATOMICAL)[0]) is True
self.assertRaises(
ConversionError, convert_philips.dicom_to_nifti,
read_dicom_directory(
test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
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),
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_anatomical(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_philips.dicom_to_nifti(read_dicom_directory(test_data.PHILIPS_ANATOMICAL),
None)
self.assertTrue(results.get('NII_FILE') is None)
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_philips.dicom_to_nifti(read_dicom_directory(test_data.PHILIPS_ANATOMICAL),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.PHILIPS_ANATOMICAL)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_philips.dicom_to_nifti(read_dicom_directory(test_data.PHILIPS_ANATOMICAL_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.PHILIPS_ANATOMICAL_IMPLICIT)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_philips.dicom_to_nifti(read_dicom_directory(test_data.PHILIPS_ENHANCED_ANATOMICAL),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.PHILIPS_ENHANCED_ANATOMICAL)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
self.assertRaises(ConversionError,
convert_philips.dicom_to_nifti,
read_dicom_directory(test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
finally:
shutil.rmtree(tmp_output_dir)
def test_anatomical(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_ANATOMICAL),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GE_ANATOMICAL)[0]) == True
results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_ANATOMICAL_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GE_ANATOMICAL_IMPLICIT)[0]) == True
finally:
shutil.rmtree(tmp_output_dir)
def test_diffusion_images_old(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI_OLD),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GE_DTI_OLD)[0]) is True
finally:
shutil.rmtree(tmp_output_dir)
def test_diffusion_images_old(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI_OLD),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GE_DTI_OLD)[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_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_FMRI), None)
self.assertTrue(results.get('NII_FILE') is None)
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_FMRI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.PHILIPS_FMRI)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_FMRI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.PHILIPS_FMRI_IMPLICIT)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_ENHANCED_FMRI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.PHILIPS_ENHANCED_FMRI)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
self.assertRaises(
ConversionError, convert_philips.dicom_to_nifti,
read_dicom_directory(test_data.PHILIPS_ENHANCED_FMRI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
finally:
shutil.rmtree(tmp_output_dir)
def test_anatomical_implicit(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.disable_validate_multiframe_implicit()
results = convert_philips.dicom_to_nifti(read_dicom_directory(
test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
settings.enable_validate_multiframe_implicit()
finally:
shutil.rmtree(tmp_output_dir)
def test_anatomical_implicit(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.disable_validate_multiframe_implicit()
results = convert_philips.dicom_to_nifti(
read_dicom_directory(
test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_ENHANCED_ANATOMICAL_IMPLICIT)[0]) is True
settings.enable_validate_multiframe_implicit()
finally:
shutil.rmtree(tmp_output_dir)
def test_anatomical(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_generic.dicom_to_nifti(read_dicom_directory(test_data.GE_ANATOMICAL),
None)
self.assertTrue(results.get('NII_FILE') is None)
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_generic.dicom_to_nifti(read_dicom_directory(test_data.GE_ANATOMICAL),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GE_ANATOMICAL)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
finally:
shutil.rmtree(tmp_output_dir)
def test_single_slice(self):
tmp_output_dir = tempfile.mkdtemp()
try:
settings.disable_validate_slicecount()
results = convert_generic.dicom_to_nifti(
read_dicom_directory(test_data.GE_ANATOMICAL_SINGLE_SLICE),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GE_ANATOMICAL_SINGLE_SLICE)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
finally:
settings.enable_validate_slicecount()
shutil.rmtree(tmp_output_dir)
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 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 test_diffusion_images(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_ge.dicom_to_nifti(
read_dicom_directory(test_data.GE_DTI), None)
self.assertTrue(results.get('NII_FILE') is None)
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
self.assertTrue(results.get('BVAL_FILE') is None)
self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
self.assertTrue(results.get('BVEC_FILE') is None)
self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
results = convert_ge.dicom_to_nifti(
read_dicom_directory(test_data.GE_DTI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GE_DTI)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
assert_compare_bval(results['BVAL_FILE'],
ground_thruth_filenames(test_data.GE_DTI)[2])
self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
assert_compare_bval(results['BVEC_FILE'],
ground_thruth_filenames(test_data.GE_DTI)[3])
self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
convert_ge.dicom_to_nifti(
read_dicom_directory(test_data.GE_DTI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
assert_compare_bval(
results['BVAL_FILE'],
ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[2])
self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
assert_compare_bval(
results['BVEC_FILE'],
ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[3])
self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
finally:
shutil.rmtree(tmp_output_dir)
def test_diffusion_images(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GE_DTI)[0]) == True
assert compare_bval(results['BVAL_FILE'],
ground_thruth_filenames(test_data.GE_DTI)[2]) == True
assert compare_bvec(results['BVEC_FILE'],
ground_thruth_filenames(test_data.GE_DTI)[3]) == True
convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[0]) == True
assert compare_bval(results['BVAL_FILE'],
ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[2]) == True
assert compare_bvec(results['BVEC_FILE'],
ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[3]) == True
finally:
shutil.rmtree(tmp_output_dir)
def test_diffusion_images(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI),
None)
self.assertTrue(results.get('NII_FILE') is None)
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
self.assertTrue(results.get('BVAL_FILE') is None)
self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
self.assertTrue(results.get('BVEC_FILE') is None)
self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
results = convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GE_DTI)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
assert_compare_bval(results['BVAL_FILE'],
ground_thruth_filenames(test_data.GE_DTI)[2])
self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
assert_compare_bval(results['BVEC_FILE'],
ground_thruth_filenames(test_data.GE_DTI)[3])
self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
convert_ge.dicom_to_nifti(read_dicom_directory(test_data.GE_DTI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[0])
self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
assert_compare_bval(results['BVAL_FILE'],
ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[2])
self.assertTrue(isinstance(results['BVAL'], numpy.ndarray))
assert_compare_bval(results['BVEC_FILE'],
ground_thruth_filenames(test_data.GE_DTI_IMPLICIT)[3])
self.assertTrue(isinstance(results['BVEC'], numpy.ndarray))
finally:
shutil.rmtree(tmp_output_dir)
def test_anatomical(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL)[0]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL)[1]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL_IMPLICIT)[1]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL)[0]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL)[1]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL_IMPLICIT)[0]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL_IMPLICIT)[1]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_COMPRESSED)[0]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_COMPRESSED)[1]) is True
results = convert_dicom.dicom_series_to_nifti(
test_data.HITACHI_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.HITACHI_ANATOMICAL)[1]) is True
finally:
shutil.rmtree(tmp_output_dir)
def test_anatomical(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL, None, False)
self.assertTrue(results.get('NII_FILE') is None)
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL_IMPLICIT)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL_IMPLICIT)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL_IMPLICIT)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_NON_ISOTROPIC,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_NON_ISOTROPIC)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[0])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
results = convert_dicom.dicom_series_to_nifti(
test_data.HITACHI_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.HITACHI_ANATOMICAL)[1])
self.assertTrue(
isinstance(results['NII'], nibabel.nifti1.Nifti1Image))
finally:
shutil.rmtree(tmp_output_dir)
def test_main_function(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = dicom2nifti.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[0])
results = dicom2nifti.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[1])
results = dicom2nifti.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0])
results = dicom2nifti.dicom_series_to_nifti(
test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.SIEMENS_ANATOMICAL_IMPLICIT)[1])
results = dicom2nifti.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[0])
results = dicom2nifti.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[1])
results = dicom2nifti.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL_IMPLICIT)[0])
results = dicom2nifti.dicom_series_to_nifti(
test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.GENERIC_ANATOMICAL_IMPLICIT)[1])
results = dicom2nifti.dicom_series_to_nifti(
test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'), False)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[0])
results = dicom2nifti.dicom_series_to_nifti(
test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'), True)
assert_compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[1])
finally:
shutil.rmtree(tmp_output_dir)
def test_diffusion_imaging(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_DTI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.PHILIPS_DTI)[0]) is True
assert compare_bval(
results['BVAL_FILE'],
ground_thruth_filenames(test_data.PHILIPS_DTI)[2]) is True
assert compare_bvec(
results['BVEC_FILE'],
ground_thruth_filenames(test_data.PHILIPS_DTI)[3]) is True
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_DTI_002),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(test_data.PHILIPS_DTI_002)[0]) is True
assert compare_bval(
results['BVAL_FILE'],
ground_thruth_filenames(test_data.PHILIPS_DTI_002)[2]) is True
assert compare_bvec(
results['BVEC_FILE'],
ground_thruth_filenames(test_data.PHILIPS_DTI_002)[3]) is True
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_ENHANCED_DTI),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_ENHANCED_DTI)[0]) is True
assert compare_bval(
results['BVAL_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_ENHANCED_DTI)[2]) is True
assert compare_bvec(
results['BVEC_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_ENHANCED_DTI)[3]) is True
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_DTI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_DTI_IMPLICIT)[0]) is True
assert compare_bval(
results['BVAL_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_DTI_IMPLICIT)[2]) is True
assert compare_bvec(
results['BVEC_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_DTI_IMPLICIT)[3]) is True
results = convert_philips.dicom_to_nifti(
read_dicom_directory(test_data.PHILIPS_DTI_IMPLICIT_002),
os.path.join(tmp_output_dir, 'test.nii.gz'))
assert compare_nifti(
results['NII_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_DTI_IMPLICIT_002)[0]) is True
assert compare_bval(
results['BVAL_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_DTI_IMPLICIT_002)[2]) is True
assert compare_bvec(
results['BVEC_FILE'],
ground_thruth_filenames(
test_data.PHILIPS_DTI_IMPLICIT_002)[3]) is True
self.assertRaises(
ConversionError, convert_philips.dicom_to_nifti,
read_dicom_directory(test_data.PHILIPS_ENHANCED_DTI_IMPLICIT),
os.path.join(tmp_output_dir, 'test.nii.gz'))
finally:
shutil.rmtree(tmp_output_dir)
def test_main_function(self):
tmp_output_dir = tempfile.mkdtemp()
try:
results = dicom2nifti.dicom_series_to_nifti(test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'),
False)
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[0])
results = dicom2nifti.dicom_series_to_nifti(test_data.SIEMENS_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'),
True)
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL)[1])
results = dicom2nifti.dicom_series_to_nifti(test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'),
False)
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL_IMPLICIT)[0])
results = dicom2nifti.dicom_series_to_nifti(test_data.SIEMENS_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'),
True)
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.SIEMENS_ANATOMICAL_IMPLICIT)[1])
results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'),
False)
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[0])
results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_ANATOMICAL,
os.path.join(tmp_output_dir, 'test.nii.gz'),
True)
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_ANATOMICAL)[1])
results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'),
False)
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_ANATOMICAL_IMPLICIT)[0])
results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_ANATOMICAL_IMPLICIT,
os.path.join(tmp_output_dir, 'test.nii.gz'),
True)
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_ANATOMICAL_IMPLICIT)[1])
results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'),
False)
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[0])
results = dicom2nifti.dicom_series_to_nifti(test_data.GENERIC_COMPRESSED,
os.path.join(tmp_output_dir, 'test.nii.gz'),
True)
assert_compare_nifti(results['NII_FILE'],
ground_thruth_filenames(test_data.GENERIC_COMPRESSED)[1])
finally:
shutil.rmtree(tmp_output_dir)
