def test_write_struct():
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
# Trigger a warning
pfo_study_in = os.path.join(root_dir, 'test_data', 'bru_banana')
scan2struct(pfo_study_in)
# manage warning in python 2 or python 3:
if sys.version_info[0] == 3:
assert len(w) == 1
assert issubclass(w[-1].category, UserWarning)
else:
import exceptions
assert len(w) == 1
assert issubclass(w[-1].category, exceptions.UserWarning)
pfo_scan_in = os.path.join(root_dir, 'test_data', 'bru_banana', '1')
banana_struct = scan2struct(pfo_scan_in)
pfo_output = os.path.join(root_dir, 'test_data', 'nifti_banana', 'write_struct_here')
if not os.path.exists(pfo_output):
os.system('mkdir {}'.format(pfo_output))
write_struct(banana_struct, pfo_output, fin_scan='test')
assert os.path.exists(os.path.join(pfo_output, 'acquisition_method.txt'))
assert os.path.exists(os.path.join(pfo_output, 'test.nii.gz'))
def test_scan2struct_with_banana_data_slope_no_slope():
pfo_scan_in = os.path.join(root_dir, 'test_data', 'bru_banana', '1')
struct_no_slope_corrected = scan2struct(pfo_scan_in, correct_slope=False)
struct_yes_slope_corrected = scan2struct(pfo_scan_in, correct_slope=True)
parsed_slope_from_no = struct_no_slope_corrected['visu_pars_list'][0]['VisuCoreDataSlope']
parsed_slope_from_yes = struct_yes_slope_corrected['visu_pars_list'][0]['VisuCoreDataSlope']
ground_slope = np.array([11.02701887, ] * 5)
# check general structure:
assert_equal(struct_no_slope_corrected['nib_scans_list'][0].shape,
struct_yes_slope_corrected['nib_scans_list'][0].shape)
assert_array_equal(parsed_slope_from_no, parsed_slope_from_yes)
np.testing.assert_array_almost_equal(parsed_slope_from_no, ground_slope)
assert_equal(struct_no_slope_corrected['acqp'], {})
assert_equal(struct_no_slope_corrected['reco'], {})
assert_equal(struct_no_slope_corrected['method'], {})
# check data of the nibabel images:
np.testing.assert_array_almost_equal(ground_slope[0] * struct_no_slope_corrected['nib_scans_list'][0].get_data(),
struct_yes_slope_corrected['nib_scans_list'][0].get_data(), decimal=4)
def test_scan2struct_with_banana_data_slope_no_slope():
pfo_scan_in = os.path.join(root_dir, "test_data", "bru_banana", "1")
struct_no_slope_corrected = scan2struct(pfo_scan_in, correct_slope=False)
struct_yes_slope_corrected = scan2struct(pfo_scan_in, correct_slope=True)
parsed_slope_from_no = struct_no_slope_corrected["visu_pars_list"][0][
"VisuCoreDataSlope"]
parsed_slope_from_yes = struct_yes_slope_corrected["visu_pars_list"][0][
"VisuCoreDataSlope"]
ground_slope = np.array([11.02701887] * 5)
# check general structure:
assert_equal(
struct_no_slope_corrected["nib_scans_list"][0].shape,
struct_yes_slope_corrected["nib_scans_list"][0].shape,
)
assert_array_equal(parsed_slope_from_no, parsed_slope_from_yes)
np.testing.assert_array_almost_equal(parsed_slope_from_no, ground_slope)
assert_equal(struct_no_slope_corrected["acqp"], {})
assert_equal(struct_no_slope_corrected["reco"], {})
assert_equal(struct_no_slope_corrected["method"], {})
# check data of the nibabel images:
np.testing.assert_array_almost_equal(
ground_slope[0] *
struct_no_slope_corrected["nib_scans_list"][0].get_data(),
struct_yes_slope_corrected["nib_scans_list"][0].get_data(),
decimal=4,
)
def convert_scan(self,
pfo_input_scan,
pfo_output_converted,
nifti_file_name=None,
create_output_folder_if_not_exists=True):
"""
:param pfo_input_scan: path to folder (pfo) containing a scan from Bruker, see documentation for the difference
between Bruker 'scan' and Bruker 'study'.
:param pfo_output_converted: path to the folder where the converted scan will be stored.
:param create_output_folder_if_not_exists: [True] if the output folder does not exist will be created.
:param nifti_file_name: [None] filename of the nifti image that will be saved into the pfo_output folder.
If None, the filename will be obtained from the parameter file of the study.
:return: [None] save the data parsed from the raw Bruker scan into a folder, including the nifti image.
"""
if not os.path.isdir(pfo_input_scan):
raise IOError('Input folder does not exist.')
if create_output_folder_if_not_exists:
os.makedirs(pfo_output_converted)
print('FRAME BODY {}'.format(self.frame_body_as_frame_head))
print('UPSIDE DOWN {}'.format(self.sample_upside_down))
struct_scan = scan2struct(
pfo_input_scan,
correct_slope=self.correct_slope,
correct_offset=self.correct_offset,
sample_upside_down=self.sample_upside_down,
nifti_version=self.nifti_version,
qform_code=self.qform_code,
sform_code=self.sform_code,
get_acqp=self.get_acqp,
get_method=self.get_method,
get_reco=self.get_reco,
frame_body_as_frame_head=self.frame_body_as_frame_head)
if struct_scan is not None:
write_struct(
struct_scan,
pfo_output_converted,
fin_scan=nifti_file_name,
save_human_readable=self.save_human_readable,
save_b0_if_dwi=self.save_b0_if_dwi,
verbose=self.verbose,
)
