def test_multiple_files(self):
params = make_params()
params.file_name = TEST_DIR
find_rotation_axis(params)
self.assertEqual(params.rotation_axis, 31.5)
# Check YAML file
with open(YAML_FILE, mode='r') as yfp:
yaml_output = yaml.safe_load(yfp.read())
self.assertEqual(yaml_output['test_tomogram.h5']['rotation-axis'],
31.5)
def read_rot_center(params):
"""
Read the rotation center from /process group in the DXchange file.
Return: rotation center from this dataset or None if it doesn't exist.
"""
log.info(' *** *** rotation axis')
#First, try to read from the /process/tomopy-cli parameters
with h5py.File(params.file_name, 'r') as file_name:
try:
dataset = '/process' + '/tomopy-cli-' + __version__ + '/' + 'find-rotation-axis' + '/' + 'rotation-axis'
params.rotation_axis = float(file_name[dataset][0])
log.info(
' *** *** Rotation center read from HDF5 file: {0:f}'.format(
params.rotation_axis))
return params
except (KeyError, ValueError):
log.warning(' *** *** No rotation center stored in the HDF5 file')
#If we get here, we need to either find it automatically or from config file.
log.warning(' *** *** No rotation axis stored in DXchange file')
if (params.rotation_axis_auto == True):
log.warning(' *** *** Auto axis location requested')
log.warning(' *** *** Computing rotation axis')
params.rotation_axis = find_center.find_rotation_axis(params)
log.info(' *** *** using config file value of {:f}'.format(
params.rotation_axis))
return params
def read_rot_center(params):
"""
Read the rotation center from /process group in the HDF file.
Return: rotation center from this dataset or None if it doesn't exist.
"""
log.info(' *** *** rotation axis')
# Handle case of manual only: this is the easiest
if params.rotation_axis_auto == 'manual':
log.info(' *** *** Force use of config file value = {:f}'.format(
params.rotation_axis))
elif params.rotation_axis_auto == 'auto':
log.info(
' *** *** Force auto calculation without reading config value')
log.info(' *** *** Computing rotation axis')
params = find_center.find_rotation_axis(params)
else:
# Try to read from HDF5 file
log.info(' *** *** Try to read rotation center from file {}'.format(
params.file_name))
with h5py.File(params.file_name, 'r') as file_name:
try:
dataset = '/process/tomopy-cli-{}/find-rotation-axis/rotation-axis'.format(
__version__)
params.rotation_axis = float(file_name[dataset][0])
dataset = '/process/tomopy-cli-{}/find-rotation-axis/rotation-axis-flip'.format(
__version__)
params.rotation_axis_flip = float(file_name[dataset][0])
log.info(
' *** *** Rotation center read from HDF5 file: {0:f}'.
format(params.rotation_axis))
log.info(
' *** *** Rotation center flip read from HDF5 file: {0:f}'
.format(params.rotation_axis_flip))
return params
except (KeyError, ValueError):
log.warning(
' *** *** No rotation center stored in the HDF5 file')
# If we get here, we need to either find it automatically or from config file.
log.warning(' *** *** No rotation axis stored in the HDF file')
if (params.rotation_axis_auto == 'read_auto'):
log.warning(' *** *** fall back to auto calculation')
log.warning(' *** *** Computing rotation axis')
params = find_center.find_rotation_axis(params)
else:
log.warning(' *** *** using config file value of {:f}'.format(
params.rotation_axis))
return params
def run_find_center(args):
if (str(args.file_format) in KNOWN_FORMATS):
log.warning('find center start')
args = find_center.find_rotation_axis(args)
log.warning('find center end')
# update tomopy.conf
sections = config.RECON_PARAMS
config.update_config(args, is_reconstruction=False)
else:
log.error(" *** %s is not a supported file format" % args.file_format)
exit()
def test_single_file(self):
params = make_params()
find_rotation_axis(params)
self.assertEqual(params.rotation_axis, 31.5)