def testDefaultConstruction(self):
""" Testing the default construction of the class using a dictionary. """
# Attempt to construct an instance of the class.
parameters = EMCOrientationParameters()
# Check instance and inheritance.
self.assertIsInstance(parameters, EMCOrientationParameters)
self.assertIsInstance(parameters, AbstractCalculatorParameters)
# Check all parameters are set to default values.
self.assertTrue(parameters.beamstop)
self.assertTrue(parameters.detailed_output)
self.assertEqual(parameters.initial_number_of_quaternions, 1)
self.assertEqual(parameters.max_number_of_quaternions, 2)
self.assertEqual(parameters.min_error, 1.e-5)
self.assertEqual(parameters.max_number_of_iterations, 100)
def testConstructionParameters(self):
""" Testing the construction of the class with a parameters object. """
# Construct the object.
emc_parameters = EMCOrientationParameters(
initial_number_of_quaternions=2,
max_number_of_quaternions=4,
max_number_of_iterations=5,
min_error=1.e-6,
beamstop=False,
detailed_output=False)
analyzer = EMCOrientation(parameters=emc_parameters)
# Test a parameter.
self.assertEqual(analyzer.parameters.initial_number_of_quaternions, 2)
self.assertIsInstance(analyzer, EMCOrientation)
def testLegacyDictionary(self):
""" Check parameter object can be initialized via a old-style dictionary. """
parameter_dict = {
'initial_number_of_quaternions': 1,
'max_number_of_quaternions': 9,
'max_number_of_iterations': 200,
'min_error': 1.0e-8,
'beamstop': False,
'detailed_output': False
}
parameters = EMCOrientationParameters(
parameters_dictionary=parameter_dict)
# Check all parameters are set to default values.
self.assertFalse(parameters.beamstop)
self.assertFalse(parameters.detailed_output)
self.assertEqual(parameters.initial_number_of_quaternions, 1)
self.assertEqual(parameters.max_number_of_quaternions, 9)
self.assertEqual(parameters.min_error, 1.e-8)
self.assertEqual(parameters.max_number_of_iterations, 200)
def __init__(self,
parameters=None,
input_path=None,
output_path=None,
tmp_files_path=None,
run_files_path=None):
"""
:param parameters: Parameters for the EMC orientation calculator.
:type parameters: EMCOrientationParameters instance
:param input_path: Path to directory holding input data for EMC.
:type input_path: str
:param output_path: Path to file where output data will be stored.
:type output_path: str
:param tmp_files_path: Path to directory where temporary files will be stored.
:type tmp_files_path: str
:param run_files_path: Path to directory where run data will be stored, in particular the sparse photons file 'photons.dat' and 'detector.dat'.
:type run_files_path: str
:note: If 'run_files_path' is an existing directory that contains data from a previous EMC run, the current run will append to the
existing data. A consistency check is performed.
"""
# Check parameters.
if isinstance(parameters, dict):
parameters = EMCOrientationParameters(
parameters_dictionary=parameters)
# Set default parameters is no parameters given.
if parameters is None:
parameters = checkAndSetInstance(EMCOrientationParameters,
parameters,
EMCOrientationParameters())
else:
parameters = checkAndSetInstance(EMCOrientationParameters,
parameters, None)
# Initialize base class.
super(EMCOrientation, self).__init__(parameters, input_path,
output_path)
self.__provided_data = [
'data/data',
'data/angle',
'data/center',
'params/info',
'version',
]
self.__expected_data = [
'/data/data',
'/data/diffr',
'/data/angle',
'/params/geom/detectorDist',
'/params/geom/pixelWidth',
'/params/geom/pixelHeight',
'/params/geom/mask',
'/params/beam/photonEnergy',
'/params/beam/photons',
'/params/beam/focusArea',
]
# Set run and tmp files paths.
if _checkPaths(run_files_path, tmp_files_path):
self.run_files_path = run_files_path
self.tmp_files_path = tmp_files_path