def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: Parameters of the calculation (not data).
:type parameters: dict || AbstractCalculatorParameters
:param input_path: Path to hdf5 file holding the input data.
:type input_path: str
:param output_path: Path to hdf5 file for output.
:type output_path: str
"""
# Check input path. Raises if none given.
input_path = checkAndSetInstance(str, input_path, None)
# Check output path. Set default if none given.
output_path = checkAndSetInstance(str, output_path, 'source')
# Init base class.
super(AbstractPhotonSource, self).__init__(parameters, input_path, output_path)
# Setup provided data groups and sets.
self.__provided_data = ['/data/arrEhor',
'/data/arrEver',
'/params/Mesh/nSlices',
'/params/Mesh/nx',
'/params/Mesh/ny',
'/params/Mesh/sliceMax',
'/params/Mesh/sliceMin',
'/params/Mesh/xMax',
'/params/Mesh/xMin',
'/params/Mesh/yMax',
'/params/Mesh/yMin',
'/params/Mesh/zCoord',
'/params/Rx',
'/params/Ry',
'/params/dRx',
'/params/dRy',
'/params/nval',
'/params/photonEnergy',
'/params/wDomain',
'/params/wEFieldUnit',
'/params/wFloatType',
'/params/wSpace',
'/params/xCentre',
'/params/yCentre',
'/history/parent/info/data_description',
'/history/parent/info/package_version',
'/history/parent/misc/FAST2XY.DAT',
'/history/parent/misc/angular_distribution',
'/history/parent/misc/spot_size',
'/history/parent/misc/gain_curve',
'/history/parent/misc/nzc',
'/history/parent/misc/temporal_struct',
'/version',
]
# Setup expected data.
self.__expected_data = [d for d in self.__provided_data]
def testCheckAndSetInstanceDerived(self):
""" Test the check and set utility works correctly also for abstract data and derived types. """
# Check works for a derived type.
class my_baseclass(object):
def __init__(self, var1, var2):
self.__var1 = var1
self.__var2 = var2
class my_derived_class(my_baseclass):
def __init__(self, var1, var2, var3):
super(my_derived_class, self).__init__(1.0, 2.0)
self.__var3 = var3
mc_base = my_baseclass(1.0, 2.0)
mc_derived = my_derived_class(1.0, 2.0, 3.0)
check_ok = True
try:
checked_base_class = checkAndSetInstance(my_baseclass, mc_base)
checked_derived_class = checkAndSetInstance(my_derived_class, mc_derived)
checked_derived_class2 = checkAndSetInstance(my_baseclass, mc_derived)
except:
check_ok = False
self.assertTrue(check_ok)
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
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
Constructor for the Abstract Photon Detector.
"""
# Check input path. Set to default if none given.
input_path = checkAndSetInstance(str, input_path, 'diffr')
# Check output path. Set default if none given.
output_path = checkAndSetInstance(str, output_path, 'detector')
# Initialize the base class.
super(AbstractPhotonDetector, self).__init__(parameters, input_path, output_path)
def checkAndSetModelSee( model ):
"""
Utility to check if the model is a valid model for the high frequency (dynamic) feature.
@param model : The model to check.
<br/><b>type</b> : str
@return : The checked model
@raise ValueError if not a string or not a valid See0 model ('RPA', 'BMA', 'BMA+sLFC', 'BMA+dLFC', 'LFC', 'Landen')
"""
# Default handling.
model = checkAndSetInstance( str, model, 'RPA')
# Valid models.
valid_models = ['RPA',
'Lindhard',
'static LFC',
'dynamic LFC',
'BMA',
'BMA+sLFC',
'BMA+dLFC',
]
if model not in valid_models:
raise ValueError( "The See model must be a valid See0 model. Valid See0 models are %s." % (str(valid_models)) )
# Return
return model
def pmi_stop_ID(self, value):
""" Set the 'pmi_stop_ID' parameter to a given value.
:param value: The value to set 'pmi_stop_ID' to.
"""
pmi_stop_ID = checkAndSetInstance(int, value, 1)
if pmi_stop_ID >= 0:
self.__pmi_stop_ID = pmi_stop_ID
else:
raise ValueError("The parameters 'pmi_stop_ID' must be a positive integer.")
def photon_response(self, val):
""" Set the panel photon_response. """
if val is not None:
val = checkAndSetInstance(float, val, None)
self.__photon_response = val
# Invalidate energy response.
if val is not None and self.__energy_response is not None:
self.__energy_response = None
def pmi_stop_ID(self, value):
""" Set the 'pmi_stop_ID' parameter to a given value.
:param value: The value to set 'pmi_stop_ID' to.
"""
pmi_stop_ID = checkAndSetInstance(int, value, 1)
if pmi_stop_ID >= 0:
self.__pmi_stop_ID = pmi_stop_ID
else:
raise ValueError(
"The parameters 'pmi_stop_ID' must be a positive integer.")
def min_error(self, value):
""" Set the 'min_error' parameter to a given value.
:param value: The value to set 'min_error' to.
"""
min_error = checkAndSetInstance( float, value, 1.e-5 )
if min_error > 0:
self.__min_error = min_error
else:
raise ValueError( "The parameter 'min_error' must be a positive float.")
def max_number_of_iterations(self, value):
""" Set the 'max_number_of_iterations' parameter to a given value.
:param value: The value to set 'max_number_of_iterations' to.
"""
max_number_of_iterations = checkAndSetInstance( int, value, 100 )
if max_number_of_iterations > 0:
self.__max_number_of_iterations = max_number_of_iterations
else:
raise ValueError( "The parameter 'max_number_of_iterations' must be a positive integer.")
def number_of_MPI_processes(self, value):
""" Set the 'number_of_MPI_processes' parameter to a given value.
:param value: The value to set 'number_of_MPI_processes' to.
"""
number_of_MPI_processes = checkAndSetInstance(int, value, 2)
if number_of_MPI_processes > 0:
self.__number_of_MPI_processes = number_of_MPI_processes
else:
raise ValueError("The parameters 'number_of_MPI_processes' must be a positive integer.")
def initial_number_of_quaternions(self, value):
""" Set the 'initial_number_of_quaternions' parameter to a given value.
:param value: The value to set 'initial_number_of_quaternions' to.
"""
initial_number_of_quaternions = checkAndSetInstance( int, value, 1 )
if all([initial_number_of_quaternions > 0, initial_number_of_quaternions < 10]):
self.__initial_number_of_quaternions = initial_number_of_quaternions
else:
raise ValueError( "Parameter 'initial_number_of_quaternions' must be an integer (0 < n < 10)")
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: Parameters of the calculation (not data).
:type parameters: dict || AbstractCalculatorParameters
:param input_path: Path to hdf5 file holding the input data.
:type input_path: str
:param output_path: Path to hdf5 file for output.
:type output_path: str
"""
# Check input path. Set to default if none given.
input_path = checkAndSetInstance(str, input_path, 'prop')
# Check output path. Set default if none given.
output_path = checkAndSetInstance(str, output_path, 'pmi')
super(AbstractPhotonInteractor, self).__init__(parameters, input_path, output_path)
def checkAndSetLFC(lfc):
""" Utility to check if input is a valid local field correction factor.
@param lfc : The lfc to check.
<br/><b>type</b> : double
@return : The checked lfc.
"""
lfc = checkAndSetInstance(float, lfc, 0.0)
return lfc
def number_of_diffraction_patterns(self, value):
""" Set the 'number_of_diffraction_patterns' parameter to a given value.
:param value: The value to set 'number_of_diffraction_patterns' to.
"""
number_of_diffraction_patterns = checkAndSetInstance( int, value, 1 )
if number_of_diffraction_patterns > 0:
self.__number_of_diffraction_patterns = number_of_diffraction_patterns
else:
raise ValueError("The parameters 'number_of_diffraction_patterns' must be a positive integer.")
def slice_interval(self, value):
""" Set the 'slice_interval' parameter to a given value.
:param value: The value to set 'slice_interval' to.
"""
slice_interval = checkAndSetInstance(int, value, 100)
if slice_interval > 0:
self.__slice_interval = slice_interval
else:
raise ValueError("The parameter 'slice_interval' must be a positive integer.")
def number_of_diffraction_patterns(self, value):
""" Set the 'number_of_diffraction_patterns' parameter to a given value.
:param value: The value to set 'number_of_diffraction_patterns' to.
"""
number_of_diffraction_patterns = checkAndSetInstance(int, value, 1)
if number_of_diffraction_patterns > 0:
self.__number_of_diffraction_patterns = number_of_diffraction_patterns
else:
raise ValueError("The parameters 'number_of_diffraction_patterns' must be a positive integer.")
def number_of_shrink_cycles(self, value):
""" Set the 'number_of_shrink_cycles' parameter to a given value.
:param value : The value to set 'number_of_shrink_cycles' to.
:type value: int
"""
number_of_shrink_cycles = checkAndSetInstance(int, value, 10)
if number_of_shrink_cycles > 0:
self.__number_of_shrink_cycles = number_of_shrink_cycles
else:
raise ValueError("The parameter 'number_of_shrink_cycles' must be a positive integer.")
def max_number_of_quaternions(self, value):
""" Set the 'max_number_of_quaternions' parameter to a given value.
:param value: The value to set 'max_number_of_quaternions' to.
"""
max_number_of_quaternions = checkAndSetInstance( int, value, self.__initial_number_of_quaternions+1 )
if all([ max_number_of_quaternions <= 10, max_number_of_quaternions > self.initial_number_of_quaternions]):
self.__max_number_of_quaternions = max_number_of_quaternions
else:
raise ValueError( "Parameter 'max_number_of_quaternions' must be an integer (initial_number_of_quaternions < n <= 10)")
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: Parameters of the calculation (not data).
:type parameters: dict || AbstractCalculatorParameters
:param input_path: Path to hdf5 file holding the input data.
:type input_path: str
:param output_path: Path to hdf5 file for output.
:type output_path: str
"""
# Check input path. Set to default if none given.
input_path = checkAndSetInstance(str, input_path, 'prop')
# Check output path. Set default if none given.
output_path = checkAndSetInstance(str, output_path, 'pmi')
super(AbstractPhotonInteractor, self).__init__(parameters, input_path, output_path)
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: Phasing parameters.
:type parameters: DMPhasingParameters instance
:param input_path: Path to input data (file or directory).
:type input_path: str
:param output_path: Path to output data (file or directory).
:type output_path: str
"""
# Check parameters.
if isinstance(parameters, dict):
parameters = DMPhasingParameters(parameters_dictionary=parameters)
# Set default parameters is no parameters given.
if parameters is None:
parameters = checkAndSetInstance(DMPhasingParameters, parameters,
DMPhasingParameters())
else:
parameters = checkAndSetInstance(DMPhasingParameters, parameters,
None)
super(DMPhasing, self).__init__(parameters, input_path, output_path)
self.__expected_data = [
'/data/data',
'/data/angle',
'/data/center',
'/params/info',
'/version',
]
self.__provided_data = [
'/data/electronDensity',
'/params/info',
'/history',
'/info',
'/misc',
'/version',
]
def checkAndSetLFC(lfc):
""" Utility to check if input is a valid local field correction factor.
@param lfc : The lfc to check.
<br/><b>type</b> : double
@return : The checked lfc.
"""
lfc = checkAndSetInstance(float, lfc, 0.0)
return lfc
def checkAndSetPhotonDetector(var=None, default=None):
"""
Check if passed object is an AbstractPhotonDetector instance. If non is given, set to given default.
:param var: The object to check.
:param default: The default to use.
:return: The checked photon source object.
:raises RuntimeError: if no valid PhotonDetector was given.
"""
return checkAndSetInstance(AbstractPhotonDetector, var, default)
def min_error(self, value):
""" Set the 'min_error' parameter to a given value.
:param value: The value to set 'min_error' to.
"""
min_error = checkAndSetInstance(float, value, 1.e-5)
if min_error > 0:
self.__min_error = min_error
else:
raise ValueError(
"The parameter 'min_error' must be a positive float.")
def checkAndSetPhotonDiffractor(var=None, default=None):
"""
Check if passed object is an AbstractPhotonDiffractor instance. If non is given, set to given default.
@param var : The object to check.
@param default : The default to use.
@return : The checked photon source object.
@throw : RuntimeError if no valid PhotonDiffractor was given.
"""
return checkAndSetInstance(AbstractPhotonDiffractor, var, default)
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: Parameters of the calculation (not data).
:type parameters: CrystFELPhotonDiffractorParameters
:param input_path: Path to hdf5 file holding the input data.
:type input_path: str
:param output_path: Path to hdf5 file for output.
:type output_path: str
"""
# Set default parameters if no parameters given.
if parameters is None:
raise ValueError( "Parameters must at least specify the sample structure, e.g. in pdb format.")
else:
self.__parameters = checkAndSetInstance( CrystFELPhotonDiffractorParameters, parameters, None )
# Dummy input path since none required (we don't read from a beam propgation yet.)
if input_path is None:
input_path = os.path.dirname(__file__)
else:
if parameters.beam_parameters is not None:
raise RuntimeError("Beam parameters can only be passed through the parameters object or via the input_path argument.")
parameters.beam_parameters = propToBeamParameters( input_path )
if output_path is None:
output_path = os.path.join(os.path.dirname(__file__), "diffr")
# Init base class.
super(CrystFELPhotonDiffractor, self).__init__(parameters,input_path,output_path)
### FIXME
self.__provided_data = [
'/data/data',
'/data/diffr',
'/data/angle',
'/history/parent/detail',
'/history/parent/parent',
'/info/package_version',
'/info/contact',
'/info/data_description',
'/info/method_description',
'/params/geom/detectorDist',
'/params/geom/pixelWidth',
'/params/geom/pixelHeight',
'/params/geom/mask',
'/params/beam/photonEnergy',
'/params/beam/photons',
'/params/beam/focusArea',
'/params/info',
]
def leash(self, value):
""" Set the 'leash' parameter to a given value.
:param value: The value to set 'leash' to.
:type value: float
"""
leash = checkAndSetInstance(float, value, 0.2)
if leash > 0:
self.__leash = leash
else:
raise ValueError("The parameter 'leash' must be a positive integer.")
def number_of_trials(self, value):
""" Set the 'number_of_trials' parameter to a given value.
:param value: The value to set 'number_of_trials' to.
:type value: int
"""
number_of_trials = checkAndSetInstance(int, value, 500)
if all([number_of_trials > 0]):
self.__number_of_trials = number_of_trials
else:
raise ValueError("Parameter 'number_of_trials' must be an integer (n > 0)")
def averaging_start(self, value):
""" Set the 'averaging_start' parameter to a given value.
:param value: The value to set 'averaging_start' to.
:type value: int
"""
averaging_start = checkAndSetInstance(int, value, 15)
if averaging_start > 0:
self.__averaging_start = averaging_start
else:
raise ValueError("The parameter 'averaging_start' must be a positive integer.")
def geometry(self, value):
""" Set the 'geometry' parameter to a given value.
:param value: The value to set 'geometry' to.
"""
self.__geometry = checkAndSetInstance( str, value, None )
if self.__geometry is not None:
if not os.path.isfile( self.__geometry):
raise IOError("The geometry %s is not a valid file or filename." % (self.__geometry) )
else:
print ("WARNING: Geometry file not set, calculation will most probably fail.")
def slice_interval(self, value):
""" Set the 'slice_interval' parameter to a given value.
:param value: The value to set 'slice_interval' to.
"""
slice_interval = checkAndSetInstance(int, value, 100)
if slice_interval > 0:
self.__slice_interval = slice_interval
else:
raise ValueError(
"The parameter 'slice_interval' must be a positive integer.")
def checkAndSetPhotonPropagator(var=None, default=None):
"""
Check if passed object is an AbstractPhotonPropagator instance. If non is given, set to given default.
:param var: The object to check
:param default: The default to use
:return: The checked photon source object
:raise RuntimeError: if no valid PhotonPropagator was given.
"""
return checkAndSetInstance(AbstractPhotonPropagator, var, default)
def checkAndSetPhotonAnalyzer(var=None, default=None):
"""
Check if passed object is an AbstractPhotonAnalyzer instance. If non is given, set to given default.
@param var : The object to check.
@param default : The default to use.
@return : The checked photon source object.
@throw : RuntimeError if no valid PhotonAnalyzer was given.
"""
return checkAndSetInstance(AbstractPhotonAnalyzer, var, default)
def number_of_slices(self, value):
""" Set the 'number_of_slices' parameter to a given value.
:param value: The value to set 'number_of_slices' to.
"""
number_of_slices = checkAndSetInstance(int, value, 1)
if number_of_slices > 0:
self.__number_of_slices = number_of_slices
else:
raise ValueError(
"The parameter 'slice_interval' must be a positive integer.")
def number_of_trials(self, value):
""" Set the 'number_of_trials' parameter to a given value.
:param value: The value to set 'number_of_trials' to.
:type value: int
"""
number_of_trials = checkAndSetInstance(int, value, 500)
if all([number_of_trials > 0]):
self.__number_of_trials = number_of_trials
else:
raise ValueError(
"Parameter 'number_of_trials' must be an integer (n > 0)")
def number_of_shrink_cycles(self, value):
""" Set the 'number_of_shrink_cycles' parameter to a given value.
:param value : The value to set 'number_of_shrink_cycles' to.
:type value: int
"""
number_of_shrink_cycles = checkAndSetInstance(int, value, 10)
if number_of_shrink_cycles > 0:
self.__number_of_shrink_cycles = number_of_shrink_cycles
else:
raise ValueError(
"The parameter 'number_of_shrink_cycles' must be a positive integer."
)
def averaging_start(self, value):
""" Set the 'averaging_start' parameter to a given value.
:param value: The value to set 'averaging_start' to.
:type value: int
"""
averaging_start = checkAndSetInstance(int, value, 15)
if averaging_start > 0:
self.__averaging_start = averaging_start
else:
raise ValueError(
"The parameter 'averaging_start' must be a positive integer.")
def leash(self, value):
""" Set the 'leash' parameter to a given value.
:param value: The value to set 'leash' to.
:type value: float
"""
leash = checkAndSetInstance(float, value, 0.2)
if leash > 0:
self.__leash = leash
else:
raise ValueError(
"The parameter 'leash' must be a positive integer.")
def max_number_of_iterations(self, value):
""" Set the 'max_number_of_iterations' parameter to a given value.
:param value: The value to set 'max_number_of_iterations' to.
"""
max_number_of_iterations = checkAndSetInstance(int, value, 100)
if max_number_of_iterations > 0:
self.__max_number_of_iterations = max_number_of_iterations
else:
raise ValueError(
"The parameter 'max_number_of_iterations' must be a positive integer."
)
def checkAndSetIO(io):
""" Check the passed io path/filenames and set appropriately. """
# Check we have a tuple.
io = checkAndSetInstance(tuple, io)
if len(io) != 2:
raise exceptions.RuntimeError("The parameter 'io' can only be a tuple of two strings.")
# Check if input exists, if not, raise.
i = checkAndSetInstance(str, io[0])
if i is None:
raise exceptions.IOError("The parameter 'input_path' must be a valid filename.")
i = os.path.abspath(i)
#
# Check if output file exists, otherwise attempt to create it.
o = checkAndSetInstance(str, io[1])
if o is None:
raise exceptions.IOError("The parameter 'output_path' must be a valid filename.")
o = os.path.abspath(o)
return (i, o)
def checkAndSetIO(io):
""" Check the passed io path/filenames and set appropriately. """
# Check we have a tuple.
io = checkAndSetInstance(tuple, io)
if len(io) != 2:
raise RuntimeError("The parameter 'io' can only be a tuple of two strings.")
# Check if input exists, if not, raise.
i = checkAndSetInstance(str, io[0])
if i is None:
raise IOError("The parameter 'input_path' must be a valid filename.")
i = os.path.abspath(i)
#
# Check if output file exists, otherwise attempt to create it.
o = checkAndSetInstance(str, io[1])
if o is None:
raise IOError("The parameter 'output_path' must be a valid filename.")
o = os.path.abspath(o)
return (i, o)
def __init__(self, input_path=None):
"""
:param input_path: Path to hdf5 file holding the data to analyze. Single file or directory.
:type input_path: str
"""
if input_path is None:
raise ValueError("The parameter 'input_path' cannot be None.")
self.__input_path = checkAndSetInstance(str, input_path, None)
def beam_parameters(self, value):
""" Set the 'beam_parameters' parameter to a given value.
:param value: The value to set 'beam_parameters' to.
"""
if value is None:
print ("WARNING: Beam parameters not set, will use crystFEL/pattern_sim defaults.")
self.__beam_parameters = checkAndSetInstance( (str, PhotonBeamParameters), value, None )
if isinstance(self.__beam_parameters, str):
if not os.path.isfile( self.__beam_parameters):
raise IOError("The beam_parameters %s is not a valid file or filename." % (self.__beam_parameters) )
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
Constructor for the phasing analyser.
:param parameters: Phasing parameters.
:type parameters: DMPhasingParameters instance
:param input_path: Path to input data (file or directory).
:type input_path: str
:param output_path: Path to output data (file or directory).
:type output_path: str
"""
# Check parameters.
if isinstance( parameters, dict ):
parameters = DMPhasingParameters( parameters_dictionary = parameters )
# Set default parameters is no parameters given.
if parameters is None:
parameters = checkAndSetInstance( DMPhasingParameters, parameters, DMPhasingParameters() )
else:
parameters = checkAndSetInstance( DMPhasingParameters, parameters, None )
super(DMPhasing, self).__init__(parameters,input_path,output_path)
self.__expected_data = ['/data/data',
'/data/angle',
'/data/center',
'/params/info',
'/version',]
self.__provided_data = ['/data/electronDensity',
'/params/info',
'/history',
'/info',
'/misc',
'/version',
]
def beam_geometry_file(self, value):
""" Set the 'beam_geometry_file' parameter to a given value.
:param value: The value to set 'beam_geometry_file' to.
"""
self.__beam_geometry_file = checkAndSetInstance(str, value, None)
if self.__beam_geometry_file is not None:
if not os.path.isfile(self.__beam_geometry_file):
raise IOError(
"The beam_parameter_file %s is not a valid file or filename." % (self.__beam_geometry_file)
)
else:
print("WARNING: Geometry file not set, calculation will most probably fail.")
def checkAndSetElectronTemperature(electron_temperature):
""" Utility to check if input is a valid electron temperature.
@param electron_temperature : The electron temperature to check.
<br/><b>type</b> : double
@return : The checked electron temperature.
"""
if electron_temperature is None:
raise RuntimeError( "Electron temperature not specified.")
electron_temperature = checkAndSetInstance( float, electron_temperature, None)
if electron_temperature <= 0.0:
raise ValueError( "Electron temperature must be positive.")
return electron_temperature
def testCheckAndSetInstanceDefault(self):
""" Check that setting the default works correctly. """
# Setup default, and class.
default = 1.0
tp = int
# Check raises because default not of correct type.
self.assertRaises(exceptions.TypeError, checkAndSetInstance, tp, None, default)
default = 1
# Use the utility to set the variable to the default.
var = checkAndSetInstance(tp, None, default)
self.assertEqual(var, default)
def checkAndSetElectronTemperature(electron_temperature):
""" Utility to check if input is a valid electron temperature.
@param electron_temperature : The electron temperature to check.
<br/><b>type</b> : double
@return : The checked electron temperature.
"""
if electron_temperature is None:
raise RuntimeError("Electron temperature not specified.")
electron_temperature = checkAndSetInstance(float, electron_temperature,
None)
if electron_temperature <= 0.0:
raise ValueError("Electron temperature must be positive.")
return electron_temperature
def checkAndSetElements(elements):
""" Utility to check if input is a valid list of elements.
@param elements: The elements to check.
<br/><b>type</b> elements: list
@return: The checked list of elements.
"""
if elements is None:
raise RuntimeError( "No element(s) specified. Give at least one chemical element.")
elements = checkAndSetInstance( list, elements, None )
# Check each element.
for element in elements:
symbol, stoch, chrg = checkAndSetInstance( list, element, None )
if symbol not in ALL_ELEMENTS:
raise ValueError( '%s is not a valid chemical element symbol.' % (symbol) )
stoch = checkAndSetPositiveInteger(stoch)
chrg = checkAndSetInteger(chrg)
if chrg < -1:
raise ValueError( "Charge must be >= -1.")
element = [symbol, stoch, chrg]
return elements
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: Parameters of the calculation (not data).
:type parameters: dict || AbstractCalculatorParameters
:param input_path: Path to hdf5 file holding the input data.
:type input_path: str
:param output_path: Path to hdf5 file for output.
:type output_path: str
"""
# Check input path. Set to default if none given.
input_path = checkAndSetInstance(str, input_path, 'detector')
# Check output path. Set default if none given.
o_path = checkAndSetInstance(str, output_path, 'analysis')
if output_path is None:
os.makedirs( os.path.abspath( o_path) )
output_path = o_path
# Initialize the base class.
super(AbstractPhotonAnalyzer, self).__init__(parameters, input_path, output_path)
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: Parameters of the calculation (not data).
:type parameters: dict || AbstractCalculatorParameters
:param input_path: Path to hdf5 file holding the input data.
:type input_path: str
:param output_path: Path to hdf5 file for output.
:type output_path: str
"""
# Check input path. Set to default if none given.
input_path = checkAndSetInstance(str, input_path, 'detector')
# Check output path. Set default if none given.
o_path = checkAndSetInstance(str, output_path, 'analysis')
if output_path is None:
os.makedirs( os.path.abspath( o_path) )
output_path = o_path
# Initialize the base class.
super(AbstractPhotonAnalyzer, self).__init__(parameters, input_path, output_path)
def testCheckAndSetInstanceDefault(self):
""" Check that setting the default works correctly. """
# Setup default, and class.
default = 1.0
tp = int
# Check raises because default not of correct type.
self.assertRaises(TypeError, checkAndSetInstance, tp, None, default)
default = 1
# Use the utility to set the variable to the default.
var = checkAndSetInstance(tp, None, default)
self.assertEqual(var, default)
def initial_number_of_quaternions(self, value):
""" Set the 'initial_number_of_quaternions' parameter to a given value.
:param value: The value to set 'initial_number_of_quaternions' to.
"""
initial_number_of_quaternions = checkAndSetInstance(int, value, 1)
if all([
initial_number_of_quaternions > 0,
initial_number_of_quaternions < 10
]):
self.__initial_number_of_quaternions = initial_number_of_quaternions
else:
raise ValueError(
"Parameter 'initial_number_of_quaternions' must be an integer (0 < n < 10)"
)
def checkAndSetBaseCalculator(var=None, default=None):
"""
Check if passed object is an AbstractAnalysis instance. If non is given, set to given default.
:param var: The object to check.
:param default: The default to use.
:return: The checked object.
:raises RuntimeError: if no valid Analysis object was given.
"""
return checkAndSetInstance(AbstractAnalysis, var, default)
def checkAndSetBandGap(band_gap):
""" Utility to check if input is a valid bandgap.
@param band_gap: The bandgap to check.
<br/><b>type</b> : double
<br/><b>default</b> 0.0.
@return : The checked bandgap.
"""
if band_gap is None:
return None
band_gap = checkAndSetInstance( float, band_gap, 0.0)
if band_gap < 0.0:
raise ValueError( "Debye temperature must be positive.")
return band_gap
def checkAndSetDebyeTemperature(debye_temperature):
""" Utility to check if input is a valid Debye temperature.
@param debye_temperature : The Debye temperature to check.
<br/><b>type</b> : double
<br/><b>default</b> : 0.0
@return : The checked Debye temperature.
"""
if debye_temperature is None:
return None
debye_temperature = checkAndSetInstance(float, debye_temperature, 0.0)
if debye_temperature < 0.0:
raise ValueError("Debye temperature must be non-negative.")
return debye_temperature
def beam_parameters(self, value):
""" Set the 'beam_parameters' parameter to a given value.
:param value: The value to set 'beam_parameters' to.
"""
value = checkAndSetInstance((str, PhotonBeamParameters), value, None)
if isinstance(value, str):
if not os.path.isfile(value):
raise IOError(
"The beam_parameters %s is not a valid file or filename." %
(value))
raise TypeError(
"Passing beam parameters as a file is currently unsupported. Please use the PhotonBeamParameters class."
)
self.__beam_parameters = value
def checkAndSetDebyeTemperature(debye_temperature):
""" Utility to check if input is a valid Debye temperature.
@param debye_temperature : The Debye temperature to check.
<br/><b>type</b> : double
<br/><b>default</b> : 0.0
@return : The checked Debye temperature.
"""
if debye_temperature is None:
return None
debye_temperature = checkAndSetInstance( float, debye_temperature, 0.0)
if debye_temperature < 0.0:
raise ValueError( "Debye temperature must be non-negative.")
return debye_temperature
def checkAndSetBandGap(band_gap):
""" Utility to check if input is a valid bandgap.
@param band_gap: The bandgap to check.
<br/><b>type</b> : double
<br/><b>default</b> 0.0.
@return : The checked bandgap.
"""
if band_gap is None:
return None
band_gap = checkAndSetInstance(float, band_gap, 0.0)
if band_gap < 0.0:
raise ValueError("Debye temperature must be positive.")
return band_gap
def max_number_of_quaternions(self, value):
""" Set the 'max_number_of_quaternions' parameter to a given value.
:param value: The value to set 'max_number_of_quaternions' to.
"""
max_number_of_quaternions = checkAndSetInstance(
int, value, self.__initial_number_of_quaternions + 1)
if all([
max_number_of_quaternions <= 10,
max_number_of_quaternions > self.initial_number_of_quaternions
]):
self.__max_number_of_quaternions = max_number_of_quaternions
else:
raise ValueError(
"Parameter 'max_number_of_quaternions' must be an integer (initial_number_of_quaternions < n <= 10)"
)