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 testCheckAndSetPositiveInteger(self):
""" Test the check method for positive integers. """
# Check with correct parameter.
self.assertEqual( 1, checkAndSetPositiveInteger(1) )
# Check default.
self.assertEqual( 1, checkAndSetPositiveInteger(None, 1) )
# Check exception if parameter not an int.
self.assertRaises( TypeError, checkAndSetPositiveInteger, "not an integer")
# Check exception if parameter < 0.
self.assertRaises( TypeError, checkAndSetPositiveInteger, -1)
# Check exception if parameter = 0.
self.assertRaises( TypeError, checkAndSetPositiveInteger, 0)
def testCheckAndSetPositiveInteger(self):
""" Test the check method for positive integers. """
# Check with correct parameter.
self.assertEqual( 1, checkAndSetPositiveInteger(1) )
# Check default.
self.assertEqual( 1, checkAndSetPositiveInteger(None, 1) )
# Check exception if parameter not an int.
self.assertRaises( TypeError, checkAndSetPositiveInteger, "not an integer")
# Check exception if parameter < 0.
self.assertRaises( TypeError, checkAndSetPositiveInteger, -1)
# Check exception if parameter = 0.
self.assertRaises( TypeError, checkAndSetPositiveInteger, 0)
def _checkAndSetNodesPerTask(value=None):
""" """
""" Utility function to check validity of input for number of nodes per
task.
:param value: The value to check.
:type value: int
:return: The checked value, default 1.
"""
return checkAndSetPositiveInteger(value, 1)
def _checkAndSetCPUsPerTask(value=None):
""" """
""" Utility function to check validity of input for number of cpus per task.
:param value: The value to check.
:type value: (int | str)
:return: The checked value, default 1.
"""
# Check type
if isinstance(value, str):
if not value == "MAX":
raise ValueError(
'cpus_per_task must be a positive integer or string "MAX".')
return value
return checkAndSetPositiveInteger(value, 1)
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):
"""
Constructor for the xfel photon propagator.
@param parameters : singFEL parameters.
<br/><b>type</b> : dict
<br/><b>example</b> : parameters={ 'uniform_rotation' : True,
'calculate_Compton' : False,
'pmi_start_ID' : 1,
'pmi_stop_ID' : 1,
'number_of_diffraction_patterns' : 2,
'number_of_MPI_processes' : 2,
'slice_interval' : 10,
'number_of_slices' : 100,
'beam_parameter_file' : 's2e.beam',
'beam_geometry_file' : 's2e.geom',
}
@param parameters['uniform_rotation'] : Whether or not to apply uniform sampling of the sample's rotations.
<br/><b>type</b> : boolean
@param parameters['calculate_Compton'] : Whether or not to calculate incoherent (Compton) scattering.
<br/><b>type</b> : Bool
@param parameters['pmi_start_ID'] : Index of the pmi file to start from.
<br/><b>type</b> : int
@param parameters['pmi_stop_ID'] : Index of the pmi file to stop at.
<br/><b>type</b> : int
@param parameters['number_of_diffraction_patterns'] : The number of diffraction patterns to calculate from each photon-matter interaction trajectory.
<br/><b>type</b> : int
@param parameters['number_of_MPI_processes'] : The number of MPI processes to use
<br/><b>type</b> : int
@param parameters['slice_interval'] : The number of time slices to skip between two samplings of the photon-matter interaction trajectory.
<br/><b>type</b> : int
@param parameters['number_of_slices'] : Total number of slices in the pmi files."
<br/><b>type</b> : int
@param parameters['beam_parameter_file'] : Path of the beam parameter (.beam) file.
<br/><b>type</b> : string
@param parameters['beam_geometry_file'] : Path of the beam geometry (.geom) file.
<br/><b>type</b> : string
<br/><b>note</b>: The number of generated files is the number of pmi data files * number_of_diffraction_patterns.
"""
super(SingFELPhotonDiffractor, self).__init__(parameters,input_path,output_path)
# Check parameters.
# Check that only accepted parameters are present.
accepted_keys = ['uniform_rotation',
'calculate_Compton',
'slice_interval',
'number_of_slices',
'number_of_diffraction_patterns',
'number_of_MPI_processes',
'pmi_start_ID',
'pmi_stop_ID',
'beam_parameter_file',
'beam_geometry_file']
for k in self.parameters.keys():
if k not in accepted_keys:
raise RuntimeError( "The parameter '%s' is not a valid parameter for the SingFELPhotonDiffractor. " % (k))
# Check each parameter individually and set defaults if not set.
self.parameters['uniform_rotation'] = checkAndSetInstance(bool, self.parameters['uniform_rotation'], True)
self.parameters['calculate_Compton'] = checkAndSetInstance(bool, self.parameters['calculate_Compton'], True)
self.parameters['slice_interval'] = checkAndSetPositiveInteger(self.parameters['slice_interval'], 1)
self.parameters['number_of_slices'] = checkAndSetPositiveInteger(self.parameters['number_of_slices'], 1)
self.parameters['number_of_diffraction_patterns'] = checkAndSetPositiveInteger(self.parameters['number_of_diffraction_patterns'], 1)
self.parameters['number_of_MPI_processes'] = checkAndSetPositiveInteger(self.parameters.get('number_of_MPI_processes',2))
self.parameters['pmi_start_ID'] = checkAndSetPositiveInteger(self.parameters['pmi_start_ID'], 1)
self.parameters['pmi_stop_ID'] = checkAndSetPositiveInteger(self.parameters['pmi_stop_ID'], 1)
self.parameters['beam_parameter_file'] = checkAndSetInstance(str, self.parameters['beam_parameter_file'])
if not os.path.isfile(self.parameters['beam_parameter_file']):
raise IOError("%s is not a file." % (self.parameters['beam_parameter_file']))
self.parameters['beam_geometry_file'] = checkAndSetInstance(str, self.parameters['beam_geometry_file'])
if not os.path.isfile(self.parameters['beam_geometry_file']):
raise IOError("%s is not a file." % (self.parameters['beam_geometry_file']))
self.__expected_data = ['/data/snp_<7 digit index>/ff',
'/data/snp_<7 digit index>/halfQ',
'/data/snp_<7 digit index>/Nph',
'/data/snp_<7 digit index>/r',
'/data/snp_<7 digit index>/T',
'/data/snp_<7 digit index>/Z',
'/data/snp_<7 digit index>/xyz',
'/data/snp_<7 digit index>/Sq_halfQ',
'/data/snp_<7 digit index>/Sq_bound',
'/data/snp_<7 digit index>/Sq_free',
'/history/parent/detail',
'/history/parent/parent',
'/info/package_version',
'/info/contact',
'/info/data_description',
'/info/method_description',
'/version']
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 __init__(self, parameters=None, input_path=None, output_path=None):
"""
Constructor for the xfel photon propagator.
@param parameters : singFEL parameters.
<br/><b>type</b> : dict
<br/><b>example</b> : parameters={ 'uniform_rotation' : True,
'calculate_Compton' : False,
'pmi_start_ID' : 1,
'pmi_stop_ID' : 1,
'number_of_diffraction_patterns' : 2,
'number_of_MPI_processes' : 2,
'slice_interval' : 10,
'number_of_slices' : 100,
'beam_parameter_file' : 's2e.beam',
'beam_geometry_file' : 's2e.geom',
}
@param parameters['uniform_rotation'] : Whether or not to apply uniform sampling of the sample's rotations.
<br/><b>type</b> : boolean
@param parameters['calculate_Compton'] : Whether or not to calculate incoherent (Compton) scattering.
<br/><b>type</b> : Bool
@param parameters['pmi_start_ID'] : Index of the pmi file to start from.
<br/><b>type</b> : int
@param parameters['pmi_stop_ID'] : Index of the pmi file to stop at.
<br/><b>type</b> : int
@param parameters['number_of_diffraction_patterns'] : The number of diffraction patterns to calculate from each photon-matter interaction trajectory.
<br/><b>type</b> : int
@param parameters['number_of_MPI_processes'] : The number of MPI processes to use
<br/><b>type</b> : int
@param parameters['slice_interval'] : The number of time slices to skip between two samplings of the photon-matter interaction trajectory.
<br/><b>type</b> : int
@param parameters['number_of_slices'] : Total number of slices in the pmi files."
<br/><b>type</b> : int
@param parameters['beam_parameter_file'] : Path of the beam parameter (.beam) file.
<br/><b>type</b> : string
@param parameters['beam_geometry_file'] : Path of the beam geometry (.geom) file.
<br/><b>type</b> : string
<br/><b>note</b>: The number of generated files is the number of pmi data files * number_of_diffraction_patterns.
"""
super(SingFELPhotonDiffractor, self).__init__(parameters, input_path,
output_path)
# Check parameters.
# Check that only accepted parameters are present.
accepted_keys = [
'uniform_rotation', 'calculate_Compton', 'slice_interval',
'number_of_slices', 'number_of_diffraction_patterns',
'number_of_MPI_processes', 'pmi_start_ID', 'pmi_stop_ID',
'beam_parameter_file', 'beam_geometry_file'
]
for k in self.parameters.keys():
if k not in accepted_keys:
raise RuntimeError(
"The parameter '%s' is not a valid parameter for the SingFELPhotonDiffractor. "
% (k))
# Check each parameter individually and set defaults if not set.
self.parameters['uniform_rotation'] = checkAndSetInstance(
bool, self.parameters['uniform_rotation'], True)
self.parameters['calculate_Compton'] = checkAndSetInstance(
bool, self.parameters['calculate_Compton'], True)
self.parameters['slice_interval'] = checkAndSetPositiveInteger(
self.parameters['slice_interval'], 1)
self.parameters['number_of_slices'] = checkAndSetPositiveInteger(
self.parameters['number_of_slices'], 1)
self.parameters[
'number_of_diffraction_patterns'] = checkAndSetPositiveInteger(
self.parameters['number_of_diffraction_patterns'], 1)
self.parameters[
'number_of_MPI_processes'] = checkAndSetPositiveInteger(
self.parameters.get('number_of_MPI_processes', 2))
self.parameters['pmi_start_ID'] = checkAndSetPositiveInteger(
self.parameters['pmi_start_ID'], 1)
self.parameters['pmi_stop_ID'] = checkAndSetPositiveInteger(
self.parameters['pmi_stop_ID'], 1)
self.parameters['beam_parameter_file'] = checkAndSetInstance(
str, self.parameters['beam_parameter_file'])
if not os.path.isfile(self.parameters['beam_parameter_file']):
raise IOError("%s is not a file." %
(self.parameters['beam_parameter_file']))
self.parameters['beam_geometry_file'] = checkAndSetInstance(
str, self.parameters['beam_geometry_file'])
if not os.path.isfile(self.parameters['beam_geometry_file']):
raise IOError("%s is not a file." %
(self.parameters['beam_geometry_file']))
self.__expected_data = [
'/data/snp_<7 digit index>/ff', '/data/snp_<7 digit index>/halfQ',
'/data/snp_<7 digit index>/Nph', '/data/snp_<7 digit index>/r',
'/data/snp_<7 digit index>/T', '/data/snp_<7 digit index>/Z',
'/data/snp_<7 digit index>/xyz',
'/data/snp_<7 digit index>/Sq_halfQ',
'/data/snp_<7 digit index>/Sq_bound',
'/data/snp_<7 digit index>/Sq_free', '/history/parent/detail',
'/history/parent/parent', '/info/package_version', '/info/contact',
'/info/data_description', '/info/method_description', '/version'
]
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',
]