def __init__(self, parameters=None, input_path=None, output_path=None):
### TODO
"""
Constructor for the reconstruction analyser.
@param parameters : Dictionary of reconstruction parameters.
<br/><b>type</b> : dict
<br/><b>example</b> : parameters={}
"""
# Initialize base class.
super(S2EReconstruction, self).__init__(parameters,input_path,output_path)
self.__provided_data = ['/data/electronDensity',
'/params/info',
'/history',
'/info',
'/misc',
'/version',
]
self.__expected_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',
]
emc_parameters = None
dm_parameters = None
# Construct emc and dm calculators.
if self.parameters != {}:
emc_parameters = self.parameters['EMC_Parameters']
dm_parameters = self.parameters['DM_Parameters']
if os.path.isdir( self.output_path ):
intermediate_output_path = os.path.join( self.output_path, 'orient_out.h5' )
else:
intermediate_output_path = 'orient_out.h5'
self.__emc = EMCOrientation(emc_parameters, self.input_path, intermediate_output_path )
self.__dm = DMPhasing(dm_parameters, intermediate_output_path, self.output_path)
class S2EReconstruction(AbstractPhotonAnalyzer):
"""
Class representing photon data analysis for electron density reconstruction from 2D diffraction patterns.
Uses the EMC orientation module and the DM phasing module.
"""
def __init__(self, parameters=None, input_path=None, output_path=None):
### TODO
"""
Constructor for the reconstruction analyser.
@param parameters : Dictionary of reconstruction parameters.
<br/><b>type</b> : dict
<br/><b>example</b> : parameters={}
"""
# Initialize base class.
super(S2EReconstruction, self).__init__(parameters,input_path,output_path)
self.__provided_data = ['/data/electronDensity',
'/params/info',
'/history',
'/info',
'/misc',
'/version',
]
self.__expected_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',
]
emc_parameters = None
dm_parameters = None
# Construct emc and dm calculators.
if self.parameters != {}:
emc_parameters = self.parameters['EMC_Parameters']
dm_parameters = self.parameters['DM_Parameters']
if os.path.isdir( self.output_path ):
intermediate_output_path = os.path.join( self.output_path, 'orient_out.h5' )
else:
intermediate_output_path = 'orient_out.h5'
self.__emc = EMCOrientation(emc_parameters, self.input_path, intermediate_output_path )
self.__dm = DMPhasing(dm_parameters, intermediate_output_path, self.output_path)
def expectedData(self):
""" Query for the data expected by the Analyzer. """
return self.__expected_data
def providedData(self):
""" Query for the data provided by the Analyzer. """
return self.__provided_data
@property
def data(self):
""" Query for the field data. """
return self.__data
def _readH5(self):
""" """
""" Private method for reading the hdf5 input and extracting the parameters and data relevant to initialize the object. """
pass # Nothing to be done since IO happens in backengine.
def saveH5(self):
""" """
"""
Private method to save the object to a file.
@param output_path : The file where to save the object's data.
<br/><b>type</b> : string
<br/><b>default</b> : None
"""
pass # No action required since output is written in backengine.
def backengine(self):
emc_status = self.__emc.backengine()
if emc_status!= 0:
return emc_status
dm_status = self.__dm.backengine()
return dm_status
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: The parameters for the reconstruction.
:type parameters: dict
:example parameters: parameters={'EMC_Parameters' : EMCOrientationParameters(), 'DM_Parameters' : DMPhasingParameters()} # Use default parameters for EMC and DM.
:param input_path: Path for input data.
:type input_path: str
:param output_path: Path where to write output to.
:type output_path: str
"""
# Initialize base class.
super(S2EReconstruction, self).__init__(parameters, input_path,
output_path)
self.__provided_data = [
'/data/electronDensity',
'/params/info',
'/history',
'/info',
'/misc',
'/version',
]
self.__expected_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',
]
emc_parameters = None
dm_parameters = None
# Construct emc and dm calculators.
if self.parameters != {}:
emc_parameters = self.parameters['EMC_Parameters']
dm_parameters = self.parameters['DM_Parameters']
if os.path.isdir(self.output_path):
intermediate_output_path = os.path.join(self.output_path,
'orient_out.h5')
else:
intermediate_output_path = 'orient_out.h5'
self.__emc = EMCOrientation(emc_parameters, self.input_path,
intermediate_output_path)
self.__dm = DMPhasing(dm_parameters, intermediate_output_path,
self.output_path)
class S2EReconstruction(AbstractPhotonAnalyzer):
"""
Class representing photon data analysis for electron density reconstruction from 2D diffraction patterns.
Uses the EMC orientation module and the DM phasing module.
"""
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: The parameters for the reconstruction.
:type parameters: dict
:example parameters: parameters={'EMC_Parameters' : EMCOrientationParameters(), 'DM_Parameters' : DMPhasingParameters()} # Use default parameters for EMC and DM.
:param input_path: Path for input data.
:type input_path: str
:param output_path: Path where to write output to.
:type output_path: str
"""
# Initialize base class.
super(S2EReconstruction, self).__init__(parameters, input_path,
output_path)
self.__provided_data = [
'/data/electronDensity',
'/params/info',
'/history',
'/info',
'/misc',
'/version',
]
self.__expected_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',
]
emc_parameters = None
dm_parameters = None
# Construct emc and dm calculators.
if self.parameters != {}:
emc_parameters = self.parameters['EMC_Parameters']
dm_parameters = self.parameters['DM_Parameters']
if os.path.isdir(self.output_path):
intermediate_output_path = os.path.join(self.output_path,
'orient_out.h5')
else:
intermediate_output_path = 'orient_out.h5'
self.__emc = EMCOrientation(emc_parameters, self.input_path,
intermediate_output_path)
self.__dm = DMPhasing(dm_parameters, intermediate_output_path,
self.output_path)
def expectedData(self):
""" Query for the data expected by the Analyzer. """
return self.__expected_data
def providedData(self):
""" Query for the data provided by the Analyzer. """
return self.__provided_data
@property
def data(self):
""" Query for the field data. """
return self.__data
def _readH5(self):
""" """
""" Private method for reading the hdf5 input and extracting the parameters and data relevant to initialize the object. """
pass # Nothing to be done since IO happens in backengine.
def saveH5(self):
""" """
"""
Private method to save the object to a file.
:param output_path: The file where to save the object's data.
:type output_path: str
"""
pass # No action required since output is written in backengine.
def backengine(self):
""" Run the EMC and DM backengine executables. """
# Run EMC.
emc_status = self.__emc.backengine()
# If EMC was not successful, return with error code.
if emc_status != 0:
return emc_status
# Else run DM.
return self.__dm.backengine()
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: The parameters for the reconstruction.
:type parameters: dict
:example parameters: parameters={'EMC_Parameters' : EMCOrientationParameters(), 'DM_Parameters' : DMPhasingParameters()} # Use default parameters for EMC and DM.
:param input_path: Path for input data.
:type input_path: str
:param output_path: Path where to write output to.
:type output_path: str
"""
# Initialize base class.
super(S2EReconstruction, self).__init__(parameters,input_path,output_path)
self.__provided_data = ['/data/electronDensity',
'/params/info',
'/history',
'/info',
'/misc',
'/version',
]
self.__expected_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',
]
emc_parameters = None
dm_parameters = None
# Construct emc and dm calculators.
if self.parameters != {}:
emc_parameters = self.parameters['EMC_Parameters']
dm_parameters = self.parameters['DM_Parameters']
if os.path.isdir( self.output_path ):
intermediate_output_path = os.path.join( self.output_path, 'orient_out.h5' )
else:
intermediate_output_path = 'orient_out.h5'
self.__emc = EMCOrientation(emc_parameters, self.input_path, intermediate_output_path )
self.__dm = DMPhasing(dm_parameters, intermediate_output_path, self.output_path)
class S2EReconstruction(AbstractPhotonAnalyzer):
"""
Class representing photon data analysis for electron density reconstruction from 2D diffraction patterns.
Uses the EMC orientation module and the DM phasing module.
"""
def __init__(self, parameters=None, input_path=None, output_path=None):
"""
:param parameters: The parameters for the reconstruction.
:type parameters: dict
:example parameters: parameters={'EMC_Parameters' : EMCOrientationParameters(), 'DM_Parameters' : DMPhasingParameters()} # Use default parameters for EMC and DM.
:param input_path: Path for input data.
:type input_path: str
:param output_path: Path where to write output to.
:type output_path: str
"""
# Initialize base class.
super(S2EReconstruction, self).__init__(parameters,input_path,output_path)
self.__provided_data = ['/data/electronDensity',
'/params/info',
'/history',
'/info',
'/misc',
'/version',
]
self.__expected_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',
]
emc_parameters = None
dm_parameters = None
# Construct emc and dm calculators.
if self.parameters != {}:
emc_parameters = self.parameters['EMC_Parameters']
dm_parameters = self.parameters['DM_Parameters']
if os.path.isdir( self.output_path ):
intermediate_output_path = os.path.join( self.output_path, 'orient_out.h5' )
else:
intermediate_output_path = 'orient_out.h5'
self.__emc = EMCOrientation(emc_parameters, self.input_path, intermediate_output_path )
self.__dm = DMPhasing(dm_parameters, intermediate_output_path, self.output_path)
def expectedData(self):
""" Query for the data expected by the Analyzer. """
return self.__expected_data
def providedData(self):
""" Query for the data provided by the Analyzer. """
return self.__provided_data
@property
def data(self):
""" Query for the field data. """
return self.__data
def _readH5(self):
""" """
""" Private method for reading the hdf5 input and extracting the parameters and data relevant to initialize the object. """
pass # Nothing to be done since IO happens in backengine.
def saveH5(self):
""" """
"""
Private method to save the object to a file.
:param output_path: The file where to save the object's data.
:type output_path: str
"""
pass # No action required since output is written in backengine.
def backengine(self):
""" Run the EMC and DM backengine executables. """
# Run EMC.
emc_status = self.__emc.backengine()
# If EMC was not successful, return with error code.
if emc_status!= 0:
return emc_status
# Else run DM.
return self.__dm.backengine()