""" :module CrystFELPhotonDiffractorParameters: Module that holds the CrystFELPhotonDiffractorParameters class. """
##########################################################################
# #
# Copyright (C) 2016-2017 Carsten Fortmann-Grote #
# Contact: Carsten Fortmann-Grote <carsten.grote@xfel.eu> #
# #
# This file is part of simex_platform. #
# simex_platform is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# simex_platform is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program. If not, see <http://www.gnu.org/licenses/>. #
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##########################################################################
import os
from SimEx.Parameters.AbstractCalculatorParameters import AbstractCalculatorParameters
from SimEx.Utilities.EntityChecks import checkAndSetInstance, checkAndSetPhysicalQuantity
from SimEx.Utilities import IOUtilities
from SimEx.Utilities.Units import meter
from SimEx.Parameters.PhotonBeamParameters import PhotonBeamParameters
from SimEx.Parameters.DetectorGeometry import DetectorGeometry
[docs]class CrystFELPhotonDiffractorParameters(AbstractCalculatorParameters):
"""
:class CrystFELPhotonDiffractorParameters: Encapsulates parameters for the CrystFELPhotonDiffractor.
"""
def __init__(self,
sample=None,
uniform_rotation=None,
number_of_diffraction_patterns=None,
powder=None,
intensities_file=None,
crystal_size_min=None,
crystal_size_max=None,
poissonize=None,
number_of_background_photons=None,
suppress_fringes=None,
beam_parameters=None,
detector_geometry=None,
**kwargs
):
"""
:param sample: Location of file that contains the sample definition (pdb or crystfel format)
:type sample: str
:param uniform_rotation: Whether to perform uniform sampling of rotation space.
:type uniform_rotation: bool, default True
:param powder: Whether to sum all patterns to generate a simulated powder diffraction pattern.
:type powder: bool
:param intensities_file: Location of file that contains intensities and phases at reciprocal lattice points. See CrystFEL documentation for more info. Default: Constant intensities and phases across entire sample.
:type intensities_file: str
:param crystal_size_min: Minimum crystal size.
:type crystal_size_min: PhysicalQuantity with unit of length (meter).
:param crystal_size_max: Maximum crystal size.
:type crystal_size_max: PhysicalQuantity with unit of length (meter).
:param poissonize: Whether to add Poisson noise to pixel values.
:type poissonize: bool
:param number_of_background_photons: Add this number of Poisson distributed photons uniformly over the detector surface (default 0).
:type number_of_background_photons: int
:param number_of_diffraction_patterns: Number of diffraction patterns to calculate from each trajectory.
:type number_of_diffraction_patterns: int, default 1
:param suppress_fringes: Whether to suppress subsidiary maxima beyond first minimum of the shape transform (default False).
:type suppress_fringes: bool
:param beam_parameters: Path of the beam parameter file.
:type beam_parameters: str
:param detector_geometry: Path of the beam geometry file.
:type detector_geometry: str
:param kwargs: Key-value pairs to pass to the parent class.
"""
# Check all parameters.
self.sample = sample
self.uniform_rotation = uniform_rotation
self.powder = powder
self.intensities_file = intensities_file
self.crystal_size_min = crystal_size_min
self.crystal_size_max = crystal_size_max
self.poissonize = poissonize
self.number_of_background_photons = number_of_background_photons
self.suppress_fringes = suppress_fringes
self.beam_parameters = beam_parameters
self.detector_geometry = detector_geometry
self.number_of_diffraction_patterns = number_of_diffraction_patterns
# Handle single size case:
if self.crystal_size_min is None or self.crystal_size_max is None:
if self.crystal_size_min is None:
self.crystal_size_min = self.crystal_size_max
else:
self.crystal_size_max = self.crystal_size_min
super(CrystFELPhotonDiffractorParameters, self).__init__(**kwargs)
def _setDefaults(self):
""" Set default for required inherited parameters. """
self._AbstractCalculatorParameters__cpus_per_task_default = "MAX"
### Setters and queries.
@property
def sample(self):
""" Query the 'sample' parameter. """
return self.__sample
@sample.setter
def sample(self, val):
""" Set the 'sample' parameter to val."""
if val is None:
raise ValueError( "A sample must be defined.")
if val.split(".")[-1] == "pdb":
print("Checking presence of %s. Will query from PDB if not found in $PWD." % (val))
self.__sample = IOUtilities.checkAndGetPDB(val)
print("Sample path is set to %s." % (self.__sample))
@property
def powder(self):
""" Query the 'powder' parameter. """
return self.__powder
@powder.setter
def powder(self, val):
""" Set the 'powder' parameter to val."""
self.__powder = checkAndSetInstance( bool, val, False)
@property
def intensities_file(self):
""" Query the 'intensities_file' parameter. """
return self.__intensities_file
@intensities_file.setter
def intensities_file(self, val):
""" Set the 'intensities_file' parameter to val."""
self.__intensities_file = checkAndSetInstance( str, val, None)
@property
def crystal_size_min(self):
""" Query the 'crystal_size_min' parameter. """
return self.__crystal_size_min
@crystal_size_min.setter
def crystal_size_min(self, val):
""" Set the 'crystal_size_min' parameter to val."""
# Check if iterable.
self.__crystal_size_min = checkAndSetPhysicalQuantity(val, None, meter )
@property
def crystal_size_max(self):
""" Query the 'crystal_size_max' parameter. """
return self.__crystal_size_max
@crystal_size_max.setter
def crystal_size_max(self, val):
""" Set the 'crystal_size_max' parameter to val."""
# Check if iterable.
self.__crystal_size_max = checkAndSetPhysicalQuantity(val, None, meter )
@property
def poissonize(self):
""" Query the 'poissonize' parameter. """
return self.__poissonize
@poissonize.setter
def poissonize(self, val):
""" Set the 'poissonize' parameter to val."""
self.__poissonize = checkAndSetInstance( bool, val, False)
@property
def number_of_background_photons(self):
""" Query the 'number_of_background_photons' parameter. """
return self.__number_of_background_photons
@number_of_background_photons.setter
def number_of_background_photons(self, val):
""" Set the 'number_of_background_photons' parameter to val."""
self.__number_of_background_photons = checkAndSetInstance( int, val, 0)
@property
def suppress_fringes(self):
""" Query the 'suppress_fringes' parameter. """
return self.__suppress_fringes
@suppress_fringes.setter
def suppress_fringes(self, val):
""" Set the 'suppress_fringes' parameter to val."""
self.__suppress_fringes = checkAndSetInstance( bool, val, False)
@property
def uniform_rotation(self):
""" Query for the 'uniform_rotation' parameter. """
return self.__uniform_rotation
@uniform_rotation.setter
def uniform_rotation(self, value):
""" Set the 'uniform_rotation' parameter to a given value.
:param value: The value to set 'uniform_rotation' to.
"""
self.__uniform_rotation = checkAndSetInstance( bool, value, True )
@property
def beam_parameters(self):
""" Query for the 'beam_parameters' parameter. """
return self.__beam_parameters
@beam_parameters.setter
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) )
@property
def detector_geometry(self):
""" Query for the 'detector_geometry' parameter. """
return self.__detector_geometry
@detector_geometry.setter
def detector_geometry(self, value):
""" Set the 'detector_geometry' parameter to a given value.
:param value: The value to set 'detector_geometry' to.
"""
self.__detector_geometry = checkAndSetInstance( (str, DetectorGeometry), value, None )
if isinstance(self.__detector_geometry, str):
if not os.path.isfile( self.__detector_geometry):
raise IOError("The detector_geometry %s is not a valid file or filename." % (self.__detector_geometry) )
if self.__detector_geometry is None:
print ("WARNING: Geometry file not set, calculation will most probably fail.")
@property
def number_of_diffraction_patterns(self):
""" Query for the 'number_of_diffraction_patterns_file' parameter. """
return self.__number_of_diffraction_patterns
@number_of_diffraction_patterns.setter
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.")
