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sans_reducer.py
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sans_reducer.py
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# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source,
# Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
# SPDX - License - Identifier: GPL - 3.0 +
"""
SANS-specific implementation of the Reducer. The SANSReducer class implements
a predefined set of reduction steps to be followed. The actual ReductionStep objects
executed for each of those steps can be modified.
"""
from reduction import Reducer
from reduction import ReductionStep
from reduction import validate_step
import sans_reduction_steps
import mantid.simpleapi as api
import warnings
import inspect
## Version number
__version__ = '0.0'
class SANSReducer(Reducer):
"""
SANS-specific implementation of the Reducer
"""
## Normalization options
#TODO: those also correspond to the timer and monitor spectra -> store this in instr conf instead
NORMALIZATION_NONE = None
NORMALIZATION_TIME = 1
NORMALIZATION_MONITOR = 0
## Reduction setup
_reduction_setup = None
## Beam center finder ReductionStep object
_beam_finder = None
## Normalization option
_normalizer = None
_absolute_scale = None
## Dark current data file
_dark_current_subtracter = None
_dark_current_subtracter_class = None
## Sensitivity correction ReductionStep object
_sensitivity_correcter = None
## Solid angle correcter
_solid_angle_correcter = None
## Azimuthal averaging
_azimuthal_averager = None
## I(Qx,Qy)
_two_dim_calculator = None
## Transmission calculator
_transmission_calculator = None
## Masking step
_mask = None
## Output saving step
_save_iq = None
## Background subtracter
_background_subtracter = None
## Data loader
_data_loader = None
## Q resolution calculation
_resolution_calculator = None
## Extra data files
_extra_files = {}
geometry_correcter = None
def __init__(self):
super(SANSReducer, self).__init__()
# Default beam finder
self._beam_finder = sans_reduction_steps.BaseBeamFinder()
# Default normalization
self._normalizer = None
# Default data loader
self._data_loader = None
# Default mask object
self._mask = sans_reduction_steps.Mask()
# Default dark current subtracter class
self._dark_current_subtracter_class = api.HFIRDarkCurrentSubtraction
# Resolution calculator
self._resolution_calculator = api.ReactorSANSResolution
# Sample geometry correction
self.geometry_correcter = None
def set_instrument(self, configuration):
"""
Sets the instrument and put in the default beam center (usually the
center of the detector)
@param configuration: instrument object
"""
super(SANSReducer, self).set_instrument(configuration)
center = self.instrument.get_default_beam_center()
self._beam_finder = sans_reduction_steps.BaseBeamFinder(center[0], center[1])
@validate_step
def set_normalizer(self, normalizer):
"""
Set normalization
@param normalizer: normalization step object
"""
self._normalizer = normalizer
def get_normalizer(self):
return self._normalizer
@validate_step
def set_reduction(self, setup_algorithm):
self._reduction_setup = setup_algorithm
@validate_step
def set_geometry_correcter(self, correcter):
"""
Set the ReductionStep object that takes care of the geometry correction
@param subtracter: ReductionStep object
"""
self.geometry_correcter = correcter
def set_transmission(self, trans):
"""
Set the reduction step that will apply the transmission correction
@param trans: ReductionStep object
"""
if issubclass(trans.__class__, sans_reduction_steps.BaseTransmission) or trans is None:
self._transmission_calculator = trans
else:
raise RuntimeError("Reducer.set_transmission expects an object of class ReductionStep")
def get_transmission(self):
return self._transmission_calculator
@validate_step
def set_mask(self, mask):
"""
Set the reduction step that will apply the mask
@param mask: ReductionStep object
"""
self._mask = mask
def get_mask(self):
return self._mask
def get_beam_center(self):
"""
Return the beam center position
"""
return self._beam_finder.get_beam_center()
def set_beam_finder(self, finder):
"""
Set the ReductionStep object that finds the beam center
@param finder: BaseBeamFinder object
"""
if issubclass(finder.__class__, sans_reduction_steps.BaseBeamFinder) or finder is None:
self._beam_finder = finder
else:
raise RuntimeError("Reducer.set_beam_finder expects an object of class ReductionStep")
@validate_step
def set_absolute_scale(self, scaler):
"""
"""
self._absolute_scale = scaler
def set_data_loader(self, loader):
"""
Set the loader for all data files
@param loader: ReductionStep object
"""
if issubclass(loader.__class__, ReductionStep):
self._data_loader = loader
else:
raise RuntimeError("Reducer.set_data_loader expects an object of class ReductionStep")
def get_data_loader(self):
return self._data_loader
@validate_step
def set_sensitivity_correcter(self, correcter):
"""
Set the ReductionStep object that applies the sensitivity correction.
The ReductionStep object stores the sensitivity, so that the object
can be re-used on multiple data sets and the sensitivity will not be
recalculated.
@param correcter: ReductionStep object
"""
self._sensitivity_correcter = correcter
def get_sensitivity_correcter(self):
return self._sensitivity_correcter
@validate_step
def set_sensitivity_beam_center(self, beam_center):
if self._sensitivity_correcter is not None:
self._sensitivity_correcter.set_beam_center(beam_center)
else:
raise RuntimeError("Set the sensitivity correction before setting its beam center")
@validate_step
def set_dark_current_subtracter(self, subtracter):
"""
Set the ReductionStep object that subtracts the dark current from the data.
The loaded dark current is stored by the ReductionStep object so that the
subtraction can be applied to multiple data sets without reloading it.
@param subtracter: ReductionStep object
"""
self._dark_current_subtracter = subtracter
@validate_step
def set_solid_angle_correcter(self, correcter):
"""
Set the ReductionStep object that performs the solid angle correction.
@param subtracter: ReductionStep object
"""
if issubclass(correcter.__class__, ReductionStep) or correcter is None:
self._solid_angle_correcter = correcter
else:
raise RuntimeError("Reducer.set_solid_angle_correcter expects an object of class ReductionStep")
@validate_step
def set_azimuthal_averager(self, averager):
"""
Set the ReductionStep object that performs azimuthal averaging
and transforms the 2D reduced data set into I(Q).
@param averager: ReductionStep object
"""
self._azimuthal_averager = averager
def get_azimuthal_averager(self):
"""
Return the azimuthal average reduction step
"""
return self._azimuthal_averager
@validate_step
def set_save_Iq(self, save_iq):
"""
Set the ReductionStep object that saves the I(q) output
@param averager: ReductionStep object
"""
self._save_iq = save_iq
def set_bck_transmission(self, trans):
"""
Set the reduction step that will apply the transmission correction
@param trans: ReductionStep object
"""
lineno = inspect.currentframe().f_code.co_firstlineno
warnings.warn_explicit("SANSReducer.set_bck_transmission id deprecated: use get_background().set_transmission()",
DeprecationWarning, __file__, lineno)
if issubclass(trans.__class__, sans_reduction_steps.BaseTransmission) or trans is None:
self._background_subtracter.set_transmission(trans)
else:
raise RuntimeError("Reducer.set_bck_transmission expects an object of class ReductionStep")
@validate_step
def set_IQxQy(self, calculator):
"""
Set the algorithm to compute I(Qx,Qy)
@param calculator: ReductionStep object
"""
self._two_dim_calculator = calculator
def pre_process(self):
"""
Reduction steps that are meant to be executed only once per set
of data files. After this is executed, all files will go through
the list of reduction steps.
"""
if self.instrument is None:
raise RuntimeError("SANSReducer: trying to run a reduction with no instrument specified")
if self._reduction_setup is not None:
result = self._reduction_setup.execute(self)
self.log_text += "%s\n" % str(result)
if self._beam_finder is not None:
result = self._beam_finder.execute(self)
self.log_text += "%s\n" % str(result)
# Create the list of reduction steps
self._to_steps()
def _2D_steps(self):
"""
Creates a list of reduction steps to be applied to
each data set, including the background file.
Only the steps applied to a data set
before azimuthal averaging are included.
"""
reduction_steps = []
# Load file
reduction_steps.append(self._data_loader)
# Dark current subtraction
if self._dark_current_subtracter is not None:
reduction_steps.append(self._dark_current_subtracter)
# Normalize
if self._normalizer is not None:
reduction_steps.append(self._normalizer)
# Mask
if self._mask is not None:
reduction_steps.append(self._mask)
# Solid angle correction
if self._solid_angle_correcter is not None:
reduction_steps.append(self._solid_angle_correcter)
# Sensitivity correction
if self._sensitivity_correcter is not None:
reduction_steps.append(self._sensitivity_correcter)
return reduction_steps
def _to_steps(self):
"""
Creates a list of reduction steps for each data set
following a predefined reduction approach. For each
predefined step, we check that a ReductionStep object
exists to take of it. If one does, we append it to the
list of steps to be executed.
"""
# Get the basic 2D steps
self._reduction_steps = self._2D_steps()
# Apply transmission correction
if self._transmission_calculator is not None:
self.append_step(self._transmission_calculator)
# Subtract the background
if self._background_subtracter is not None:
self.append_step(self._background_subtracter)
if self._absolute_scale is not None:
self.append_step(self._absolute_scale)
# Sample geometry correction
if self.geometry_correcter is not None:
self.append_step(self.geometry_correcter)
# Perform azimuthal averaging
if self._azimuthal_averager is not None:
self.append_step(self._azimuthal_averager)
# Perform I(Qx,Qy) calculation
if self._two_dim_calculator is not None:
self.append_step(self._two_dim_calculator)
# Save output to file
if self._save_iq is not None:
self.append_step(self._save_iq)