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SANSBeamSpreaderTransmission.py
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SANSBeamSpreaderTransmission.py
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#pylint: disable=no-init,invalid-name
from __future__ import (absolute_import, division, print_function)
import mantid.simpleapi as api
from mantid.api import *
from mantid.kernel import *
import os
from reduction_workflow.find_data import find_data
class SANSBeamSpreaderTransmission(PythonAlgorithm):
def category(self):
return "Workflow\\SANS\\UsesPropertyManager"
def name(self):
return "SANSBeamSpreaderTransmission"
def summary(self):
return "Compute transmission using the beam spreader method"
def PyInit(self):
self.declareProperty(MatrixWorkspaceProperty("InputWorkspace", "",
direction=Direction.Input))
self.declareProperty(FileProperty("SampleSpreaderFilename", "",
action=FileAction.Load,
extensions=['xml', 'nxs', 'nxs.h5']))
self.declareProperty(FileProperty("DirectSpreaderFilename", "",
action=FileAction.Load,
extensions=['xml', 'nxs', 'nxs.h5']))
self.declareProperty(FileProperty("SampleScatteringFilename", "",
action=FileAction.Load,
extensions=['xml', 'nxs', 'nxs.h5']))
self.declareProperty(FileProperty("DirectScatteringFilename", "",
action=FileAction.Load,
extensions=['xml', 'nxs', 'nxs.h5']))
self.declareProperty("SpreaderTransmissionValue", 1.0,
"Transmission of the beam spreader")
self.declareProperty("SpreaderTransmissionError", 0.0,
"Error on the transmission of the beam spreader")
self.declareProperty("ThetaDependent", True,
"If true, a theta-dependent correction will be applied")
self.declareProperty(FileProperty("DarkCurrentFilename", "",
action=FileAction.OptionalLoad,
extensions=['xml', 'nxs', 'nxs.h5']))
self.declareProperty("UseSampleDarkCurrent", False,
"If true, the sample dark current will be used")
self.declareProperty("ReductionProperties", "__sans_reduction_properties",
validator=StringMandatoryValidator(),
doc="Property manager name for the reduction")
self.declareProperty(MatrixWorkspaceProperty("OutputWorkspace", "",
direction = Direction.Output))
self.declareProperty("MeasuredTransmission", 0.0,
direction=Direction.Output)
self.declareProperty("MeasuredError", 0.0,
direction=Direction.Output)
self.declareProperty("OutputMessage", "",
direction=Direction.Output, doc = "Output message")
#pylint: disable=too-many-locals,too-many-branches
def PyExec(self):
# Get the reduction property manager
property_manager_name = self.getProperty("ReductionProperties").value
property_manager = PropertyManagerDataService.retrieve(property_manager_name)
# Build the name we are going to give the transmission workspace
sample_scatt = self.getPropertyValue("SampleScatteringFilename")
sample_basename = os.path.basename(sample_scatt)
entry_name = "TransmissionSpreader%s" % sample_scatt
trans_ws_name = "__transmission_fit_%s" % sample_basename
trans_ws = None
# If we have already computed the transmission, used the
# previously computed workspace
if property_manager.existsProperty(entry_name):
trans_ws_name = property_manager.getProperty(entry_name)
if AnalysisDataService.doesExist(trans_ws_name):
trans_ws = AnalysisDataService.retrieve(trans_ws_name)
# Get instrument to use with FileFinder
instrument = ''
if property_manager.existsProperty("InstrumentName"):
instrument = property_manager.getProperty("InstrumentName").value
# Get the data loader
def _load_data(filename, output_ws):
if not property_manager.existsProperty("LoadAlgorithm"):
Logger("SANSBeamSpreaderTransmission").error("SANS reduction not set up properly: missing load algorithm")
raise RuntimeError("SANS reduction not set up properly: missing load algorithm")
p=property_manager.getProperty("LoadAlgorithm")
alg=Algorithm.fromString(p.valueAsStr)
alg.setProperty("Filename", filename)
alg.setProperty("OutputWorkspace", output_ws)
if alg.existsProperty("ReductionProperties"):
alg.setProperty("ReductionProperties", property_manager_name)
alg.execute()
msg = ''
if alg.existsProperty("OutputMessage"):
msg = alg.getProperty("OutputMessage").value
return msg
# Compute the transmission if we don't already have it
if trans_ws is None:
# Load data files
sample_spreader_ws = "__trans_sample_spreader"
direct_spreader_ws = "__trans_direct_spreader"
sample_scatt_ws = "__trans_sample_scatt"
direct_scatt_ws = "__trans_direct_scatt"
sample_spread = self.getPropertyValue("SampleSpreaderFilename")
direct_spread = self.getPropertyValue("DirectSpreaderFilename")
direct_scatt = self.getPropertyValue("DirectScatteringFilename")
ws_names = [[sample_spread, sample_spreader_ws],
[direct_spread, direct_spreader_ws],
[sample_scatt, sample_scatt_ws],
[direct_scatt, direct_scatt_ws]]
for f in ws_names:
filepath = find_data(f[0], instrument=instrument)
_load_data(filepath, f[1])
self._subtract_dark_current(f[1], property_manager)
# Get normalization for transmission calculation
monitor_det_ID = None
if property_manager.existsProperty("TransmissionNormalisation"):
sample_ws = AnalysisDataService.retrieve(sample_scatt_ws)
if property_manager.getProperty("TransmissionNormalisation").value=="Monitor":
monitor_det_ID = int(sample_ws.getInstrument().getNumberParameter("default-incident-monitor-spectrum")[0])
else:
monitor_det_ID = int(sample_ws.getInstrument().getNumberParameter("default-incident-timer-spectrum")[0])
elif property_manager.existsProperty("NormaliseAlgorithm"):
def _normalise(workspace):
p=property_manager.getProperty("NormaliseAlgorithm")
alg=Algorithm.fromString(p.valueAsStr)
alg.setProperty("InputWorkspace", workspace)
alg.setProperty("OutputWorkspace", workspace)
if alg.existsProperty("ReductionProperties"):
alg.setProperty("ReductionProperties", property_manager_name)
alg.execute()
msg = ''
if alg.existsProperty("OutputMessage"):
msg += alg.getProperty("OutputMessage").value+'\n'
return msg
for f in ws_names:
_normalise(f[1])
# Calculate transmission. Use the reduction method's normalization channel (time or beam monitor)
# as the monitor channel.
spreader_t_value = self.getPropertyValue("SpreaderTransmissionValue")
spreader_t_error = self.getPropertyValue("SpreaderTransmissionError")
alg = AlgorithmManager.createUnmanaged('CalculateTransmissionBeamSpreader')
alg.initialize()
alg.setProperty("SampleSpreaderRunWorkspace", sample_spreader_ws)
alg.setProperty("DirectSpreaderRunWorkspace", direct_spreader_ws)
alg.setProperty("SampleScatterRunWorkspace", sample_scatt_ws)
alg.setProperty("DirectScatterRunWorkspace", direct_scatt_ws)
alg.setProperty("IncidentBeamMonitor", monitor_det_ID)
alg.setProperty("OutputWorkspace",trans_ws_name)
alg.setProperty("SpreaderTransmissionValue",spreader_t_value)
alg.setProperty("SpreaderTransmissionError",spreader_t_error)
alg.execute()
trans_ws = AnalysisDataService.retrieve(trans_ws_name)
for f in ws_names:
if AnalysisDataService.doesExist(f[1]):
AnalysisDataService.remove(f[1])
# 2- Apply correction (Note: Apply2DTransCorr)
input_ws_name = self.getPropertyValue("InputWorkspace")
if not AnalysisDataService.doesExist(input_ws_name):
Logger("SANSBeamSpreaderTransmission").error("Could not find input workspace")
workspace = AnalysisDataService.retrieve(input_ws_name).name()
# Clone workspace to make boost-python happy
api.CloneWorkspace(InputWorkspace=workspace,
OutputWorkspace='__'+workspace)
workspace = '__'+workspace
self._apply_transmission(workspace, trans_ws_name)
trans = trans_ws.dataY(0)[0]
error = trans_ws.dataE(0)[0]
output_str = ''
if len(trans_ws.dataY(0))==1:
self.setProperty("MeasuredTransmission", trans)
self.setProperty("MeasuredError", error)
output_str = "\n%s T = %6.2g += %6.2g\n" % (output_str, trans, error)
output_msg = "Transmission correction applied [%s]%s\n" % (trans_ws_name, output_str)
output_ws = AnalysisDataService.retrieve(workspace)
self.setProperty("OutputWorkspace", output_ws)
self.setPropertyValue("OutputMessage", output_msg)
def _apply_transmission(self, workspace, trans_workspace):
"""
Apply transmission correction
@param workspace: workspace to apply correction to
@param trans_workspace: workspace name for of the transmission
"""
# Make sure the binning is compatible
api.RebinToWorkspace(WorkspaceToRebin=trans_workspace,
WorkspaceToMatch=workspace,
OutputWorkspace=trans_workspace+'_rebin',
PreserveEvents=False)
# Apply angle-dependent transmission correction using the zero-angle transmission
theta_dependent = self.getProperty("ThetaDependent").value
api.ApplyTransmissionCorrection(InputWorkspace=workspace,
TransmissionWorkspace=trans_workspace+'_rebin',
OutputWorkspace=workspace,
ThetaDependent=theta_dependent)
if AnalysisDataService.doesExist(trans_workspace+'_rebin'):
AnalysisDataService.remove(trans_workspace+'_rebin')
def _subtract_dark_current(self, workspace_name, property_manager):
"""
Subtract the dark current
@param workspace_name: name of the workspace to subtract from
@param property_manager: property manager object
"""
# Subtract dark current
use_sample_dc = self.getProperty("UseSampleDarkCurrent").value
dark_current_data = self.getPropertyValue("DarkCurrentFilename")
property_manager_name = self.getProperty("ReductionProperties").value
def _dark(workspace, dark_current_property):
if property_manager.existsProperty(dark_current_property):
p=property_manager.getProperty(dark_current_property)
# Dark current subtraction for sample data
alg=Algorithm.fromString(p.valueAsStr)
alg.setProperty("InputWorkspace", workspace)
alg.setProperty("OutputWorkspace", workspace)
alg.setProperty("Filename", dark_current_data)
if alg.existsProperty("PersistentCorrection"):
alg.setProperty("PersistentCorrection", False)
if alg.existsProperty("ReductionProperties"):
alg.setProperty("ReductionProperties", property_manager_name)
alg.execute()
msg = "Dark current subtracted"
if alg.existsProperty("OutputMessage"):
msg += alg.getProperty("OutputMessage").value
return msg
if use_sample_dc is True:
_dark(workspace_name, "DarkCurrentAlgorithm")
elif len(dark_current_data.strip())>0:
_dark(workspace_name, "DefaultDarkCurrentAlgorithm")
#############################################################################################
AlgorithmFactory.subscribe(SANSBeamSpreaderTransmission)