def quick_explicit(run, i0_monitor_index, lambda_min, lambda_max, background_min, background_max, int_min, int_max,
point_detector_start=0, point_detector_stop=0, multi_detector_start=0, theta=None,
pointdet=True,roi=[0,0], db=[0,0], trans='', debug=False, correction_strategy=NullCorrectionStrategy(),
stitch_start_overlap=None, stitch_end_overlap=None, stitch_params=None,
polcorr=False, crho=None, calpha=None, cAp=None, cPp=None, detector_component_name='point-detector',
sample_component_name='some-surface-holder', correct_positions=True ):
'''
Version of quick where all parameters are explicitly provided.
'''
_sample_ws = ConvertToWavelength.to_single_workspace(run)
nHist = _sample_ws.getNumberHistograms()
to_lam = ConvertToWavelength(run)
if pointdet:
detector_index_ranges = (point_detector_start, point_detector_stop)
else:
detector_index_ranges = (multi_detector_start, nHist-1)
_monitor_ws, _detector_ws = to_lam.convert(wavelength_min=lambda_min, wavelength_max=lambda_max, detector_workspace_indexes=detector_index_ranges, monitor_workspace_index=i0_monitor_index, correct_monitor=True, bg_min=background_min, bg_max=background_max )
inst = _sample_ws.getInstrument()
# Some beamline constants from IDF
print i0_monitor_index
print nHist
if (run=='0'):
RunNumber = '0'
else:
RunNumber = groupGet(_sample_ws.getName(),'samp','run_number')
if not pointdet:
# Proccess Multi-Detector; assume MD goes to the end:
# if roi or db are given in the function then sum over the apropriate channels
print "This is a multidetector run."
_I0M = RebinToWorkspace(WorkspaceToRebin=_monitor_ws,WorkspaceToMatch=_detector_ws)
IvsLam = _detector_ws / _I0M
if (roi != [0,0]) :
ReflectedBeam = SumSpectra(InputWorkspace=IvsLam, StartWorkspaceIndex=roi[0], EndWorkspaceIndex=roi[1])
if (db != [0,0]) :
DirectBeam = SumSpectra(InputWorkspace=_detector_ws, StartWorkspaceIndex=db[0], EndWorkspaceIndex=db[1])
ReflectedBeam = ReflectedBeam / DirectBeam
polCorr(polcorr, IvsLam, crho, calpha, cAp, cPp)
if (theta and correct_positions):
IvsQ = l2q(ReflectedBeam, detector_component_name, theta, sample_component_name)
else:
IvsQ = ConvertUnits(InputWorkspace=ReflectedBeam, Target="MomentumTransfer")
# Single Detector processing-------------------------------------------------------------
else:
print "This is a Point-Detector run."
# handle transmission runs
# process the point detector reflectivity
_I0P = RebinToWorkspace(WorkspaceToRebin=_monitor_ws,WorkspaceToMatch=_detector_ws)
IvsLam = Scale(InputWorkspace=_detector_ws,Factor=1)
if not trans:
print "No transmission file. Trying default exponential/polynomial correction..."
IvsLam = correction_strategy.apply(_detector_ws)
IvsLam = Divide(LHSWorkspace=IvsLam, RHSWorkspace=_I0P)
else: # we have a transmission run
_monInt = Integration(InputWorkspace=_I0P,RangeLower=int_min,RangeUpper=int_max)
IvsLam = Divide(LHSWorkspace=_detector_ws,RHSWorkspace=_monInt)
names = mtd.getObjectNames()
IvsLam = transCorr(trans, IvsLam, lambda_min, lambda_max, background_min, background_max,
int_min, int_max, detector_index_ranges, i0_monitor_index, stitch_start_overlap,
stitch_end_overlap, stitch_params )
IvsLam = polCorr(polcorr, IvsLam, crho, calpha, cAp, cPp)
# Convert to I vs Q
# check if detector in direct beam
if (theta == None or theta == 0 or theta == ''):
inst = groupGet('IvsLam','inst')
detLocation=inst.getComponentByName(detector_component_name).getPos()
sampleLocation=inst.getComponentByName(sample_component_name).getPos()
detLocation=inst.getComponentByName(detector_component_name).getPos()
sample2detector=detLocation-sampleLocation # metres
source=inst.getSource()
beamPos = sampleLocation - source.getPos()
PI = 3.1415926535
theta = groupGet(str(_sample_ws),'samp','theta')
if not theta:
theta = inst.getComponentByName(detector_component_name).getTwoTheta(sampleLocation, beamPos)*180.0/PI/2.0
print "Det location: ", detLocation, "Calculated theta = ",theta
if correct_positions: # detector is not in correct place
# Get detector angle theta from NeXuS
logger.information('The detectorlocation is not at Y=0')
print 'Nexus file theta =', theta
IvsQ = l2q(IvsLam, detector_component_name, theta, sample_component_name)
else:
IvsQ = ConvertUnits(InputWorkspace=IvsLam,OutputWorkspace="IvsQ",Target="MomentumTransfer")
else:
if correct_positions:
theta = float(theta)
try:
IvsQ = l2q(IvsLam, detector_component_name, theta, sample_component_name)
except AttributeError:
logger.warning("detector_component_name " + detector_component_name + " is unknown")
IvsQ = ConvertUnits(InputWorkspace=IvsLam,OutputWorkspace="IvsQ",Target="MomentumTransfer")
else:
IvsQ = ConvertUnits(InputWorkspace=IvsLam,OutputWorkspace="IvsQ",Target="MomentumTransfer")
RenameWorkspace(InputWorkspace=IvsLam,OutputWorkspace=RunNumber+'_IvsLam')
if isinstance(IvsLam, WorkspaceGroup):
counter = 0
for ws in IvsLam:
RenameWorkspace(ws, OutputWorkspace=RunNumber+'_IvsLam_'+str(counter))
counter += 1
RenameWorkspace(InputWorkspace=IvsQ,OutputWorkspace=RunNumber+'_IvsQ')
# delete all temporary workspaces unless in debug mode (debug=1)
if not debug:
cleanup()
if mtd.doesExist('IvsLam'):
DeleteWorkspace('IvsLam')
return mtd[RunNumber+'_IvsLam'], mtd[RunNumber+'_IvsQ'], theta
def quick_explicit(run, i0_monitor_index, lambda_min, lambda_max, background_min, background_max, int_min, int_max,
point_detector_start=0, point_detector_stop=0, multi_detector_start=0, theta=None,
pointdet=True,roi=[0,0], db=[0,0], trans='', debug=False, correction_strategy=NullCorrectionStrategy(),
stitch_start_overlap=None, stitch_end_overlap=None, stitch_params=None,
polcorr=False, crho=None, calpha=None, cAp=None, cPp=None, detector_component_name='point-detector',
sample_component_name='some-surface-holder', correct_positions=True ):
'''
Version of quick where all parameters are explicitly provided.
'''
_sample_ws = ConvertToWavelength.to_single_workspace(run)
nHist = _sample_ws.getNumberHistograms()
to_lam = ConvertToWavelength(run)
if pointdet:
detector_index_ranges = (point_detector_start, point_detector_stop)
else:
detector_index_ranges = (multi_detector_start, nHist-1)
_monitor_ws, _detector_ws = to_lam.convert(wavelength_min=lambda_min, wavelength_max=lambda_max, detector_workspace_indexes=detector_index_ranges, monitor_workspace_index=i0_monitor_index, correct_monitor=True, bg_min=background_min, bg_max=background_max )
inst = _sample_ws.getInstrument()
# Some beamline constants from IDF
print i0_monitor_index
print nHist
if (run=='0'):
RunNumber = '0'
else:
RunNumber = groupGet(_sample_ws.getName(),'samp','run_number')
if not pointdet:
# Proccess Multi-Detector; assume MD goes to the end:
# if roi or db are given in the function then sum over the apropriate channels
print "This is a multidetector run."
_I0M = RebinToWorkspace(WorkspaceToRebin=_monitor_ws,WorkspaceToMatch=_detector_ws)
IvsLam = _detector_ws / _I0M
if (roi != [0,0]) :
ReflectedBeam = SumSpectra(InputWorkspace=IvsLam, StartWorkspaceIndex=roi[0], EndWorkspaceIndex=roi[1])
if (db != [0,0]) :
DirectBeam = SumSpectra(InputWorkspace=_detector_ws, StartWorkspaceIndex=db[0], EndWorkspaceIndex=db[1])
ReflectedBeam = ReflectedBeam / DirectBeam
polCorr(polcorr, IvsLam, crho, calpha, cAp, cPp)
if (theta and correct_positions):
IvsQ = l2q(ReflectedBeam, detector_component_name, theta, sample_component_name)
else:
IvsQ = ConvertUnits(InputWorkspace=ReflectedBeam, Target="MomentumTransfer")
# Single Detector processing-------------------------------------------------------------
else:
print "This is a Point-Detector run."
# handle transmission runs
# process the point detector reflectivity
_I0P = RebinToWorkspace(WorkspaceToRebin=_monitor_ws,WorkspaceToMatch=_detector_ws)
IvsLam = Scale(InputWorkspace=_detector_ws,Factor=1)
if not trans:
print "No transmission file. Trying default exponential/polynomial correction..."
IvsLam = correction_strategy.apply(_detector_ws)
IvsLam = Divide(LHSWorkspace=IvsLam, RHSWorkspace=_I0P)
else: # we have a transmission run
_monInt = Integration(InputWorkspace=_I0P,RangeLower=int_min,RangeUpper=int_max)
IvsLam = Divide(LHSWorkspace=_detector_ws,RHSWorkspace=_monInt)
names = mtd.getObjectNames()
IvsLam = transCorr(trans, IvsLam, lambda_min, lambda_max, background_min, background_max,
int_min, int_max, detector_index_ranges, i0_monitor_index, stitch_start_overlap,
stitch_end_overlap, stitch_params )
IvsLam = polCorr(polcorr, IvsLam, crho, calpha, cAp, cPp)
# Convert to I vs Q
# check if detector in direct beam
if (theta == None or theta == 0 or theta == ''):
inst = groupGet('IvsLam','inst')
detLocation=inst.getComponentByName(detector_component_name).getPos()
sampleLocation=inst.getComponentByName(sample_component_name).getPos()
detLocation=inst.getComponentByName(detector_component_name).getPos()
sample2detector=detLocation-sampleLocation # metres
source=inst.getSource()
beamPos = sampleLocation - source.getPos()
theta = groupGet(str(_sample_ws),'samp','theta')
if not theta:
theta = inst.getComponentByName(detector_component_name).getTwoTheta(sampleLocation, beamPos)*180.0/math.pi/2.0
print "Det location: ", detLocation, "Calculated theta = ",theta
if correct_positions: # detector is not in correct place
# Get detector angle theta from NeXuS
logger.information('The detectorlocation is not at Y=0')
print 'Nexus file theta =', theta
IvsQ = l2q(IvsLam, detector_component_name, theta, sample_component_name)
else:
IvsQ = ConvertUnits(InputWorkspace=IvsLam,OutputWorkspace="IvsQ",Target="MomentumTransfer")
else:
if correct_positions:
theta = float(theta)
try:
IvsQ = l2q(IvsLam, detector_component_name, theta, sample_component_name)
except AttributeError:
logger.warning("detector_component_name " + detector_component_name + " is unknown")
IvsQ = ConvertUnits(InputWorkspace=IvsLam,OutputWorkspace="IvsQ",Target="MomentumTransfer")
else:
IvsQ = ConvertUnits(InputWorkspace=IvsLam,OutputWorkspace="IvsQ",Target="MomentumTransfer")
RenameWorkspace(InputWorkspace=IvsLam,OutputWorkspace=RunNumber+'_IvsLam')
if isinstance(IvsLam, WorkspaceGroup):
counter = 0
for ws in IvsLam:
RenameWorkspace(ws, OutputWorkspace=RunNumber+'_IvsLam_'+str(counter))
counter += 1
RenameWorkspace(InputWorkspace=IvsQ,OutputWorkspace=RunNumber+'_IvsQ')
# delete all temporary workspaces unless in debug mode (debug=1)
if not debug:
cleanup()
if mtd.doesExist('IvsLam'):
DeleteWorkspace('IvsLam')
return mtd[RunNumber+'_IvsLam'], mtd[RunNumber+'_IvsQ'], theta
def quick(run, theta=0, roi=[0,0], db=[0,0], trans='', outputType='pd', debug=0):
'''
call signature(s)::
x=quick(RunNumber)
x=quick(RunNumber, roi=[0,0], db=[0,0], trans=0, outputType='pd')
x=quick(RunNumber,[1,10])
x=quick(RunNumber,[1,10],[20,40])
x=quick(RunNumber, trans=2568)
x=quick(RunNumber, trans='SomeSavedWorkspaceName')
Reduces a ISIS raw or nexus file created on one of the reflectometers applying
only a minimum ammount of corrections. The data is left in terms of lambda.
Required arguments
========= =====================================================================
RunNumber Either an ISIS run number when the paths are set up correctly or
the full path and filename if an ISIS raw file.
========= =====================================================================
Optional keyword arguments:
========= =====================================================================
Keyword Description
========= =====================================================================
roi Region of interest marking the extent of the reflected beam.
default [0,0]
db Region of interest marking the extent of the direct beam.
default [0,0]
trans transmission run number or saved workspace. The default is 0 (No
transmission run). trans=-1 will supress the division of the
detector by the monitor.
outputType 'pd' = point detector (Default), 'md'= Multidetector Will use
this to build the equivalent of gd in the old matlab code but
keep all of the simple detector processing in one well organized
function. This should not be used by the average user.
========= =====================================================================
Outputs:
========= =====================================================================
x Either a single mantid workspace or worspace group or an array
of them.
========= =====================================================================
Working examples:
>>> # reduce a data set with the default parameters
>>> x=quick(/Users/trc/Dropbox/Work/PolrefTest/POLREF00003014.raw")
>>> # reduce a data set with a transmission run
>>> t=quick(/Users/trc/Dropbox/Work/PolrefTest/POLREF00003010.raw")
>>> x=quick(/Users/trc/Dropbox/Work/PolrefTest/POLREF00003014.raw", trans=t)
>>> # reduce a data set using the multidetector and output a single reflectivity
>>> # where the reflected beam is between channel 121 and 130.
>>> x=quick(/Users/trc/Dropbox/Work/PolrefTest/POLREF00003014.raw", [121,130])
Also see: pol
ToDo:
1) code for the transmisson DONE!
2) Similar to the genie on polref add extraction from the multidetector
3) need to make the variables stored in the frame work contain the run number. DONE!
'''
''' Notes for developers:
Naming conventions for workspaces which live in the mantid framework are as follows:
It's nearly random. this needs to be fixed so that name clashes do not occur.
May try adding a pair of underscores to the front of the name.
'''
[I0MonitorIndex, MultiDetectorStart, nHist] = toLam(run,'')
print I0MonitorIndex
print nHist
if (nHist > 5):
# Proccess Multi-Detector; assume MD goes to the end:
# if roi or db are given in the function then sum over the apropriate channels
print "This is a multidetector run."
try:
CropWorkspace(InputWorkspace="_D",OutputWorkspace="_DM",StartWorkspaceIndex=MultiDetectorStart)
RebinToWorkspace(WorkspaceToRebin="_M",WorkspaceToMatch="_DM",OutputWorkspace="_M_M")
CropWorkspace(InputWorkspace="_M_M",OutputWorkspace="_I0M",StartWorkspaceIndex=I0MonitorIndex)
Divide(LHSWorkspace="_DM",RHSWorkspace="_I0M",OutputWorkspace="IvsLam")
if (roi != [0,0]) :
SumSpectra(InputWorkspace="IvsLam",OutputWorkspace="DMR",StartWorkspaceIndex=roi[0], EndWorkspaceIndex=roi[1])
ReflectedBeam=mtd['DMR']
if (db != [0,0]) :
SumSpectra(InputWorkspace="_DM",OutputWorkspace="_DMD",StartWorkspaceIndex=db[0], EndWorkspaceIndex=db[1])
DirectBeam=mtd['_DMD']
except SystemExit:
print "Point-Detector only run."
RunNumber = groupGet('IvsLam','samp','run_number')
if (theta):
IvsQ = l2q(mtd['DMR'], 'linear-detector', theta)
else:
ConvertUnits(InputWorkspace='DMR',OutputWorkspace="IvsQ",Target="MomentumTransfer")
# Single Detector processing-------------------------------------------------------------
else:
print "This is a Point-Detector run."
# handle transmission runs
# process the point detector reflectivity
RebinToWorkspace(WorkspaceToRebin="_M",WorkspaceToMatch="_DP",OutputWorkspace="_M_P")
CropWorkspace(InputWorkspace="_M_P",OutputWorkspace="_I0P",StartWorkspaceIndex=I0MonitorIndex,EndWorkspaceIndex=I0MonitorIndex)
Scale("_DP","IvsLam",1)
#Divide(LHSWorkspace="_DP",RHSWorkspace="_I0P",OutputWorkspace="IvsLam")
# Normalise by good frames
GoodFrames = groupGet('IvsLam','samp','goodfrm')
print "run frames: ", GoodFrames
if (run=='0'):
RunNumber = '0'
else:
RunNumber = groupGet('IvsLam','samp','run_number')
#mtd['IvsLam'].getSampleDetails().getLogData("goodfrm").value
#Scale('IvsLam','IvsLam',GoodFrames**-1,'Multiply')
#IvsLam = mtd['IvsLam']*GoodFrames**-1
if (trans==''):
#monitor2Eff('M') # This doesn't seem to work.
#heliumDetectorEff('DP') # point detector #Nor does this.
# Multidetector (Flood) TODO
print "No transmission file. Using monitor spectrum"
# normalise by monitor spectrum
# RebinToWorkspace(WorkspaceToRebin="_M",WorkspaceToMatch="_DP",OutputWorkspace="_M_M")
# CropWorkspace(InputWorkspace="M_M",OutputWorkspace="I0M",StartWorkspaceIndex=I0MonitorIndex)
# Divide(LHSWorkspace="DM",RHSWorkspace="I0M",OutputWorkspace="RM")
Divide(LHSWorkspace="_DP",RHSWorkspace="_I0P",OutputWorkspace="IvsLam")
else: # we have a transmission run
names = mtd.getWorkspaceNames()
if trans in names:
Divide(LHSWorkspace="_DP",RHSWorkspace="_I0P",OutputWorkspace="IvsLam")
RebinToWorkspace(trans,"IvsLam",trans)
#IvsLam = mtd['IvsLam']*GoodFrames**-1
Divide(LHSWorkspace="IvsLam",RHSWorkspace=trans,OutputWorkspace="IvsLam")
else:
Divide(LHSWorkspace="_DP",RHSWorkspace="_I0P",OutputWorkspace="IvsLam")
#IvsLam = mtd['IvsLam']*GoodFrames**-1
[I0MonitorIndex, MultiDetectorStart, nHist] = toLam(trans,'_TRANS')
RebinToWorkspace(WorkspaceToRebin="_M_TRANS",WorkspaceToMatch="_DP_TRANS",OutputWorkspace="_M_P_TRANS")
CropWorkspace(InputWorkspace="_M_P_TRANS",OutputWorkspace="_I0P_TRANS",StartWorkspaceIndex=I0MonitorIndex)
Divide(LHSWorkspace="_DP_TRANS",RHSWorkspace="_I0P_TRANS",OutputWorkspace=str(trans)+"_IvsLam_TRANS")
# Normalise TRANS run by good frames
print str(trans)+'_IvsLam_TRANS'
GoodFramesTr = groupGet(str(trans)+'_IvsLam_TRANS','samp','goodfrm')
print "trans frames: ", GoodFramesTr
#mtd['IvsLam_TRANS'].getSampleDetails().getLogData("goodfrm").value
#Scale(str(trans)+'_IvsLam_TRANS',Factor=GoodFramesTr**-1,OutputWorkspace=str(trans)+'_IvsLam_TRANS')
#got sometimes very slight binning diferences, so do this again:
RebinToWorkspace(WorkspaceToRebin=str(trans)+'_IvsLam_TRANS',WorkspaceToMatch="IvsLam",OutputWorkspace=str(trans)+'_IvsLam_TRANS')
Divide(LHSWorkspace="IvsLam",RHSWorkspace=str(trans)+"_IvsLam_TRANS",OutputWorkspace="IvsLam")
# try:
# Divide(LHSWorkspace=str(trans)+"_IvsLam",RHSWorkspace=str(trans)+"_IvsLam_TRANS",OutputWorkspace="IvsLam")
# except:
# try:
# Divide(LHSWorkspace="IvsLam_1",RHSWorkspace=str(trans)+"_IvsLam_TRANS_1",OutputWorkspace="IvsLam_1")
# print 'Handling run-time error: possibly empty periods...'
# except:
# print 'Handling run-time error: possibly empty periods...'
# Need to process the optional args to see what needs to be output and what division needs to be made
# Convert to I vs Q
# check if detector in direct beam
if (theta == 0 or theta == ''):
if (theta == ''):
theta = 0
print "given theta = ",theta
inst = groupGet('IvsLam','inst')
detLocation=inst.getComponentByName('point-detector').getPos()
sampleLocation=inst.getComponentByName('some-surface-holder').getPos()
detLocation=inst.getComponentByName('point-detector').getPos()
sample2detector=detLocation-sampleLocation # meters
source=inst.getSource()
beamPos = sampleLocation - source.getPos()
PI = 3.1415926535
theta = inst.getComponentByName('point-detector').getTwoTheta(sampleLocation, beamPos)*180.0/PI
print "Det location: ", detLocation, "Calculated theta = ",theta
if detLocation.getY() == 0: # detector is not in correct place
print "det at 0"
# Load corresponding NeXuS file
runno = '_' + str(run)
#templist.append(runno)
if type(run)==type(int()):
LoadNexus(Filename=run,OutputWorkspace=runno)
else:
LoadNexus(Filename=run.replace("raw","nxs",1),OutputWorkspace=runno)
# Get detector angle theta from NeXuS
theta = groupGet(runno,'samp','theta')
print 'Nexus file theta =', theta
IvsQ = l2q(IvsLam, 'point-detector', theta)
else:
ConvertUnits(InputWorkspace='IvsLam',OutputWorkspace="IvsQ",Target="MomentumTransfer",AlignBins="1")
else:
theta = float(theta)
IvsQ = l2q(mtd['IvsLam'], 'point-detector', theta)
RenameWorkspace('IvsLam',RunNumber+'_IvsLam')
RenameWorkspace('IvsQ',RunNumber+'_IvsQ')
# delete all temporary workspaces unless in debug mode (debug=1)
if debug == 0:
cleanup()
return mtd[RunNumber+'_IvsLam'], mtd[RunNumber+'_IvsQ'], theta