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Merge branch 'feature/8388_correct_temp_normalisation'
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@abuts
abuts committed Nov 18, 2013
2 parents 0696ddc + 7bd8f8b commit 80ed3a6
Showing 1 changed file with 112 additions and 60 deletions.
172 changes: 112 additions & 60 deletions Code/Mantid/scripts/Inelastic/IndirectDataAnalysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -348,109 +348,147 @@ def elwin(inputFiles, eRange, log_type='sample', Normalise = False,
datTx = np.append(datTx,Txa)
datTy = np.append(datTy,iqa)
datTe = np.append(datTe,eqa)
DeleteWorkspace(tempWS)

DeleteWorkspace('__eq1')
DeleteWorkspace('__eq2')
DeleteWorkspace('__elf')

if (nr == 1):
ename = first[:-1]
else:
ename = first+'to_'+last

elfWS = ename+'_elf' # interchange Q & T

#check if temp was increasing of decreasing
#check if temp was increasing or decreasing
if(datTx[0] > datTx[-1]):
# if so reverse data to follow natural ordering
datTx = datTx[::-1]
datTy = datTy[::-1]
datTe = datTe[::-1]

CreateWorkspace(OutputWorkspace=elfWS, DataX=datTx, DataY=datTy, DataE=datTe,
Nspec=nQ, UnitX='Energy', VerticalAxisUnit='MomentumTransfer', VerticalAxisValues=q1)
DeleteWorkspace('__elf')
label = unit[0]+' / '+unit[1]
AddSampleLog(Workspace=elfWS, LogName="Vaxis", LogType="String", LogText=label)

elfWS = ename+'_elf'
e1WS = ename+'_eq1'
CreateWorkspace(OutputWorkspace=e1WS, DataX=datX1, DataY=datY1, DataE=datE1,
Nspec=nr, UnitX='MomentumTransfer', VerticalAxisUnit='Energy', VerticalAxisValues=Taxis)
label = unit[0]+' / '+unit[1]
AddSampleLog(Workspace=e1WS, LogName="Vaxis", LogType="String", LogText=label)
e2WS = ename+'_eq2'
CreateWorkspace(OutputWorkspace=e2WS, DataX=datX2, DataY=datY2, DataE=datE2,
Nspec=nr, UnitX='QSquared', VerticalAxisUnit='Energy', VerticalAxisValues=Taxis)
AddSampleLog(Workspace=e2WS, LogName="Vaxis", LogType="String", LogText=label)
#elt only created if we normalise
eltWS = None

wsnames = [elfWS, e1WS, e2WS]

#x,y,e data for the elf, e1 and e2 workspaces
data = [[datTx, datTy, datTe],
[datX1, datY1, datE1],
[datX2, datY2, datE2]]

#x and vertical units for the elf, e1 and e2 workspaces
xunits = ['Energy', 'MomentumTransfer', 'QSquared']
vunits = ['MomentumTransfer', 'Energy', 'Energy']

#vertical axis values for the elf, e1 and e2 workspaces
vvalues = [q1, Taxis, Taxis]

#number of spectra in each workspace
nspecs = [nQ, nr, nr]

#x-axis units label
label = unit[0]+' / '+unit[1]

wsInfo = zip(wsnames,data, xunits, vunits, vvalues, nspecs)

#Create output workspaces and add sample logs
for wsname, wsdata, xunit, vunit, vvalue, nspec in wsInfo:
x, y, e = wsdata

CreateWorkspace(OutputWorkspace=wsname, DataX=x, DataY=y, DataE=e,
Nspec=nspec, UnitX=xunit, VerticalAxisUnit=vunit, VerticalAxisValues=vvalue)

#add sample logs to new workspace
CopyLogs(InputWorkspace=tempWS, OutputWorkspace=wsname)
addElwinLogs(wsname, label, eRange, Range2)

# remove the temp workspace now we've copied the logs
DeleteWorkspace(tempWS)

if unit[0] == 'Temperature':
nT = len(Tvalue)
if Tvalue[0] < Tvalue[nT-1]:
lo = 0
hi = nT-1
else:
lo = nT-1
hi = 0
text = 'Temperature range : '+str(Tvalue[lo])+' to '+str(Tvalue[hi])
AddSampleLog(Workspace=e1WS, LogName="Temperature normalise", LogType="String", LogText=str(Normalise))

AddSampleLog(Workspace=e1WS, LogName="temp_normalise",
LogType="String", LogText=str(Normalise))

#create workspace normalized to the lowest temperature
if Normalise:
yval = mtd[e1WS].readY(lo)
normFactor = 1.0/yval[0]
Scale(InputWorkspace=e1WS, OutputWorkspace=e1WS, Factor=normFactor, Operation='Multiply')
AddSampleLog(Workspace=e1WS, LogName="Temperature value", LogType="Number", LogText=str(Tvalue[0]))
if Verbose:
text = 'Temperature range : '+str(Tvalue[lo])+' to '+str(Tvalue[hi])
logger.notice(text)
logger.notice('Normalised eq1 by scale factor : '+str(normFactor))
eltWS = ename+'_elt'

#create elt workspace
mtd[elfWS].clone(OutputWorkspace=eltWS)
elwinNormalizeToLowestTemp(eltWS)

#set labels and meta data
unitx = mtd[eltWS].getAxis(0).setUnit("Label")
unitx.setLabel(unit[0], unit[1])
addElwinLogs(eltWS, label, eRange, Range2)

#append workspace name to output files list
wsnames.append(eltWS)

#set labels on workspace axes
unity = mtd[e1WS].getAxis(1).setUnit("Label")
unity.setLabel(unit[0], unit[1])
label = unit[0]+' / '+unit[1]
addElwinLogs(e1WS, label, eRange, Range2)

unity = mtd[e2WS].getAxis(1).setUnit("Label")
unity.setLabel(unit[0], unit[1])
addElwinLogs(e2WS, label, eRange, Range2)

unitx = mtd[elfWS].getAxis(0).setUnit("Label")
unitx.setLabel(unit[0], unit[1])
addElwinLogs(elfWS, label, eRange, Range2)

if Save:
e1_path = os.path.join(workdir, e1WS+'.nxs') # path name for nxs file
e2_path = os.path.join(workdir, e2WS+'.nxs') # path name for nxs file
elf_path = os.path.join(workdir, elfWS+'.nxs') # path name for nxs file

if Verbose:
logger.notice('Creating file : '+e1_path)
logger.notice('Creating file : '+e2_path)
logger.notice('Creating file : '+elf_path)

SaveNexusProcessed(InputWorkspace=e1WS, Filename=e1_path)
SaveNexusProcessed(InputWorkspace=e2WS, Filename=e2_path)
SaveNexusProcessed(InputWorkspace=elfWS, Filename=elf_path)
elwinSaveWorkspaces(wsnames, workdir, Verbose)

if Plot:
elwinPlot(label,e1WS,e2WS,elfWS)
elwinPlot(label,e1WS,e2WS,elfWS,eltWS)

EndTime('Elwin')
return e1WS,e2WS

#normalize workspace to the lowest temperature
def elwinNormalizeToLowestTemp(eltWS):
nhist = mtd[eltWS].getNumberHistograms()

#normalize each spectrum in the workspace
for n in range(0,nhist):
y = mtd[eltWS].readY(n)
scale = 1.0/y[0]
yscaled = scale * y
mtd[eltWS].setY(n, yscaled)

# Write each of the created workspaces to file
def elwinSaveWorkspaces(flist, dir, Verbose):
for fname in flist:
fpath = os.path.join(dir, fname+'.nxs')

if Verbose:
logger.notice('Creating file : '+ fpath)

SaveNexusProcessed(InputWorkspace=fname, Filename=fpath)

# Add sample log to each of the workspaces created by Elwin
def addElwinLogs(ws, label, eRange, Range2):

AddSampleLog(Workspace=ws, LogName="Vaxis", LogType="String", LogText=label)
AddSampleLog(Workspace=ws, LogName="Range1 start", LogType="Number", LogText=str(eRange[0]))
AddSampleLog(Workspace=ws, LogName="Range1 end", LogType="Number", LogText=str(eRange[1]))
AddSampleLog(Workspace=ws, LogName="Two ranges", LogType="String", LogText=str(Range2))
AddSampleLog(Workspace=ws, LogName="vert_axis", LogType="String", LogText=label)
AddSampleLog(Workspace=ws, LogName="range1_start", LogType="Number", LogText=str(eRange[0]))
AddSampleLog(Workspace=ws, LogName="range1_end", LogType="Number", LogText=str(eRange[1]))
AddSampleLog(Workspace=ws, LogName="two_ranges", LogType="String", LogText=str(Range2))

if Range2:
AddSampleLog(Workspace=ws, LogName="Range2 start", LogType="Number", LogText=str(eRange[2]))
AddSampleLog(Workspace=ws, LogName="Range2 end", LogType="Number", LogText=str(eRange[3]))
AddSampleLog(Workspace=ws, LogName="range2_start", LogType="Number", LogText=str(eRange[2]))
AddSampleLog(Workspace=ws, LogName="range2_end", LogType="Number", LogText=str(eRange[3]))

#Plot each of the workspace output by elwin
def elwinPlot(label,eq1,eq2,elf):
def elwinPlot(label,eq1,eq2,elf,elt):
plotElwinWorkspace(eq1, yAxisTitle='Elastic Intensity', setScale=True)
plotElwinWorkspace(eq2, yAxisTitle='log(Elastic Intensity)', setScale=True)
plotElwinWorkspace(elf, xAxisTitle=label)

if elt is not None:
plotElwinWorkspace(elt, xAxisTitle=label)

#Plot a workspace generated by Elwin
def plotElwinWorkspace(ws, xAxisTitle=None, yAxisTitle=None, setScale=False):
ws = mtd[ws]
Expand Down Expand Up @@ -891,6 +929,14 @@ def msdfitParsToWS(Table, xData):
dataY1 = map(lambda x : -x, yA1)
eA1 = ws.column(4)
wsname = Table

#check if temp was increasing or decreasing
if(dataX[0] > dataX[-1]):
# if so reverse data to follow natural ordering
dataX = dataX[::-1]
dataY1 = dataY1[::-1]
eA1 = eA1[::-1]

CreateWorkspace(OutputWorkspace=wsname+'_a0', DataX=dataX, DataY=yA0, DataE=eA0,
Nspec=1, UnitX='')
CreateWorkspace(OutputWorkspace=wsname+'_a1', DataX=dataX, DataY=dataY1, DataE=eA1,
Expand Down Expand Up @@ -928,8 +974,8 @@ def msdfit(inputs, startX, endX, Save=False, Verbose=False, Plot=True):
ws_run = ws.getRun()
vertAxisValues = ws.getAxis(1).extractValues()
x_list = vertAxisValues
if 'Vaxis' in ws_run:
xlabel = ws_run.getLogData('Vaxis').value
if 'vert_axis' in ws_run:
xlabel = ws_run.getLogData('vert_axis').value
for nr in range(0, nHist):
nsam,ntc = CheckHistZero(root)
lnWS = '__lnI_'+str(nr)
Expand Down Expand Up @@ -984,6 +1030,12 @@ def msdfit(inputs, startX, endX, Save=False, Verbose=False, Plot=True):
DeleteWorkspace(inWS)
DeleteWorkspace('__data')
GroupWorkspaces(InputWorkspaces=gro,OutputWorkspace=calcWS)

#add sample logs to output workspace
CopyLogs(InputWorkspace=root, OutputWorkspace=msdWS)
AddSampleLog(Workspace=msdWS, LogName="start_x", LogType="Number", LogText=str(startX))
AddSampleLog(Workspace=msdWS, LogName="end_x", LogType="Number", LogText=str(endX))

if Plot:
msdfitPlotSeq(msdWS, xlabel)
msdfitPlotFits(calcWS, 0)
Expand Down

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