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Commit b70757af authored by Roman Tolchenov's avatar Roman Tolchenov
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Revert "Re #5974. Adde changes by Spencer Howells." 

This reverts commit 94511568.
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Code/Mantid/scripts/Inelastic/IndirectDataAnalysis.py
+ 60
− 111
View file @ b70757af
......@@ -3,7 +3,7 @@ from IndirectImport import import_mantidplot
mp = import_mantidplot()
from IndirectCommon import *
from mantid import config, logger
import math, re, os.path, numpy as np
import math, re, os.path
##############################################################################
# Misc. Helper Functions
......@@ -143,13 +143,11 @@ def elwin(inputFiles, eRange, Save=False, Verbose=True, Plot=False):
elif ( len(eRange) == 2 ):
logger.notice('Using 1 energy range from '+range1)
for file in inputFiles:
(direct, file) = os.path.split(file)
(root, ext) = os.path.splitext(file)
savefile = root[:-3]
LoadNexus(Filename=file, OutputWorkspace=tempWS)
if Verbose:
logger.notice('Reading file : '+file)
nsam,ntc = CheckHistZero(tempWS)
savefile = getWSprefix(tempWS)
if ( len(eRange) == 4 ):
ElasticWindow(InputWorkspace=tempWS, Range1Start=eRange[0], Range1End=eRange[1],
Range2Start=eRange[2], Range2End=eRange[3],
......@@ -174,17 +172,11 @@ def elwin(inputFiles, eRange, Save=False, Verbose=True, Plot=False):
return eq1, eq2
def elwinPlot(eq1,eq2):
nBins = mtd[eq1[0]].blocksize()
if nBins >= 10:
nBins = 10
lastXeq1 = mtd[eq1[0]].readX(0)[nBins-1]
lastXeq1 = mtd[eq1[0]].readX(0)[-1]
graph1 = mp.plotSpectrum(eq1, 0)
layer = graph1.activeLayer()
layer.setScale(mp.Layer.Bottom, 0.0, lastXeq1)
nBins = mtd[eq2[0]].blocksize()
if nBins >= 10:
nBins = 10
lastXeq2 = mtd[eq2[0]].readX(0)[nBins-1]
lastXeq2 = mtd[eq2[0]].readX(0)[-1]
graph2 = mp.plotSpectrum(eq2, 0)
layer = graph2.activeLayer()
layer.setScale(mp.Layer.Bottom, 0.0, lastXeq2)
......@@ -278,67 +270,43 @@ def fury(sam_files, res_file, rebinParam, RES=True, Save=False, Verbose=False,
# FuryFit
##############################################################################
def furyfitParsToWS(Table, Data, option):
nopt = len(option)
if nopt == 2:
npeak = option[0]
type = option[1]
elif nopt == 4:
npeak = 2
type = 'SE'
else:
logger.notice('Bad option : ' +option)
Q = createQaxis(Data)
nQ = len(Q)
Q.append(2*Q[nQ-1]-Q[nQ-2])
def furyfitParsToWS(Table, Data):
dataX = createQaxis(Data)
dataY = []
dataE = []
names = ""
xAxisVals = []
ws = mtd[Table]
rCount = ws.rowCount()
cCount = ws.columnCount()
rCount = ws.rowCount()
cName = ws.getColumnNames()
Qa = np.array(Q)
A0v = ws.column(1) #bgd value
A0e = ws.column(2) #bgd error
Iy1 = ws.column(5) #intensity1 value
Ie1 = ws.column(2) #intensity1 error = bgd
dataX = Qa
dataY = np.array(Iy1)
dataE = np.array(Ie1)
names = cName[5]
Ty1 = ws.column(7) #tau1 value
Te1 = ws.column(8) #tau1 error
dataX = np.append(dataX,Qa)
dataY = np.append(dataY,np.array(Ty1))
dataE = np.append(dataE,np.array(Te1))
names += ","+cName[7]
nSpec = 2
logger.notice(' Option : '+str(npeak)+' '+type)
if npeak == 1:
By1 = ws.column(9) #beta1 value
Be1 = ws.column(10) #beta2 error
dataX = np.append(dataX,Qa)
dataY = np.append(dataY,np.array(By1))
dataE = np.append(dataE,np.array(Be1))
names += ","+cName[9]
nSpec += 1
logger.notice(' Nspec : '+str(nSpec)+' '+names)
if npeak == 2:
Iy2 = ws.column(9) #intensity2 value
Ie2 = ws.column(10) #intensity2 error
dataX = np.append(dataX,Qa)
dataY = np.append(dataY,np.array(Iy2))
dataE = np.append(dataE,np.array(Ie2))
names += ","+cName[9]
nSpec += 1
Ty2 = ws.column(11) #tau2 value
Te2 = ws.column(12) #tau2 error
dataX = np.append(dataX,Qa)
dataY = np.append(dataY,np.array(Ty2))
dataE = np.append(dataE,np.array(Te2))
names += ","+cName[11]
nSpec += 1
logger.notice(' Ns : '+str(nSpec)+' '+names)
nSpec = ( cCount - 1 ) / 2
yA0 = ws.column(1)
eA0 = ws.column(2)
logger.notice(str(yA0))
logger.notice(str(eA0))
xAxis = cName[0]
stretched = 0
for spec in range(0,nSpec):
yCol = (spec*2)+1
yAxis = cName[(spec*2)+1]
if ( re.search('Intensity$', yAxis) or re.search('Tau$', yAxis) or
re.search('Beta$', yAxis) ):
xAxisVals += dataX
if (len(names) > 0):
names += ","
names += yAxis
eCol = (spec*2)+2
eAxis = cName[(spec*2)+2]
for row in range(0, rCount):
dataY.append(ws.cell(row,yCol))
dataE.append(ws.cell(row,eCol))
if ( re.search('Beta$', yAxis) ): # need to know how many of curves
stretched += 1 # are stretched exponentials
else:
nSpec -= 1
wsname = Table + "_Workspace"
CreateWorkspace(OutputWorkspace=wsname, DataX=dataX, DataY=dataY, DataE=dataE,
CreateWorkspace(OutputWorkspace=wsname, DataX=xAxisVals, DataY=dataY, DataE=dataE,
Nspec=nSpec, UnitX='MomentumTransfer', VerticalAxisUnit='Text',
VerticalAxisValues=names)
return wsname
......@@ -369,13 +337,11 @@ def furyfitSeq(inputWS, func, ftype, startx, endx, Save, Plot, Verbose = True):
for i in range(1,nHist):
input += ';'+inputWS+',i'+str(i)
outNm = getWSprefix(inputWS) + 'fury_' + ftype + "0_to_" + str(nHist-1)
option = ftype[:-2]
if Verbose:
logger.notice('Option: '+option)
logger.notice(func)
PlotPeakByLogValue(Input=input, OutputWorkspace=outNm, Function=func,
StartX=startx, EndX=endx, FitType='Sequential')
wsname = furyfitParsToWS(outNm, inputWS, option)
wsname = furyfitParsToWS(outNm, inputWS)
RenameWorkspace(InputWorkspace=outNm, OutputWorkspace=outNm+"_Parameters")
if Save:
opath = os.path.join(workdir, wsname+'.nxs') # path name for nxs file
......@@ -389,8 +355,6 @@ def furyfitSeq(inputWS, func, ftype, startx, endx, Save, Plot, Verbose = True):
def furyfitMultParsToWS(Table, Data):
dataX = []
dataA0v = []
dataA0e = []
dataY1 = []
dataE1 = []
dataY2 = []
......@@ -399,24 +363,21 @@ def furyfitMultParsToWS(Table, Data):
dataE3 = []
ws = mtd[Table+'_Parameters']
rCount = ws.rowCount()
cCount = ws.columnCount()
logger.notice(' Cols : '+str(cCount))
nSpec = ( rCount - 1 ) / 5
for spec in range(0,nSpec):
A0val = 1
A0err = 2
n1 = spec*5
rowi = n1 + 2 #intensity
ival = 5 #intensity value
ierr = 6 #intensity error
tval = 7 #tau value
terr = 8 #tau error
rowt = n1 + 3 #tau
rowb = 4 #beta
bval = 9 #beta value
bval = 10 #beta error
dataX.append(spec)
dataA0v.append(ws.cell(spec,A0val))
dataA0e.append(ws.cell(spec,A0err))
dataY1.append(ws.cell(spec,ival))
dataE1.append(ws.cell(spec,A0err))
dataE1.append(ws.cell(spec,ierr))
dataY2.append(ws.cell(spec,tval))
dataE2.append(ws.cell(spec,terr))
dataY3.append(ws.cell(spec,bval))
......@@ -518,14 +479,8 @@ def msdfitPlotFits(lniWS, fitWS, n):
mfit_plot = mp.plotSpectrum(lniWS,n,True)
mp.mergePlots(mfit_plot,mp.plotSpectrum(fitWS+'_line',n,False))
def getInstrRun(file):
mo = re.match('([a-zA-Z]+)([0-9]+)',file)
instr_and_run = mo.group(0) # instr name + run number
instr = mo.group(1) # instrument prefix
run = mo.group(2) # run number as string
return instr,run
def msdfit(inputs, startX, endX, Save=False, Verbose=True, Plot=True):
import re
StartTime('msdFit')
workdir = config['defaultsave.directory']
log_type = 'sample'
......@@ -540,10 +495,6 @@ def msdfit(inputs, startX, endX, Save=False, Verbose=True, Plot=True):
if Verbose:
logger.notice('Reading Run : '+file)
LoadNexusProcessed(FileName=file, OutputWorkspace=root)
eiq = root[:-1]+'1'
LoadNexusProcessed(FileName=eiq+'.nxs', OutputWorkspace='__eiq')
(instr, run) = getInstrRun(root)
run_name = instr + run
nsam,ntc = CheckHistZero(root)
inX = mtd[root].readX(0)
inY = mtd[root].readY(0)
......@@ -564,30 +515,32 @@ def msdfit(inputs, startX, endX, Save=False, Verbose=True, Plot=True):
lnWS = root[:-3] + 'lnI'
CreateWorkspace(OutputWorkspace=lnWS, DataX=inX, DataY=logy, DataE=loge,
Nspec=1)
log_name = run_name+'_'+log_type
mo = re.match('([a-zA-Z]+)([0-9]+)',root)
log_name_root = mo.group(0) # instr name + run number
run_number = mo.group(2) # run number as string
log_name = log_name_root+'_'+log_type
log_file = log_name+'.txt'
log_path = FileFinder.getFullPath(log_file)
if (log_path == ''):
logger.notice(' Run : '+run_name +' ; Temperature file not found')
xval = int(run[-3:])
logger.notice(' Run : '+log_name_root +' ; Temperature file not found')
#xval = int(root[5:8])
xval = int(run_number[-3:]) # take 3 last digits of the run number
xlabel = 'Run'
else:
else:
logger.notice('Found '+log_path)
LoadLog(Workspace=root, Filename=log_path)
run_logs = mtd[root].getRun()
tmp = run_logs[log_name].value
temp = tmp[len(tmp)-1]
logger.notice(' Run : '+run_name+' ; Temperature = '+str(temp))
logger.notice(' Run : '+log_name_root +' ; Temperature = '+str(temp))
xval = temp
xlabel = 'Temp'
if (np == 0):
RenameWorkspace(InputWorkspace='__eiq',OutputWorkspace='eiq')
first = run_name
last = run
first = log_name_root
last = log_name_root
run_list = lnWS
else:
ConjoinWorkspaces(InputWorkspace1='eiq', InputWorkspace2='__eiq', CheckOverlapping=False)
last = run
last = log_name_root
run_list += ';'+lnWS
x_list.append(xval)
DeleteWorkspace(root)
......@@ -596,13 +549,16 @@ def msdfit(inputs, startX, endX, Save=False, Verbose=True, Plot=True):
logger.notice('Fitting Runs '+first+' to '+last)
logger.notice('Q-range from '+str(startX)+' to '+str(endX))
function = 'name=LinearBackground, A0=0, A1=0'
mname = first+'_to_'+last
#mname = first[0:8]+'_to_'+last[3:8]
mo = re.match('[a-zA-Z]+[0-9]+',first)
mname = mo.group(0)+'_to_'
mo = re.match('[a-zA-Z]+([0-9]+)',last)
mname += mo.group(1)
msdWS = mname+'_msd'
PlotPeakByLogValue(Input=run_list, OutputWorkspace=msdWS+'_Table', Function=function,
StartX=startX, EndX=endX, FitType = 'Sequential')
msdfitParsToWS(msdWS, x_list)
np = 0
eiqWS = mname+'_eiq'
lniWS = mname+'_lnI'
fitWS = mname+'_Fit'
a0 = mtd[msdWS+'_a0'].readY(0)
......@@ -633,20 +589,13 @@ def msdfit(inputs, startX, endX, Save=False, Verbose=True, Plot=True):
np += 1
group = fitWS+'_data,'+ fitWS+'_line'
GroupWorkspaces(InputWorkspaces=group,OutputWorkspace=fitWS)
RenameWorkspace(InputWorkspace='eiq',OutputWorkspace=eiqWS)
if Plot:
msdfitPlotSeq(msdWS, xlabel)
msdfitPlotFits(lniWS, fitWS, 0)
if Save:
eiq_path = os.path.join(workdir, eiqWS+'.nxs') # path name for nxs file
SaveNexusProcessed(InputWorkspace=eiqWS, Filename=eiq_path, Title=eiqWS)
lni_path = os.path.join(workdir, lniWS+'.nxs') # path name for nxs file
SaveNexusProcessed(InputWorkspace=lniWS, Filename=lni_path, Title=lniWS)
msd_path = os.path.join(workdir, msdWS+'.nxs') # path name for nxs file
SaveNexusProcessed(InputWorkspace=msdWS, Filename=msd_path, Title=msdWS)
if Verbose:
logger.notice('Output eiq file : '+eiq_path)
logger.notice('Output lnI file : '+lni_path)
logger.notice('Output msd file : '+msd_path)
EndTime('msdFit')
return msdWS
......
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