From b70757afc0e2516554faece48060e225212f5bde Mon Sep 17 00:00:00 2001
From: Roman Tolchenov <roman.tolchenov@stfc.ac.uk>
Date: Tue, 23 Oct 2012 10:29:44 +0100
Subject: [PATCH] Revert "Re #5974. Adde changes by Spencer Howells."
This reverts commit 945115686478d7fe1df9afdc5bbfe8b3ce8221c5.
---
.../scripts/Inelastic/IndirectDataAnalysis.py | 171 ++++++------------
1 file changed, 60 insertions(+), 111 deletions(-)
diff --git a/Code/Mantid/scripts/Inelastic/IndirectDataAnalysis.py b/Code/Mantid/scripts/Inelastic/IndirectDataAnalysis.py
index 9fbd6acde2b..6b6873346ea 100644
--- a/Code/Mantid/scripts/Inelastic/IndirectDataAnalysis.py
+++ b/Code/Mantid/scripts/Inelastic/IndirectDataAnalysis.py
@@ -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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