Merge branch 'feature/5421_IDA_bayes_interface' into develop

Conflicts:
	Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt
	Code/Mantid/scripts/Inelastic/IndirectBayes.py

Refs #5421

Code/Mantid/MantidQt/CustomInterfaces/CMakeLists.txt

@@ -114,7 +114,6 @@ set ( MOC_FILES inc/MantidQtCustomInterfaces/Background.h
                 inc/MantidQtCustomInterfaces/CreateMDWorkspace.h
                 inc/MantidQtCustomInterfaces/CreateMDWorkspaceAlgDialog.h
                 inc/MantidQtCustomInterfaces/Elwin.h
-
                 inc/MantidQtCustomInterfaces/Fury.h
                 inc/MantidQtCustomInterfaces/FuryFit.h
                 inc/MantidQtCustomInterfaces/Homer.h

Code/Mantid/MantidQt/CustomInterfaces/src/JumpFit.cpp

@@ -89,7 +89,7 @@ namespace MantidQt
 			QString pyInput = 
 				"from IndirectJumpFit import JumpRun\n";
 
-			pyInput += "JumpRun("+sample+","+fitFunction+","+widthTxt+","+QMin+","+QMax+","
+			pyInput += "JumpRun('"+sample+"','"+fitFunction+"',"+widthTxt+","+QMin+","+QMax+","
 									"Save="+save+", Plot='"+plot+"', Verbose="+verbose+")\n";
 
 			runPythonScript(pyInput);

Code/Mantid/MantidQt/CustomInterfaces/src/Stretch.cpp

@@ -92,7 +92,7 @@ namespace MantidQt
 			if(m_uiForm.chkElasticPeak->isChecked()) { elasticPeak = "True"; }
 			if(m_uiForm.chkSequentialFit->isChecked()) { sequence = "True"; }
 
-			QString fitOps = "[" + elasticPeak + ", '" + background + "', 0, 0]";
+			QString fitOps = "[" + elasticPeak + ", '" + background + "', False, False]";
 
 			//Collect input from the properties browser
 			QString eMin = m_properties["EMin"]->valueText();

Code/Mantid/scripts/Inelastic/IndirectBayes.py

@@ -49,7 +49,6 @@ def GetXYE(inWS,n,array_len):
 	E=PadArray(Ein,array_len)
 	return N,X,Y,E
 
-
 def GetResNorm(resnormWS,ngrp):
 	if ngrp == 0:                                # read values from WS
 		dtnorm = mtd[resnormWS+'_Intensity'].readY(0)
@@ -75,7 +74,7 @@ def ReadNormFile(readRes,resnormWS,nsam,Verbose):            # get norm & scale
 			sys.exit(error)
 		Xin = mtd[resnormWS+'_Stretch'].readX(0)					# no. points from length of x array
 		if len(Xin) == 0:				
-			error = 'ResNorm file has no xscale points'			
+			error = 'ResNorm file has no xscale points'
 			logger.notice('ERROR *** ' + error)
 			sys.exit(error)
 		if nrm != nsam:				# check that no. groups are the same
@@ -140,6 +139,7 @@ def ReadWidthFile(readWidth,widthFile,numSampleGroups,Verbose):
 
 # QLines programs
 def QLRun(program,samWS,resWS,resnormWS,erange,nbins,Fit,wfile,Loop,Verbose=False,Plot='None',Save=False):
+
 	StartTime(program)
 
 	#expand fit options
@@ -218,8 +218,9 @@ def QLRun(program,samWS,resWS,resnormWS,erange,nbins,Fit,wfile,Loop,Verbose=Fals
 	wrkr=resWS
 	wrkr.ljust(140,' ')
 	wrk = [wrks, wrkr]
-#
-	if program == 'QL':						   # initialise probability list
+
+	# initialise probability list
+	if program == 'QL':
 		prob0 = []
 		prob1 = []
 		prob2 = []
@@ -333,12 +334,19 @@ def QLRun(program,samWS,resWS,resnormWS,erange,nbins,Fit,wfile,Loop,Verbose=Fals
 		outWS = C2Se(fname)
 		if (Plot != 'None'):
 			QLPlotQSe(fname,Plot,res_plot,Loop)
-
+
+	#Add some sample logs to the output workspace
+	AddSampleLog(Workspace=outWS, LogName="Fit Program", LogType="String", LogText=prog)
+	AddSampleLog(Workspace=outWS, LogName="Energy min", LogType="Number", LogText=str(erange[0]))
+	AddSampleLog(Workspace=outWS, LogName="Energy max", LogType="Number", LogText=str(erange[1]))
 	AddSampleLog(Workspace=outWS, LogName="Elastic", LogType="String", LogText=str(elastic))
+
 	AddSampleLog(Workspace=outWS, LogName="ResNorm", LogType="String", LogText=str(resnorm))
 	if resnorm:
 		AddSampleLog(Workspace=outWS, LogName="ResNorm file", LogType="String", LogText=resnormWS)
+
 	AddSampleLog(Workspace=outWS, LogName="Width", LogType="String", LogText=str(width))
+
 	if width:
 		AddSampleLog(Workspace=outWS, LogName="Width file", LogType="String", LogText=wfile)
 
@@ -467,6 +475,7 @@ def C2Fw(prog,sname):
 
 	CreateWorkspace(OutputWorkspace=outWS, DataX=dataX, DataY=dataY, DataE=dataE, Nspec=nhist,
 		UnitX='MomentumTransfer', VerticalAxisUnit='Text', VerticalAxisValues=Vaxis, YUnitLabel='')
+
 	return outWS
 
 def SeBlock(a,first):                                 #read Ascii block of Integers
@@ -601,7 +610,6 @@ def QLPlotQSe(inputWS,Plot,res_plot,Loop):
 		f_plot=mp.plotSpectrum(fWS,res_plot,False)
 
 # Quest programs
-
 def CheckBetSig(nbs):
 	Nsig = int(nbs[1])
 	if Nsig == 0:
@@ -623,10 +631,25 @@ def CheckBetSig(nbs):
 		sys.exit(error)
 	return Nbet,Nsig
 
-def QuestRun(samWS,resWS,rsname,nbs,erange,nbins,Fit,Loop,Verbose,Plot,Save):
+def QuestRun(samWS,resWS,nbs,erange,nbins,Fit,Loop,Verbose,Plot,Save):
 	StartTime('Quest')
+	#expand fit options
+	elastic, background, width, resnorm = Fit
+
+	#convert true/false to 1/0 for fortran
+	o_el = 1 if elastic else 0
+	o_w1 = 1 if width else 0
+	o_res = 1 if resnorm else 0
 
-	resnorm = (Fit[:3] == 1)
+	#fortran code uses background choices defined using the following numbers
+	if background == 'Sloping':
+		o_bgd = 2
+	elif background == 'Flat':
+		o_bgd = 1
+	elif background == 'Zero':
+		o_bgd = 0
+
+	fitOp = [o_el, o_bgd, o_w1, o_res]
 
 	workdir = config['defaultsave.directory']
 	array_len = 4096                           # length of array in Fortran
@@ -637,22 +660,10 @@ def QuestRun(samWS,resWS,rsname,nbs,erange,nbins,Fit,Loop,Verbose,Plot,Save):
 		logger.notice('Resolution is ' + resWS)
 	CheckAnalysers(samWS,resWS,Verbose)
 	nsam,ntc = CheckHistZero(samWS)
+
 	if Loop != True:
 		nsam = 1
-	if Fit[0]:
-		elastic = True
-		o_el = 1
-	else:
-		elastic = False
-		o_el = 0
-	if Fit[1] == 'Sloping':
-		o_bgd = 2
-	if Fit[1] == 'Flat':
-		o_bgd = 1
-	if Fit[1] == 'Zero':
-		o_bgd = 0
-	background = Fit[1]
-	fitOp = [o_el, o_bgd, 0, 0]
+
 	efix = getEfixed(samWS)
 	theta,Q = GetThetaQ(samWS)
 	nres,ntr = CheckHistZero(resWS)
@@ -666,7 +677,6 @@ def QuestRun(samWS,resWS,rsname,nbs,erange,nbins,Fit,Loop,Verbose,Plot,Save):
 		logger.notice(' Number of spectra = '+str(nsam))
 		logger.notice(' Erange : '+str(erange[0])+' to '+str(erange[1]))
 
-	dtn,xsc = ReadNormFile(resnorm,rsname,nsam,Verbose)
 	fname = samWS[:-4] + '_'+ prog
 	wrks=workdir + samWS[:-4]
 	if Verbose:
@@ -757,8 +767,7 @@ def QuestPlot(inputWS,Plot):
 		mp.mergePlots(sig_plot,beta_plot)
 
 # ResNorm programs
-
-def ResNormRun(vname,rname,erange,nbin,Verbose=False,Plot=False,Save=False):
+def ResNormRun(vname,rname,erange,nbin,Verbose=False,Plot='None',Save=False):
 	StartTime('ResNorm')
 	workdir = config['defaultsave.directory']
 	array_len = 4096                                    # length of Fortran array

Code/Mantid/scripts/Inelastic/IndirectJumpFit.py

@@ -71,4 +71,4 @@ def JumpRun(samWS,jumpFunc,width,qmin,qmax,Verbose=False,Plot=False,Save=False):
 	EndTime('Jump fit : '+jumpFunc+' ; ')
 
 def JumpPlot(inputWS):
-    j_plot=mp.plotSpectrum(inputWS,[0,1,2],True)
+    mp.plotSpectrum(inputWS,[0,1,2],True)