Refs #4867 - Addition of several PyAlgs from Spencer.

Code/Mantid/Framework/PythonAPI/PythonAlgorithms/ILLines.py

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+# Algorithm to start Bayes programs
+from MantidFramework import *
+from IndirectImport import run_f2py_compatibility_test, is_supported_f2py_platform
+
+if is_supported_f2py_platform():
+	import IndirectBayes as Main
+
+class ILLines(PythonAlgorithm):
+
+	def category(self):
+		return "Workflow\\MIDAS;PythonAlgorithms"
+
+	def PyInit(self):
+		self.declareProperty(Name='InputType',DefaultValue='File',Validator=ListValidator(['File','Workspace']),Description = 'Origin of data input - File (*.nxs) or Workspace')
+		self.declareProperty(Name='Instrument',DefaultValue='IN10',Validator=ListValidator(['IN10','IN16']),Description = 'Instrument')
+		self.declareProperty(Name='Program',DefaultValue='QL',Validator=ListValidator(['QL','QSe']),Description = 'Name of program to run')
+		self.declareProperty(Name='SamNumber',DefaultValue='',Validator=MandatoryValidator(),Description = 'Sample run number')
+		self.declareProperty(Name='ResInputType',DefaultValue='File',Validator=ListValidator(['File','Workspace']),Description = 'Origin of res input - File (*_res.nxs) or Workspace')
+		self.declareProperty(Name='ResType',DefaultValue='Res',Validator=ListValidator(['Res','Data']),Description = 'Format of Resolution file')
+		self.declareProperty(Name='ResNumber',DefaultValue='',Validator=MandatoryValidator(),Description = 'Resolution run number')
+		self.declareProperty(Name='BackgroundOption',DefaultValue='Sloping',Validator=ListValidator(['Sloping','Flat','Zero']),Description = 'Form of background to fit')
+		self.declareProperty(Name='ElasticOption',DefaultValue=True,Description = 'Include elastic peak in fit')
+		self.declareProperty(Name='FixWidth',DefaultValue=False,Description = 'Fix one of the widths')
+		self.declareProperty(Name='WidthFile', DefaultValue='',Description = 'Name of file containing fixed width values')
+		self.declareProperty(Name='ResNorm',DefaultValue=False,Description = 'Use ResNorm output file')
+		self.declareProperty(Name='ResNormNumber', DefaultValue='',Description = 'Name of file containing fixed width values')
+		self.declareProperty(Name='EnergyMin', DefaultValue=-0.5,Description = 'Minimum energy for fit. Default=-0.5')
+		self.declareProperty(Name='EnergyMax', DefaultValue=0.5,Description = 'Maximum energy for fit. Default=0.5')
+		self.declareProperty(Name='SamBinning', DefaultValue=1,Description = 'Binning value (integer) for sample. Default=1')
+		self.declareProperty(Name='ResBinning', DefaultValue=1,Description = 'Binning value (integer) for resolution - QLd only. Default=1')
+		self.declareProperty(Name='Plot',DefaultValue='None',Validator=ListValidator(['None','ProbBeta','Intensity','FwHm','Fit','All']),Description = 'Plot options')
+		self.declareProperty(Name='Verbose',DefaultValue=True,Description = 'Switch Verbose Off/On')
+		self.declareProperty(Name='Save',DefaultValue=False,Description = 'Switch Save result to nxs file Off/On')
+
+	def PyExec(self):
+		run_f2py_compatibility_test()
+
+		self.log().information('ILLines input')
+		inType = self.getPropertyValue('InputType')
+		instr = self.getPropertyValue('Instrument')
+		prog = self.getPropertyValue('Program')
+		sam = self.getPropertyValue('SamNumber')
+		rinType = self.getPropertyValue('ResInputType')
+		rtype = self.getPropertyValue('ResType')
+		res = self.getPropertyValue('ResNumber')
+		elastic = self.getProperty('ElasticOption')
+		bgd = self.getPropertyValue('BackgroundOption')
+		width = self.getProperty('FixWidth')
+		wfile = self.getPropertyValue('WidthFile')
+		resnorm = self.getProperty('ResNorm')
+		resn = self.getPropertyValue('ResNormNumber')
+		emin = self.getPropertyValue('EnergyMin')
+		emax = self.getPropertyValue('EnergyMax')
+		nbin = self.getPropertyValue('SamBinning')
+		nrbin = self.getPropertyValue('ResBinning')
+		nbins = [nbin, nrbin]
+
+		sname = instr+'_'+sam
+		rname = instr+'_'+res
+		rsname = instr+resn
+		erange = [emin, emax]
+		if elastic:
+			o_el = 1
+		else:
+			o_el = 0
+		if bgd == 'Sloping':
+			o_bgd = 2
+		if bgd == 'Flat':
+			o_bgd = 1
+		if bgd == 'Zero':
+			o_bgd = 0
+		if width:
+			o_w1 = 1
+		else:
+			o_w1 = 0
+		if resnorm:
+			o_res = 1
+		else:
+			o_res = 0
+		fitOp = [o_el, o_bgd, o_w1, o_res]
+		verbOp = self.getProperty('Verbose')
+		plotOp = self.getPropertyValue('Plot')
+		saveOp = self.getProperty('Save')
+		Main.QLStart(prog,inType,sname,rinType,rname,rtype,rsname,erange,nbins,fitOp,wfile,verbOp,plotOp,saveOp)
+#def QLStart(program,ana,samWS,resWS,rtype,rsname,erange,nbins,fitOp,wfile,Verbose,Plot,Save):
+
+mantid.registerPyAlgorithm(ILLines())         # Register algorithm with Mantid

Code/Mantid/Framework/PythonAPI/PythonAlgorithms/JumpFit.py

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+# Algorithm to start Jump fit programs
+from MantidFramework import *
+from IndirectImport import run_f2py_compatibility_test, is_supported_f2py_platform
+
+if is_supported_f2py_platform():
+	import IndirectBayes as Main
+
+class JumpFit(PythonAlgorithm):
+
+	def category(self):
+		return "Workflow\\MIDAS;PythonAlgorithms"
+
+	def PyInit(self):
+		self.declareProperty(Name='InputType',DefaultValue='File',Validator=ListValidator(['File','Workspace']),Description = 'Origin of data input - File (*.nxs) or Workspace')
+		self.declareProperty(Name='Instrument',DefaultValue='IRIS',Validator=ListValidator(['IRIS','OSIRIS']),Description = 'Instrument name')
+		self.declareProperty(Name='Analyser',DefaultValue='graphite002',Validator=ListValidator(['graphite002','graphite004']),Description = 'Analyser & reflection')
+		self.declareProperty(Name='QLprogram',DefaultValue='QLr',Validator=ListValidator(['QLr','QLd']),Description = 'QL output from Res or Data')
+		self.declareProperty(Name='Fit',DefaultValue='CE',Validator=ListValidator(['CE','SS']),Description = 'Chudley-Elliott or Singwi-Sjolander')
+		self.declareProperty(Name='Width',DefaultValue='FW11',Validator=ListValidator(['FW11','FW21','FW22']),Description = 'FullWidth type')
+		self.declareProperty(Name='SamNumber',DefaultValue='',Validator=MandatoryValidator(),Description = 'Sample run number')
+		self.declareProperty(Name='Plot',DefaultValue=False,Description = 'Switch Plot Off/On')
+		self.declareProperty(Name='Verbose',DefaultValue=True,Description = 'Switch Verbose Off/On')
+		self.declareProperty(Name='Save',DefaultValue=False,Description = 'Switch Save result to nxs file Off/On')
+
+	def PyExec(self):
+		run_f2py_compatibility_test()
+
+		self.log().information('Jump input')
+		inType = self.getPropertyValue('InputType')
+		instr = self.getPropertyValue('Instrument')
+		if instr == 'IRIS':
+			prefix = 'irs'
+		if instr == 'OSIRIS':
+			prefix = 'osi'
+		ana = self.getPropertyValue('Analyser')
+		prog = self.getPropertyValue('QLprogram')
+		jump = self.getPropertyValue('Fit')
+		fw = self.getPropertyValue('Width')
+		sam = self.getPropertyValue('SamNumber')
+
+		sname = prefix+sam+'_'+ana+'_'+prog
+		verbOp = self.getProperty('Verbose')
+		plotOp = self.getProperty('Plot')
+		saveOp = self.getProperty('Save')
+		Main.JumpStart(inType,sname,jump,prog,fw,verbOp,plotOp,saveOp)
+
+mantid.registerPyAlgorithm(JumpFit())         # Register algorithm with Mantid

Code/Mantid/Framework/PythonAPI/PythonAlgorithms/Symmetrise.py

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+# Algorithm to start Symmetrise
+from MantidFramework import *
+import IndirectSymm as Main
+
+class Symmetrise(PythonAlgorithm):
+
+	def category(self):
+		return "Workflow\\MIDAS;PythonAlgorithms"
+
+	def PyInit(self):
+		self.declareProperty(Name='InputType',DefaultValue='File',Validator=ListValidator(['File','Workspace']),Description = 'Origin of data input - File (_red.nxs) or Workspace')
+		self.declareProperty(Name='Instrument',DefaultValue='IRIS',Validator=ListValidator(['IRIS','OSIRIS']),Description = 'Instrument')
+		self.declareProperty(Name='Analyser',DefaultValue='graphite002',Validator=ListValidator(['graphite002','graphite004']),Description = 'Analyser & reflection')
+		self.declareProperty(Name='SamNumber',DefaultValue='',Validator=MandatoryValidator(),Description = 'Sample run number')
+		self.declareProperty(Name='Xcut',DefaultValue='',Validator=MandatoryValidator(),Description = 'X cutoff value')
+		self.declareProperty('Verbose',DefaultValue=True,Description = 'Switch Verbose Off/On')
+		self.declareProperty('Plot',DefaultValue=True,Description = 'Switch Plot Off/On')
+		self.declareProperty('Save',DefaultValue=False,Description = 'Switch Save result to nxs file Off/On')
+
+	def PyExec(self):
+
+		self.log().information('Symmetrise')
+		inType = self.getPropertyValue('InputType')
+		instr = self.getPropertyValue('Instrument')
+		if instr == 'IRIS':
+			prefix = 'irs'
+		if instr == 'OSIRIS':
+			prefix = 'osi'
+		ana = self.getPropertyValue('Analyser')
+		sn = self.getPropertyValue('SamNumber')
+		sam = prefix+sn+'_'+ana+'_red'
+		cut = self.getPropertyValue('Xcut')
+		cut = float(cut)
+
+		verbOp = self.getProperty('Verbose')
+		plotOp = self.getProperty('Plot')
+		saveOp = self.getProperty('Save')
+		Main.SymmStart(inType,sam,cut,verbOp,plotOp,saveOp)
+
+mantid.registerPyAlgorithm(Symmetrise())         # Register algorithm with Mantid

Code/Mantid/Framework/PythonAPI/PythonAlgorithms/iFudge.py

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+# Algorithm to start Bayes programs
+from MantidFramework import *
+from mantid.simpleapi import *
+from mantid import config, logger, mtd
+
+class iFudge(PythonAlgorithm):
+
+	def category(self):
+		return "Workflow\\MIDAS;PythonAlgorithms"
+
+	def PyInit(self):
+		self.declareProperty(Name='InputType',DefaultValue='File',Validator=ListValidator(['File','Workspace']),Description = 'Origin of data input - File (_red.nxs) or Workspace')
+		self.declareProperty(Name='Instrument',DefaultValue='IRIS',Validator=ListValidator(['IRIS','OSIRIS']),Description = 'Instrument')
+		self.declareProperty(Name='Analyser',DefaultValue='graphite002',Validator=ListValidator(['graphite002','graphite004']),Description = 'Analyser & reflection')
+		self.declareProperty(Name='InNumber',DefaultValue='',Validator=MandatoryValidator(),Description = 'Sample run number')
+		self.declareProperty(Name='MultiplyBy',DefaultValue='',Validator=MandatoryValidator(),Description = 'Multiplicative scale factor')
+		self.declareProperty(Name='OutNumber',DefaultValue='',Validator=MandatoryValidator(),Description = 'Sample run number')
+
+	def PyExec(self):
+
+		self.log().information('Scale input')
+		workdir = config['defaultsave.directory']
+		inType = self.getPropertyValue('InputType')
+		instr = self.getPropertyValue('Instrument')
+		if instr == 'IRIS':
+			prefix = 'irs'
+		if instr == 'OSIRIS':
+			prefix = 'osi'
+		ana = self.getPropertyValue('Analyser')
+		InNumb = self.getPropertyValue('InNumber')
+		inWS = prefix+InNumb+'_'+ana+'_red'
+		factor = self.getPropertyValue('MultiplyBy')
+		if inType == 'File':
+			spath = os.path.join(workdir, inWS+'.nxs')		# path name for sample nxs file
+			logger.notice('Input from File : '+spath)
+			LoadNexusProcessed(Filename=spath, OutputWorkspace=inWS)
+		else:
+			logger.notice('Input from Workspace : '+inWS)
+		OutNumb = self.getPropertyValue('OutNumber')
+		outWS = prefix+OutNumb+'_'+ana+'_red'
+		Scale(InputWorkspace=inWS, OutputWorkspace=outWS, Factor=float(factor), Operation='Multiply')
+
+mantid.registerPyAlgorithm(iFudge())         # Register algorithm with Mantid

Code/Mantid/scripts/Inelastic/IndirectSymm.py

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+# SYMMetrise 
+#
+from mantid.simpleapi import *
+from mantid import config, logger, mtd
+from IndirectCommon import *
+from IndirectImport import import_mantidplot
+import sys, platform, math, os.path, numpy as np
+mp = import_mantidplot()
+
+def SymmRun(sample,cut,Verbose,Plot,Save):
+	workdir = config['defaultsave.directory']
+	symWS = sample[:-3] + 'sym'
+	hist = mtd[sample].getNumberHistograms()       # no. of hist/groups in sam
+	Xin = mtd[sample].readX(0)
+	npt = len(Xin)-1
+	delx = Xin[1]-Xin[0]
+	for n in range(0,npt):
+		x = Xin[n]-cut
+		if math.fabs(x) < delx:
+			ineg = n
+	for n in range(0,npt):
+		x = Xin[n]+Xin[ineg]
+		if math.fabs(x) < delx:
+			ipos = n
+	ncut = npt-ipos+1
+	if Verbose:
+		logger.notice('No. points = '+str(npt))
+		logger.notice('Negative : at i ='+str(ineg)+' ; x = '+str(Xin[ineg]))
+		logger.notice('Positive : at i ='+str(ipos)+' ; x = '+str(Xin[ipos]))
+		logger.notice('Cut points = '+str(ncut))
+	for m in range(0,hist):
+		Xin = mtd[sample].readX(m)
+		Yin = mtd[sample].readY(m)
+		Ein = mtd[sample].readE(m)
+		Xout = []
+		Yout = []
+		Eout = []
+		for n in range(0,ncut):
+			icut = npt-n-1
+			Xout.append(-Xin[icut])
+			Yout.append(Yin[icut])
+			Eout.append(Ein[icut])
+		for n in range(ncut,npt):
+			Xout.append(Xin[n])
+			Yout.append(Yin[n])
+			Eout.append(Ein[n])
+		if m == 0:
+			CreateWorkspace(OutputWorkspace=symWS, DataX=Xout, DataY=Yout, DataE=Eout,
+				Nspec=1, UnitX='DeltaE')
+		else:
+			CreateWorkspace(OutputWorkspace='__tmp', DataX=Xout, DataY=Yout, DataE=Eout,
+				Nspec=1, UnitX='DeltaE')
+			ConjoinWorkspaces(InputWorkspace1=symWS, InputWorkspace2='__tmp',CheckOverlapping=False)				
+#		Nspec=nt, UnitX='MomentumTransfer', VerticalAxisUnit='Text', VerticalAxisValues='Taxis')
+# start output
+	if Save:
+		path = os.path.join(workdir,symWS+'.nxs')
+		SaveNexusProcessed(InputWorkspace=symWS, Filename=path)
+		if Verbose:
+			logger.notice('Output file : ' + path)
+	if Plot:
+		plotSymm('','',Plot)
+
+def SymmStart(inType,sname,cut,Verbose,Plot,Save):
+	StartTime('Symmetrise')
+	workdir = config['defaultsave.directory']
+	if inType == 'File':
+		spath = os.path.join(workdir, sname+'.nxs')		# path name for sample nxs file
+		LoadNexusProcessed(FileName=spath, OutputWorkspace=sname)
+		message = 'Input from File : '+spath
+	else:
+		message = 'Input from Workspace : '+sname
+	if Verbose:
+		logger.notice(message)
+	SymmRun(sname,cut,Verbose,Plot,Save)
+	EndTime('Symmetrise')
+
+def plotSymm(inWS,spec_list,Plot):
+	if (Plot == 'Totals' or Plot == 'All'):
+		tot_plot=mp.plotSpectrum(inWS+'_Totals',spec_list)
+	if (Plot == 'Scat1' or Plot == 'All'):
+		mp.importMatrixWorkspace(inWS+'_1').plotGraph2D()