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CRY_ini.py
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from mantid.simpleapi import *
import CRY_utils
import re
import os
EnvAnalysisdir=''
print '--------------------- '
print 'Using the B:\\MantidPowderFocus\\\scripts2\\CRY_ini.py scripts... '
print '--------------------- '
class files:
def __init__(self,instr, RawDir="",Analysisdir="",UnitTest=False, debugMode=False):
global EnvAnalysisdir
self.debugMode=False
if debugMode:
self.debugMode=True
self.instr = instr.lower()
self.InsDir = os.path.dirname(os.path.realpath( __file__ ))+'/'+instr
print '--------------------- '
print 'INSTRUMENT DIRECTORY: '+self.InsDir
print '--------------------- '
self.RawDir = RawDir
self.user = ""
self.basefile = instr[0:3]
self.LstPrefDir = ""
self.LstPreffil = ""
self.VanFile = []
self.VEmptyFile = []
self.SEmptyFile = []
self.CorrVanFile = ""
self.ExistV = "no"
self.VGrpfocus = "van"
self.Path2DatGrpFile = ""
self.VHeight = "2"
self.VRadius = "0.4"
self.VAttenuationXSection = "5.1"
self.VScatteringXSection = "5.08"
self.VanaNumberDensity = "0.072"
self.VNumberOfSlices = "10"
self.VNumberOfAnnuli = "10"
self.VNumberOfWavelengthPoints= "100"
self.VExpMethod = "Normal"
self.VanSmooth = "100"
self.VanSplineCoef = "15"
# Peak removal, default, interpolation
self.VanPeakRemove = "interpol"
self.VanPeakFile = 'VanaPeaks.dat'
self.VanPeakList = []
# Peak removal, in the future, stripeaks with params....
# self.VanPeakRemove = "strip"
self.VanPeakWdt = [20, 50, 0]
self.VanPeakTol = [4, 4, 0]
#
self.CorrectSampleAbs = "no"
self.SampleAbsCorrected = False
self.SampleHeight = "0.0"
self.SampleRadius = "0.0"
self.SampleAttenuationXSection = "0.0"
self.SampleScatteringXSection = "0.0"
self.SampleNumberDensity = "1"
self.SampleNumberOfSlices = "10"
self.SampleNumberOfAnnuli = "10"
self.SampleNumberOfWavelengthPoints= "100"
self.SampleExpMethod = "Normal"
# Efficiency correction : Hard Coded for HRPD
self.LowerLambda = 1.4
self.UpperLambda = 3.0
#
self.OutSuf = ""
self.XYEDspc = "yes"
self.XYEtof = "yes"
self.GSS = "yes"
self.Nex = "yes"
self.NBank = 3
self.bankList = [1,2,3]
self.Drange = []
# Default values if none given in Arguments
os.chdir(self.InsDir)
if UnitTest:
self.Analysisdir=self.InsDir+'/UnitTest/'
self.RawDir=self.InsDir+'/UnitTest/RAW'
else:
if RawDir<>"":
self.RawDir= RawDir
else:
self.RawDir= ''
if Analysisdir<>"":
self.Analysisdir = Analysisdir
else:
self.Analysisdir = EnvAnalysisdir
self.OffDir=self.Analysisdir+"/GrpOff/"
self.GrpDir=self.Analysisdir+"/GrpOff/"
def initialize(self,Cycle,user,prefFile="", prefDir="", Verbose=False):
msg=""
ierr=0
self.cycle=self.Analysisdir+"/"+Cycle
if not os.path.exists(self.cycle):
os.makedirs(self.cycle)
self.calib=self.Analysisdir+"/"+Cycle+"/Calibration"
if not os.path.exists(self.calib):
os.makedirs(self.calib)
self.user=self.Analysisdir+Cycle+"/"+user+"/"
if not os.path.exists(self.user):
os.makedirs(self.user)
if prefFile<>"":
self.LstPreffil=prefFile
else:
self.LstPreffil="mtd.pref"
if prefDir<>"":
self.LstPrefDir=prefDir
else:
self.LstPrefDir=self.user
# Check existence of preference file
os.chdir(self.LstPrefDir)
print 'look for file --->'
print self.LstPrefDir+self.LstPreffil
fexist=os.path.exists(self.LstPrefDir+self.LstPreffil)
if not fexist:
msg = msg + "Abort: Required Preference file :"+self.LstPreffil
msg=msg + "\n NOT FOUND in the directory :"+self.LstPrefDir+'\n'
print msg
ierr=1
return (msg,ierr)
else:
msg = "Preference file :"+self.LstPreffil+" FOUND in the directory :"+self.LstPrefDir+"\n"
print msg
# Read preference file: default, read_prefline-label ALWAYS REQUIRED in pref-file
# Read preference file: optional params read with updatePrefVal
self.OffDir=self.updatePrefVal("OffDir",self.OffDir)
self.GrpDir=self.updatePrefVal("GrpDir",self.GrpDir)
self.OffFile=self.read_prefline("Offsets")
self.GrpFile=self.read_prefline("Grouping")
if self.RawDir=='':
self.RawDir= '//isis/inst$/ndx'+self.instr+'/instrument/data/'+Cycle+'/'
else:
self.RawDir = self.updatePrefVal("RawDir",self.RawDir)
self.VanDir = self.RawDir
self.VEmptyDir = self.RawDir
self.SEmptyDir = self.RawDir
self.VanDir=self.updatePrefVal("VanDir",self.VanDir)
self.VEmptyDir=self.updatePrefVal("VEmptyDir",self.VEmptyDir)
self.SEmptyDir=self.updatePrefVal("SEmptyDir",self.SEmptyDir)
self.VrunnoList = self.read_prefline("Vanadium")
self.VErunnoList = self.read_prefline("V-Empty")
self.SErunnoList = self.read_prefline("S-Empty")
# ===== Vanadium file handling =====
AutoVan=False
self.ExistV = self.read_prefline("ExistingV")
self.CorrVanFile = self.updatePrefVal("CorrVanFile",self.CorrVanFile)
if self.CorrVanFile == "":
AutoVan=True
self.CorrVanDir = self.Analysisdir+"/"+Cycle+"/Calibration"
self.CorrVanDir = self.updatePrefVal("CorrVanDir",self.CorrVanDir)
#
self.VHeight = self.updatePrefVal("VHeight",self.VHeight)
self.VRadius = self.updatePrefVal("VRadius",self.VRadius)
self.VAttenuationXSection = self.updatePrefVal("VAttenuationXSection",self.VAttenuationXSection)
self.VScatteringXSection = self.updatePrefVal("VScatteringXSection",self.VScatteringXSection)
self.VanaNumberDensity = self.updatePrefVal("VanaNumberDensity",self.VanaNumberDensity)
self.VNumberOfSlices = self.updatePrefVal("VNumberOfSlices",self.VNumberOfSlices)
self.VNumberOfAnnuli = self.updatePrefVal("VNumberOfAnnuli",self.VNumberOfAnnuli)
self.VNumberOfWavelengthPoints = self.updatePrefVal("VNumberOfWavelengthPoints",self.VNumberOfWavelengthPoints)
self.VExpMethod = self.updatePrefVal("VExpMethod",self.VExpMethod)
self.VanPeakRemove = self.updatePrefVal("VanPeakRemove",self.VanPeakRemove)
self.VanPeakFile = self.updatePrefVal("VanPeakFile",self.VanPeakFile)
self.VanSmooth = self.updatePrefVal("VanSmooth",self.VanSmooth)
self.VanSplineCoef = self.updatePrefVal("VanSplineCoef",self.VanSplineCoef)
# ===== Sac and Efficcinecy correction file handling =====
self.LowerLambda=self.updatePrefVal("LowerLambda",self.LowerLambda)
self.UpperLambda=self.updatePrefVal("UpperLambda",self.UpperLambda)
self.SacEffDir=self.Analysisdir+"/"+Cycle+"/Calibration"
self.SacEffDir=self.updatePrefVal("SacEffDir",self.SacEffDir)
self.SacEffFile=self.CorrVanFile+"_detcorr"
if AutoVan:
self.CorrVanFile="van_"+self.VrunnoList+"_"+self.VErunnoList
self.SacEffFile="corr_"+self.VrunnoList+"_"+self.VErunnoList
else:
self.SacEffFile=self.updatePrefVal("SacEffFile",self.SacEffFile)
# ===== Set all Calibration file access =====
self.updateCalib()
self.VanCorrFileLookup()
#
# ===== output params =====
self.CorrectSampleAbs = self.updatePrefVal("CorrectSampleAbs",self.CorrectSampleAbs)
self.SampleHeight = self.updatePrefVal("SampleHeight",self.SampleHeight)
self.SampleHeight = self.updatePrefVal("SampleHeight",self.SampleHeight)
self.SampleRadius = self.updatePrefVal("SampleRadius",self.SampleRadius)
self.SampleAttenuationXSection = self.updatePrefVal("SampleAttenuationXSection",self.SampleAttenuationXSection)
self.SampleScatteringXSection = self.updatePrefVal("SampleScatteringXSection",self.SampleScatteringXSection)
self.SampleNumberDensity = self.updatePrefVal("SampleNumberDensity",self.SampleNumberDensity)
self.SampleNumberOfSlices = self.updatePrefVal("SampleNumberOfSlices",self.SampleNumberOfSlices)
self.SampleNumberOfAnnuli = self.updatePrefVal("SampleNumberOfAnnuli",self.SampleNumberOfAnnuli)
self.SampleNumberOfWavelengthPoints = self.updatePrefVal("SampleNumberOfWavelengthPoints",self.SampleNumberOfWavelengthPoints)
self.SampleExpMethod = self.updatePrefVal("SampleExpMethod",self.SampleExpMethod)
self.scale = self.read_prefline("Scale")
if self.scale == "":
self.scale="1"
self.OutSuf=self.updatePrefVal("Output",self.OutSuf)
self.XYEtof = self.read_prefline("XYE-TOF")
self.XYEdspc = self.read_prefline("XYE-D")
self.GSS = self.read_prefline("GSS")
self.Nex = self.read_prefline("Nexus")
self.saveXYEtof= (self.XYEtof == "yes")
self.saveXYEd = (self.XYEdspc == "yes")
Nbank = self.read_prefline("Nbank")
self.Nbank = int(Nbank)
self.CropRange = self.read_multprefline("CropRange",self.Nbank)
self.Bining = self.read_multprefline("Bining",self.Nbank)
self.dataRangeSet = False
if self.saveXYEtof or self.saveXYEd:
bankList = self.read_prefline("BankList")
self.bankList = CRY_utils.getListInt(bankList)
print "Done"
if Verbose:
self.tell()
return ierr
def VanCorrFileLookup(self):
msg=''
VanOK=0
for i in self.bankList:
spec=i-1
fexist=os.path.exists(self.CorrVanFile+"-"+str(spec)+".nxs")
if not fexist:
VanOK=i
if self.ExistV == "yes" or self.ExistV =="sam":
if VanOK <> 0:
msg = msg + "At least the corrected vanadium file "+self.CorrVanFile+"-"+str(i)+".nxs is missing \n"
if self.ExistV =="sam" :
msg = msg + "Vanadium runs will be created in due time according to the grouping deduced from 1st sample dead detector list\n"
msg = msg + "Using as parameters: \n"
self.VGrpfocus = "sam"
if self.ExistV =="yes" :
msg = msg + "I'm re-creating the van nexus files using as parameters: \n"
self.ExistV = "no"
else:
msg = msg + "All the corrected vanadium file "+self.CorrVanFile+"-i.nxs exists and will be used \n"
self.ExistV = "load"
print 'got Here!!!'
else:
if self.ExistV == "over":
msg = msg + "A corrected Van file will be created with base name "+self.CorrVanFile+" overriding any previous one created before\n"
else :
msg = msg + "At least the corrected Van file "+self.CorrVanFile+"-"+str(i)+".nxs given in the pref file already exists,\n"
self.CorrVanFile = self.CorrVanFile+"_new"
msg = msg + "New ones will be created changing the base name to : "
self.ExistV = "no"
if self.ExistV == "no" :
msg = msg + "File : "+self.CorrVanFile+".nxs, using as parameters:\n"
msg = msg + "VHeight = "+self.VHeight +"\n"
msg = msg + "VRadius = "+self.VRadius +"\n"
msg = msg + "AttenuationXSection = "+self.VAttenuationXSection +"\n"
msg = msg + "ScatteringXSection = "+self.VScatteringXSection +"\n"
msg = msg + "SampleNumberDensity = "+self.VanaNumberDensity +"\n"
msg = msg + "NumberOfSlices = "+self.VNumberOfSlices +"\n"
msg = msg + "NumberOfAnnuli = "+self.VNumberOfAnnuli +"\n"
msg = msg + "NumberOfWavelengthPoints= "+self.VNumberOfWavelengthPoints +"\n"
msg = msg + "ExpMethod = "+self.VExpMethod
print 'after Lookup: '+self.ExistV
#
if self.VanPeakRemove == "interpol" or self.VanPeakRemove == "spline":
fexist=os.path.exists(self.InsDir+"/"+self.VanPeakFile)
if not fexist:
msg = msg + "Vanadium Peak file "+self.InsDir+"/"+self.VanPeakFile+" not found, \n"
msg = msg + "I will not strip any peak...! \n"
else:
fvan = open(self.InsDir+"/"+self.VanPeakFile,'r')
b=-1
for line in fvan:
p=re.compile("bank")
m=p.search(line)
if m <> None:
self.VanPeakList.append([])
b=b+1
continue
numbers=line.rstrip().split()
self.VanPeakList[b].append([float(numbers[0]),float(numbers[1])])
print "Vana Peaks will be removed by interpolation in ranges given in"
print self.InsDir+"/"+self.VanPeakFile+'\n'
fvan.close()
else:
self.VanPeakWdt = self.updatePrefVal("VanPeakWdt",self.VanPeakWdt)
self.VanPeakTol = self.updatePrefVal("VanPeakTol",self.VanPeakTol)
print msg
def setCommonRawDir(self,RawDir=""):
if RawDir <> "":
self.RawDir = RawDir
self.VanDir = self.RawDir
self.VEmptyDir = self.RawDir
self.SEmptyDir = self.RawDir
def updateCalib(self):
self.VanFile = CRY_utils.ListOfList2List(CRY_utils.getSampleList(self.basefile,self.VrunnoList,self.VanDir))
self.VEmptyFile = CRY_utils.ListOfList2List(CRY_utils.getSampleList(self.basefile,self.VErunnoList,self.VEmptyDir))
self.SEmptyFile = CRY_utils.ListOfList2List(CRY_utils.getSampleList(self.basefile,self.SErunnoList,self.SEmptyDir))
self.Path2OffFile = self.OffDir+"/"+self.OffFile
self.Path2GrpFile = self.GrpDir+"/"+self.GrpFile
self.CorrVanFile = self.CorrVanDir+"/"+self.CorrVanFile
self.SacEffFile = self.SacEffDir+"/"+self.SacEffFile
def updatePrefVal(self,Label,updated):
Field2Update = self.read_prefline(Label,optional=True)
if Field2Update=="":
return updated
else:
return Field2Update
def setRawFile(self,runno):
if runno == 0:
return "none"
else:
return self.RawDir+"/"+self.basefile+str(runno)+".raw"
def read_prefline(self,label,optional=False):
os.chdir(self.LstPrefDir)
fin =open(self.LstPreffil,"r")
found=False
for line in fin:
pattern2match=label+'[ ]*(.*)'
p = re.compile(pattern2match)
m = p.match(line)
if m <> None:
found = True
break
fin.close()
if found:
return m.group(1).rstrip()
else:
if optional:
return ""
else:
print "Severe Warning: Field "+label+" required in pref file"
print "PROGRAM MIGHT CRASH!..."
return ""
def write_prefline(self,label,value):
os.chdir(self.LstPrefDir)
fin=open(self.LstPreffil,"r")
fileline=[]
for line in fin:
pattern2match='('+label+'[ ]+)'
p = re.compile(pattern2match)
m = p.match(line)
if m <> None:
line=m.group()+value+"\n"
fileline.append(line)
fin.close()
fin =open(self.LstPreffil,"w")
for line in fileline:
fin.write(line)
fin.close()
def read_multprefline(self,label,n):
fin =open(self.LstPreffil,"r")
found=False
output=[]
i=0
for line in fin:
pattern2match=label+'[ ]+(.+)'
p = re.compile(pattern2match)
m = p.match(line)
if m <> None:
found = True
i+=1
output.append(m.group(1).rstrip())
if i==n:
break
fin.close()
return output
def read_dir(self,fin,col):
for line in fin:
if line[0]<>"#":
break
alist = line.rstrip().split()
return alist[col-1]
def tell(self):
msg = ""
msg = msg + "InsDir " + self.InsDir +"\n"
msg = msg + "RawDir " + self.RawDir +"\n"
msg = msg + "Analysisdir " + self.Analysisdir +"\n"
msg = msg + "user " + self.user +"\n"
msg = msg + "basefile " + self.basefile +"\n"
msg = msg + "OffFile " + self.Path2OffFile + "\n"
msg = msg + "GrpFile " + self.Path2GrpFile + "\n"
msg = msg + "LstPrefDir " + self.LstPrefDir +"\n"
msg = msg + "LstPreffil " + self.LstPreffil +"\n"
msg = msg + "Analysisdir " + self.Analysisdir +"\n"
for afile in self.VanFile:
msg = msg + "VanFile " + afile +"\n"
for afile in self.VEmptyFile:
msg = msg + "VEmptyFile " + afile +"\n"
for afile in self.SEmptyFile:
msg = msg + "SEmptyFile " + afile +"\n"
msg = msg + "ExistingV " + self.ExistV +"\n"
msg = msg + "CorrVanFile " + self.CorrVanFile+".nxs" +"\n"
msg = msg + "VHeight " + self.VHeight +"\n"
msg = msg + "VRadius " + self.VRadius +"\n"
msg = msg + "AttenuationXSection " + self.VAttenuationXSection +"\n"
msg = msg + "ScatteringXSection " + self.VScatteringXSection +"\n"
msg = msg + "SampleNumberDensity " + self.VanaNumberDensity +"\n"
msg = msg + "NumberOfSlices " + self.VNumberOfSlices +"\n"
msg = msg + "NumberOfAnnuli " + self.VNumberOfAnnuli +"\n"
msg = msg + "NumberOfWavelengthPoints" + self.VNumberOfWavelengthPoints +"\n"
msg = msg + "ExpMethod " + self.VExpMethod +"\n"
msg = msg + "VanSmooth " + self.VanSmooth +"\n"
msg = msg + "VanPeakRemove " + self.VanPeakRemove +"\n"
msg = msg + "SacEffFile " + self.SacEffFile +"\n"
msg = msg + "SampleHeight " + self.SampleHeight +"\n"
msg = msg + "SampleRadius " + self.SampleRadius +"\n"
msg = msg + "SampleAttenuationXSection " + self.SampleAttenuationXSection +"\n"
msg = msg + "SampleScatteringXSection " + self.SampleScatteringXSection +"\n"
msg = msg + "SampleSampleNumberDensity " + self.SampleNumberDensity +"\n"
msg = msg + "SampleNumberOfSlices " + self.SampleNumberOfSlices +"\n"
msg = msg + "SampleNumberOfAnnuli " + self.SampleNumberOfAnnuli +"\n"
msg = msg + "SampleNumberOfWavelengthPoints" + self.SampleNumberOfWavelengthPoints +"\n"
msg = msg + "SampleExpMethod " + self.SampleExpMethod +"\n"
msg = msg + "OutSuf " + self.OutSuf +"\n"
msg = msg + "XYEDspc " + self.XYEDspc +"\n"
msg = msg + "XYEtof " + self.XYEtof +"\n"
msg = msg + "GSS " + self.GSS +"\n"
msg = msg + "Nbank " + str(self.Nbank) +"\n"
for i in range(0,self.Nbank):
msg = msg + "Bank: " + str(i) +"\n"
msg = msg + " CropRange " + self.CropRange[i] +"\n"
msg = msg + " Bining " + self.Bining[i] +"\n"
for i in self.bankList:
msg = msg + "bankUsed " + str(i)+"\n"
print msg
if __name__ == '__main__':
# Opt : expt=files("hrpd",RawDir="",Analysisdir="")
expt=files("hrpd")
# default
expt.initialize('Cycle08_2','Si')
# Opt : expt.initialize('Cycle09_2','tests',prefFile='mtd.pref', prefDir="")