def nrnDoAll( nrnType, nrnNumber, nrnVersion="",nrnDate=""):
versionSuffix = "" if not nrnVersion else " "+nrnVersion
dateSuffix = "" if not nrnDate else " " + nrnDate
srcFileNRN = srcDir+"%s %s/%s %s nrn%s%s.txt"%(nrnType,nrnNumber,nrnType,nrnNumber, dateSuffix, versionSuffix)
srcFileNS = srcDir+"%s %s/%s %s ns%s%s.txt"%(nrnType,nrnNumber, nrnType,nrnNumber, dateSuffix, versionSuffix)
print "nrnType = " + nrnType
print "nrnNumber = " + nrnNumber
print "versionSuffix = " + versionSuffix
print "dateSuffix = " + dateSuffix
print "srcFileNRN:" + srcFileNRN
print "srcFileNS:" + srcFileNS
transFileNRN = outDir+"%s %s/%s %s nrn%s%s.transl.txt"%(nrnType,nrnNumber,nrnType,nrnNumber,dateSuffix,versionSuffix)
transFileNS = outDir+"%s %s/%s %s ns%s%s.transl.txt"%(nrnType,nrnNumber,nrnType,nrnNumber,dateSuffix,versionSuffix)
print "transFileNRN:" + transFileNRN
print "transFileNS:" + transFileNS
invTransFileNRN = outDir+"%s %s/%s %s nrn%s%s.transl.invX.txt"%(nrnType,nrnNumber,nrnType,nrnNumber,dateSuffix,versionSuffix)
invTransFileNS = outDir+"%s %s/%s %s ns%s%s.transl.invX.txt"%(nrnType,nrnNumber,nrnType,nrnNumber,dateSuffix,versionSuffix)
scaledInvTransFileNRN = outDir+"%s %s/%s %s nrn%s%s.transl.invX.scaled.txt"%(nrnType,nrnNumber,nrnType,nrnNumber,dateSuffix,versionSuffix)
scaledInvTransFileNS = outDir+"%s %s/%s %s ns%s%s.transl.invX.scaled.txt"%(nrnType,nrnNumber,nrnType,nrnNumber,dateSuffix,versionSuffix)
invTransFileConCat = outDir+"%s %s/%s %s nrn + ns%s%s.transl.invX.scaled.txt"%(nrnType,nrnNumber,nrnType,nrnNumber,dateSuffix,versionSuffix)
invTransFileConCatSWC = outDir+"%s %s/%s %s nrn + ns%s%s.transl.invX.scaled.swc"%(nrnType,nrnNumber,nrnType,nrnNumber,dateSuffix,versionSuffix)
matlabscriptname = outDir+"%s %s/mscript.m"%(nrnType,nrnNumber) #,nrnType,nrnNumber,versionSuffix)
invTransFileConCatSWCStraight = outDir+"%s %s/%s %s nrn + ns%s%s.transl.invX.scaled.straightened.swc"%(nrnType,nrnNumber,nrnType,nrnNumber,dateSuffix,versionSuffix)
#Old version without unique folder for each cellID
#final = swcs_outDir+"%s %s nrn + ns%s%s.transl.invX.scaled.straightened.swc"%(nrnType,nrnNumber,dateSuffix,versionSuffix)
final = swcs_outDir+"%s %s/%s %s nrn + ns%s%s.transl.invX.scaled.straightened.swc"%(nrnType,nrnNumber,nrnType,nrnNumber,dateSuffix,versionSuffix)
print "final: " + final
print "Source Files"
print "\t", srcFileNRN
print "\t", srcFileNS
print "Producing"
print "\t",transFileNRN
print "\t",transFileNS
print "\t",invTransFileNRN
print "\t",invTransFileNS
print "\t",scaledInvTransFileNRN
print "\t",scaledInvTransFileNS
print "\t",invTransFileConCat
print "\t",invTransFileConCatSWC
print "\t",invTransFileConCatSWCStraight
print "Executing:"
nrnTranslate(
nsFilenameSrc=srcFileNS,
nrnFilenameSrc=srcFileNRN,
nsFilenameSink=transFileNS,
nrnFilenameSink=transFileNRN)
nrnInvertX( srcFilename=transFileNS, sinkFilename=invTransFileNS)
nrnInvertX( srcFilename=transFileNRN, sinkFilename=invTransFileNRN)
nrnScale(srcFilename=invTransFileNS, sinkFilename=scaledInvTransFileNS, scaleFactor=1.28)
nrnScale(srcFilename=invTransFileNRN, sinkFilename=scaledInvTransFileNRN, scaleFactor=1.28)
nrnConcatenateXYZS( srcFilename1=scaledInvTransFileNRN, srcFilename2=scaledInvTransFileNS, sinkFilename=invTransFileConCat)
nrnXYZToSWC(srcFilename=invTransFileConCat, sinkFilename=invTransFileConCatSWC)
nrnStraighten( srcFilename = invTransFileConCatSWC, sinkFilename=invTransFileConCatSWCStraight,matlabscriptname=matlabscriptname)
#Create Unique output folder for each unique cellID if the folder doesn't exist
if not os.path.exists(swcs_outDir+"%s %s/"%(nrnType,nrnNumber)): os.makedirs(swcs_outDir+"%s %s/"%(nrnType,nrnNumber))
shutil.copyfile(invTransFileConCatSWCStraight,final)
def nrnDoAll( nrnType, nrnNumber, nrnVersion="",nrnDate=""):
versionSuffix = "" if not nrnVersion else " "+nrnVersion
dateSuffix = "" if not nrnDate else " " + nrnDate
srcFileNRN = srcDir+"%s %s%s/%s %s nrn%s%s.txt"%(nrnType,nrnNumber, versionSuffix,nrnType,nrnNumber, dateSuffix, versionSuffix)
srcFileNS = srcDir+"%s %s%s/%s %s ns%s%s.txt"%(nrnType,nrnNumber, versionSuffix,nrnType,nrnNumber, dateSuffix, versionSuffix)
transFileNRN = outDir+"%s %s%s/%s %s nrn%s.transl.txt"%(nrnType,nrnNumber,versionSuffix,nrnType,nrnNumber,versionSuffix)
transFileNS = outDir+"%s %s%s/%s %s ns%s.transl.txt"%(nrnType,nrnNumber,versionSuffix,nrnType,nrnNumber,versionSuffix)
invTransFileNRN = outDir+"%s %s%s/%s %s nrn%s.transl.invX.txt"%(nrnType,nrnNumber,versionSuffix,nrnType,nrnNumber,versionSuffix)
invTransFileNS = outDir+"%s %s%s/%s %s ns%s.transl.invX.txt"%(nrnType,nrnNumber,versionSuffix,nrnType,nrnNumber,versionSuffix)
scaledInvTransFileNRN = outDir+"%s %s%s/%s %s nrn%s.transl.invX.scaled.txt"%(nrnType,nrnNumber,versionSuffix,nrnType,nrnNumber,versionSuffix)
scaledInvTransFileNS = outDir+"%s %s%s/%s %s ns%s.transl.invX.scaled.txt"%(nrnType,nrnNumber,versionSuffix,nrnType,nrnNumber,versionSuffix)
invTransFileConCat = outDir+"%s %s%s/%s %s nrn + ns%s.transl.invX.scaled.txt"%(nrnType,nrnNumber,versionSuffix,nrnType,nrnNumber,versionSuffix)
invTransFileConCatSWC = outDir+"%s %s%s/%s %s nrn + ns%s.transl.invX.scaled.swc"%(nrnType,nrnNumber,versionSuffix,nrnType,nrnNumber,versionSuffix)
matlabscriptname = outDir+"%s %s%s/mscript.m"%(nrnType,nrnNumber,versionSuffix) #,nrnType,nrnNumber,versionSuffix)
invTransFileConCatSWCStraight = outDir+"%s %s%s/%s %s nrn + ns%s.transl.invX.scaled.straightened.swc"%(nrnType,nrnNumber,versionSuffix,nrnType,nrnNumber,versionSuffix)
final = swcs_outDir+"%s %s nrn + ns%s.transl.invX.scaled.straightened.swc"%(nrnType,nrnNumber,versionSuffix)
print "Source Files"
print "\t", srcFileNRN
print "\t", srcFileNS
print "Producing"
print "\t",transFileNRN
print "\t",transFileNS
print "\t",invTransFileNRN
print "\t",invTransFileNS
print "\t",scaledInvTransFileNRN
print "\t",scaledInvTransFileNS
print "\t",invTransFileConCat
print "\t",invTransFileConCatSWC
print "\t",invTransFileConCatSWCStraight
print "Executing:"
nrnTranslate(
nsFilenameSrc=srcFileNS,
nrnFilenameSrc=srcFileNRN,
nsFilenameSink=transFileNS,
nrnFilenameSink=transFileNRN)
nrnInvertX( srcFilename=transFileNS, sinkFilename=invTransFileNS)
nrnInvertX( srcFilename=transFileNRN, sinkFilename=invTransFileNRN)
nrnScale(srcFilename=invTransFileNS, sinkFilename=scaledInvTransFileNS, scaleFactor=1.28)
nrnScale(srcFilename=invTransFileNRN, sinkFilename=scaledInvTransFileNRN, scaleFactor=1.28)
nrnConcatenateXYZS( srcFilename1=scaledInvTransFileNRN, srcFilename2=scaledInvTransFileNS, sinkFilename=invTransFileConCat)
nrnXYZToSWC(srcFilename=invTransFileConCat, sinkFilename=invTransFileConCatSWC)
nrnStraighten( srcFilename = invTransFileConCatSWC, sinkFilename=invTransFileConCatSWCStraight,matlabscriptname=matlabscriptname)
if not os.path.exists(swcs_outDir): os.makedirs(swcs_outDir)
shutil.copyfile(invTransFileConCatSWCStraight,final)