def joinBnxFiles(varsP, bnxFiles):
"""After image processing, merge results into all.bnx.
"""
#the old way was to use this fn which simply copies lines
# while this is fine most of the time, RefAligner is more sophisticated,
# so it should be more robust to use RefAligner
#molecule.joinBnxFiles(bnxFiles, self.bnxFile)
#this used to be called writeIntermediate
varsP.writeListToFile(bnxFiles, varsP.bnxTarget)
# args, jobName, expectedResultFile, uniqueString
args = [varsP.RefAlignerBin, "-if", varsP.bnxTarget, "-merge", "-bnx", "-o", varsP.bnxFile.replace(".bnx",""), "-f"]
if varsP.stdoutlog :
args.extend( ['-stdout', '-stderr'] )
#print "joinBnxFiles: args:", args
jobwrapper = mthread.jobWrapper(varsP, "joinBnxFiles")
jobwrapper.addJob( mthread.singleJob(args, "joinBnxFiles", varsP.bnxFile, "joinBnxFiles") )
jobwrapper.multiThreadRunJobs(1)
jobwrapper.doAllPipeReport()
success = jobwrapper.allResultsFound()
if not success :
varsP.updatePipeReport("ERROR in performImageAnalysis: joinBnxFiles failed. Check: "+varsP.bnxTarget+"\n")
# this is just putting the path of bnxFile in bnxTarget
# on second thought, if I don't do this, then SampleCharModule will run on each bnx individually
#if success :
# varsP.writeListToFile([varsP.bnxFile], varsP.bnxTarget)
#sense of return of allResultsFound is opposite of return of performImageAnalysis:
# allResultsFound is True for all jobs success, False for any jobs fail
# performImage analysis return is 1 for failure
return not success
def performImageAnalysis(varsP, bypass=False, quality=True, forceonecolor=False):
"""Top level function for instrument scaling, image handling, bnx encoding
"""
#print "bypass = "******"ERROR in performImageAnalysis: no images found in paths in "+varsP.imgFile+"\n")
return 1 #this is an error--new convention is to return 1 on error
processImagesJobSet = mthread.jobWrapper(varsP, groupName = 'Image Transfer and Processing', throttle=8)
expID = 1
devices = []
allJobs = []
bnxFiles = [] #only used if bypass--see below
for remoteDataLocation in remoteDataLocations:
expTag = '%02d' % expID
expID += 1
localPath = os.path.join(varsP.localRoot, expTag + '/')
#if expTag == "04" : #debug
#print "data\n:", remoteDataLocation, "\n" #debug
curDevice = Device(varsP, expTag, remoteDataLocation, localPath, bypass, quality, forceonecolor)
for sJob in curDevice.getTargetJobs():
if sJob : #empty list is returned if target mol file already exists
processImagesJobSet.addJob(sJob)
devices.append(curDevice)
if bypass :
bnxFiles.append(curDevice.bnxFile)
if bypass:
return #bnxFiles #no longer need to return anything--this is not an error
processImagesJobSet.multiThreadRunJobs(varsP.nThreads, sleepTime =0.25)
#pipeReport += processImagesJobSet.makeRunReport()
#pipeReport += processImagesJobSet.makeParseReport()
#varsP.updatePipeReport(pipeReport, printalso=False)
processImagesJobSet.doAllPipeReport()
if varsP.lambdaRef:
mapLambdaJobSet = mthread.jobWrapper(varsP, groupName = 'Map Lambda')
for device in devices:
device.findSNRCutoff()
if varsP.lambdaRef:
for sJob in device.getLambdaMapJobs():
if sJob :
mapLambdaJobSet.addJob(sJob)
if varsP.lambdaRef:
mapLambdaJobSet.multiThreadRunJobs(varsP.nThreads, sleepTime =0.25)
pipeReport = mapLambdaJobSet.makeRunReport()
pipeReport += mapLambdaJobSet.makeParseReport()
for device in devices:
device.processLambdaMapResults()
varsP.updatePipeReport(pipeReport, printalso=False)
#still need to writeCorrectedBnx
targetLog = ''
scanLog = ''
deviceLog = ''
bnxFiles = []
for i,device in enumerate(devices):
device.writeCorrectedBnx()
if device.bnxFile : #this is nulled if above failed
bnxFiles.append(device.bnxFile)
if i == 0:
#targetLog += device.getTargetReport(headerOnly=True) + '\n'
deviceLog += device.getDeviceReport(headerOnly=True) + '\n'
scanLog += device.getScanReport() + '\n'
#targetLog += device.getTargetReport() + '\n'
deviceLog += device.getDeviceReport() + '\n'
#remove targetLog here; put it in pipeReport also,
# and do it at the beginning, not the end, of processing
#varsP.updateInfoReport(targetLog + '\n' + scanLog + '\n' + deviceLog + '\n')
varsP.updateInfoReport(scanLog + '\n' + deviceLog + '\n')
#return bnxFiles #instead of returning here, merge here, then return
return joinBnxFiles(varsP, bnxFiles) #see return of this fn
