def averageSubStack(partlist, stackfile, bin=1):
if len(partlist) > 300:
partlist = partlist[:300]
boxsize = apImagicFile.getBoxsize(stackfile)
if len(partlist) == 0:
binboxsize = boxsize/bin
blank = numpy.ones((binboxsize, binboxsize), dtype=numpy.float32)
return blank
if not os.path.isfile(stackfile):
apDisplay.printWarning("could not find stack, "+stackfile)
return False
partdatalist = apImagicFile.readParticleListFromStack(stackfile, partlist, boxsize, msg=False)
partdataarray = numpy.asarray(partdatalist)
finaldata = partdataarray.mean(0)
if bin > 1:
finaldata = apImage.binImg(finaldata, bin)
return finaldata
def createMontageInMemory(self, apix):
self.cluster_resolution = []
apDisplay.printMsg("Converting files")
### Set binning of images
boxsize = apImagicFile.getBoxsize(self.instack)
bin = 1
while boxsize/bin > 200:
bin+=1
binboxsize = boxsize/bin
### create averages
files = glob.glob(self.timestamp+".[0-9]*")
files.sort(self.sortFile)
montage = []
montagepngs = []
i = 0
for listname in files:
i += 1
apDisplay.printMsg("%d of %d classes"%(i,len(files)))
pngfile = listname+".png"
if not os.path.isfile(listname) or apFile.fileSize(listname) < 1:
### create a ghost particle
sys.stderr.write("skipping "+listname+"\n")
blank = numpy.ones((binboxsize, binboxsize), dtype=numpy.float32)
### add to montage stack
montage.append(blank)
self.cluster_resolution.append(None)
### create png
apImage.arrayToPng(blank, pngfile)
else:
### read particle list
partlist = self.readListFile(listname)
### average particles
partdatalist = apImagicFile.readParticleListFromStack(self.instack, partlist, boxsize, msg=False)
partdataarray = numpy.asarray(partdatalist)
finaldata = partdataarray.mean(0)
if bin > 1:
finaldata = apImage.binImg(finaldata, bin)
### add to montage stack
montage.append(finaldata)
res = apFourier.spectralSNR(partdatalist, apix)
self.cluster_resolution.append(res)
### create png
apImage.arrayToPng(finaldata, pngfile)
### check for png file
if os.path.isfile(pngfile):
montagepngs.append(pngfile)
else:
apDisplay.printError("failed to create montage")
stackname = "kerdenstack"+self.timestamp+".hed"
apImagicFile.writeImagic(montage, stackname)
### create montage
montagecmd = ("montage -geometry +4+4 -tile %dx%d "%(self.params['xdim'], self.params['ydim']))
for monpng in montagepngs:
montagecmd += monpng+" "
montagecmd += "montage.png"
apEMAN.executeEmanCmd(montagecmd, showcmd=True, verbose=False)
time.sleep(1)
apFile.removeFilePattern(self.timestamp+".*.png")
return bin
def makeNewStacks(self, parttree):
### untilted stack
self.notstackdata = apStack.getOnlyStackData(self.params['notstackid'])
notstackfile = os.path.join(self.notstackdata['path']['path'], self.notstackdata['name'])
### tilted stack
if not self.tiltstackdata:
self.tiltstackdata = apStack.getOnlyStackData(self.params['tiltstackid'])
tiltstackfile = os.path.join(self.tiltstackdata['path']['path'], self.tiltstackdata['name'])
### make doc file of Euler angles
#eulerfile = self.makeEulerDoc(parttree)
eulerfile = os.path.join(self.params['rundir'], "eulersdoc"+self.timestamp+".spi")
if os.path.isfile(eulerfile):
apFile.removeFile(eulerfile)
count = 0
notstacklist = []
tiltstacklist = []
sizelimit = 2048
notbox = apImagicFile.getBoxsize(notstackfile)
tiltbox = apImagicFile.getBoxsize(tiltstackfile)
tiltstacks = []
notstacks = []
t0 = time.time()
for partdict in parttree:
### print friendly message
if count % 100 == 0:
backs = "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b"
sys.stderr.write(backs+backs+backs+backs)
if count > sizelimit:
esttime = (len(parttree)/float(count)-1.0)*(time.time()-t0)
sys.stderr.write(str(count)+" particles of "+str(len(parttree))
+", "+apDisplay.timeString(esttime)+" remaining")
else:
sys.stderr.write(str(count)+" particles of "+str(len(parttree)))
### save stacks to file to save memory
if count%sizelimit == 0:
if count > 1:
apDisplay.printMsg("Writing stacks to file")
t1 = time.time()
tiltname = os.path.join(self.params['rundir'], "tiltstack%d.hed"%(count))
apFile.removeStack(tiltname)
apImagicFile.writeImagic(tiltstacklist, tiltname, msg=False)
tiltstacks.append(tiltname)
apDisplay.printMsg("finished tilted stack in "+apDisplay.timeString(time.time()-t1))
t1 = time.time()
notname = os.path.join(self.params['rundir'], "notstack%d.hed"%(count))
apFile.removeStack(notname)
apImagicFile.writeImagic(notstacklist, notname, msg=False)
notstacks.append(notname)
apDisplay.printMsg("finished untilted stack in "+apDisplay.timeString(time.time()-t1))
### reset stacks
apDisplay.printMsg("Reset stacks in memory")
notstacklist = []
tiltstacklist = []
### increment count
count += 1
### write to Euler doc
self.appendEulerDoc(eulerfile, partdict['tilt'], count)
### untilted stack
notpartarray = apImagicFile.readSingleParticleFromStack(notstackfile, partdict['not'], notbox, False)
notstacklist.append(notpartarray)
### tilted stack
tiltpartarray = apImagicFile.readSingleParticleFromStack(tiltstackfile, partdict['tilt'], tiltbox, False)
tiltstacklist.append(tiltpartarray)
### write remaining particles to stack
if len(notstacklist) > 0:
apDisplay.printMsg("Writing stacks to file")
t1 = time.time()
tiltname = os.path.join(self.params['rundir'], "tiltstack%d.hed"%(count))
apFile.removeStack(tiltname)
apImagicFile.writeImagic(tiltstacklist, tiltname, msg=False)
tiltstacks.append(tiltname)
apDisplay.printMsg("finished tilted stack in "+apDisplay.timeString(time.time()-t1))
t1 = time.time()
notname = os.path.join(self.params['rundir'], "notstack%d.hed"%(count))
apFile.removeStack(notname)
apImagicFile.writeImagic(notstacklist, notname, msg=False)
notstacks.append(notname)
apDisplay.printMsg("finished untilted stack in "+apDisplay.timeString(time.time()-t1))
### merge NOT stack
notname = os.path.join(self.params['rundir'], "notstack.hed")
apImagicFile.mergeStacks(notstacks, notname)
for stackname in notstacks:
apFile.removeStack(stackname, warn=False)
### merge TILT stack
tiltname = os.path.join(self.params['rundir'], "tiltstack.hed")
apImagicFile.mergeStacks(tiltstacks, tiltname)
for stackname in tiltstacks:
apFile.removeStack(stackname, warn=False)
### upload results
if self.params['commit'] is True:
self.uploadResults()
