def assemblePngs(keys, tag, montagestack):
apDisplay.printMsg("assembling pngs into montage")
# get path from montagestack
stackpath = os.path.dirname(os.path.abspath(montagestack))
montagecmd = "montage -geometry +4+4 "
montagestackdata = apImagicFile.readImagic(montagestack)
for i,key in enumerate(keys):
if i % 20 == 0:
sys.stderr.write(".")
pngfile = key+".png"
array = montagestackdata['images'][i]
apImage.arrayToPng(array, pngfile, normalize=True, msg=False)
#proccmd = "proc2d "+montagestack+" "+pngfile+" first="+str(i)+" last="+str(i)
#apEMAN.executeEmanCmd(proccmd, verbose=False, showcmd=False)
montagecmd += pngfile+" "
apDisplay.printMsg("montaging")
montagefile = os.path.join(stackpath,"montage"+tag+".png")
montagecmd += montagefile
apEMAN.executeEmanCmd(montagecmd, verbose=True)
#rotatecmd = "mogrify -rotate 180 -flop "+montagefile
#apEMAN.executeEmanCmd(rotatecmd, verbose=False)
for key in keys:
apFile.removeFile(key+".png")
if not os.path.isfile(montagefile):
apDisplay.printWarning("failed to create montage file")
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