def arrayToJpegPlusPeak(numer, outfile, peak=None, normalize=True):
"""
takes a numpy and writes a JPEG
best for micrographs and photographs
"""
if normalize:
numer = imagenorm.maxNormalizeImage(numer)
else:
numer = numer * 255
image = _arrayToImage(numer)
image = image.convert("RGB")
if peak != None:
draw = ImageDraw.Draw(image)
peak2 = numpy.asarray(peak)
for i in range(2):
if peak[i] < 0:
peak2[i] = (numer.shape)[i] + peak[i]
elif peak[i] > (numer.shape)[i]:
peak2[i] = peak[i] - (numer.shape)[i]
drawPeak(peak2, draw, numer.shape)
print " ... writing JPEG: ", outfile
image.save(outfile, "JPEG", quality=85)
return
def arrayToJpegPlusPeak(numer, outfile, peak=None, normalize=True):
"""
takes a numpy and writes a JPEG
best for micrographs and photographs
"""
if normalize:
numer = imagenorm.maxNormalizeImage(numer)
else:
numer = numer*255
image = _arrayToImage(numer)
image = image.convert("RGB")
if peak != None:
draw = ImageDraw.Draw(image)
peak2 = numpy.asarray(peak)
for i in range(2):
if peak[i] < 0:
peak2[i] = (numer.shape)[i] + peak[i]
elif peak[i] > (numer.shape)[i]:
peak2[i] = peak[i] - (numer.shape)[i]
drawPeak(peak2, draw, numer.shape)
print " ... writing JPEG: ",outfile
image.save(outfile, "JPEG", quality=85)
return
def arrayToImage(numer, normalize=True, stdevLimit=3.0):
"""
takes a numpy and writes a JPEG
best for micrographs and photographs
"""
if normalize:
numer = imagenorm.maxNormalizeImage(numer, stdevLimit)
else:
numer = numer * 255
image = _arrayToImage(numer)
return image
def arrayToImage(numer, normalize=True, stdevLimit=3.0):
"""
takes a numpy and writes a JPEG
best for micrographs and photographs
"""
if normalize:
numer = imagenorm.maxNormalizeImage(numer, stdevLimit)
else:
numer = numer*255
image = _arrayToImage(numer)
return image
def arrayToPng(numer, filename, normalize=True, msg=True):
"""
takes a numpy and writes a PNG
best for masks and line art
"""
if normalize:
numer = imagenorm.maxNormalizeImage(numer)
else:
numer = numer * 255
image = _arrayToImage(numer)
if msg is True:
apDisplay.printMsg("writing PNG: " + apDisplay.short(filename))
image.save(filename, "PNG")
return
def arrayToJpeg(numer, filename, normalize=True, msg=True, quality=85):
"""
takes a numpy and writes a JPEG
best for micrographs and photographs
"""
if normalize:
numer = imagenorm.maxNormalizeImage(numer)
else:
numer = numer * 255
image = _arrayToImage(numer)
if msg is True:
apDisplay.printMsg("writing JPEG: " + apDisplay.short(filename))
image.save(filename, "JPEG", quality=quality)
return
def arrayToPng(numer, filename, normalize=True, msg=True):
"""
takes a numpy and writes a PNG
best for masks and line art
"""
if normalize:
numer = imagenorm.maxNormalizeImage(numer)
else:
numer = numer*255
image = _arrayToImage(numer)
if msg is True:
apDisplay.printMsg("writing PNG: "+apDisplay.short(filename))
image.save(filename, "PNG")
return
def arrayToJpeg(numer, filename, normalize=True, msg=True, quality=85):
"""
takes a numpy and writes a JPEG
best for micrographs and photographs
"""
if normalize:
numer = imagenorm.maxNormalizeImage(numer)
else:
numer = numer*255
image = _arrayToImage(numer)
if msg is True:
apDisplay.printMsg("writing JPEG: "+apDisplay.short(filename))
image.save(filename, "JPEG", quality=quality)
return
def updateTemplateStack(self, alignedstack, partlist, iternum):
"""
Function to Average particles that match template to create new templates
"""
#templatestr = os.path.join(self.params['rundir'], "templates/filt*.mrc")
#oldfilelist = glob.glob(templatestr)
### clear old stacks
templatestack = os.path.join(self.params['rundir'], ("templatestack%02d.spi" % iternum))
apFile.removeFile(templatestack, warn=True)
### calculate correlation stats
statlist = []
for partdict in partlist:
statlist.append(partdict['score'])
statlist.sort()
cutoff = statlist[int(0.1*len(partlist))]*0.999
apDisplay.printMsg("using a 10% correlation cutoff of: "+str(round(cutoff)))
### init list of files
keeplists = []
for templatenum in range(1, self.params['numtemplate']+1):
f = open(("templates/keeplist%02d-%02d.list" % (iternum, templatenum)), "w")
keeplists.append(f)
junk = open(("templates/rejectlist%02d.list" % (iternum)), "w")
### allocate particles to keep lists
numjunk = 0
for partdict in partlist:
#EMAN lists start at zero
if partdict['score'] > cutoff:
keeplists[partdict['template']-1].write(str(partdict['num']-1)+"\n")
else:
numjunk+=1
junk.write(str(partdict['num']-1)+"\n")
for f in keeplists:
f.close()
junk.close()
### average junk for fun
apDisplay.printMsg(str(numjunk)+" particles were marked as junk")
if numjunk == 0:
junk = open(("templates/rejectlist%02d.list" % (iternum)), "w")
randpart = random.random()*(len(partlist)-1)
junk.write(str(randpart)+"\n")
junk.close()
junklist = "templates/rejectlist%02d.list" % (iternum)
junkmrcfile = "templates/junkavg%02d.mrc" % (iternum)
emancmd = ("proc2d "+alignedstack+" "+junkmrcfile
+" list="+junklist
+" edgenorm average norm=0,1 ")
apEMAN.executeEmanCmd(emancmd, showcmd=False)
### create averaged templates
filelist = []
for templatenum in range(1, self.params['numtemplate']+1):
keeplist = "templates/keeplist%02d-%02d.list" % (iternum, templatenum)
mrcfile = "templates/templateavg%02d-%02d.mrc" % (iternum, templatenum)
if os.path.isfile(keeplist) and os.stat(keeplist)[6] > 1:
emancmd = ("proc2d "+alignedstack+" "+mrcfile
+" list="+keeplist
+" edgenorm average norm=0,1 ")
if self.params['csym'] is not None:
emancmd += "sym=c%d"%(self.params['csym'])
apEMAN.executeEmanCmd(emancmd, showcmd=False)
else:
apDisplay.printWarning("No particles aligned to template "+str(templatenum))
if numjunk == 0:
apDisplay.printWarning("Using random particle as new template")
else:
apDisplay.printWarning("Using worst 10% of particles as new template")
lasttemplate = "templates/templateavg%02d-%02d.mrc" % (iternum-1, templatenum)
if not os.path.isfile(lasttemplate):
lasttemplate = "templates/scaledTemplate%d.mrc" % (templatenum)
lastdata = imagenorm.maxNormalizeImage(imagefile.mrcToArray(lasttemplate))
junkdata = imagenorm.maxNormalizeImage(imagefile.mrcToArray(junkmrcfile))
imagefile.arrayToMrc((lastdata+3.0*junkdata), "temp.mrc")
emancmd = ("proc2d temp.mrc "+mrcfile
+" addnoise=1.5 "
+" edgenorm norm=0,1 ")
apEMAN.executeEmanCmd(emancmd, showcmd=False)
filelist.append(mrcfile)
### create new template stack
for mrcfile in filelist:
emancmd = ("proc2d "+mrcfile+" "+templatestack
+" clip="+str(self.boxsize)+","+str(self.boxsize)
+" edgenorm norm=0,1 spider ")
apEMAN.executeEmanCmd(emancmd, showcmd=False)
return templatestack
def updateTemplateStack(self, alignedstack, partlist, iternum):
"""
Function to Average particles that match template to create new templates
"""
#templatestr = os.path.join(self.params['rundir'], "templates/filt*.mrc")
#oldfilelist = glob.glob(templatestr)
### clear old stacks
templatestack = os.path.join(self.params['rundir'], ("templatestack%02d.spi" % iternum))
apFile.removeFile(templatestack, warn=True)
### calculate correlation stats
statlist = []
for partdict in partlist:
statlist.append(partdict['score'])
statlist.sort()
cutoff = statlist[int(0.1*len(partlist))]*0.999
apDisplay.printMsg("using a 10% correlation cutoff of: "+str(round(cutoff)))
### init list of files
keeplists = []
for templatenum in range(1, self.params['numtemplate']+1):
f = open(("templates/keeplist%02d-%02d.list" % (iternum, templatenum)), "w")
keeplists.append(f)
junk = open(("templates/rejectlist%02d.list" % (iternum)), "w")
### allocate particles to keep lists
numjunk = 0
for partdict in partlist:
#EMAN lists start at zero
if partdict['score'] > cutoff:
keeplists[partdict['template']-1].write(str(partdict['num']-1)+"\n")
else:
numjunk+=1
junk.write(str(partdict['num']-1)+"\n")
for f in keeplists:
f.close()
junk.close()
### average junk for fun
apDisplay.printMsg(str(numjunk)+" particles were marked as junk")
if numjunk == 0:
junk = open(("templates/rejectlist%02d.list" % (iternum)), "w")
randpart = random.random()*(len(partlist)-1)
junk.write(str(randpart)+"\n")
junk.close()
junklist = "templates/rejectlist%02d.list" % (iternum)
junkmrcfile = "templates/junkavg%02d.mrc" % (iternum)
emancmd = ("proc2d "+alignedstack+" "+junkmrcfile
+" list="+junklist
+" edgenorm average norm=0,1 ")
apEMAN.executeEmanCmd(emancmd, showcmd=False)
### create averaged templates
filelist = []
for templatenum in range(1, self.params['numtemplate']+1):
keeplist = "templates/keeplist%02d-%02d.list" % (iternum, templatenum)
mrcfile = "templates/templateavg%02d-%02d.mrc" % (iternum, templatenum)
if os.path.isfile(keeplist) and os.stat(keeplist)[6] > 1:
emancmd = ("proc2d "+alignedstack+" "+mrcfile
+" list="+keeplist
+" edgenorm average norm=0,1 ")
if self.params['csym'] is not None:
emancmd += "sym=c%d"%(self.params['csym'])
apEMAN.executeEmanCmd(emancmd, showcmd=False)
else:
apDisplay.printWarning("No particles aligned to template "+str(templatenum))
if numjunk == 0:
apDisplay.printWarning("Using random particle as new template")
else:
apDisplay.printWarning("Using worst 10% of particles as new template")
lasttemplate = "templates/templateavg%02d-%02d.mrc" % (iternum-1, templatenum)
if not os.path.isfile(lasttemplate):
lasttemplate = "templates/scaledTemplate%d.mrc" % (templatenum)
lastdata = imagenorm.maxNormalizeImage(imagefile.mrcToArray(lasttemplate))
junkdata = imagenorm.maxNormalizeImage(imagefile.mrcToArray(junkmrcfile))
imagefile.arrayToMrc((lastdata+3.0*junkdata), "temp.mrc")
emancmd = ("proc2d temp.mrc "+mrcfile
+" addnoise=1.5 "
+" edgenorm norm=0,1 ")
apEMAN.executeEmanCmd(emancmd, showcmd=False)
filelist.append(mrcfile)
### create new template stack
for mrcfile in filelist:
emancmd = ("proc2d "+mrcfile+" "+templatestack
+" clip="+str(self.boxsize)+","+str(self.boxsize)
+" edgenorm norm=0,1 spider ")
apEMAN.executeEmanCmd(emancmd, showcmd=False)
return templatestack