def createAlignedReferenceStack(self):
searchstr = "part"+self.params['timestamp']+"_ref0*.xmp"
files = glob.glob(searchstr)
files.sort()
stack = []
reflist = self.readRefDocFile()
for i in range(len(files)):
fname = files[i]
refdict = reflist[i]
if refdict['partnum'] != i+1:
print i, refdict['partnum']
apDisplay.printError("sorting error in reflist, see neil")
refarray = spider.read(fname)
xyshift = (refdict['xshift'], refdict['yshift'])
alignrefarray = apImage.xmippTransform(refarray, rot=refdict['inplane'],
shift=xyshift, mirror=refdict['mirror'])
stack.append(alignrefarray)
stackarray = numpy.asarray(stack, dtype=numpy.float32)
#print stackarray.shape
avgstack = "part"+self.params['timestamp']+"_average.hed"
apFile.removeStack(avgstack, warn=False)
apImagicFile.writeImagic(stackarray, avgstack)
### create a average mrc
avgdata = stackarray.mean(0)
apImage.arrayToMrc(avgdata, "average.mrc")
return
def createAlignedStacks(self, partlist):
stackid = self.params['stackid']
stackdata = apStack.getOnlyStackData(stackid)
origstackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
imagesdict = apImagicFile.readImagic(origstackfile)
i = 0
t0 = time.time()
apDisplay.printMsg("rotating and shifting particles at "+time.asctime())
alignstack = []
while i < len(partlist):
partimg = imagesdict['images'][i]
partdict = partlist[i]
partnum = i+1
#print partnum, partdict, partimg.shape
if partdict['partnum'] != partnum:
apDisplay.printError("particle shifting "+str(partnum)+" != "+str(partdict))
xyshift = (partdict['xshift'], partdict['yshift'])
alignpartimg = apImage.xmippTransform(partimg, rot=partdict['inplane'],
shift=xyshift, mirror=partdict['mirror'])
alignstack.append(alignpartimg)
i += 1
apDisplay.printMsg("rotate then shift %d particles in %s"%(i,apDisplay.timeString(time.time()-t0)))
alignstackarray = numpy.asarray(alignstack)
self.alignimagicfile = "alignstack.hed"
apImagicFile.writeImagic(alignstackarray, self.alignimagicfile)
def createAlignedStacks(self, partlist):
stackid = self.params['stackid']
stackdata = apStack.getOnlyStackData(stackid)
origstackfile = os.path.join(stackdata['path']['path'],
stackdata['name'])
imagesdict = apImagicFile.readImagic(origstackfile)
i = 0
t0 = time.time()
apDisplay.printMsg("rotating and shifting particles at " +
time.asctime())
alignstack = []
while i < len(partlist):
partimg = imagesdict['images'][i]
partdict = partlist[i]
partnum = i + 1
#print partnum, partdict, partimg.shape
if partdict['partnum'] != partnum:
apDisplay.printError("particle shifting " + str(partnum) +
" != " + str(partdict))
xyshift = (partdict['xshift'], partdict['yshift'])
alignpartimg = apImage.xmippTransform(partimg,
rot=partdict['inplane'],
shift=xyshift,
mirror=partdict['mirror'])
alignstack.append(alignpartimg)
i += 1
apDisplay.printMsg("rotate then shift %d particles in %s" %
(i, apDisplay.timeString(time.time() - t0)))
alignstackarray = numpy.asarray(alignstack)
self.alignimagicfile = "alignstack.hed"
apImagicFile.writeImagic(alignstackarray, self.alignimagicfile)
def createAlignedStacks(self, partlist, origstackfile):
partperiter = min(4096,apImagicFile.getPartSegmentLimit(origstackfile))
numpart = len(partlist)
if numpart < partperiter:
partperiter = numpart
t0 = time.time()
imgnum = 0
stacklist = []
apDisplay.printMsg("rotating and shifting particles at "+time.asctime())
while imgnum < len(partlist):
index = imgnum % partperiter
if imgnum % 100 == 0:
sys.stderr.write(".")
if index == 0:
### deal with large stacks
if imgnum > 0:
sys.stderr.write("\n")
stackname = "alignstack%d.hed"%(imgnum)
apDisplay.printMsg("writing aligned particles to file "+stackname)
stacklist.append(stackname)
apFile.removeStack(stackname, warn=False)
apImagicFile.writeImagic(alignstack, stackname, msg=False)
perpart = (time.time()-t0)/imgnum
apDisplay.printColor("particle %d of %d :: %s per part :: %s remain"%
(imgnum+1, numpart, apDisplay.timeString(perpart),
apDisplay.timeString(perpart*(numpart-imgnum))), "blue")
alignstack = []
imagesdict = apImagicFile.readImagic(origstackfile, first=imgnum+1, last=imgnum+partperiter, msg=False)
### align particles
partimg = imagesdict['images'][index]
partdict = partlist[imgnum]
partnum = imgnum+1
if partdict['partnum'] != partnum:
apDisplay.printError("particle shifting "+str(partnum)+" != "+str(partdict))
xyshift = (partdict['xshift'], partdict['yshift'])
alignpartimg = apImage.xmippTransform(partimg, rot=partdict['inplane'],
shift=xyshift, mirror=partdict['mirror'])
alignstack.append(alignpartimg)
imgnum += 1
### write remaining particle to file
sys.stderr.write("\n")
stackname = "alignstack%d.hed"%(imgnum)
apDisplay.printMsg("writing aligned particles to file "+stackname)
stacklist.append(stackname)
apImagicFile.writeImagic(alignstack, stackname, msg=False)
### merge stacks
alignimagicfile = "alignstack.hed"
apFile.removeStack(alignimagicfile, warn=False)
apImagicFile.mergeStacks(stacklist, alignimagicfile)
#for stackname in stacklist:
# emancmd = "proc2d %s %s"%(stackname, alignimagicfile)
# apEMAN.executeEmanCmd(emancmd, verbose=False)
filepart = apFile.numImagesInStack(alignimagicfile)
if filepart != numpart:
apDisplay.printError("number aligned particles (%d) not equal number expected particles (%d)"%
(filepart, numpart))
for stackname in stacklist:
apFile.removeStack(stackname, warn=False)
### summarize
apDisplay.printMsg("rotated and shifted %d particles in %s"%(imgnum, apDisplay.timeString(time.time()-t0)))
return alignimagicfile