コード例 #1
0
	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
コード例 #2
0
	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)
コード例 #3
0
 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)
コード例 #4
0
	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