def getTiltGeom(self):
		# get the tilt geometry parameters
		self.params['aligndir'],self.params['imagedir'] =	apProTomo.setProtomoDir(self.params['rundir'])

		# self.params['imagedir'] when not testing with renamed images
		rawimagenames = apProTomo.linkImageFiles(self.ordered_imagelist, "/ami/data17/leginon/10nov10z/rawdatatest")
		shifts = apTomo.getGlobalShift(self.ordered_imagelist, self.corr_bin, self.refimg)

		tltparams = apProTomo.convertShiftsToParams(self.tilts, shifts, self.center, rawimagenames)
		return tltparams
示例#2
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    def getTiltGeom(self):
        # get the tilt geometry parameters
        self.params['aligndir'], self.params[
            'imagedir'] = apProTomo.setProtomoDir(self.params['rundir'])

        # self.params['imagedir'] when not testing with renamed images
        rawimagenames = apProTomo.linkImageFiles(
            self.ordered_imagelist, "/ami/data17/leginon/10nov10z/rawdatatest")
        shifts = apTomo.getGlobalShift(self.ordered_imagelist, self.corr_bin,
                                       self.refimg)

        tltparams = apProTomo.convertShiftsToParams(self.tilts, shifts,
                                                    self.center, rawimagenames)
        return tltparams
示例#3
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	def start(self):
		commit = self.params['commit']
		tiltdatalist = apTomo.getTiltdataList(self.params['tiltseries'],self.params['othertiltseries'])
		sessiondata = tiltdatalist[0]['session']
		description = self.params['description']
		alignsample = self.params['sample']
		cycle = self.params['cycle']
		alignmethod = self.params['alignmethod']
		apDisplay.printMsg("getting imagelist")
		imagelist = apTomo.getImageList(tiltdatalist)
		tilts,ordered_imagelist,ordered_mrc_files,refimg = apTomo.orderImageList(imagelist)
		
		# This parameter is needed for protomo, but not protomo2
		if self.params['refimg']:
			refimg = self.params['refimg']

		if alignmethod != 'protomo2':
			for file in ordered_mrc_files:
				# protomo can not function with a negative origin
				# protomo2 CAN function with negative origin
				apImage.shiftMRCStartToZero(file)
				
			apDisplay.printMsg("getting pixelsize")
			pixelsize = apTomo.getTomoPixelSize(ordered_imagelist[refimg])
			if pixelsize is None:
				apDisplay.printError('Pixel Size not retrieved. Invalid tilt series for processing')

		imgshape = apTomo.getTomoImageShape(ordered_imagelist[refimg])
		corr_bin = apTomo.getCorrelatorBinning(imgshape)
		center = {'x':imgshape[1]/2,'y':imgshape[0]/2}
		default_azimuth = apTomo.getDefaultAzimuthFromLeginon(ordered_imagelist[refimg])

		processdir = os.path.abspath(self.params['rundir'])
		imodseriesname = apTomo.getFilename(tiltdatalist)
		
		# protomo2 does not write out text files, intermediate info is in memory and the final result is binary
		seriesname = 'tomo'+ imodseriesname
		# Write tilt series stack images and tilt angles, not needed for protomo2
		if alignmethod != 'protomo2':
			stackdir = self.params['tiltseriesdir']
			stackname = imodseriesname+".st"
			apTomo.writeTiltSeriesStack(stackdir,stackname,ordered_mrc_files,1e10*pixelsize)
			apImod.writeRawtltFile(stackdir,imodseriesname,tilts)
		
		leginonxcorrlist = []
		for tiltdata in tiltdatalist:
			settingsdata = apTomo.getTomographySettings(sessiondata,tiltdata)
			leginonxcorrlist.append(settingsdata)
			
		# Run protomo2 
		if alignmethod == 'protomo2':
			self.runProtomo2(sessiondata, processdir, seriesname, ordered_imagelist, refimg, center, corr_bin, commit, tilts)
			
			# protomo2 does not need anything beyond this point, so exit
			return
			
		if cycle != 1 or alignmethod != 'protomo':
			cycles=[cycle,]
		else:
			# also process and commit protomo cycle 0 if doing cycle 1
			cycles=[0,1]
		for cycle in cycles:
			if alignmethod == 'protomo' or alignmethod == 'leginon':
				self.params['aligndir'],self.params['imagedir'] =	apProTomo.setProtomoDir(self.params['rundir'],cycle)
				aligndir = self.params['aligndir']
				# Link images into rundir/raw
				rawimagenames = apProTomo.linkImageFiles(ordered_imagelist,self.params['imagedir'])
				tltfile = os.path.join(aligndir,seriesname+'-%02d-itr.tlt' % (cycle,))
				if cycle == 0:
					# get initial shift alignment from leginon tiltcorrelator
					# Assume all tiltdata have the same tomography settings
					shifts = apTomo.getGlobalShift(ordered_imagelist, corr_bin, refimg)
					tltparams = apProTomo.convertShiftsToParams(tilts,shifts,center,default_azimuth,rawimagenames)
					apProTomo.writeTiltFile(tltfile,seriesname, tltparams[0], tltparams[1])
					refineparamdict=apProTomo.createRefineDefaults(len(tilts),
							os.path.join(processdir,'raw'),os.path.join(processdir,'out'))
					refineparamdict = apProTomo.updateRefineParams(refineparamdict,imgshape,alignsample,100,refimg)
				else:
					lasttltfile = os.path.join(aligndir,seriesname+'-%02d-fitted.tlt' % (cycle-1,))
					if self.params['goodcycle']:
						if (self.params['goodstart'] == 0 and self.params['goodend'] == len(ordered_imagelist) - 1):
							# revert goodcycle related params since nothing will be reset
							self.params['goodcycle'] = None
							self.params['goodstart'] = None
							self.params['goodend'] = None
					if not self.params['goodcycle']:
						#default uses last cycle
						shutil.copy(lasttltfile,tltfile)
					else:
						if not (self.params['goodstart'] or self.params['goodend']):
							shutil.copy(lasttltfile,tltfile)
						else:
							# Reset bad ending tilts before alignment cycle
							goodtltfile = os.path.join(aligndir,seriesname+'-%02d-fitted.tlt' % (self.params['goodcycle'],))
							goodtltparams = apProTomo.parseTilt(goodtltfile)
							lasttltparams = apProTomo.parseTilt(lasttltfile)
							tltparams = apProTomo.resetTiltParams(lasttltparams,goodtltparams,self.params['goodstart'],self.params['goodend'])
							apProTomo.writeTiltFile(tltfile,seriesname, tltparams[0], tltparams[1])
					lastrefineparamfile = os.path.join(aligndir,seriesname+'-%02d.param' % (cycle-1,))
					refineparamdict = apProTomo.parseRefineParamFile(lastrefineparamfile)
					refineparamdict = apProTomo.updateRefineParams(refineparamdict,imgshape,alignsample,self.params['region'],refimg)
				# Write param file in rundir/align
				paramfilepath = os.path.join(seriesname+'-%02d.param' % (cycle))
				fullparamfilepath = os.path.join(aligndir,paramfilepath)
				apProTomo.writeRefineParamFile(refineparamdict,fullparamfilepath)
				# run porjalign script
				os.chdir(aligndir)
				if cycle > 0:
					self.runProjalign(paramfilepath)
				else:
					lasttltfile = os.path.join(aligndir,seriesname+'-%02d-itr.tlt' % (cycle,))
					newtltfile = os.path.join(aligndir,seriesname+'-%02d-fitted.tlt' % (cycle,))
					shutil.copy(lasttltfile,newtltfile)
				# convert to imod alignment
				alignpathprefix = os.path.join(processdir, seriesname)
				centertuple = (center['x'],center['y'])
				apProTomo.convertGlobalTransformProtomoToImod(seriesname+'-%02d' %(cycle),imodseriesname, centertuple)
			elif alignmethod == 'imod-shift':
				# Correlation by Coarse correlation in IMOD
				aligndir = processdir
				imodxcorrdata = apImod.coarseAlignment(stackdir, processdir, imodseriesname, commit)
				# Global Transformation
				gtransforms = apImod.convertToGlobalAlignment(processdir, imodseriesname)
			# Create Aligned Stack for record
			bin = int(math.ceil(min(imgshape) / 512.0))
			apImod.createAlignedStack(stackdir, aligndir, imodseriesname,bin)
			if alignmethod == 'protomo' or alignmethod == 'leginon':
				alifilename = imodseriesname+'-%02d.ali' % cycle
				os.rename(imodseriesname+'.ali',alifilename)
			else:
				alifilename = imodseriesname+'.ali'
			alifilepath = os.path.join(aligndir,alifilename)
			# commit to database
			if commit:
				if alignmethod == 'protomo' or alignmethod == 'leginon':
					# -- Commit Parameters --
					protomodata = apProTomo.insertProtomoParams(seriesname)
					alignrun = apTomo.insertTomoAlignmentRun(sessiondata,leginonxcorrlist[0],None,protomodata,None,1,self.params['runname'],self.params['rundir'],self.params['description'])
					self.cycle_description = self.params['description']
					self.params['cycle'] = cycle
					if cycle == 0:
						# temporarily change aligner description on the initial 0 cycle
						self.params['description'] = 'leginon correlation results'
					# insert sample and window size and all the other user defined params into ApProtomoRefinementParamsData
					alignerdata = apProTomo.insertAlignIteration(alignrun, protomodata, self.params, refineparamdict,ordered_imagelist[refimg])
					# -- Commit Results --
					resulttltfile = os.path.join(aligndir,seriesname+'-%02d-fitted.tlt' % (cycle,))
					resulttltparams = apProTomo.parseTilt(resulttltfile)
					if resulttltparams:
						# commit the geometry parameters (psi, theta, phi, azimuth)
						modeldata = apProTomo.insertModel(alignerdata, resulttltparams)
						# insert results into ApProtomoAlignmentData (also used by imod) for each image
						for i,imagedata in enumerate(ordered_imagelist):
							apProTomo.insertTiltAlignment(alignerdata,imagedata,i,resulttltparams[0][i],center)
					self.params['description'] = self.cycle_description
				else:
					alignrun = apTomo.insertTomoAlignmentRun(sessiondata,None,imodxcorrdata,None,None,1,self.params['runname'],self.params['rundir'],self.params['description'])
					alignerdata = apTomo.insertAlignerParams(alignrun,self.params)
					#results
					prexgfile = os.path.join(aligndir,imodseriesname+'.prexg')
					shifts = apImod.readShiftPrexgFile(aligndir, imodseriesname)
					resulttltparams = apProTomo.convertShiftsToParams(tilts,shifts,center,default_azimuth)
					if resulttltparams:
						modeldata = apProTomo.insertModel(alignerdata, resulttltparams)
						for i,imagedata in enumerate(ordered_imagelist):
							apProTomo.insertTiltAlignment(alignerdata,imagedata,i,resulttltparams[0][i],center)
				# multiple tilt series in one alignrun
				for i in range(0,len(tiltdatalist)):
					if i == 0:
						primary = True
					else:
						primary = False
					apTomo.insertTiltsInAlignRun(alignrun, tiltdatalist[i],leginonxcorrlist[i],primary)
			apTomo.makeAlignStackMovie(alifilepath)
			os.chdir(processdir)