def setupTiltSeries(self):
         tilts,self.ordered_imagelist,ordered_mrc_files,refindex = apTomo.orderImageList(self.orig_imagelist)
         self.seriesname = apTomo.getFilename(self.tiltdatalist)
         stackdir = self.params['tiltseriesdir']
         stackname = self.seriesname+".st"
         apTomo.writeTiltSeriesStack(stackdir,stackname,ordered_mrc_files,1e10*self.pixelsize)
         apImod.writeRawtltFile(stackdir,self.seriesname,tilts)
Exemple #2
0
 def setupTiltSeries(self):
     tilts, self.ordered_imagelist, ordered_mrc_files, refindex = apTomo.orderImageList(
         self.orig_imagelist)
     self.seriesname = apTomo.getFilename(self.tiltdatalist)
     stackdir = self.params['tiltseriesdir']
     stackname = self.seriesname + ".st"
     apTomo.writeTiltSeriesStack(stackdir, stackname, ordered_mrc_files,
                                 1e10 * self.pixelsize)
     apImod.writeRawtltFile(stackdir, self.seriesname, tilts)
Exemple #3
0
	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)
Exemple #4
0
    def start(self):
        # set local parameters
        commit = self.params['commit']
        tiltdatalist = apTomo.getTiltdataList(self.params['tiltseries'],
                                              self.params['othertiltseries'])
        sessiondata = tiltdatalist[0]['session']
        description = self.params['description']
        runname = self.params['runname']
        alignmethod = self.params['alignmethod']
        reconbin = int(self.params['reconbin'])
        thickness_pixel = int(self.params['reconthickness'])
        markersize_nm = int(self.params['markersize'])
        markernumber = int(self.params['markernumber'])

        apDisplay.printMsg("getting imagelist")
        imagelist = apTomo.getImageList(tiltdatalist)
        tilts, ordered_imagelist, ordered_mrc_files, refimg = apTomo.orderImageList(
            imagelist)
        apDisplay.printMsg("getting pixelsize")
        pixelsize = apTomo.getTomoPixelSize(ordered_imagelist[refimg])
        imgshape = apTomo.getTomoImageShape(ordered_imagelist[refimg])
        #thickness_binnedpixel = int(thickness_nm * 1e-9 / (pixelsize * reconbin))
        markersize_pixel = int(markersize_nm * 1e-9 / pixelsize)
        processdir = os.path.abspath(self.params['rundir'])
        imodseriesname = apTomo.getFilename(tiltdatalist)
        seriesname = imodseriesname
        # Write tilt series stack images and tilt angles
        stackdir = self.params['tiltseriesdir']
        stackname = imodseriesname + ".st"
        apTomo.writeTiltSeriesStack(stackdir, stackname, ordered_mrc_files,
                                    1e10 * pixelsize)
        apRaptor.linkStToMrcExtension(stackdir, imodseriesname)
        apImod.writeRawtltFile(stackdir, imodseriesname, tilts)
        # Get Leginon tomography settings
        leginontomosettingslist = []
        for tiltdata in tiltdatalist:
            settingsdata = apTomo.getTomographySettings(sessiondata, tiltdata)
            leginontomosettingslist.append(settingsdata)
        aligndir = processdir
        # run the script and get alignment results when raptor can output alignment results in the future. raptoraligndata is None for now.
        returncode, raptoraligndata, raptorfailed = apRaptor.alignAndRecon(
            stackdir, stackname, processdir, markersize_pixel, reconbin,
            thickness_pixel, markernumber, commit)
        # Create Aligned Stack for record, not done in apRaptor yet, currently raptoraligndata is None
        if not raptorfailed:
            alifilename = imodseriesname + '.ali'
            alifilepath = os.path.join(aligndir, 'align', alifilename)
            print alifilepath
        # commit to database
        if commit:
            # parameters
            raptorparamsdata = apRaptor.insertRaptorParams(
                markersize_nm, markernumber)
            alignrun = apTomo.insertTomoAlignmentRun(
                sessiondata, None, None, None, raptorparamsdata, 1,
                self.params['runname'], self.params['rundir'],
                self.params['description'], raptorfailed)
            # to accomodate iterative alignment, one alignmentrun may have
            # used the aligner several times, for this case a single
            # aligner params data is inserted as in the case of Imod xcorr
            alignerdata = apTomo.insertAlignerParams(alignrun, self.params)
            #results
            if raptoraligndata:
                # if raptor has alignment result, it is converted to protomo
                # format which is more parameterized and saved
                prexgfile = os.path.join(aligndir, imodseriesname + '.prexg')
                shifts = apImod.readShiftPrexgFile(aligndir, imodseriesname)
                resulttltparams = apProTomo.convertShiftsToParams(
                    tilts, shifts, center)
                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
                # Record tilts in align run allows more than one tilt series to be
                # used in one align run.
                apTomo.insertTiltsInAlignRun(alignrun, tiltdatalist[i],
                                             leginontomosettingslist[i],
                                             primary)
            if not raptorfailed:
                apTomo.makeAlignStackMovie(alifilepath)
            os.chdir(processdir)

            # Full tomogram created with raptor is ???? handness?????
            if not raptorfailed:
                '''
				voltransform = '????'
				origtomopath = os.path.join(processdir, seriesname+"_full.rec")
				currenttomopath = apImod.transformVolume(origtomopath,voltransform)
				shutil.move(currenttomopath, origtomopath)
				'''
                zprojectfile = apImod.projectFullZ(processdir, runname,
                                                   seriesname, reconbin, False,
                                                   False)
                try:
                    zimagedata = apTomo.uploadZProjection(
                        runname, imagelist[0], zprojectfile)
                except:
                    zimagedata = None
                fullrundata = apTomo.insertFullTomoRun(sessiondata, processdir,
                                                       runname, 'imod-wbp')
                fulltomodata = apTomo.insertFullTomogram(
                    sessiondata, tiltdatalist[0], alignerdata, fullrundata,
                    runname, description, zimagedata, thickness_pixel,
                    reconbin)

                # if raptor succeeded, upload data and parameters to database
                session_time = sessiondata.timestamp
                description = self.params['description']
                raptordatabase = apRaptor.commitToJensenDatabase(
                    session_time, fulltomodata, stackdir, processdir,
                    stackname, description)
                if raptordatabase == 0:
                    apDisplay.printMsg(
                        "RAPTOR and uploading to Jensen database done.")
                else:
                    apDisplay.printWarning(
                        "Uploading to Jensen database failed.")
        def start(self):
                # set local parameters
                commit = self.params['commit']
                tiltdatalist = apTomo.getTiltdataList(self.params['tiltseries'],self.params['othertiltseries'])
                sessiondata = tiltdatalist[0]['session']
                description = self.params['description']
                runname = self.params['runname']
                alignmethod = self.params['alignmethod']
                reconbin = int(self.params['reconbin'])
                thickness_pixel = int(self.params['reconthickness'])
                markersize_nm = int(self.params['markersize'])
                markernumber = int(self.params['markernumber'])

                apDisplay.printMsg("getting imagelist")
                imagelist = apTomo.getImageList(tiltdatalist)
                tilts,ordered_imagelist,ordered_mrc_files,refimg = apTomo.orderImageList(imagelist)
                apDisplay.printMsg("getting pixelsize")
                pixelsize = apTomo.getTomoPixelSize(ordered_imagelist[refimg])
                imgshape = apTomo.getTomoImageShape(ordered_imagelist[refimg])
                #thickness_binnedpixel = int(thickness_nm * 1e-9 / (pixelsize * reconbin))
                markersize_pixel = int(markersize_nm * 1e-9 / pixelsize)
                processdir = os.path.abspath(self.params['rundir'])
                imodseriesname = apTomo.getFilename(tiltdatalist)
                seriesname = imodseriesname
                # Write tilt series stack images and tilt angles
                stackdir = self.params['tiltseriesdir']
                stackname = imodseriesname+".st"
                apTomo.writeTiltSeriesStack(stackdir,stackname,ordered_mrc_files,1e10*pixelsize)
                apRaptor.linkStToMrcExtension(stackdir,imodseriesname)
                apImod.writeRawtltFile(stackdir,imodseriesname,tilts)
                # Get Leginon tomography settings
                leginontomosettingslist = []
                for tiltdata in tiltdatalist:
                        settingsdata = apTomo.getTomographySettings(sessiondata,tiltdata)
                        leginontomosettingslist.append(settingsdata)
                aligndir = processdir
                # run the script and get alignment results when raptor can output alignment results in the future. raptoraligndata is None for now.
                returncode, raptoraligndata, raptorfailed = apRaptor.alignAndRecon(stackdir, stackname, processdir, markersize_pixel, reconbin, thickness_pixel, markernumber, commit)
                # Create Aligned Stack for record, not done in apRaptor yet, currently raptoraligndata is None
                if not raptorfailed:
                        alifilename = imodseriesname+'.ali'
                        alifilepath = os.path.join(aligndir,'align',alifilename)
                        print alifilepath
                # commit to database
                if commit:
                        # parameters
                        raptorparamsdata = apRaptor.insertRaptorParams(markersize_nm,markernumber)
                        alignrun = apTomo.insertTomoAlignmentRun(sessiondata,None,None,None,raptorparamsdata,1,self.params['runname'],self.params['rundir'],self.params['description'],raptorfailed)
                        # to accomodate iterative alignment, one alignmentrun may have 
                        # used the aligner several times, for this case a single 
                        # aligner params data is inserted as in the case of Imod xcorr
                        alignerdata = apTomo.insertAlignerParams(alignrun,self.params)
                        #results
                        if raptoraligndata:
                                # if raptor has alignment result, it is converted to protomo
                                # format which is more parameterized and saved
                                prexgfile = os.path.join(aligndir,imodseriesname+'.prexg')
                                shifts = apImod.readShiftPrexgFile(aligndir, imodseriesname)
                                resulttltparams = apProTomo.convertShiftsToParams(tilts,shifts,center)
                                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
                                # Record tilts in align run allows more than one tilt series to be
                                # used in one align run.
                                apTomo.insertTiltsInAlignRun(alignrun, tiltdatalist[i],leginontomosettingslist[i],primary)
                        if not raptorfailed:
                                apTomo.makeAlignStackMovie(alifilepath)
                        os.chdir(processdir)

                        # Full tomogram created with raptor is ???? handness?????
                        if not raptorfailed:
                                '''
                                voltransform = '????'
                                origtomopath = os.path.join(processdir, seriesname+"_full.rec")
                                currenttomopath = apImod.transformVolume(origtomopath,voltransform)
                                shutil.move(currenttomopath, origtomopath)
                                '''
                                zprojectfile = apImod.projectFullZ(processdir, runname, seriesname,reconbin,False,False)
                                try:
                                        zimagedata = apTomo.uploadZProjection(runname,imagelist[0],zprojectfile)
                                except:
                                        zimagedata = None
                                fullrundata = apTomo.insertFullTomoRun(sessiondata,processdir,runname,'imod-wbp')
                                fulltomodata = apTomo.insertFullTomogram(sessiondata,tiltdatalist[0],alignerdata,
                                                fullrundata,runname,description,zimagedata,thickness_pixel,reconbin)


                                # if raptor succeeded, upload data and parameters to database
                                session_time = sessiondata.timestamp
                                description = self.params['description']
                                raptordatabase = apRaptor.commitToJensenDatabase(session_time, fulltomodata, stackdir, processdir, stackname, description)
                                if raptordatabase == 0:
                                        apDisplay.printMsg("RAPTOR and uploading to Jensen database done.")
                                else:
                                        apDisplay.printWarning("Uploading to Jensen database failed.")