コード例 #1
0
 def createTransformFile(self):
         # Get alignment from database
         specimen_euler, tiltaz, origins, rotations = apTomo.getAlignmentFromDB(self.alignerdata,self.imgcenter)
         centertuple = (self.imgcenter['x'],self.imgcenter['y'])
         imodaffines = apProTomo.convertProtomoToImod(specimen_euler, tiltaz, origins, rotations,centertuple)
         processdir = self.params['rundir']
         apImod.writeTransformFile(processdir, self.seriesname,imodaffines,ext='xf')
         imodlocalaffines = apTomo.convertGlobalToLocalAffines(imodaffines)
         apImod.writeTransformFile(processdir, self.seriesname,imodlocalaffines,ext='prexf')
コード例 #2
0
    def start(self):

        ###do queries
        sessiondata = apDatabase.getSessionDataFromSessionName(
            self.params['sessionname'])
        self.sessiondata = sessiondata
        tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(
            self.params['tiltseries'], sessiondata)
        tiltseriessettings = apTomo.getTomographySettings(
            sessiondata, tiltseriesdata)
        tiltdata = apTomo.getImageList([tiltseriesdata])
        description = self.params['description']
        apDisplay.printMsg("getting imagelist")
        print "ordering list"
        tilts, ordered_imagelist, ordered_mrc_files, refimg = apTomo.orderImageList(
            tiltdata)
        #tilts are tilt angles, ordered_imagelist are imagedata, ordered_mrc_files are paths to files, refimg is an int

        ###set up files
        seriesname = 'series' + str(self.params['tiltseries'])
        tiltfilename = seriesname + '.tlt'
        param_out = seriesname + '.param'
        maxtilt = max([abs(tilts[0]), abs(tilts[-1])])
        apDisplay.printMsg("highest tilt angle is %f" % maxtilt)
        self.params['cos_alpha'] = math.cos(maxtilt * math.pi / 180)
        self.params['raw_path'] = os.path.join(self.params['rundir'], 'raw')

        rawexists = apParam.createDirectory(self.params['raw_path'])

        apDisplay.printMsg("copying raw images")
        newfilenames = apProTomo.getImageFiles(ordered_imagelist,
                                               self.params['raw_path'],
                                               link=False)

        #get alignment data
        alignerdata = apTomo.getAlignerdata(self.params['alignerid'])
        imgshape = apTomo.getTomoImageShape(ordered_imagelist[0])
        imgcenter = {'x': self.imgshape[1] / 2, 'y': self.imgshape[0] / 2}
        specimen_euler, azimuth, origins, rotations = apTomo.getAlignmentFromDB(
            alignerdata, imgcenter)

        #write protomo2 tilt file
        outtltfile = 'series.tlt'
        seriesname = 'series'

        apProTomo.writeTiltFile2(outfilename, seriesname, specimen_eulers,
                                 azimuth, referenceimage)
コード例 #3
0
 def createTransformFile(self):
     # Get alignment from database
     specimen_euler, tiltaz, origins, rotations = apTomo.getAlignmentFromDB(
         self.alignerdata, self.imgcenter)
     centertuple = (self.imgcenter['x'], self.imgcenter['y'])
     imodaffines = apProTomo.convertProtomoToImod(specimen_euler, tiltaz,
                                                  origins, rotations,
                                                  centertuple)
     processdir = self.params['rundir']
     apImod.writeTransformFile(processdir,
                               self.seriesname,
                               imodaffines,
                               ext='xf')
     imodlocalaffines = apTomo.convertGlobalToLocalAffines(imodaffines)
     apImod.writeTransformFile(processdir,
                               self.seriesname,
                               imodlocalaffines,
                               ext='prexf')
コード例 #4
0
	def start(self):
	
	
		###do queries
		sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
		self.sessiondata = sessiondata
		tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params['tiltseries'],sessiondata)
		tiltseriessettings= apTomo.getTomographySettings(sessiondata,tiltseriesdata)
		tiltdata=apTomo.getImageList([tiltseriesdata])
		description = self.params['description']
		apDisplay.printMsg("getting imagelist")
		print "ordering list"
		tilts,ordered_imagelist,ordered_mrc_files,refimg = apTomo.orderImageList(tiltdata)
		#tilts are tilt angles, ordered_imagelist are imagedata, ordered_mrc_files are paths to files, refimg is an int

		###set up files
		seriesname='series'+str(self.params['tiltseries'])
		tiltfilename=seriesname+'.tlt'
		param_out=seriesname+'.param'
		maxtilt=max([abs(tilts[0]),abs(tilts[-1])])
		apDisplay.printMsg("highest tilt angle is %f" % maxtilt)
		self.params['cos_alpha']=math.cos(maxtilt*math.pi/180)
		self.params['raw_path']=os.path.join(self.params['rundir'],'raw')

		rawexists=apParam.createDirectory(self.params['raw_path'])

		apDisplay.printMsg("copying raw images")
		newfilenames=apProTomo.getImageFiles(ordered_imagelist,self.params['raw_path'], link=False)
		
		#get alignment data
		alignerdata = apTomo.getAlignerdata(self.params['alignerid'])
		imgshape = apTomo.getTomoImageShape(ordered_imagelist[0])
		imgcenter = {'x':self.imgshape[1]/2,'y':self.imgshape[0]/2}
		specimen_euler, azimuth, origins, rotations = apTomo.getAlignmentFromDB(alignerdata,imgcenter)

		#write protomo2 tilt file
		outtltfile='series.tlt'
		seriesname='series'
		
		apProTomo.writeTiltFile2(outfilename, seriesname, specimen_eulers, azimuth, referenceimage )