def start(self):
		commit = self.params['commit']
		description = self.params['description']
		processdir = self.params['fulltomodir']
		runname = self.params['runname']
		offsetz = self.params['offsetz']
		subbin = self.params['bin']
		invert = self.params['invert']
		fulltomodata = apTomo.getFullTomoData(self.params['fulltomoId'])
		#subvolume making
		if (self.params['selexonId'] is not None or self.params['stackId']) and fulltomodata is not None:
			sessiondata = fulltomodata['session']
			seriesname = fulltomodata['name'].rstrip('_full')
			fullbin = fulltomodata['bin']
			if not fullbin:
				apDisplay.printWarning("no binning in full tomogram, something is wrong, use alignment bin for now")
				fullbin = fulltomodata['aligner']['alignrun']['bin']
			fulltomopath = os.path.join(fulltomodata['reconrun']['path']['path'], seriesname+"_full.rec")
			fulltomoheader = mrc.readHeaderFromFile(fulltomopath)
			fulltomoshape = fulltomoheader['shape']
			if self.params['sizez'] > fulltomoshape[1]*fullbin :
				self.params['sizez'] = fulltomoshape[1]*fullbin
			subrunname = self.params['subrunname']
			volumeindex = apTomo.getLastVolumeIndex(fulltomodata) + 1
			dimension = {'x':int(self.params['sizex']),'y':int(self.params['sizey']),'z':int(self.params['sizez'])}
			zprojimagedata = fulltomodata['zprojection']
			apDisplay.printMsg("getting pixelsize")
			pixelsize = apTomo.getTomoPixelSize(zprojimagedata) * fullbin * subbin
			gtransform = [1,0,0,1,0,0]
			if self.params['selexonId']:
				particles = apParticle.getParticles(zprojimagedata, self.params['selexonId'])
			if self.params['stackId']:
				particles,stackparticles = apStack.getImageParticles(zprojimagedata, self.params['stackId'])
				stackdata = apStack.getOnlyStackData(self.params['stackId'])
			for p, particle in enumerate(particles):
				print particle['xcoord'],particle['ycoord'],fullbin
				center = apTomo.transformParticleCenter(particle,fullbin,gtransform)
				size = (dimension['x']/fullbin,dimension['y']/fullbin,dimension['z']/fullbin)
				volumename = 'volume%d'% (volumeindex,)
				volumedir = os.path.join(processdir,subrunname+'/',volumename+'/')
				apParam.createDirectory(volumedir)
				apImod.trimVolume(processdir, subrunname,seriesname,volumename,center,offsetz,size,True)
				long_volumename = seriesname+'_'+volumename
				subvolumepath = os.path.join(processdir, runname+"/",volumename+"/",long_volumename+".rec")
				if subbin > 1 or invert:
					apTomo.modifyVolume(subvolumepath,subbin,invert)
				if commit:
					subtomorundata = apTomo.insertSubTomoRun(sessiondata,
							self.params['selexonId'],self.params['stackId'],subrunname,invert,subbin)
					subtomodata = apTomo.insertSubTomogram(fulltomodata,subtomorundata,
							particle,offsetz,dimension,
							volumedir,long_volumename,volumeindex,pixelsize,
							description)
					apTomo.makeMovie(subvolumepath)
					apTomo.makeProjection(subvolumepath)
				volumeindex += 1
	def start(self):
		commit = self.params['commit']
		description = self.params['description']
		processdir = self.params['fulltomodir']
		runname = self.params['runname']
		offsetz = self.params['offsetz']
		subbin = self.params['bin']
		invert = self.params['invert']
		fulltomodata = apTomo.getFullTomoData(self.params['fulltomoId'])
		#subvolume making
		if (self.params['selexonId'] is not None or self.params['stackId']) and fulltomodata is not None:
			sessiondata = fulltomodata['session']
			seriesname = fulltomodata['name'].rstrip('_full')
			fullbin = fulltomodata['bin']
			if not fullbin:
				apDisplay.printWarning("no binning in full tomogram, something is wrong, use alignment bin for now")
				fullbin = fulltomodata['aligner']['alignrun']['bin']
			fulltomopath = os.path.join(fulltomodata['reconrun']['path']['path'], seriesname+"_full.rec")
			fulltomoheader = mrc.readHeaderFromFile(fulltomopath)
			fulltomoshape = fulltomoheader['shape']
			if self.params['sizez'] > fulltomoshape[1]*fullbin :
				self.params['sizez'] = fulltomoshape[1]*fullbin
			subrunname = self.params['subrunname']
			volumeindex = apTomo.getLastVolumeIndex(fulltomodata) + 1
			dimension = {'x':int(self.params['sizex']),'y':int(self.params['sizey']),'z':int(self.params['sizez'])}
			zprojimagedata = fulltomodata['zprojection']
			apDisplay.printMsg("getting pixelsize")
			pixelsize = apTomo.getTomoPixelSize(zprojimagedata) * fullbin * subbin
			gtransform = [1,0,0,1,0,0]
			if self.params['selexonId']:
				particles = apParticle.getParticles(zprojimagedata, self.params['selexonId'])
			if self.params['stackId']:
				particles,stackparticles = apStack.getImageParticles(zprojimagedata, self.params['stackId'])
				stackdata = apStack.getOnlyStackData(self.params['stackId'])
			for p, particle in enumerate(particles):
				print particle['xcoord'],particle['ycoord'],fullbin
				center = apTomo.transformParticleCenter(particle,fullbin,gtransform)
				size = (dimension['x']/fullbin,dimension['y']/fullbin,dimension['z']/fullbin)
				volumename = 'volume%d'% (volumeindex,)
				volumedir = os.path.join(processdir,subrunname+'/',volumename+'/')
				apParam.createDirectory(volumedir)
				apImod.trimVolume(processdir, subrunname,seriesname,volumename,center,offsetz,size,True)
				long_volumename = seriesname+'_'+volumename
				subvolumepath = os.path.join(processdir, runname+"/",volumename+"/",long_volumename+".rec")
				if subbin > 1 or invert:
					apTomo.modifyVolume(subvolumepath,subbin,invert)
				if commit:
					subtomorundata = apTomo.insertSubTomoRun(sessiondata,
							self.params['selexonId'],self.params['stackId'],subrunname,invert,subbin)
					subtomodata = apTomo.insertSubTomogram(fulltomodata,subtomorundata,
							particle,offsetz,dimension,
							volumedir,long_volumename,volumeindex,pixelsize,
							description)
					apTomo.makeMovie(subvolumepath)
					apTomo.makeProjection(subvolumepath)
				volumeindex += 1
	def recon3D(self,particle,volumeindex):
		processdir = self.params['fulltomodir']
		subrunname = self.params['subrunname']
		subbin = self.params['bin']
		invert = self.params['invert']
		gtransform = [1,0,0,1,0,0]
		size = self.getSubTomogramSize()
		volumename = self.setSubVolumePath(volumeindex)
		center = apTomo.transformParticleCenter(particle,self.fullbin,gtransform)
		apImod.trimVolume(processdir, subrunname,self.seriesname,volumename,center,self.params['offsetz'],size,True)
		offsetz = self.getOffsetZ()
		if subbin > 1 or invert:
			apTomo.modifyVolume(self.subvolumepath,subbin,invert)
		return size, self.params['offsetz']
示例#4
0
 def recon3D(self, particle, volumeindex):
     processdir = self.params['fulltomodir']
     subrunname = self.params['subrunname']
     subbin = self.params['bin']
     invert = self.params['invert']
     gtransform = [1, 0, 0, 1, 0, 0]
     size = self.getSubTomogramSize()
     volumename = self.setSubVolumePath(volumeindex)
     center = apTomo.transformParticleCenter(particle, self.fullbin,
                                             gtransform)
     apImod.trimVolume(processdir, subrunname, self.seriesname, volumename,
                       center, self.params['offsetz'], size, True)
     offsetz = self.getOffsetZ()
     if subbin > 1 or invert:
         apTomo.modifyVolume(self.subvolumepath, subbin, invert)
     return size, self.params['offsetz']