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']
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']