def getParticlesInImage(self, imgdata):
if self.params['defocpair'] is True and self.params[
'selectionid'] is not None:
# using defocal pairs and particle picks
partdatas, shiftdata = apParticle.getDefocPairParticles(
imgdata, self.params['selectionid'],
self.params['particlelabel'])
elif self.params['fromstackid'] is not None:
# using previous stack to make a new stack
fromstackdata = appiondata.ApStackData.direct_query(
self.params['fromstackid'])
partdatas, shiftdata = self.getParticlesFromStack(
fromstackdata,
imgdata,
self.params['defocpair'],
)
else:
# using particle picks
partdatas = apParticle.getParticles(imgdata,
self.params['selectionid'],
self.params['particlelabel'])
shiftdata = {'shiftx': 0, 'shifty': 0, 'scale': 1}
apDisplay.printMsg("Found %d particles" % (len(partdatas)))
### apply correlation limits
if self.params['correlationmin'] or self.params['correlationmax']:
partdatas = self.eliminateMinMaxCCParticles(partdatas)
### apply masks
if self.params['checkmask']:
partdatas = self.eliminateMaskedParticles(partdatas, imgdata)
return partdatas, shiftdata
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 getParticlePicks(self, imgdata):
particles = []
if self.params['pickrunids'] is not None:
self.params['pickrunidlist'] = self.params['pickrunids'].split(",")
for pickrunid in self.params['pickrunidlist']:
newparticles = apParticle.getParticles(imgdata, pickrunid)
particles.extend(newparticles)
targets = self.particlesToTargets(particles)
#apDisplay.printMsg("Found "+str(len(targets))+" particles for image "+apDisplay.short(imgdata['filename']))
return targets
def getParticlePicks(self, imgdata):
particles = []
if self.params['pickrunids'] is not None:
self.params['pickrunidlist'] = self.params['pickrunids'].split(",")
for pickrunid in self.params['pickrunidlist']:
newparticles = apParticle.getParticles(imgdata, pickrunid)
particles.extend(newparticles)
targets = self.particlesToTargets(particles)
#apDisplay.printMsg("Found "+str(len(targets))+" particles for image "+apDisplay.short(imgdata['filename']))
return targets
def getParticlePicks(self, imgdata): if not self.params['pickrunid']: if not self.params['pickrunname']: return [] self.params['pickrunid'] = apParticle.getSelectionRun(imgdata, self.params['pickrunname']) if not self.params['pickrunname']: rundata = apParticle.getSelectionRunDataFromID(self.params['pickrunid']) self.params['pickrunname'] = rundata['name'] particles = apParticle.getParticles(imgdata, self.params['pickrunid']) targets = self.particlesToTargets(particles) return targets
def getParticlesInImage(self,imgdata):
if self.params['defocpair'] is True and self.params['selectionid'] is not None:
# using defocal pairs and particle picks
partdatas, shiftdata = apParticle.getDefocPairParticles(imgdata, self.params['selectionid'], self.params['particlelabel'])
elif self.params['fromstackid'] is not None:
# using previous stack to make a new stack
fromstackdata = appiondata.ApStackData.direct_query(self.params['fromstackid'])
partdatas, shiftdata = self.getParticlesFromStack(fromstackdata,imgdata,self.params['defocpair'],)
else:
# using particle picks
partdatas = apParticle.getParticles(imgdata, self.params['selectionid'], self.params['particlelabel'])
shiftdata = {'shiftx':0, 'shifty':0, 'scale':1}
apDisplay.printMsg("Found %d particles"%(len(partdatas)))
### apply correlation limits
if self.params['correlationmin'] or self.params['correlationmax']:
partdatas = self.eliminateMinMaxCCParticles(partdatas)
### apply masks
if self.params['checkmask']:
partdatas = self.eliminateMaskedParticles(partdatas, imgdata)
return partdatas,shiftdata
def getParticles(self,zprojimagedata): '''Return a list of ApParticleData for reconstruction''' return apParticle.getParticles(zprojimagedata, self.params['selexonId'])
def getParticles(self, zprojimagedata):
'''Return a list of ApParticleData for reconstruction'''
return apParticle.getParticles(zprojimagedata,
self.params['selexonId'])
