def getParticles(self, zprojimagedata):
'''
start Etomo
insert particles
'''
os.chdir(self.params['fulltomodir'])
proc = subprocess.Popen("etomo --fg %s.edf" % (self.seriesname),
shell=True)
proc.wait()
xrange = apImod.getSubTomoBoundary(self.params['fulltomodir'],
self.seriesname, 'x')
if not len(xrange):
apDisplay.printError(
'Subtomogram coordinate not generated, can not commit to database.'
)
# get subtomogram center from edf log
xmin, xmax = apImod.getSubTomoBoundary(self.params['fulltomodir'],
self.seriesname, 'x')
ymin, ymax = apImod.getSubTomoBoundary(self.params['fulltomodir'],
self.seriesname, 'y')
xcenter = self.fullbin * (xmin + xmax) / 2
ycenter = self.fullbin * (ymin + ymax) / 2
peaktree = [{'xcoord': xcenter, 'ycoord': ycenter, 'peakarea': 1}]
# Use the same selection run name for all subtomogram centers
selectionrunname = zprojimagedata['session']['name'] + '_subtomo'
self.insertCenterSelectionRunData(zprojimagedata['session'],
selectionrunname)
apParticle.insertParticlePeaks(peaktree, zprojimagedata,
selectionrunname)
particles = apParticle.getParticlesForImageFromRunName(
zprojimagedata, selectionrunname)
return [particles[0]]
def getParticles(self,zprojimagedata):
'''
start Etomo
insert particles
'''
os.chdir(self.params['fulltomodir'])
proc = subprocess.Popen("etomo --fg %s.edf" % (self.seriesname), shell=True)
proc.wait()
xrange = apImod.getSubTomoBoundary(self.params['fulltomodir'],self.seriesname,'x')
if not len(xrange):
apDisplay.printError('Subtomogram coordinate not generated, can not commit to database.')
# get subtomogram center from edf log
xmin,xmax = apImod.getSubTomoBoundary(self.params['fulltomodir'],self.seriesname,'x')
ymin,ymax = apImod.getSubTomoBoundary(self.params['fulltomodir'],self.seriesname,'y')
xcenter = self.fullbin * (xmin+xmax) / 2
ycenter = self.fullbin * (ymin+ymax) / 2
peaktree = [{'xcoord':xcenter,'ycoord':ycenter,'peakarea':1}]
# Use the same selection run name for all subtomogram centers
selectionrunname = zprojimagedata['session']['name']+'_subtomo'
self.insertCenterSelectionRunData(zprojimagedata['session'],selectionrunname)
apParticle.insertParticlePeaks(peaktree, zprojimagedata, selectionrunname)
particles = apParticle.getParticlesForImageFromRunName(zprojimagedata,selectionrunname)
return [particles[0]]
def getOffsetZ(self): processdir = self.params['fulltomodir'] zmin,zmax = apImod.getSubTomoBoundary(self.params['fulltomodir'],self.seriesname,'z') offsetz = ((zmax + zmin) - self.fulltomoshape[1] ) / 2 return offsetz
def getOffsetZ(self):
processdir = self.params['fulltomodir']
zmin, zmax = apImod.getSubTomoBoundary(self.params['fulltomodir'],
self.seriesname, 'z')
offsetz = ((zmax + zmin) - self.fulltomoshape[1]) / 2
return offsetz
