def setRunDir(self):
"""
this function only runs if no rundir is defined at the command line
"""
subtomorunq = appiondata.ApSubTomogramRunData()
subtomorundata = subtomorunq.direct_query(self.params['subtomoId'])
subtomoq = appiondata.ApTomogramData(subtomorun=subtomorundata)
results = subtomoq.query(results=1)
if results:
subtomodir = results[0]['path']['path']
tiltdirs = subtomodir.split('/tiltseries')
self.params['rundir'] = os.path.join(tiltdirs[0],"average",self.params['runname'])
def insertSubTomoRun(sessiondata,
selectionrunid,
stackid,
name,
invert=False,
subbin=1):
if selectionrunid:
qpick = appiondata.ApSelectionRunData()
pickdata = qpick.direct_query(selectionrunid)
else:
pickdata = None
if stackid:
qstack = appiondata.ApStackData()
stackdata = qstack.direct_query(stackid)
else:
stackdata = None
qrun = appiondata.ApSubTomogramRunData(session=sessiondata,
pick=pickdata,
stack=stackdata,
runname=name,
invert=invert,
subbin=subbin)
return publish(qrun)
def start(self):
subtomorunq = appiondata.ApSubTomogramRunData()
subtomorundata = subtomorunq.direct_query(self.params['subtomoId'])
volshape, totalbin, pixelsize = apTomo.getSubvolumeInfo(subtomorundata)
if volshape is None:
apDisplay.printError('No subvolume exists for the subtomoId')
sessionname = subtomorundata['session']['name']
stackq = appiondata.ApStackData()
stackdata = stackq.direct_query(self.params['stackId'])
diameter = apStack.getStackParticleDiameter(stackdata)
diameterpixel = diameter * 1e-10 / pixelsize
halfwidth = diameterpixel / 4
ztolerance = halfwidth
zbackgroundrange = max(((volshape[0] - diameterpixel * 3) / 2, 10))
if self.params['commit']:
avgrundata = apTomo.insertTomoAverageRun(
self.params['runname'],
self.params['rundir'],
subtomorundata,
stackdata,
halfwidth,
self.params['description'],
)
profiles = {}
sumvol = numpy.zeros(volshape)
substacktype, conditionstackdata = apStack.findSubStackConditionData(
stackdata)
if substacktype in ['clustersub', 'alignsub']:
alignstack = apStack.getAlignStack(substacktype,
conditionstackdata)
alignpackage = apAlignment.getAlignPackage(alignstack['alignrun'])
stackprtls = apStack.getStackParticlesFromId(stackdata.dbid)
i = 0
for stackp in stackprtls:
alignp = apAlignment.getAlignParticle(stackp, alignstack)
shift = apAlignment.getAlignShift(alignp, alignpackage)
subtomodata = apTomo.getSubTomogramData(subtomorundata, stackp)
subtomofile = os.path.join(subtomodata['path']['path'],
subtomodata['name'] + '.rec')
subvolume = apTomo.getTomoVolume(subtomodata)
if subvolume is not None:
zcenter = volshape[0] / 2
profile = apTomo.getParticleCenterZProfile(
subvolume, shift, halfwidth, zbackgroundrange)
subtomoid = subtomodata.dbid
profiles[subtomoid] = profile
center = apTomo.gaussianCenter(profile)
if center > zcenter - ztolerance and center < zcenter + ztolerance:
i += 1
shiftz = zcenter - center
transformedvolume = apTomo.transformTomo(
subvolume, subtomofile, alignpackage, alignp,
shiftz, totalbin)
## write transformed mrc file to check the result
filename = os.path.join(
self.params['rundir'],
'./transformed%05d.mrc' % subtomoid)
mrc.write(transformedvolume, filename)
sumvol += transformedvolume
t = numpy.sum(transformedvolume, axis=0)
filename = os.path.join(self.params['rundir'],
'./p%05d.mrc' % subtomoid)
mrc.write(transformedvolume, filename)
if self.params['commit']:
apTomo.insertTomoAvgParticle(
avgrundata, subtomodata, alignp, shiftz)
if i < 1:
apDisplay.printError('no subtomogram qualifies for averaging')
else:
avgvol = sumvol / i
avgvolfilename = sessionname + "_" + self.params['runname'] + ".mrc"
avgvolpath = os.path.join(self.params['rundir'], avgvolfilename)
mrc.write(avgvol, avgvolpath)
if not os.path.isfile(avgvolpath):
apDisplay.printError("tomogram not exist")
apTomo.makeMovie(avgvolpath, self.params['maxsize'])
apTomo.makeProjection(avgvolpath, self.params['maxsize'])
proshape = profile.shape
for id in profiles.keys():
out = open('profile_%05d.txt' % id, 'w')
for z in range(0, proshape[0]):
str = "%5d\t" % z
str += "%6.3f\t" % profiles[id][z]
str += "\n"
out.write(str)
out.close()
