def start(self):
tomogram = self.params['rundir']+'/'+self.tomodata['name']+'.rec'
if not os.path.isfile(tomogram):
tomogram = self.params['rundir']+'/'+self.tomodata['name']+'.mrc'
if not os.path.isfile(tomogram):
apDisplay.printError("tomogram not exist")
apTomo.makeMovie(tomogram,self.params['maxsize'])
apTomo.makeProjection(tomogram,self.params['maxsize'])
def start(self):
tomogram = self.params['rundir']+'/'+self.tomodata['name']+'.rec'
if not os.path.isfile(tomogram):
tomogram = self.params['rundir']+'/'+self.tomodata['name']+'.mrc'
if not os.path.isfile(tomogram):
apDisplay.printError("tomogram not exist")
apTomo.makeMovie(tomogram,self.params['maxsize'])
apTomo.makeProjection(tomogram,self.params['maxsize'])
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 start(self):
commit = self.params['commit']
processdir = self.params['fulltomodir']
runname = self.params['runname']
subbin = self.params['bin']
invert = self.params['invert']
self.fulltomodata = apTomo.getFullTomoData(self.params['fulltomoId'])
if self.fulltomodata is None:
return
#subvolume making
self.seriesname = self.fulltomodata['name'].rstrip('_full')
self.fulltomoshape = self.getFullTomoShape()
sessiondata = self.fulltomodata['session']
self.fullbin = self.fulltomodata['bin']
if not self.fullbin:
apDisplay.printWarning(
"no binning in full tomogram, something is wrong, use alignment bin for now"
)
self.fullbin = self.fulltomodata['aligner']['alignrun']['bin']
volumeindex = apTomo.getLastVolumeIndex(self.fulltomodata) + 1
zprojimagedata = self.fulltomodata['zprojection']
apDisplay.printMsg("getting pixelsize")
pixelsize = apTomo.getTomoPixelSize(
zprojimagedata) * self.fullbin * subbin
particles = self.getParticles(zprojimagedata)
for p, particle in enumerate(particles):
size, offsetz = self.recon3D(particle, volumeindex)
volumedir = os.path.dirname(self.subvolumepath)
# not include .rec
long_volumename = os.path.basename(self.subvolumepath)[:-4]
# size is the subtomogram dimension tuple after full tomogram binning
if commit:
subtomorundata = apTomo.insertSubTomoRun(
sessiondata, self.getParticleSelectionRunId(),
self.getStackId(), self.params['subrunname'], invert,
subbin)
description = self.updateDescription()
subtomodata = apTomo.insertSubTomogram(
self.fulltomodata, subtomorundata, particle, offsetz, {
'x': size[0],
'y': size[1],
'z': size[2]
}, volumedir, long_volumename, volumeindex, pixelsize,
description)
apTomo.makeMovie(self.subvolumepath)
apTomo.makeProjection(self.subvolumepath)
volumeindex += 1
def start(self):
commit = self.params['commit']
processdir = self.params['fulltomodir']
runname = self.params['runname']
subbin = self.params['bin']
invert = self.params['invert']
self.fulltomodata = apTomo.getFullTomoData(self.params['fulltomoId'])
if self.fulltomodata is None:
return
#subvolume making
self.seriesname = self.fulltomodata['name'].rstrip('_full')
self.fulltomoshape = self.getFullTomoShape()
sessiondata = self.fulltomodata['session']
self.fullbin = self.fulltomodata['bin']
if not self.fullbin:
apDisplay.printWarning("no binning in full tomogram, something is wrong, use alignment bin for now")
self.fullbin = self.fulltomodata['aligner']['alignrun']['bin']
volumeindex = apTomo.getLastVolumeIndex(self.fulltomodata) + 1
zprojimagedata = self.fulltomodata['zprojection']
apDisplay.printMsg("getting pixelsize")
pixelsize = apTomo.getTomoPixelSize(zprojimagedata) * self.fullbin * subbin
particles = self.getParticles(zprojimagedata)
for p, particle in enumerate(particles):
size,offsetz = self.recon3D(particle,volumeindex)
volumedir = os.path.dirname(self.subvolumepath)
# not include .rec
long_volumename = os.path.basename(self.subvolumepath)[:-4]
# size is the subtomogram dimension tuple after full tomogram binning
if commit:
subtomorundata = apTomo.insertSubTomoRun(sessiondata,
self.getParticleSelectionRunId(),self.getStackId(),self.params['subrunname'],invert,subbin)
description = self.updateDescription()
subtomodata = apTomo.insertSubTomogram(self.fulltomodata,subtomorundata,
particle,offsetz,{'x':size[0],'y':size[1],'z':size[2]},
volumedir,long_volumename,volumeindex,pixelsize,
description)
apTomo.makeMovie(self.subvolumepath)
apTomo.makeProjection(self.subvolumepath)
volumeindex += 1
def start(self):
cleanlist = []
# imod needs the recon files named as .rec It may need some fix later
if self.params["name"] is None:
self.setNewFileName()
apDisplay.printColor("Naming tomogram as: " + self.params["name"], "cyan")
newtomopath = os.path.join(self.params["rundir"], self.params["name"] + ".rec")
origtomopath = self.params["file"]
origxfpath = self.params["oldxffile"]
apParam.createDirectory(self.params["aligndir"])
newxfpath = os.path.join(self.params["aligndir"], self.params["newxffile"])
order = self.params["order"]
voltransform = self.params["transform"]
bin = self.params["bin"]
self.getImageShapeFromTiltSeries()
self.getOriginalVolumeShape()
if os.path.isfile(newtomopath):
uploaded_before = self.checkExistingFile()
if uploaded_before:
return
else:
currenttomopath = origtomopath
if self.params["full"]:
### full tomogram upload, may need to pad to the image size
if self.params["order"] == "XZY" and not voltransform:
apDisplay.printMsg("Default full tomogram orientation with original handness")
else:
if voltransform:
apDisplay.printMsg("Transforming original tomogram....")
currenttomopath = apImod.transformVolume(origtomopath, voltransform)
cleanlist.append(currenttomopath)
### padding the XZY tomogram to the image size
currentheader = mrc.readHeaderFromFile(currenttomopath)
currentshape = currentheader["shape"]
currentxyshape = currentshape[0], currentshape[2]
imageshape = self.imageshape
if currentxyshape[0] < imageshape[0] / bin or currentxyshape[1] < imageshape[1] / bin:
currenttomopath = apImod.pad(currenttomopath, currentxyshape, imageshape, bin, "XZY")
cleanlist.append(currenttomopath)
else:
### subtomogram simple upload, just copy file to Tomo folder
if self.params["order"] == "XYZ" and not voltransform:
apDisplay.printMsg("Default sub tomogram orientation")
else:
if voltransform:
apDisplay.printMsg("Transforming original tomogram....")
currenttomopath = apImod.transformVolume(origtomopath, voltransform)
cleanlist.append(currenttomopath)
### simple upload, just copy file to Tomo folder
apDisplay.printMsg("Copying original tomogram to a new location: " + newtomopath)
shutil.copyfile(currenttomopath, newtomopath)
if origxfpath and os.path.isfile(origxfpath):
apDisplay.printMsg("Copying original alignment to a new location: " + newxfpath)
shutil.copyfile(origxfpath, newxfpath)
if self.params["image"]:
shutil.copyfile(self.params["image"], self.params["rundir"] + "/snapshot.png")
### inserting tomogram
tomoheader = mrc.readHeaderFromFile(newtomopath)
self.params["shape"] = tomoheader["shape"]
if self.params["full"]:
seriesname = "%s_%03d" % (self.params["sessionname"], self.params["tiltseriesnumber"])
self.params["zprojfile"] = apImod.projectFullZ(
self.params["rundir"], self.params["runname"], seriesname, bin, True, False
)
else:
apTomo.makeMovie(newtomopath)
apTomo.makeProjection(newtomopath)
apTomo.uploadTomo(self.params)
### clean up
for tmpfilepath in cleanlist:
apFile.removeFile(tmpfilepath)
def start(self):
cleanlist = []
# imod needs the recon files named as .rec It may need some fix later
if self.params['name'] is None:
self.setNewFileName()
apDisplay.printColor("Naming tomogram as: " + self.params['name'],
"cyan")
newtomopath = os.path.join(self.params['rundir'],
self.params['name'] + ".rec")
origtomopath = self.params['file']
origxfpath = self.params['oldxffile']
apParam.createDirectory(self.params['aligndir'])
newxfpath = os.path.join(self.params['aligndir'],
self.params['newxffile'])
order = self.params['order']
voltransform = self.params['transform']
bin = self.params['bin']
self.getImageShapeFromTiltSeries()
self.getOriginalVolumeShape()
if os.path.isfile(newtomopath):
uploaded_before = self.checkExistingFile()
if uploaded_before:
return
else:
currenttomopath = origtomopath
if self.params['full']:
### full tomogram upload, may need to pad to the image size
if self.params['order'] == 'XZY' and not voltransform:
apDisplay.printMsg(
"Default full tomogram orientation with original handness"
)
else:
if voltransform:
apDisplay.printMsg(
"Transforming original tomogram....")
currenttomopath = apImod.transformVolume(
origtomopath, voltransform)
cleanlist.append(currenttomopath)
### padding the XZY tomogram to the image size
currentheader = mrc.readHeaderFromFile(currenttomopath)
currentshape = currentheader['shape']
currentxyshape = currentshape[0], currentshape[2]
imageshape = self.imageshape
if currentxyshape[0] < imageshape[0] / bin or currentxyshape[
1] < imageshape[1] / bin:
currenttomopath = apImod.pad(currenttomopath,
currentxyshape, imageshape,
bin, 'XZY')
cleanlist.append(currenttomopath)
else:
### subtomogram simple upload, just copy file to Tomo folder
if self.params['order'] == 'XYZ' and not voltransform:
apDisplay.printMsg("Default sub tomogram orientation")
else:
if voltransform:
apDisplay.printMsg(
"Transforming original tomogram....")
currenttomopath = apImod.transformVolume(
origtomopath, voltransform)
cleanlist.append(currenttomopath)
### simple upload, just copy file to Tomo folder
apDisplay.printMsg(
"Copying original tomogram to a new location: " + newtomopath)
shutil.copyfile(currenttomopath, newtomopath)
if origxfpath and os.path.isfile(origxfpath):
apDisplay.printMsg(
"Copying original alignment to a new location: " +
newxfpath)
shutil.copyfile(origxfpath, newxfpath)
if self.params['image']:
shutil.copyfile(self.params['image'],
self.params['rundir'] + '/snapshot.png')
### inserting tomogram
tomoheader = mrc.readHeaderFromFile(newtomopath)
self.params['shape'] = tomoheader['shape']
if self.params['full']:
seriesname = "%s_%03d" % (self.params['sessionname'],
self.params['tiltseriesnumber'])
self.params['zprojfile'] = apImod.projectFullZ(
self.params['rundir'], self.params['runname'], seriesname, bin,
True, False)
else:
apTomo.makeMovie(newtomopath)
apTomo.makeProjection(newtomopath)
apTomo.uploadTomo(self.params)
### clean up
for tmpfilepath in cleanlist:
apFile.removeFile(tmpfilepath)
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()
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()
