def runRmeasure(self, volfile):
emancmd = "proc3d %s %s"%(volfile, "rmeasure.mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
apix = apStack.getStackPixelSizeFromStackId(self.params['tiltstackid'])*self.params['tiltbin']
self.rmeasureresolution = apRecon.runRMeasure(apix, "rmeasure.mrc")
#apDisplay.printColor("Final Rmeasure resolution: "+str(self.rmeasureresolution), "cyan")
apFile.removeFile("rmeasure.mrc")
def runRmeasure(self):
finalrawvolfile = os.path.join(self.params['rundir'], "rawvolume%s-%03d.spi"%(self.timestamp, self.params['numiters']))
emancmd = "proc3d %s %s"%(finalrawvolfile, "rmeasure.mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
apix = apStack.getStackPixelSizeFromStackId(self.params['tiltstackid'])*self.params['tiltbin']
self.rmeasureresolution = apRecon.runRMeasure(apix, "rmeasure.mrc")
#apDisplay.printColor("Final Rmeasure resolution: "+str(self.rmeasureresolution), "cyan")
apFile.removeFile("rmeasure.mrc")
def runRmeasure(self):
finalrawvolfile = os.path.join(
self.params['rundir'],
"rawvolume%s-%03d.spi" % (self.timestamp, self.params['numiters']))
emancmd = "proc3d %s %s" % (finalrawvolfile, "rmeasure.mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
apix = apStack.getStackPixelSizeFromStackId(
self.params['tiltstackid']) * self.params['tiltbin']
self.rmeasureresolution = apRecon.runRMeasure(apix, "rmeasure.mrc")
#apDisplay.printColor("Final Rmeasure resolution: "+str(self.rmeasureresolution), "cyan")
apFile.removeFile("rmeasure.mrc")
def getRMeasureData(self, volumeDensity):
volPath = os.path.join(self.params['rundir'], volumeDensity)
if not os.path.exists(volPath):
apDisplay.printWarning("R Measure failed, volume density not found: "+volPath)
return None
resolution = apRecon.runRMeasure(self.apix, volPath)
if resolution is None:
return None
rmesq = appiondata.ApRMeasureData()
rmesq['volume']=os.path.basename(volumeDensity)
rmesq['rMeasure']=resolution
return rmesq
def getRMeasureData(self, volumeDensity):
volPath = os.path.join(self.params['rundir'], volumeDensity)
if not os.path.exists(volPath):
apDisplay.printWarning("R Measure failed, volume density not found: "+volPath)
return None
resolution = apRecon.runRMeasure(self.apix, volPath)
if resolution is None:
return None
rmesq = appiondata.ApRMeasureData()
rmesq['volume']=os.path.basename(volumeDensity)
rmesq['rMeasure']=resolution
return rmesq
def getRMeasureData(self, iteration):
volumeDensity='threed.'+iteration['num']+'a.mrc'
volPath = os.path.join(self.params['rundir'], volumeDensity)
if not os.path.exists(volPath):
apDisplay.printWarning("R Measure failed, volume density not found: "+volPath)
return None
resolution = apRecon.runRMeasure(self.params['apix'], volPath)
if resolution is None:
return None
rmesq=appiondata.ApRMeasureData()
rmesq['volume']=volumeDensity
rmesq['rMeasure']=resolution
return rmesq
def getRMeasureData(self, iteration, reference_number=1):
''' run rMeasure resolution and return database object '''
volumeDensity = os.path.join(self.resultspath, "recon_%s_it%.3d_vol%.3d.mrc" \
% (self.params['timestamp'], iteration, reference_number))
if not os.path.exists(volumeDensity):
apDisplay.printWarning("R Measure failed, volume density not found: "+volumeDensity)
return None
resolution = apRecon.runRMeasure(self.runparams['apix'], volumeDensity)
if resolution is None:
return None
### database object
rmesq = appiondata.ApRMeasureData()
rmesq['volume'] = "recon_%s_it%.3d_vol%.3d.mrc" % (self.params['timestamp'], iteration, reference_number)
rmesq['rMeasure'] = resolution
return rmesq
def getRMeasureData(self, iteration, reference_number=1):
''' run rMeasure resolution and return database object '''
volumeDensity = os.path.join(self.resultspath, "recon_%s_it%.3d_vol%.3d.mrc" \
% (self.params['timestamp'], iteration, reference_number))
if not os.path.exists(volumeDensity):
apDisplay.printWarning(
"R Measure failed, volume density not found: " + volumeDensity)
return None
resolution = apRecon.runRMeasure(self.runparams['apix'], volumeDensity)
if resolution is None:
return None
### database object
rmesq = appiondata.ApRMeasureData()
rmesq['volume'] = "recon_%s_it%.3d_vol%.3d.mrc" % (
self.params['timestamp'], iteration, reference_number)
rmesq['rMeasure'] = resolution
return rmesq
def start(self):
self.params['outputstack'] = os.path.join(self.params['rundir'],
self.params['stackname'])
particles, self.params['refineiter'] = getParticleInfo(
self.params['reconid'], self.params['iter'])
stackdata = particles[0]['particle']['stack']
stack = os.path.join(stackdata['path']['path'], stackdata['name'])
classes, cstats = determineClasses(particles)
rejectlst = []
if self.params['sigma'] is not None:
cutoff = cstats[
'meanquality'] + self.params['sigma'] * cstats['stdquality']
apDisplay.printMsg("Cutoff = " + str(cutoff))
rejectlst = self.removePtclsByQualityFactor(
particles, rejectlst, cutoff)
if self.params['avgjump'] is not None:
rejectlst = self.removePtclsByJumps(particles, rejectlst)
if self.params['rejectlst']:
rejectlst = removePtclsByLst(rejectlst, self.params)
classkeys = classes.keys()
classkeys.sort()
classnum = 0
totalptcls = 0
keepfile = open('keep.lst', 'w')
keepfile.write('#LST\n')
reject = open('reject.lst', 'w')
reject.write('#LST\n')
apDisplay.printMsg("Processing classes")
#loop through classes
for key in classkeys:
# file to hold particles of this class
clsfile = open('clstmp.lst', 'w')
clsfile.write('#LST\n')
classnum += 1
if classnum % 10 == 1:
apDisplay.printMsg(
str(classnum) + " of " + (str(len(classkeys))))
images = EMAN.EMData()
#loop through particles in class
nptcls = 0
for ptcl in classes[key]['particles']:
if ptcl['mirror']:
mirror = 1
else:
mirror = 0
rot = ptcl['euler3']
rot = rot * math.pi / 180
if ptcl['particle']['particleNumber'] not in rejectlst:
l = '%d\t%s\t%f,\t%f,%f,%f,%d\n' % (
ptcl['particle']['particleNumber'] - 1, stack,
ptcl['quality_factor'], rot, ptcl['shiftx'],
ptcl['shifty'], mirror)
keepfile.write(l)
clsfile.write(l)
totalptcls += 1
nptcls += 1
else:
reject.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' %
(ptcl['particle']['particleNumber'] - 1,
stack, ptcl['quality_factor'], rot,
ptcl['shiftx'], ptcl['shifty'], mirror))
#if ptcl['quality_factor']>cstats['meanquality']+3*cstats['stdquality']:
# high.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' % (ptcl['particle']['particleNumber']-1,
# stack,ptcl['quality_factor'],rot,ptcl['shiftx'],ptcl['shifty'],mirror))
clsfile.close()
if nptcls < 1:
continue
if self.params['skipavg'] is False:
makeClassAverages('clstmp.lst', self.params['outputstack'],
classes[key], self.params)
if self.params['eotest'] is True:
self.makeEvenOddClasses('clstmp.lst', classes[key])
apDisplay.printMsg("\n")
reject.close()
keepfile.close()
os.remove('clstmp.lst')
# make 3d density file if specified:
if self.params['make3d'] is not None:
self.params['make3d'] = os.path.basename(self.params['make3d'])
outfile = os.path.join(self.params['rundir'],
self.params['make3d'])
apEMAN.make3d(self.params['stackname'],
outfile,
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.executeEmanCmd("proc3d %s %s mask=%d norm" %
(outfile, outfile, self.params['mask']))
if self.params['eotest'] is True:
apEMAN.make3d(self.params['oddstack'],
"odd.mrc",
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.make3d(self.params['evenstack'],
"even.mrc",
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.executeEmanCmd("proc3d odd.mrc even.mrc fsc=fsc.eotest")
if os.path.exists(outfile):
# run rmeasure
apix = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
box = apVolume.getModelDimensions(outfile)
apDisplay.printMsg('inserting density into database')
symdata = apSymmetry.findSymmetry(self.params['sym'])
if not symdata:
apDisplay.printError('no symmetry associated with this model')
modq = appiondata.Ap3dDensityData()
modq['session'] = apStack.getSessionDataFromStackId(
self.params['stackid'])
modq['name'] = self.params['make3d']
modq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
modq['boxsize'] = box
modq['mask'] = self.params['mask']
modq['pixelsize'] = apix
fscres = apRecon.getResolutionFromFSCFile('fsc.eotest',
box,
apix,
msg=True)
modq['resolution'] = fscres
modq['rmeasure'] = apRecon.runRMeasure(apix, outfile)
modq['md5sum'] = apFile.md5sumfile(outfile)
modq['maxjump'] = self.params['avgjump']
modq['sigma'] = self.params['sigma']
modq['hard'] = self.params['hard']
modq['symmetry'] = symdata
modq['refineIter'] = self.params['refineiter']
if self.params['commit'] is True:
modq.insert()
apChimera.filterAndChimera(outfile,
res=fscres,
apix=apix,
box=box,
chimtype='snapshot',
zoom=self.params['zoom'],
sym=self.params['sym'],
mass=self.params['mass'])
else:
apDisplay.printError(
'no 3d volume was generated - check the class averages:')
apDisplay.printError(self.params['stackname'])
apDisplay.printError(
'hard may be set too high, or avg euler jump set too low for the # of particles'
)
stackstr = str(stackdata.dbid)
reconstr = str(self.params['reconid'])
apDisplay.printColor(
"Make a new stack with only non-jumpers:\n" +
"subStack.py --projectid=" + str(self.params['projectid']) +
" -s " + stackstr + " \\\n " + " -k " +
os.path.join(self.params['rundir'], "keep.lst") + " \\\n " +
" -d 'recon " + reconstr + " sitters' -n sitters" + reconstr +
" -C ", "purple")
def start(self):
self.params["outputstack"] = os.path.join(self.params["rundir"], self.params["stackname"])
particles, self.params["refineiter"] = getParticleInfo(self.params["reconid"], self.params["iter"])
stackdata = particles[0]["particle"]["stack"]
stack = os.path.join(stackdata["path"]["path"], stackdata["name"])
classes, cstats = determineClasses(particles)
rejectlst = []
if self.params["sigma"] is not None:
cutoff = cstats["meanquality"] + self.params["sigma"] * cstats["stdquality"]
apDisplay.printMsg("Cutoff = " + str(cutoff))
rejectlst = self.removePtclsByQualityFactor(particles, rejectlst, cutoff)
if self.params["avgjump"] is not None:
rejectlst = self.removePtclsByJumps(particles, rejectlst)
if self.params["rejectlst"]:
rejectlst = removePtclsByLst(rejectlst, self.params)
classkeys = classes.keys()
classkeys.sort()
classnum = 0
totalptcls = 0
keepfile = open("keep.lst", "w")
keepfile.write("#LST\n")
reject = open("reject.lst", "w")
reject.write("#LST\n")
apDisplay.printMsg("Processing classes")
# loop through classes
for key in classkeys:
# file to hold particles of this class
clsfile = open("clstmp.lst", "w")
clsfile.write("#LST\n")
classnum += 1
if classnum % 10 == 1:
apDisplay.printMsg(str(classnum) + " of " + (str(len(classkeys))))
images = EMAN.EMData()
# loop through particles in class
nptcls = 0
for ptcl in classes[key]["particles"]:
if ptcl["mirror"]:
mirror = 1
else:
mirror = 0
rot = ptcl["euler3"]
rot = rot * math.pi / 180
if ptcl["particle"]["particleNumber"] not in rejectlst:
l = "%d\t%s\t%f,\t%f,%f,%f,%d\n" % (
ptcl["particle"]["particleNumber"] - 1,
stack,
ptcl["quality_factor"],
rot,
ptcl["shiftx"],
ptcl["shifty"],
mirror,
)
keepfile.write(l)
clsfile.write(l)
totalptcls += 1
nptcls += 1
else:
reject.write(
"%d\t%s\t%f,\t%f,%f,%f,%d\n"
% (
ptcl["particle"]["particleNumber"] - 1,
stack,
ptcl["quality_factor"],
rot,
ptcl["shiftx"],
ptcl["shifty"],
mirror,
)
)
# if ptcl['quality_factor']>cstats['meanquality']+3*cstats['stdquality']:
# high.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' % (ptcl['particle']['particleNumber']-1,
# stack,ptcl['quality_factor'],rot,ptcl['shiftx'],ptcl['shifty'],mirror))
clsfile.close()
if nptcls < 1:
continue
if self.params["skipavg"] is False:
makeClassAverages("clstmp.lst", self.params["outputstack"], classes[key], self.params)
if self.params["eotest"] is True:
self.makeEvenOddClasses("clstmp.lst", classes[key])
apDisplay.printMsg("\n")
reject.close()
keepfile.close()
os.remove("clstmp.lst")
# make 3d density file if specified:
if self.params["make3d"] is not None:
self.params["make3d"] = os.path.basename(self.params["make3d"])
outfile = os.path.join(self.params["rundir"], self.params["make3d"])
apEMAN.make3d(
self.params["stackname"],
outfile,
sym=self.params["sym"],
mode=self.params["mode"],
hard=self.params["hard"],
)
apEMAN.executeEmanCmd("proc3d %s %s mask=%d norm" % (outfile, outfile, self.params["mask"]))
if self.params["eotest"] is True:
apEMAN.make3d(
self.params["oddstack"],
"odd.mrc",
sym=self.params["sym"],
mode=self.params["mode"],
hard=self.params["hard"],
)
apEMAN.make3d(
self.params["evenstack"],
"even.mrc",
sym=self.params["sym"],
mode=self.params["mode"],
hard=self.params["hard"],
)
apEMAN.executeEmanCmd("proc3d odd.mrc even.mrc fsc=fsc.eotest")
if os.path.exists(outfile):
# run rmeasure
apix = apStack.getStackPixelSizeFromStackId(self.params["stackid"])
box = apVolume.getModelDimensions(outfile)
apDisplay.printMsg("inserting density into database")
symdata = apSymmetry.findSymmetry(self.params["sym"])
if not symdata:
apDisplay.printError("no symmetry associated with this model")
modq = appiondata.Ap3dDensityData()
modq["session"] = self.params["sessionname"]
modq["name"] = self.params["make3d"]
modq["path"] = appiondata.ApPathData(path=os.path.abspath(self.params["rundir"]))
modq["boxsize"] = box
modq["mask"] = self.params["mask"]
modq["pixelsize"] = apix
fscres = apRecon.getResolutionFromFSCFile("fsc.eotest", box, apix, msg=True)
modq["resolution"] = fscres
modq["rmeasure"] = apRecon.runRMeasure(apix, outfile)
modq["md5sum"] = apFile.md5sumfile(outfile)
modq["maxjump"] = self.params["avgjump"]
modq["sigma"] = self.params["sigma"]
modq["hard"] = self.params["hard"]
modq["symmetry"] = symdata
modq["refineIter"] = self.params["refineiter"]
if self.params["commit"] is True:
modq.insert()
apChimera.filterAndChimera(
outfile,
res=fscres,
apix=apix,
box=box,
chimtype="snapshot",
zoom=self.params["zoom"],
sym=self.params["sym"],
mass=self.params["mass"],
)
else:
apDisplay.printError("no 3d volume was generated - check the class averages:")
apDisplay.printError(self.params["stackname"])
apDisplay.printError("hard may be set too high, or avg euler jump set too low for the # of particles")
stackstr = str(stackdata.dbid)
reconstr = str(self.params["reconid"])
apDisplay.printColor(
"Make a new stack with only non-jumpers:\n"
+ "subStack.py --projectid="
+ str(self.params["projectid"])
+ " -s "
+ stackstr
+ " \\\n "
+ " -k "
+ os.path.join(self.params["rundir"], "keep.lst")
+ " \\\n "
+ " -d 'recon "
+ reconstr
+ " sitters' -n sitters"
+ reconstr
+ " -C ",
"purple",
)
