### get all particle data for this iteration
particledata = self.readParticleFile(iteration, reference_number)
self.insertRefinementParticleData(particledata, iterationParamsq,
referenceParamsq)
### create euler freq map
if self.params['commit'] is True:
apDisplay.printMsg("creating euler frequency map")
if self.package != 'EMAN':
postrefine = True
else:
postrefine = False
apEulerDraw.createEulerImages(self.refinerunq.dbid,
iteration,
path=self.params['rundir'],
postrefine=postrefine)
for f in glob.glob("euler**png"):
shutil.move(f, os.path.join(self.resultspath, f))
return
#==================
def insertRefinementParticleData(self,
particledata,
iterationParamsq,
referenceParamsq,
euler_convention='zxz'):
''' inserts all particle data into database, based on parameters from text file '''
apDisplay.printMsg(
def insertIteration(self, iteration):
refineparamsq = appiondata.ApEmanRefineIterData()
refineparamsq['ang'] = iteration['ang']
refineparamsq['lpfilter'] = iteration['lpfilter']
refineparamsq['hpfilter'] = iteration['hpfilter']
refineparamsq['pad'] = iteration['pad']
refineparamsq['EMAN_maxshift'] = iteration['maxshift']
refineparamsq['EMAN_hard'] = iteration['hard']
refineparamsq['EMAN_classkeep'] = iteration['classkeep']
refineparamsq['EMAN_classiter'] = iteration['classiter']
refineparamsq['EMAN_filt3d'] = iteration['filt3d']
refineparamsq['EMAN_shrink'] = iteration['shrink']
refineparamsq['EMAN_euler2'] = iteration['euler2']
refineparamsq['EMAN_xfiles'] = iteration['xfiles']
refineparamsq['EMAN_median'] = iteration['median']
refineparamsq['EMAN_phasecls'] = iteration['phasecls']
refineparamsq['EMAN_fscls'] = iteration['fscls']
refineparamsq['EMAN_refine'] = iteration['refine']
refineparamsq['EMAN_goodbad'] = iteration['goodbad']
refineparamsq['EMAN_perturb'] = iteration['perturb']
refineparamsq['MsgP_cckeep'] = iteration['msgpasskeep']
refineparamsq['MsgP_minptls'] = iteration['msgpassminp']
#create Chimera snapshots
fscfile = os.path.join(self.params['rundir'],
"fsc.eotest." + iteration['num'])
halfres = apRecon.calcRes(fscfile, self.params['boxsize'],
self.params['apix'])
if self.params['snapfilter']:
halfres = self.params['snapfilter']
volumeDensity = 'threed.' + iteration['num'] + 'a.mrc'
volDensPath = os.path.join(self.params['rundir'], volumeDensity)
apChimera.filterAndChimera(volDensPath,
halfres,
self.params['apix'],
self.params['boxsize'],
'snapshot',
self.params['contour'],
self.params['zoom'],
sym=iteration['sym']['eman_name'],
mass=self.params['mass'])
## uncommment this for chimera image only runs...
if self.params['chimeraonly'] is True:
return
# insert resolution data
if halfres != True:
resData = self.getResolutionData(iteration)
else:
apDisplay.printWarning(
"resolution reported as nan, not committing results to database"
)
return
if self.params['package'] == 'EMAN':
refineclassavg = 'classes_eman.' + iteration['num'] + '.img'
postrefineclassavg = None
elif self.params['package'] == 'EMAN/SpiCoran':
refineclassavg = 'classes_eman.' + iteration['num'] + '.img'
postrefineclassavg = 'classes_coran.' + iteration['num'] + '.img'
elif self.params['package'] == 'EMAN/MsgP':
refineclassavg = 'classes_eman.' + iteration['num'] + '.img'
postrefineclassavg = 'classes_msgp.' + iteration['num'] + '.img'
else:
apDisplay.printError("Refinement Package Not Valid")
# insert refinement results
refineq = appiondata.ApRefineIterData()
refineq['refineRun'] = self.params['refineRun']
refineq['emanParams'] = refineparamsq
refineq['iteration'] = iteration['num']
refineq['resolution'] = resData
refineq['rMeasure'] = self.getRMeasureData(iteration)
refineq['mask'] = iteration['mask']
refineq['imask'] = iteration['imask']
refineq['symmetry'] = iteration['sym']
refineq['exemplar'] = False
classvar = 'classes.' + iteration['num'] + '.var.img'
refineq['refineClassAverages'] = refineclassavg
refineq['postRefineClassAverages'] = postrefineclassavg
if classvar in self.params['classvars']:
refineq['classVariance'] = classvar
if volumeDensity in self.params['volumes']:
refineq['volumeDensity'] = volumeDensity
apDisplay.printMsg("inserting Refinement Data into database")
if self.params['commit'] is True:
refineq.insert()
else:
apDisplay.printWarning("not committing results to database")
#insert FSC data
fscfile = os.path.join(self.params['rundir'],
"fsc.eotest." + iteration['num'])
self.insertFSC(fscfile, refineq, self.params['commit'])
halfres = apRecon.calcRes(fscfile, self.params['boxsize'],
self.params['apix'])
apDisplay.printColor("FSC 0.5 Resolution: " + str(halfres), "cyan")
# get projections eulers for iteration:
eulers = self.getEulersFromProj(iteration['num'])
# get list of bad particles for this iteration
badprtls = self.readParticleLog(self.params['rundir'],
iteration['num'])
# expand cls.*.tar into temp file
clsf = os.path.join(self.params['rundir'],
"cls." + iteration['num'] + ".tar")
#print "reading",clsf
clstar = tarfile.open(clsf)
clslist = clstar.getmembers()
clsnames = clstar.getnames()
#print "extracting",clsf,"into temp directory"
for clsfile in clslist:
clstar.extract(clsfile, self.params['tmpdir'])
clstar.close()
# for each class, insert particle alignment info into database
apDisplay.printColor(
"Inserting Particle Classification Data for " +
str(len(clsnames)) + " classes", "magenta")
t0 = time.time()
for cls in clsnames:
self.insertRefineParticleData(cls, iteration, eulers, badprtls,
refineq, len(clsnames))
apDisplay.printColor(
"\nFinished in " + apDisplay.timeString(time.time() - t0),
"magenta")
# remove temp directory
for file in os.listdir(self.params['tmpdir']):
os.remove(os.path.join(self.params['tmpdir'], file))
os.rmdir(self.params['tmpdir'])
#create euler freq map
apDisplay.printMsg("creating euler frequency map")
refrunid = int(self.params['refineRun'].dbid)
iternum = int(iteration['num'])
if self.params['package'] != 'EMAN':
postrefine = True
else:
postrefine = False
apEulerDraw.createEulerImages(refrunid,
iternum,
path=self.params['rundir'],
postrefine=postrefine)
return
apDisplay.printWarning("not committing results to database")
### get all particle data for this iteration
particledata = self.readParticleFile(iteration, reference_number)
self.insertRefinementParticleData(particledata, iterationParamsq, referenceParamsq)
### create euler freq map
if self.params["commit"] is True:
apDisplay.printMsg("creating euler frequency map")
if self.package != "EMAN":
postrefine = True
else:
postrefine = False
apEulerDraw.createEulerImages(
self.refinerunq.dbid, iteration, path=self.params["rundir"], postrefine=postrefine
)
for f in glob.glob("euler**png"):
shutil.move(f, os.path.join(self.resultspath, f))
return
# ==================
def insertRefinementParticleData(self, particledata, iterationParamsq, referenceParamsq, euler_convention="zxz"):
""" inserts all particle data into database, based on parameters from text file """
apDisplay.printMsg("inserting particle data into database ... this may take some time")
for i in range(len(particledata)):
prtlq = appiondata.ApRefineParticleData()
def insertIteration(self, iteration):
refineparamsq=appiondata.ApEmanRefineIterData()
refineparamsq['ang']=iteration['ang']
refineparamsq['lpfilter']=iteration['lpfilter']
refineparamsq['hpfilter']=iteration['hpfilter']
refineparamsq['pad']=iteration['pad']
refineparamsq['EMAN_maxshift']=iteration['maxshift']
refineparamsq['EMAN_hard']=iteration['hard']
refineparamsq['EMAN_classkeep']=iteration['classkeep']
refineparamsq['EMAN_classiter']=iteration['classiter']
refineparamsq['EMAN_filt3d']=iteration['filt3d']
refineparamsq['EMAN_shrink']=iteration['shrink']
refineparamsq['EMAN_euler2']=iteration['euler2']
refineparamsq['EMAN_xfiles']=iteration['xfiles']
refineparamsq['EMAN_median']=iteration['median']
refineparamsq['EMAN_phasecls']=iteration['phasecls']
refineparamsq['EMAN_fscls']=iteration['fscls']
refineparamsq['EMAN_refine']=iteration['refine']
refineparamsq['EMAN_goodbad']=iteration['goodbad']
refineparamsq['EMAN_perturb']=iteration['perturb']
refineparamsq['MsgP_cckeep']=iteration['msgpasskeep']
refineparamsq['MsgP_minptls']=iteration['msgpassminp']
#create Chimera snapshots
fscfile = os.path.join(self.params['rundir'], "fsc.eotest."+iteration['num'])
halfres = apRecon.calcRes(fscfile, self.params['boxsize'], self.params['apix'])
if self.params['snapfilter']:
halfres = self.params['snapfilter']
volumeDensity = 'threed.'+iteration['num']+'a.mrc'
volDensPath = os.path.join(self.params['rundir'], volumeDensity)
apChimera.filterAndChimera(volDensPath, halfres, self.params['apix'],
self.params['boxsize'], 'snapshot', self.params['contour'], self.params['zoom'],
sym=iteration['sym']['eman_name'], mass=self.params['mass'])
## uncommment this for chimera image only runs...
if self.params['chimeraonly'] is True:
return
# insert resolution data
if halfres != True:
resData = self.getResolutionData(iteration)
else:
apDisplay.printWarning("resolution reported as nan, not committing results to database")
return
if self.params['package']== 'EMAN':
refineclassavg='classes_eman.'+iteration['num']+'.img'
postrefineclassavg=None
elif self.params['package']== 'EMAN/SpiCoran':
refineclassavg='classes_eman.'+iteration['num']+'.img'
postrefineclassavg='classes_coran.'+iteration['num']+'.img'
elif self.params['package']== 'EMAN/MsgP':
refineclassavg='classes_eman.'+iteration['num']+'.img'
postrefineclassavg='classes_msgp.'+iteration['num']+'.img'
else:
apDisplay.printError("Refinement Package Not Valid")
# insert refinement results
refineq = appiondata.ApRefineIterData()
refineq['refineRun'] = self.params['refineRun']
refineq['emanParams'] = refineparamsq
refineq['iteration'] = iteration['num']
refineq['resolution'] = resData
refineq['rMeasure'] = self.getRMeasureData(iteration)
refineq['mask'] = iteration['mask']
refineq['imask'] = iteration['imask']
refineq['symmetry']=iteration['sym']
refineq['exemplar'] = False
classvar = 'classes.'+iteration['num']+'.var.img'
refineq['refineClassAverages'] = refineclassavg
refineq['postRefineClassAverages'] = postrefineclassavg
if classvar in self.params['classvars']:
refineq['classVariance'] = classvar
if volumeDensity in self.params['volumes']:
refineq['volumeDensity'] = volumeDensity
apDisplay.printMsg("inserting Refinement Data into database")
if self.params['commit'] is True:
refineq.insert()
else:
apDisplay.printWarning("not committing results to database")
#insert FSC data
fscfile = os.path.join(self.params['rundir'], "fsc.eotest."+iteration['num'])
self.insertFSC(fscfile, refineq, self.params['commit'])
halfres = apRecon.calcRes(fscfile, self.params['boxsize'], self.params['apix'])
apDisplay.printColor("FSC 0.5 Resolution: "+str(halfres), "cyan")
# get projections eulers for iteration:
eulers = self.getEulersFromProj(iteration['num'])
# get list of bad particles for this iteration
badprtls = self.readParticleLog(self.params['rundir'], iteration['num'])
# expand cls.*.tar into temp file
clsf=os.path.join(self.params['rundir'], "cls."+iteration['num']+".tar")
#print "reading",clsf
clstar=tarfile.open(clsf)
clslist=clstar.getmembers()
clsnames=clstar.getnames()
#print "extracting",clsf,"into temp directory"
for clsfile in clslist:
clstar.extract(clsfile,self.params['tmpdir'])
clstar.close()
# for each class, insert particle alignment info into database
apDisplay.printColor("Inserting Particle Classification Data for "
+str(len(clsnames))+" classes", "magenta")
t0 = time.time()
for cls in clsnames:
self.insertRefineParticleData(cls, iteration, eulers, badprtls, refineq, len(clsnames))
apDisplay.printColor("\nFinished in "+apDisplay.timeString(time.time()-t0), "magenta")
# remove temp directory
for file in os.listdir(self.params['tmpdir']):
os.remove(os.path.join(self.params['tmpdir'],file))
os.rmdir(self.params['tmpdir'])
#create euler freq map
apDisplay.printMsg("creating euler frequency map")
refrunid = int(self.params['refineRun'].dbid)
iternum = int(iteration['num'])
if self.params['package'] != 'EMAN':
postrefine = True
else:
postrefine = False
apEulerDraw.createEulerImages(refrunid, iternum, path=self.params['rundir'], postrefine=postrefine)
return