def applyBfactor(infile, fscfile, apix, mass=None, outfile=None):
embfactorfile = "embfactor64.exe"
embfactorexe = apParam.getExecPath("embfactor64.exe")
if embfactorexe is None:
apDisplay.printWarning("Could not find %s"%(embfactorfile))
return infile
if outfile is None:
outfile = os.path.splitext(infile)[0]+"-bfactor.mrc"
cmd = embfactorexe
cmd += " -FSC %s"%(fscfile)
cmd += " -sampling %.3f"%(apix)
### this option always failed for me -neil
#if mass is not None:
# cmd += " -molweight %d"%(mass*1000)
cmd += " %s"%(infile)
cmd += " %s"%(outfile)
apParam.runCmd(cmd, package="B-factor", verbose=True, showcmd=True)
if not apVolume.isValidVolume(outfile):
apDisplay.printWarning("B-factor correction failed %s"%(embfactorfile))
return infile
return outfile
def applyBfactor(infile, fscfile, apix, mass=None, outfile=None):
embfactorfile = "embfactor64.exe"
embfactorexe = apParam.getExecPath("embfactor64.exe")
if embfactorexe is None:
apDisplay.printWarning("Could not find %s" % (embfactorfile))
return infile
if outfile is None:
outfile = os.path.splitext(infile)[0] + "-bfactor.mrc"
cmd = embfactorexe
cmd += " -FSC %s" % (fscfile)
cmd += " -sampling %.3f" % (apix)
### this option always failed for me -neil
#if mass is not None:
# cmd += " -molweight %d"%(mass*1000)
cmd += " %s" % (infile)
cmd += " %s" % (outfile)
apParam.runCmd(cmd, package="B-factor", verbose=True, showcmd=True)
if not apVolume.isValidVolume(outfile):
apDisplay.printWarning("B-factor correction failed %s" %
(embfactorfile))
return infile
return outfile
def start(self):
if self.params['method'] == 'any':
### startAny uses class averages
clusterstack, numimages = self.getClusterStack()
else:
### starticos, startoct, startcsym uses individual particles
clusterstack, numimages = self.getClusterParticles()
if self.params['method'] != 'any':
if self.params['numkeep'] is not None and numimages/10 < int(self.params['numkeep']):
apDisplay.printWarning("particle number of "+ self.params['numkeep']
+ " is greater than 10% of the number of selected classes")
elif self.params['numkeep'] is None:
self.params['numkeep'] = int(math.floor(numimages/20.0))+1
apDisplay.printWarning("numkeep was not defined, using %d particles"%(self.params['numkeep']))
nproc = apParam.getNumProcessors()
#construct command for each of the EMAN commonline method
if self.params['method'] == 'any':
startcmd = "startAny "+clusterstack+" proc="+str(nproc)
startcmd +=" sym="+self.symmdata['eman_name']
if self.params['mask'] is not None:
startcmd +=" mask="+str(self.params['mask'])
else:
maskrad = math.floor(self.clusterstackdata['clusterrun']['boxsize']/2.0)
startcmd +=" mask=%d"%(maskrad)
if self.params['rounds'] is not None:
startcmd +=" rounds="+str(self.params['rounds'])
elif self.params['method'] == 'csym':
startcmd = "startcsym "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
startcmd +=" sym="+self.symmdata['eman_name']
if self.params['imask'] is not None:
startcmd +=" imask="+self.params['imask']
elif self.params['method'] == 'oct':
startcmd = "startoct "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
elif self.params['method'] == 'icos':
startcmd = "starticos "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
if self.params['imask'] is not None:
startcmd +=" imask="+self.params['imask']
apDisplay.printMsg("Creating 3D model with EMAN function: start"+self.params['method'])
apFile.removeFile("threed.0a.mrc")
apFile.removeFile("eman.log")
apEMAN.executeEmanCmd(startcmd, verbose=False, logfile="eman.log")
#apEMAN.executeEmanCmd(startcmd, verbose=True)
finalmodelname = "threed-%s-eman_start%s.mrc"%(self.timestamp, self.params['method'])
finalmodelpath = os.path.join(self.params['rundir'], finalmodelname)
apDisplay.printMsg("Final model name: "+finalmodelname)
finalmodel = "threed.0a.mrc"
if os.path.isfile(finalmodel):
emancmd = "proc3d %s %s norm=0,1 origin=0,0,0"%(finalmodel, finalmodelpath)
#shutil.move(finalmodel, finalmodelpath)
apEMAN.executeEmanCmd(emancmd, verbose=True)
if not apVolume.isValidVolume(finalmodelpath):
apDisplay.printError("Created volume is not valid")
else:
apDisplay.printError("No 3d model was created")
### upload it
self.uploadDensity(finalmodelpath)
### chimera imaging
apChimera.renderSnapshots(finalmodelpath, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.symmdata['eman_name'])
apChimera.renderAnimation(finalmodelpath, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.symmdata['eman_name'])
### remove stack
if apFile.stackSize(clusterstack)/1024**2 > 10:
### file bigger than 10MB
apFile.removeStack(clusterstack)
apFile.removeFile("threed.0a.mrc")
def start(self):
if self.params['method'] == 'any':
### startAny uses class averages
clusterstack, numimages = self.getClusterStack()
else:
### starticos, startoct, startcsym uses individual particles
clusterstack, numimages = self.getClusterParticles()
if self.params['method'] != 'any':
if self.params['numkeep'] is not None and numimages/10 < int(self.params['numkeep']):
apDisplay.printWarning("particle number of "+ self.params['numkeep']
+ " is greater than 10% of the number of selected classes")
elif self.params['numkeep'] is None:
self.params['numkeep'] = int(math.floor(numimages/20.0))+1
apDisplay.printWarning("numkeep was not defined, using %d particles"%(self.params['numkeep']))
nproc = apParam.getNumProcessors()
#construct command for each of the EMAN commonline method
if self.params['method'] == 'any':
startcmd = "startAny "+clusterstack+" proc="+str(nproc)
startcmd +=" sym="+self.symmdata['eman_name']
if self.params['mask'] is not None:
startcmd +=" mask="+str(self.params['mask'])
else:
maskrad = math.floor(self.clusterstackdata['clusterrun']['boxsize']/2.0)
startcmd +=" mask=%d"%(maskrad)
if self.params['rounds'] is not None:
startcmd +=" rounds="+str(self.params['rounds'])
elif self.params['method'] == 'csym':
startcmd = "startcsym "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
startcmd +=" sym="+self.symmdata['eman_name']
if self.params['imask'] is not None:
startcmd +=" imask="+self.params['imask']
elif self.params['method'] == 'oct':
startcmd = "startoct "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
elif self.params['method'] == 'icos':
startcmd = "starticos "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
if self.params['imask'] is not None:
startcmd +=" imask="+self.params['imask']
apDisplay.printMsg("Creating 3D model with EMAN function: start"+self.params['method'])
apFile.removeFile("threed.0a.mrc")
apFile.removeFile("eman.log")
apEMAN.executeEmanCmd(startcmd, verbose=False, logfile="eman.log")
#apEMAN.executeEmanCmd(startcmd, verbose=True)
finalmodelname = "threed-%s-eman_start%s.mrc"%(self.timestamp, self.params['method'])
finalmodelpath = os.path.join(self.params['rundir'], finalmodelname)
apDisplay.printMsg("Final model name: "+finalmodelname)
finalmodel = "threed.0a.mrc"
if os.path.isfile(finalmodel):
emancmd = "proc3d %s %s norm=0,1 origin=0,0,0"%(finalmodel, finalmodelpath)
#shutil.move(finalmodel, finalmodelpath)
apEMAN.executeEmanCmd(emancmd, verbose=True)
if not apVolume.isValidVolume(finalmodelpath):
apDisplay.printError("Created volume is not valid")
else:
apDisplay.printError("No 3d model was created")
### upload it
self.uploadDensity(finalmodelpath)
### chimera imaging
apChimera.renderSnapshots(finalmodelpath, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.symmdata['eman_name'])
apChimera.renderAnimation(finalmodelpath, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.symmdata['eman_name'])
### remove stack
if apFile.stackSize(clusterstack)/1024**2 > 10:
### file bigger than 10MB
apFile.removeStack(clusterstack)
apFile.removeFile("threed.0a.mrc")
