def start(self):
aligndata = appiondata.ApAlignStackData.direct_query(self.params['alignstackid'])
boxsize = aligndata['boxsize']
apix = aligndata['pixelsize']
maskpixrad = self.params['maskrad']/apix
if maskpixrad*2 > boxsize-2:
apDisplay.printError("Mask radius is too big for boxsize: %d > %d"%(maskpixrad*2,boxsize-2))
apDisplay.printMsg("Mask radius and boxsize: %.1f < %d"%(maskpixrad*2,boxsize-2))
self.instack = os.path.join(aligndata['path']['path'], aligndata['imagicfile'])
outdata = "stack.data"
apXmipp.convertStackToXmippData(self.instack, outdata, maskpixrad,
boxsize, numpart=self.params['numpart']-1)
self.runKerdenSOM(outdata)
if apFile.stackSize(self.instack) > 3.0*(1024**3):
# Big stacks use eman
self.createMontageByEMAN()
binned = None
else:
binned = self.createMontageInMemory(apix)
self.insertKerDenSOM(binned=binned)
apFile.removeFile(outdata)
apFile.removeFilePattern("*.cod")
def centerParticles(stack, mask=None, maxshift=None):
apDisplay.printMsg("Centering stack: "+stack)
stacksize = apFile.stackSize(stack)
freemem = mem.free()*1024 #convert memory to bytes
apDisplay.printMsg("file is %s, mem is %s"
%(apDisplay.bytes(stacksize), apDisplay.bytes(freemem)))
### from EMAN FAQ: need to have at least 3x as much ram as the size of the file
memsize = freemem/3.0
numfrac = int(math.ceil(stacksize/memsize))
apDisplay.printMsg("file is %s, will be split into %d fractions"
%(apDisplay.bytes(stacksize), numfrac))
for i in range(numfrac):
emancmd = "cenalignint "+stack
if numfrac > 1:
emancmd += " frac="+str(i)+"/"+str(numfrac)
if mask is not None:
emancmd += " mask="+str(mask)
if maxshift is not None:
emancmd += " maxshift="+str(maxshift)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
return
def centerParticles(stack, mask=None, maxshift=None):
apDisplay.printMsg("Centering stack: "+stack)
stacksize = apFile.stackSize(stack)
freemem = mem.free()*1024 #convert memory to bytes
apDisplay.printMsg("file is %s, mem is %s"
%(apDisplay.bytes(stacksize), apDisplay.bytes(freemem)))
### from EMAN FAQ: need to have at least 3x as much ram as the size of the file
memsize = freemem/3.0
numfrac = int(math.ceil(stacksize/memsize))
apDisplay.printMsg("file is %s, will be split into %d fractions"
%(apDisplay.bytes(stacksize), numfrac))
for i in range(numfrac):
emancmd = "cenalignint "+stack
if numfrac > 1:
emancmd += " frac="+str(i)+"/"+str(numfrac)
if mask is not None:
emancmd += " mask="+str(mask)
if maxshift is not None:
emancmd += " maxshift="+str(maxshift)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
return
def writeClusterJobFile(self):
if self.params['nproc'] is None:
nproc = 128
else:
nproc = self.params['nproc']
rundir = os.path.join("/lustre/people/vossman/xmippdata", self.params['runname'])
newrundir = "$PBSREMOTEDIR/"
xmippopts = ( " "
+" -i $PBSREMOTEDIR/partlist2.doc "
+" -nref "+str(self.params['numrefs'])
+" -iter "+str(self.params['maxiter'])
+" -o $PBSREMOTEDIR/part"+self.timestamp
+" -psi_step "+str(self.params['psistep'])
)
### fast mode
if self.params['fast'] is True:
xmippopts += " -fast "
if self.params['fastmode'] == "narrow":
xmippopts += " -C 1e-10 "
elif self.params['fastmode'] == "wide":
xmippopts += " -C 1e-18 "
### convergence criteria
if self.params['converge'] == "fast":
xmippopts += " -eps 5e-3 "
elif self.params['converge'] == "slow":
xmippopts += " -eps 5e-8 "
else:
xmippopts += " -eps 5e-5 "
### mirrors
if self.params['mirror'] is True:
xmippopts += " -mirror "
### save mem
if self.params['savemem'] is True:
xmippopts += " -save_memB "
### normalization
if self.params['norm'] is True:
xmippopts += " -norm "
### use student's T distribution
if self.params['student'] is True:
xmippopts += " -student "
### memory needed
numbytes = apFile.stackSize(self.stack['file'])
numgig = math.ceil( numbytes / (1024.0**3) / (self.params['bin']**2) )
### write to file
jobfile = "xmipp-"+self.timestamp+".job"
results = rundir+"/"+self.params['runname']+"-results.tgz"
f = open(jobfile, "w")
f.write("#PBS -l nodes=1:ppn=8\n")
#f.write("#PBS -l nodes="+str(nproc/4)+":ppn=4\n")
f.write("#PBS -l walltime=240:00:00\n")
f.write("#PBS -l cput=240:00:00\n")
f.write("#PBS -l mem=%dgb\n"%(numgig))
f.write("#PBS -r n\n")
f.write("#PBS -k oe\n")
f.write("\n")
f.write("## rundir: "+self.params['rundir']+"\n")
f.write("\n")
f.write("cd "+rundir+"\n")
f.write("/bin/rm -fv pbstempdir "+results+"\n")
f.write("ln -s $PBSREMOTEDIR pbstempdir\n")
f.write("cd $PBSREMOTEDIR\n")
f.write("tar xf "+rundir+"/particles.tar\n")
f.write("\n")
f.write("foreach line ( `cat partlist.sel | cut -f1 -d' '` )\n")
f.write(" echo $PBSREMOTEDIR/`echo $line | sed 's/^.*partfiles/partfiles/'` 1 >> partlist2.doc\n")
f.write("end\n")
f.write("\n")
f.write("setenv MPI_HOME /lustre/people/applications/openmpi-1.2.2/\n")
f.write("setenv XMIPP_HOME /lustre/people/vossman/Xmipp-2.3-src/\n")
f.write("set path = ( $MPI_HOME/bin $path )\n")
f.write("setenv LD_LIBRARY_PATH $MPI_HOME/lib:$XMIPP_HOME/lib:/usr/lib:/lib\n")
f.write("\n")
#f.write("$MPI_HOME/bin/mpirun -np "+str(nproc)+" $XMIPP_HOME/bin/xmipp_mpi_ml_align2d \\\n")
f.write("$MPI_HOME/bin/mpirun -np 8 \\\n")
f.write(" $XMIPP_HOME/bin/xmipp_mpi_ml_align2d -save_memB \\\n")
f.write(" "+xmippopts+"\n")
f.write("\n")
f.write("tar zcf "+results+" *.???\n")
f.write("\n")
f.write("exit\n")
f.close()
query = (
" UPDATE ApMaxLikeJobData "
+" SET `finished` = '1' "
+" WHERE `DEF_id` = '"+str(self.params['maxlikejobid'])+"'"
+"\n"
)
f = open("readyupload.sql", "w")
f.write(query)
f.close()
apDisplay.printMsg("mysql -u usr_object -h database_host ap"+str(self.params['projectid'])+" < readyupload.sql")
apDisplay.printMsg("tar cf particles.tar partlist.sel partfiles/")
apDisplay.printMsg("rsync -vaP "+jobfile+" cluster:"+rundir+"/")
apDisplay.printMsg("rsync -vaP particles.tar cluster:"+rundir+"/")
apDisplay.printColor("ready to run job on cluster", "cyan")
sys.exit(1)
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")