def runIMAGICclassify(self):
bfile = "msaclassify.job"
outfile = "classes"
apFile.removeStack(outfile)
numIters = int(self.params['numpart']*self.params['itermult'])
decrement = self.params['start']-self.params['end']
if self.params['iter']>0:
decrement /= float(self.params['iter'])
numClasses = self.params['start']-(decrement*self.params['currentiter'])
stackfile = self.params['alignedstack']
self.params['currentnumclasses'] = numClasses
f = open(bfile,'w')
f.write("#!/bin/csh -f\n")
f.write("setenv IMAGIC_BATCH 1\n")
f.write("%s/msa/classify.e <<EOF\n" % self.imagicroot)
f.write("IMAGES\n")
f.write("%s\n"%stackfile)
f.write("0\n")
f.write("%i\n"%self.params['activeeigen'])
f.write("YES\n")
f.write("%i\n"%numClasses)
f.write("classes_start\n")
f.write("EOF\n")
f.write("%s/msa/classum.e <<EOF\n" % self.imagicroot)
f.write("%s\n"%stackfile)
f.write("classes_start\n")
f.write("%s\n"%outfile)
f.write("YES\n")
f.write("NONE\n")
f.write("0\n")
if int(self.imagicversion) >= 120619:
f.write("NONE\n") # Mode of summing statistics
f.write("EOF\n")
## make eigenimage stack appion-compatible
f.write("proc2d eigenim.hed eigenim.hed inplace\n")
f.write("touch msaclassify_done.txt\n")
f.write("exit\n")
f.close()
## execute the batch file
aligntime0 = time.time()
apEMAN.executeEmanCmd("chmod 755 "+bfile)
apDisplay.printColor("Running IMAGIC .batch file: %s"%(os.path.abspath(bfile)), "cyan")
apIMAGIC.executeImagicBatchFile(os.path.abspath(bfile))
os.remove("msaclassify_done.txt")
if not os.path.exists(outfile+".hed"):
apDisplay.printError("ERROR IN IMAGIC SUBROUTINE")
apDisplay.printColor("finished IMAGIC in "+apDisplay.timeString(time.time()-aligntime0), "cyan")
def start(self):
### get analysis paramteres
self.analysisdata = appiondata.ApAlignAnalysisRunData.direct_query(self.params['analysisId'])
pixelsize = self.analysisdata['alignstack']['pixelsize']
boxsize = self.analysisdata['alignstack']['boxsize']
bin = self.analysisdata['imagicMSArun']['bin']
self.params['apix'] = float(pixelsize) * int(bin)
self.params['boxsize'] = int(boxsize) / int(bin)
self.params['num_particles'] = self.analysisdata['alignstack']['num_particles']
starttime=time.time()
print self.params
print "... stack pixel size: "+str(self.params['apix'])
print "... stack box size: "+str(self.params['boxsize'])
apDisplay.printColor("Running IMAGIC .batch file: See imagicMSAcluster log file(s) corresponding to # of classes for details", "cyan")
### insert run into database
self.insertClusterRun()
### split the cluster numbers
numclasslist = self.params['num_classes'].split(",")
for item in numclasslist:
numclusters = int(item)
apDisplay.printColor("\n==========================\nprocessing class averages for "
+str(numclusters)+" classes\n==========================\n", "green")
### create IMAGIC batch file
batchfile = self.createImagicBatchFile(numclusters)
### execute IMAGIC batch file
clustertime0 = time.time()
proc = subprocess.Popen("chmod 775 "+str(batchfile), shell=True)
proc.wait()
apIMAGIC.executeImagicBatchFile(batchfile)
logfile = open(os.path.join(self.params['rundir'], "imagicMSAcluster_classes_"+str(numclusters)+".log"))
loglines = logfile.readlines()
for line in loglines:
if re.search("ERROR in program", line):
apDisplay.printError("ERROR IN IMAGIC SUBROUTINE, please check the logfile: imagicMSAcluster_classes_"\
+str(numclusters)+".log")
apDisplay.printColor("finished IMAGIC in "+apDisplay.timeString(time.time()-clustertime0), "cyan")
### normalize
classfile = os.path.join(self.params['rundir'], self.params['classumfile'])
emancmd = "proc2d "+classfile+" "+classfile+".norm.hed norm"
while os.path.isfile(classfile+".norm.img"):
apStack.removeStack(alignstack+".norm.img")
apParam.runCmd(emancmd, "EMAN")
os.rename(classfile+".norm.hed", classfile)
os.rename(classfile+".norm.img", classfile[:-4]+".img")
### connect to database
self.insertClusterStack(numclusters)
def start(self):
### get analysis paramteres
self.analysisdata = appiondata.ApAlignAnalysisRunData.direct_query(self.params['analysisId'])
pixelsize = self.analysisdata['alignstack']['pixelsize']
boxsize = self.analysisdata['alignstack']['boxsize']
bin = self.analysisdata['imagicMSArun']['bin']
self.params['apix'] = float(pixelsize) * int(bin)
self.params['boxsize'] = int(boxsize) / int(bin)
self.params['num_particles'] = self.analysisdata['alignstack']['num_particles']
starttime=time.time()
print self.params
print "... stack pixel size: "+str(self.params['apix'])
print "... stack box size: "+str(self.params['boxsize'])
apDisplay.printColor("Running IMAGIC .batch file: See imagicMSAcluster log file(s) corresponding to # of classes for details", "cyan")
### insert run into database
self.insertClusterRun()
### split the cluster numbers
numclasslist = self.params['num_classes'].split(",")
for item in numclasslist:
numclusters = int(item)
apDisplay.printColor("\n==========================\nprocessing class averages for "
+str(numclusters)+" classes\n==========================\n", "green")
### create IMAGIC batch file
batchfile = self.createImagicBatchFile(numclusters)
### execute IMAGIC batch file
clustertime0 = time.time()
proc = subprocess.Popen("chmod 775 "+str(batchfile), shell=True)
proc.wait()
apIMAGIC.executeImagicBatchFile(batchfile)
logfile = open(os.path.join(self.params['rundir'], "imagicMSAcluster_classes_"+str(numclusters)+".log"))
loglines = logfile.readlines()
for line in loglines:
if re.search("ERROR in program", line):
apDisplay.printError("ERROR IN IMAGIC SUBROUTINE, please check the logfile: imagicMSAcluster_classes_"\
+str(numclusters)+".log")
apDisplay.printColor("finished IMAGIC in "+apDisplay.timeString(time.time()-clustertime0), "cyan")
### normalize
classfile = os.path.join(self.params['rundir'], self.params['classumfile'])
emancmd = "proc2d "+classfile+" "+classfile+".norm.hed norm"
while os.path.isfile(classfile+".norm.img"):
apStack.removeStack(alignstack+".norm.img")
apParam.runCmd(emancmd, "EMAN")
os.rename(classfile+".norm.hed", classfile)
os.rename(classfile+".norm.img", classfile[:-4]+".img")
### connect to database
self.insertClusterStack(numclusters)
def runIMAGICmsa(self):
bfile = "msa.job"
outfile = "msaout"
apFile.removeStack(outfile)
stackfile = self.params['alignedstack']
# convert mask to fraction for imagic
maskfrac = self.workingmask*2/self.workingboxsize
## make an msa mask file
imagicFilters.mask2D(self.workingboxsize, maskfrac, maskfile='msamask')
f = open(bfile,'w')
f.write("#!/bin/csh -f\n")
f.write("setenv IMAGIC_BATCH 1\n")
if self.params['msaproc'] > 1:
f.write("mpirun -np %i -x IMAGIC_BATCH %s/msa/msa.e_mpi << EOF\n" %(self.params['msaproc'],self.imagicroot))
if int(self.imagicversion) != 110119:
f.write("YES\n")
f.write("%i\n"%self.params['msaproc'])
else:
f.write("%s/msa/msa.e <<EOF\n" % self.imagicroot)
if int(self.imagicversion) != 110326:
f.write("NO\n")
if int(self.imagicversion) != 110119 and int(self.imagicversion) != 100312:
f.write("NO\n")
f.write("FRESH_MSA\n")
f.write("MODULATION\n")
f.write("%s\n"%stackfile)
if int(self.imagicversion) <= 100312:
f.write("NO\n")
f.write("msamask\n")
f.write("eigenim\n")
if int(self.imagicversion) < 120619:
f.write("my_pixcoos\n")
f.write("my_eigenpix\n")
else:
f.write("NO\n")
f.write("%i\n"%self.params['msaiter'])
f.write("%i\n"%self.params['numeigen'])
if int(self.imagicversion) >= 120619:
f.write("1\n")
f.write("%.02f\n"%self.params['overcorrection'])
f.write("%s\n"%outfile)
f.write("EOF\n")
f.write("touch msa_done.txt\n")
f.write("exit\n")
f.close()
## execute the batch file
aligntime0 = time.time()
apEMAN.executeEmanCmd("chmod 755 "+bfile)
apDisplay.printColor("Running IMAGIC .batch file: %s"%(os.path.abspath(bfile)), "cyan")
apIMAGIC.executeImagicBatchFile(os.path.abspath(bfile))
os.remove("msa_done.txt")
if not os.path.exists(outfile+".plt"):
apDisplay.printError("ERROR IN IMAGIC SUBROUTINE")
apDisplay.printColor("finished IMAGIC in "+apDisplay.timeString(time.time()-aligntime0), "cyan")
## run classification & class averaging
self.runIMAGICclassify()
# align resulting classes
self.alignClasses()
def runIMAGICmra(self):
bfile = "mralign.job"
outfile = "mrastack"
apFile.removeStack(outfile)
f = open(bfile,'w')
f.write("#!/bin/csh -f\n")
f.write("setenv IMAGIC_BATCH 1\n")
if self.params['nproc'] > 1:
f.write("mpirun -np %i -x IMAGIC_BATCH %s/align/mralign.e_mpi << EOF\n" %(self.params['nproc'],self.imagicroot))
if int(self.imagicversion) != 110119:
f.write("YES\n")
f.write("%i\n"%self.params['nproc'])
else:
f.write("%s/align/mralign.e <<EOF\n" % self.imagicroot)
f.write("NO\n")
f.write("FRESH\n")
f.write("ALL\n")
# 091120 or higher version 4D options:
if int(self.imagicversion) >= 91120:
f.write("ALIGNMENT\n")
f.write("ALL\n")
f.write("ROTATION_FIRST\n")
f.write("CCF\n")
f.write(self.params['alignedstack']+"\n")
f.write(outfile+"\n")
f.write(os.path.splitext(self.params['localstack'])[0]+"\n")
f.write(self.params['currentcls']+"\n")
f.write("NO_FILTER\n")
# lower than 091120 version of imagic asks for mirrors:
if int(self.imagicversion) < 91120:
f.write("NO\n")
f.write("0.31\n")
# check if there are any rotations stored in the header
#TEMPORARY HACK
hasRots=False
if self.params['currentiter'] > 1:
hasRots=True
# don't ask Max shift (during this alignment) for first iteration:
if hasRots is True:
f.write("0.2\n")
f.write("-180,180\n")
# don't ask rotation (during this alignment) for first iteration:
if hasRots is True:
f.write("-180,180\n")
f.write("MEDIUM\n")
f.write("0.0,%.2f\n"%(self.workingmask*2/self.workingboxsize))
f.write("2\n")
f.write("NO\n")
f.write("EOF\n")
f.write("\n")
### write out alignment parameters to file
f.write("%s/stand/headers.e <<EOF\n" % self.imagicroot)
if int(self.imagicversion) < 91120:
f.write(outfile+"\n")
f.write("PLT\n")
f.write("SHIFT\n")
f.write("outparams.plt\n")
f.write("*\n")
else:
f.write("PLT\n")
f.write("SHIFT\n")
f.write(outfile+"\n")
f.write("outparams.plt\n")
f.write("EOF\n")
f.write("touch mra_done.txt\n")
f.write("exit\n")
f.close()
## execute the batch file
aligntime0 = time.time()
apEMAN.executeEmanCmd("chmod 755 "+bfile)
apDisplay.printColor("Running IMAGIC .batch file: %s"%(os.path.abspath(bfile)), "cyan")
apIMAGIC.executeImagicBatchFile(os.path.abspath(bfile))
os.remove("mra_done.txt")
if not os.path.exists(outfile+".hed"):
apDisplay.printError("ERROR IN IMAGIC SUBROUTINE")
apDisplay.printColor("finished IMAGIC in "+apDisplay.timeString(time.time()-aligntime0), "cyan")
if self.params['currentiter'] > 1:
apFile.removeStack(self.params['alignedstack'])
self.params['alignedstack']=os.path.abspath(outfile)
self.params['alignedstack'] = string.replace(self.params['alignedstack'],"/jetstor/APPION","")