def alignClasses(self):
classname = "classes"
# using IMAGIC to align references
# center the particles
if self.params['mramethod'] == "imagic":
#imagic centering doesn't work as well as EMAN's unfortunately
#cenfile = imagicAlignment.alimass(classname+".hed", maxshift=0.15, ceniter=10, nproc=1)
aligntime0 = time.time()
# convert mask to fraction for imagic
maskfrac = self.workingmask*2/self.workingboxsize
# don't align references for last iteration
if self.params['currentiter'] < self.params['iter']:
if self.params['classiter'] is True:
emancmd = "e2stacksort.py classes_avg.hed outtmpcls.hdf --simalign=rotate_translate --center --useali --iterative"
apEMAN.executeEmanCmd(emancmd, verbose=False)
apFile.removeStack(classname)
classname = "a"+classname
# convert hdf back to imagic
emancmd = "proc2d outtmpcls.hdf %s.hed"%classname
apEMAN.executeEmanCmd(emancmd, verbose=False)
apFile.removeStack("outtmpcls.hdf")
else:
if self.params['nocenter'] is False and self.params['nomask'] is False:
emancmd = "proc2d %s.hed %s_cen.hed center"%(classname,classname)
## try cenalignint
emancmd = "cenalignint %s.hed"%classname
apEMAN.executeEmanCmd(emancmd, verbose=False)
## cenalignint also makes a stack with badly centered avgs
if os.path.isfile("bad.hed"):
emancmd = "proc2d bad.hed ali.hed"
apEMAN.executeEmanCmd(emancmd, verbose=False)
apFile.removeStack("bad")
if self.params['keepall'] is False:
apFile.removeStack(classname)
classname = classname+"_cen"
classname = "ali"
alifile = imagicAlignment.alirefs(classname, mask=0.99, maxshift=0.1)
if self.params['keepall'] is False:
apFile.removeStack(classname)
classname = alifile
# mask the classes
if self.params['nomask'] is False:
maskfile = imagicFilters.softMask(classname, mask=maskfrac, falloff=0.1)
if self.params['keepall'] is False:
apFile.removeStack(classname)
else:
maskfile = classname
# normalize the classes
classname = imagicFilters.normalize(maskfile, sigma=10.0)
if self.params['keepall'] is False:
apFile.removeStack(maskfile)
apDisplay.printColor("finished alignment in "+apDisplay.timeString(time.time()-aligntime0), "cyan")
else:
# for projection matching with EMAN:
# don't align references for last iteration
if self.params['currentiter'] < self.params['iter']:
emancmd = "classalign2 %s.hed 10 keep=100 saveali"%classname
apEMAN.executeEmanCmd(emancmd, verbose=False)
apFile.removeStack(classname)
classname = "a"+classname
# mask the averages
emancmd = "proc2d %s.hed %s_mask.hed mask=%i"%(classname,classname,(self.workingmask))
apEMAN.executeEmanCmd(emancmd, verbose=False)
apFile.removeStack(classname)
classname = classname+"_mask"
# normalize references
emancmd = "proc2d %s.hed %s_norm.hed norm"%(classname,classname)
apEMAN.executeEmanCmd(emancmd, verbose=False)
apFile.removeStack(classname)
classname = classname+"_norm"
outputcls = os.path.join(self.params['rundir'],"classes%02i" % self.params['currentiter'])
# copy normalized particles to run directory
emancmd = "proc2d %s.hed %s.hed"%(classname,outputcls)
apEMAN.executeEmanCmd(emancmd, verbose=False)
apFile.removeStack(classname)
self.params['currentcls'] = outputcls
def start(self):
self.insertTopolRepJob()
self.stack = {}
self.stack['apix'] = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
if self.params['virtualdata'] is not None:
self.stack['file'] = self.params['virtualdata']['filename']
else:
self.stack['file'] = os.path.join(self.stackdata['path']['path'], self.stackdata['name'])
self.dumpParameters()
self.params['canexe'] = self.getCANPath()
### process stack to local file
self.params['localstack'] = os.path.join(self.params['rundir'], self.timestamp+".hed")
a = proc2dLib.RunProc2d()
a.setValue('infile',self.stack['file'])
a.setValue('outfile',self.params['localstack'])
a.setValue('apix',self.stack['apix'])
a.setValue('bin',self.params['bin'])
a.setValue('last',self.params['numpart']-1)
a.setValue('append',False)
if self.params['lowpass'] is not None and self.params['lowpass'] > 1:
a.setValue('lowpass',self.params['lowpass'])
if self.params['highpass'] is not None and self.params['highpass'] > 1:
a.setValue('highpass',self.params['highpass'])
if self.params['invert'] is True:
a.setValue('invert',True)
if self.params['premask'] is True and self.params['mramethod'] != 'imagic':
a.setValue('mask',self.params['mask'])
if self.params['virtualdata'] is not None:
vparts = self.params['virtualdata']['particles']
plist = [int(p['particleNumber'])-1 for p in vparts]
a.setValue('list',plist)
if self.params['uploadonly'] is not True:
if os.path.isfile(os.path.join(self.params['rundir'],"stack.hed")):
self.params['localstack']=os.path.join(self.params['rundir'],"stack.hed")
else:
a.run()
if self.params['numpart'] != apFile.numImagesInStack(self.params['localstack']):
apDisplay.printError("Missing particles in stack")
### IMAGIC mask particles before alignment
if self.params['premask'] is True and self.params['mramethod'] == 'imagic':
# convert mask to fraction for imagic
maskfrac = self.workingmask*2/self.workingboxsize
maskstack = imagicFilters.softMask(self.params['localstack'],mask=maskfrac)
shutil.move(maskstack+".hed",os.path.splitext(self.params['localstack'])[0]+".hed")
shutil.move(maskstack+".img",os.path.splitext(self.params['localstack'])[0]+".img")
origstack = self.params['localstack']
### find number of processors
# if self.params['nproc'] is None:
self.params['nproc'] = apParam.getNumProcessors()
if self.params['uploadonly'] is not True:
aligntime = time.time()
# run through iterations
for i in range(0,self.params['iter']+1):
# move back to starting directory
os.chdir(self.params['rundir'])
# set up next iteration directory
self.params['currentiter'] = i
self.params['iterdir'] = os.path.abspath("iter%02i" % i)
self.params['iterdir'] = string.replace(self.params['iterdir'],"/jetstor/APPION","")
if os.path.exists(self.params['iterdir']):
apDisplay.printError("Error: directory '%s' exists, aborting alignment" % self.params['iterdir'])
# create directory for iteration
os.makedirs(self.params['iterdir'])
os.chdir(self.params['iterdir'])
# if at first iteration, create initial class averages
if i == 0:
# first rewrite localstack headers if particles not pre-masked
if self.params['premask'] is False and self.params['mramethod'] == "imagic":
imagicFilters.takeoverHeaders(self.params['localstack'],self.params['numpart'],self.workingboxsize)
self.params['alignedstack'] = os.path.splitext(self.params['localstack'])[0]
if self.params['msamethod']=='imagic':
self.runIMAGICmsa()
else:
self.runCAN()
continue
# using references from last iteration, run multi-ref alignment
if self.params['mramethod'] == "imagic":
# rewrite class headers
imagicFilters.takeoverHeaders(self.params['currentcls'],self.params['currentnumclasses'],self.workingboxsize)
self.runIMAGICmra()
else:
self.runEMANmra()
# create class averages from aligned stack
if self.params['msamethod']=='imagic':
self.runIMAGICmsa()
else:
self.runCAN()
aligntime = time.time() - aligntime
apDisplay.printMsg("Alignment time: "+apDisplay.timeString(aligntime))
## set upload information params:
else:
## get last iteration
alliters = glob.glob("iter*")
alliters.sort()
## get iteration number from iter dir
self.params['currentiter'] = int(alliters[-1][-2:])
self.params['iterdir'] = os.path.join(self.params['rundir'],alliters[-1])
self.params['currentcls'] = "classes%02i"%(self.params['currentiter'])
## go into last iteration directory
os.chdir(self.params['iterdir'])
self.params['alignedstack'] = os.path.abspath("mrastack")
if os.path.isfile(os.path.join(self.params['rundir'],self.params['currentcls']+".hed")):
p1 = os.path.join(self.params['rundir'],self.params['currentcls'])
p2 = os.path.join(self.params['iterdir'],self.params['currentcls'])
shutil.move(p1+".hed",p2+".hed")
shutil.move(p1+".img",p2+".img")
## sort the class averages
self.sortClassAverages()
### get particle information from last iteration
if self.params['mramethod']=='imagic':
partlist = self.readPartIMAGICFile()
else:
partlist = self.readPartEMANFile()
if self.params['msamethod']=='imagic':
partrefdict = self.imagicClassificationToDict()
else:
partrefdict = self.canClassificationToDict()
# move back to starting directory
os.chdir(self.params['rundir'])
# move aligned stack to current directory for appionweb
if not os.path.isfile("mrastack.hed"):
shutil.move(self.params['alignedstack']+".hed","mrastack.hed")
shutil.move(self.params['alignedstack']+".img","mrastack.img")
# rewrite header
if self.params['mramethod'] == "imagic" or self.params['msamethod'] == 'imagic':
imagicFilters.takeoverHeaders("mrastack",self.params['numpart'],self.workingboxsize)
# move actual averages to current directory
if self.params['msamethod']=='can':
if not os.path.isfile("classes_avg.hed"):
self.applySort()
# save actual class averages as refs in database
self.params['currentcls']="classes_avg"
### create an average mrc of final references
if not os.path.isfile("average.mrc"):
apStack.averageStack(stack=self.params['currentcls']+".hed")
self.dumpParameters()
### remove the filtered stack
apFile.removeStack(origstack)
### save to database
if self.params['commit'] is True:
self.insertRunIntoDatabase()
self.insertParticlesIntoDatabase(partlist, partrefdict)