for cls in clslist:
## create SPIDER batch file and run coran
spidercmd = emancoran.runCoranClass(params, cls)
print "classification complete"
print "Determining best class averages"
#Determine best averages
#Create list of cc values
for cls in range(0, len(clslist)):
clsdir = clslist[cls].split('.')[0] + '.dir'
# if no particles in class, create empty class averages
if not os.path.exists(
os.path.join(clslist[cls].split('.')[0] + '.dir',
'aligned.spi')):
# blank projection image
apEMAN.writeBlankImage('goodavgs.hed', params['boxsize'], -1)
# blank class average
apEMAN.writeBlankImage('goodavgs.hed', params['boxsize'], -1)
# blank "good" average
#apEMAN.writeBlankImage('allavgs.hed',params['boxsize'],-1)
if params['eotest'] is True:
apEMAN.writeBlankImage('goodavgs.even.hed', params['boxsize'],
-1)
apEMAN.writeBlankImage('goodavgs.odd.hed', params['boxsize'],
-1)
continue
avgname = os.path.join(clsdir, 'classes_avg.spi')
averages = EMAN.readImages(avgname, -1, -1, 0)
e = projections[cls].getEuler()
cclist = []
def runCoranClass(params,cls):
print "processing class",cls
#set up cls dir
clsdir=cls.split('.')[0]+'.dir'
os.mkdir(clsdir)
clscmd='clstoaligned.py -c ' + cls
## if multiprocessor, don't run clstoaligned yet
if params['proc'] == 1:
#make aligned stack
proc = subprocess.Popen(clscmd, shell=True)
proc.wait()
corancmd=clscmd+'\n'
coranbatch='coranfor'+cls.split('.')[0]+'.bat'
#make spider batch
params['nptcls'] = apEMAN.getNPtcls(cls)
# if no particles, create an empty class average
if params['nptcls'] == 0:
# don't run clscmd, just make directory and empty average
apEMAN.writeBlankImage(os.path.join(clsdir,'classes_avg.spi'),params['boxsize'],0,'spider')
print "WARNING!! no particles in class"
return
# if only 3 particles or less, turn particles into the class averages
elif params['nptcls'] < 4:
#this is an ugly hack, just average the particles together, no ref-free
# don't use mpi, just make directory with clscmd and average particles
proc = subprocess.Popen(clscmd, shell=True)
proc.wait()
avgcmd=("proc2d %s %s average" % (os.path.join(clsdir,'aligned.spi'),os.path.join(clsdir,'classes_avg.spi')))
proc = subprocess.Popen(avgcmd, shell=True)
proc.wait()
dummyclsdir=os.path.join(clsdir,'classes')
os.mkdir(dummyclsdir)
dummyfilename='clhc_cls0001.spi'
dummyfile=open(os.path.join(dummyclsdir,dummyfilename),'w')
dummyfile.write(';bat/spi\n')
for ptcl in range(0,params['nptcls']):
dummyfile.write('%d 1 %d\n' % (ptcl,ptcl+1))
dummyfile.close()
print "WARNING!! not enough particles in class for subclassification"
return
# otherwise, run coran
else:
makeSpiderCoranBatch(params,coranbatch,clsdir)
### this is how we should do this
#mySpider = spyder.SpiderSession(logo=False, nproc=1)
#mySpider.toSpiderQuiet("@%s\n" % coranbatch.split('.')[0])
spidercmd = ("cd %s\n" % clsdir)
if params['hp'] is not None:
spidercmd+=("proc2d aligned.spi alignedhp.spi spiderswap apix=%s hp=%s\n" % (params['apix'],params['hp']))
spidercmd+= ("spider bat/spi @%s\n" % coranbatch.split('.')[0])
## if multiprocessor, don't run spider yet
if params['proc'] == 1:
proc = subprocess.Popen(spidercmd, shell=True)
proc.wait()
corancmd+=spidercmd
return corancmd
print "ERROR!!! "+clsdir+"/"+spijobfile+" does not exist"
else:
for cls in clslist:
## create SPIDER batch file and run coran
spidercmd = emancoran.runCoranClass(params,cls)
print "classification complete"
print "Determining best class averages"
#Determine best averages
#Create list of cc values
for cls in range(0,len(clslist)):
clsdir=clslist[cls].split('.')[0]+'.dir'
# if no particles in class, create empty class averages
if not os.path.exists(os.path.join(clslist[cls].split('.')[0]+'.dir','aligned.spi')):
# blank projection image
apEMAN.writeBlankImage('goodavgs.hed',params['boxsize'],-1)
# blank class average
apEMAN.writeBlankImage('goodavgs.hed',params['boxsize'],-1)
# blank "good" average
#apEMAN.writeBlankImage('allavgs.hed',params['boxsize'],-1)
if params['eotest'] is True:
apEMAN.writeBlankImage('goodavgs.even.hed',params['boxsize'],-1)
apEMAN.writeBlankImage('goodavgs.odd.hed',params['boxsize'],-1)
continue
avgname=os.path.join(clsdir,'classes_avg.spi')
averages=EMAN.readImages(avgname,-1,-1,0)
e=projections[cls].getEuler()
cclist=[]
cutofflist=[]
projections[cls].setNImg(-1)
def runCoranClass(params, cls):
print "processing class", cls
#set up cls dir
clsdir = cls.split('.')[0] + '.dir'
os.mkdir(clsdir)
clscmd = 'clstoaligned.py -c ' + cls
## if multiprocessor, don't run clstoaligned yet
if params['proc'] == 1:
#make aligned stack
proc = subprocess.Popen(clscmd, shell=True)
proc.wait()
corancmd = clscmd + '\n'
coranbatch = 'coranfor' + cls.split('.')[0] + '.bat'
#make spider batch
params['nptcls'] = apEMAN.getNPtcls(cls)
# if no particles, create an empty class average
if params['nptcls'] == 0:
# don't run clscmd, just make directory and empty average
apEMAN.writeBlankImage(os.path.join(clsdir, 'classes_avg.spi'),
params['boxsize'], 0, 'spider')
print "WARNING!! no particles in class"
return
# if only 3 particles or less, turn particles into the class averages
elif params['nptcls'] < 4:
#this is an ugly hack, just average the particles together, no ref-free
# don't use mpi, just make directory with clscmd and average particles
proc = subprocess.Popen(clscmd, shell=True)
proc.wait()
avgcmd = ("proc2d %s %s average" % (os.path.join(
clsdir, 'aligned.spi'), os.path.join(clsdir, 'classes_avg.spi')))
proc = subprocess.Popen(avgcmd, shell=True)
proc.wait()
dummyclsdir = os.path.join(clsdir, 'classes')
os.mkdir(dummyclsdir)
dummyfilename = 'clhc_cls0001.spi'
dummyfile = open(os.path.join(dummyclsdir, dummyfilename), 'w')
dummyfile.write(';bat/spi\n')
for ptcl in range(0, params['nptcls']):
dummyfile.write('%d 1 %d\n' % (ptcl, ptcl + 1))
dummyfile.close()
print "WARNING!! not enough particles in class for subclassification"
return
# otherwise, run coran
else:
makeSpiderCoranBatch(params, coranbatch, clsdir)
### this is how we should do this
#mySpider = spyder.SpiderSession(logo=False, nproc=1)
#mySpider.toSpiderQuiet("@%s\n" % coranbatch.split('.')[0])
spidercmd = ("cd %s\n" % clsdir)
if params['hp'] is not None:
spidercmd += (
"proc2d aligned.spi alignedhp.spi spiderswap apix=%s hp=%s\n" %
(params['apix'], params['hp']))
spidercmd += ("spider bat/spi @%s\n" % coranbatch.split('.')[0])
## if multiprocessor, don't run spider yet
if params['proc'] == 1:
proc = subprocess.Popen(spidercmd, shell=True)
proc.wait()
corancmd += spidercmd
return corancmd
