def main():
(options, rawimage) = parse_command_line()
pid = EMAN.LOGbegin(sys.argv)
EMAN.LOGInfile(pid, rawimage)
imagenum = EMAN.fileCount(rawimage)[0]
for iter in range(options.iters):
projfile = "proj.%d.hdf" % (iter+1)
cmplstfile = "cmp.%d.lst" % (iter+1)
ortlstfile = "ort.%d.lst" % (iter+1)
mapfile = "threed.%da.mrc" % (iter)
mapfile2 = "threed.%da.mrc" % (iter+1)
if options.eotest:
mapfile2e = "threed.%da.e.mrc" % (iter+1)
mapfile2o = "threed.%da.o.mrc" % (iter+1)
subsetlste = "ort.%d.e.lst" % (iter+1)
subsetlsto = "ort.%d.o.lst" % (iter+1)
fscfile = "fsc.%d.txt" % (iter+1)
else:
mapfile2e = None
mapfile2o = None
subsetlste = None
subsetlsto = None
fscfile = None
if not os.path.exists(mapfile):
print "ERROR: cannot find 3D map \"%s\"" % (mapfile)
sys.exit()
else:
d = EMAN.EMData()
d.readImage(rawimage,0,1) # read header
rnx = d.xSize()
rny = d.ySize()
d.readImage(mapfile,-1,1) # read header
mnx = d.xSize()
mny = d.ySize()
mnz = d.zSize()
if rnx!=mnx or rny!=mny:
print "ERROR: raw images (%s) sizes (%dx%d) are different from the 3D map (%s) sizes (%dx%dx%d)" % (rawimage, rnx, rny, mapfile, mnx, mny, mnz)
sys.exit()
if not os.path.exists(cmplstfile):
runpar_file = "runpar.%d.ortcen.txt" % (iter+1)
n = imagenum/options.batchsize
if imagenum%n: n+=1
if n<options.cpus:
n=options.cpus
options.batchsize=imagenum/n+1
if options.batchsize==1:
n = imagenum
options.batchsize=1
num_tries = 0
max_tries = 3
while not os.path.exists(ortlstfile) and num_tries < max_tries:
runparfp = open(runpar_file, "w")
num_tries += 1
todo_num = 0
sublstfiles = []
cmpsublstfiles = []
for i in range(n):
cmplstfile_tmp = "cmp.%d.%d.lst" % (iter+1, i)
ortlstfile_tmp = "ort.%d.%d.lst" % (iter+1, i)
startNum = i * options.batchsize
endNum = (i+1) * options.batchsize
if startNum>=imagenum: break
if endNum>imagenum: endNum=imagenum
sublstfiles.append(ortlstfile_tmp)
cmpsublstfiles.append(cmplstfile_tmp)
if os.path.exists(ortlstfile_tmp): continue
else: todo_num += 1
cmd = "symrelax.py %s %s " % (rawimage, mapfile)
if options.sffile: cmd += "--sf=%s " % ( options.sffile )
if options.phasecorrected: cmd += "--phasecorrected "
cmd += "--verbose=%d " % (options.verbose )
cmd += "--mask=%d " % (options.mask)
cmd += "--startSym=%s " % (options.startSym)
cmd += "--endSym=%s " % (options.endSym)
cmd += "--first=%d --last=%d " % (startNum, endNum)
cmd += "--shrink=%d " % (options.shrink)
cmd += "--ortlstfile=%s " % (ortlstfile_tmp)
cmd += "--score=%s " % (options.scorefunc)
if options.saveprojection:
cmd += "--projection=%s " % (projfile)
cmd += "--cmplstfile=%s " % (cmplstfile_tmp)
if i: cmd += "--nocmdlog "
if i == 0: print cmd
runparfp.write("%s\n" % (cmd))
runparfp.close()
if todo_num:
cmd = "runpar proc=%d,%d file=%s" % (options.cpus, options.cpus, runpar_file)
print cmd
os.system(cmd)
#now merge all sublst file
# first test if all jobs are done properly
done = 1
for lstfile_tmp in sublstfiles:
if not os.path.exists(lstfile_tmp): done = 0
if done:
EMAN.merge_lstfiles(sublstfiles, ortlstfile, delete_lstfiles = 1)
# pool the cmplstfiles
if options.saveprojection:
EMAN.merge_lstfiles(cmpsublstfiles, cmplstfile, delete_lstfiles = 1)
if not os.path.exists(ortlstfile) or (os.path.exists(ortlstfile) and os.path.getsize(ortlstfile)<=5):
print "ERROR: raw image new orientation results lst file \"%s\" is not generated properly" % (ortlstfile)
sys.exit()
if not os.path.exists(mapfile2):
reconstruction_by_make3d(ortlstfile, mapfile2, options=options, mapfile2e=mapfile2e, mapfile2o=mapfile2o, fscfile=fscfile)
if not (os.path.exists(mapfile2) and os.path.getsize(mapfile2)):
print "ERROR: 3D map \"%s\" is not generated properly" % (mapfile2)
sys.exit()
EMAN.LOGend()
