def main():
arglist = []
for arg in sys.argv:
arglist.append(arg)
progname = os.path.basename(arglist[0])
usage = progname + " prj_stack volume [begin end step] --CTF --npad=ntimes_padding --list=file --group=ID --snr=SNR --sym=symmetry --verbose=(0|1) --xysize --MPI"
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option("--CTF",
action="store_true",
default=False,
help="apply CTF correction")
parser.add_option("--snr",
type="float",
default=1.0,
help="Signal-to-Noise Ratio")
parser.add_option("--sym", type="string", default="c1", help="symmetry")
parser.add_option(
"--list",
type="string",
help="file with list of images to be used in the first column")
parser.add_option(
"--group",
type="int",
default=-1,
help=
"perform reconstruction using images for a given group number (group is attribute in the header)"
)
parser.add_option("--MPI",
action="store_true",
default=False,
help="use MPI version ")
parser.add_option("--npad",
type="int",
default=2,
help="number of times padding (default 2)")
parser.add_option("--verbose",
type="int",
default=0,
help="verbose level: 0 no verbose, 1 verbose")
parser.add_option("--xysize",
type="int",
default=-1,
help="user expected size at xy direction")
parser.add_option("--zsize",
type="int",
default=-1,
help="user expected size at z direction")
parser.add_option("--smearstep",
type="float",
default=0.0,
help="Rotational smear step (default 0.0, no smear)")
parser.add_option(
"--interpolation_method",
type="string",
default="4nn",
help="4nn, or tril: nearest neighbor, or trillinear interpolation")
parser.add_option("--niter",
type="int",
default=10,
help="number of iterations for iterative reconstruction")
parser.add_option("--upweighted",
action="store_true",
default=False,
help="apply background noise")
parser.add_option("--compensate",
action="store_true",
default=False,
help="compensate in reconstruction")
parser.add_option("--chunk_id",
type="int",
default=-1,
help="reconstruct both odd and even groups of particles")
parser.add_option("--target_window_size",
type="int",
default=-1,
help=" size of the targeted reconstruction ")
(options, args) = parser.parse_args(arglist[1:])
if options.MPI:
from mpi import mpi_init
sys.argv = mpi_init(len(sys.argv), sys.argv)
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
if len(args) == 2:
prj_stack = args[0]
vol_stack = args[1]
nimage = EMUtil.get_image_count(prj_stack)
pid_list = list(range(0, nimage))
elif len(args) == 5:
prj_stack = args[0]
vol_stack = args[1]
begin = atoi(args[2])
end = atoi(args[3])
step = atoi(args[4])
pid_list = list(range(begin, end, step))
else:
ERROR("incomplete list of arguments", "recon3d_n", 1)
exit()
if (options.list and options.group > -1):
ERROR("options group and list cannot be used together", "recon3d_n", 1)
sys.exit()
from applications import recons3d_n, recons3d_trl_MPI
global_def.BATCH = True
if options.interpolation_method == "4nn":
recons3d_n(prj_stack, pid_list, vol_stack, options.CTF, options.snr, 1, options.npad,\
options.sym, options.list, options.group, options.verbose, options.MPI,options.xysize, options.zsize, options.smearstep, options.upweighted, options.compensate,options.chunk_id)
elif options.interpolation_method == "tril":
if options.MPI is False:
ERROR(
" trillinear interpolation reconstruction has MPI version only!"
)
sys.exit()
recons3d_trl_MPI(prj_stack, pid_list, vol_stack, options.CTF, options.snr, 1, options.npad,\
options.sym, options.verbose, options.niter, options.compensate, options.target_window_size)
else:
ERROR(
" Wrong interpolation method. The current options are 4nn, and tril. 4nn is the defalut one. "
)
global_def.BATCH = False
if options.MPI:
from mpi import mpi_finalize
mpi_finalize()
def main():
arglist = []
for arg in sys.argv:
arglist.append(arg)
progname = os.path.basename(arglist[0])
usage = progname + " prj_stack volume [begin end step] --CTF --npad=ntimes_padding --list=file --group=ID --snr=SNR --sym=symmetry --verbose=(0|1) --xysize --MPI"
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option("--CTF",
action="store_true",
default=False,
help="apply CTF correction")
parser.add_option("--snr",
type="float",
default=1.0,
help="Signal-to-Noise Ratio")
parser.add_option("--sym", type="string", default="c1", help="symmetry")
parser.add_option(
"--list",
type="string",
help="file with list of images to be used in the first column")
parser.add_option(
"--group",
type="int",
default=-1,
help=
"perform reconstruction using images for a given group number (group is attribute in the header)"
)
parser.add_option("--MPI",
action="store_true",
default=False,
help="use MPI version ")
parser.add_option("--npad",
type="int",
default=2,
help="number of times padding (default 2)")
parser.add_option("--verbose",
type="int",
default=0,
help="verbose level: 0 no verbose, 1 verbose")
parser.add_option("--xysize",
type="int",
default=-1,
help="user expected size at xy direction")
parser.add_option("--zsize",
type="int",
default=-1,
help="user expected size at z direction")
parser.add_option("--smearstep",
type="float",
default=0.0,
help="Rotational smear step (default 0.0, no smear)")
(options, args) = parser.parse_args(arglist[1:])
if options.MPI:
from mpi import mpi_init
sys.argv = mpi_init(len(sys.argv), sys.argv)
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
if len(args) == 2:
prj_stack = args[0]
vol_stack = args[1]
nimage = EMUtil.get_image_count(prj_stack)
pid_list = range(0, nimage)
elif len(args) == 5:
prj_stack = args[0]
vol_stack = args[1]
begin = atoi(args[2])
end = atoi(args[3])
step = atoi(args[4])
pid_list = range(begin, end, step)
else:
ERROR("incomplete list of arguments", "recon3d_n", 1)
exit()
if (options.list and options.group > -1):
ERROR("options group and list cannot be used together", "recon3d_n", 1)
sys.exit()
from applications import recons3d_n
global_def.BATCH = True
recons3d_n(prj_stack, pid_list, vol_stack, options.CTF, options.snr, 1, options.npad,\
options.sym, options.list, options.group, options.verbose, options.MPI,options.xysize, options.zsize, options.smearstep)
global_def.BATCH = False
if options.MPI:
from mpi import mpi_finalize
mpi_finalize()
def main():
arglist = []
for arg in sys.argv:
arglist.append( arg )
progname = os.path.basename( arglist[0] )
usage = progname + " prj_stack volume [begin end step] --CTF --npad=ntimes_padding --list=file --group=ID --snr=SNR --sym=symmetry --verbose=(0|1) --xysize --MPI"
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option("--CTF", action="store_true", default=False, help="apply CTF correction")
parser.add_option("--snr", type="float", default=1.0, help="Signal-to-Noise Ratio" )
parser.add_option("--sym", type="string", default="c1", help="symmetry" )
parser.add_option("--list", type="string", help="file with list of images to be used in the first column" )
parser.add_option("--group", type="int", default=-1, help="perform reconstruction using images for a given group number (group is attribute in the header)" )
parser.add_option("--MPI", action="store_true", default=False, help="use MPI version ")
parser.add_option("--npad", type="int", default=2, help="number of times padding (default 2)" )
parser.add_option("--verbose", type="int", default=0, help="verbose level: 0 no verbose, 1 verbose" )
parser.add_option("--xysize", type="int", default=-1, help="user expected size at xy direction" )
parser.add_option("--zsize", type="int", default=-1, help="user expected size at z direction" )
parser.add_option("--smearstep", type="float", default=0.0, help="Rotational smear step (default 0.0, no smear)" )
(options,args) = parser.parse_args(arglist[1:])
if options.MPI:
from mpi import mpi_init
sys.argv = mpi_init(len(sys.argv), sys.argv)
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
if len(args) == 2:
prj_stack = args[0]
vol_stack = args[1]
nimage = EMUtil.get_image_count( prj_stack )
pid_list = range(0, nimage)
elif len(args) == 5:
prj_stack = args[0]
vol_stack = args[1]
begin = atoi( args[2] )
end = atoi( args[3] )
step = atoi( args[4] )
pid_list = range(begin, end, step)
else:
ERROR("incomplete list of arguments","recon3d_n",1)
exit()
if(options.list and options.group > -1):
ERROR("options group and list cannot be used together","recon3d_n",1)
sys.exit()
from applications import recons3d_n
global_def.BATCH = True
recons3d_n(prj_stack, pid_list, vol_stack, options.CTF, options.snr, 1, options.npad,\
options.sym, options.list, options.group, options.verbose, options.MPI,options.xysize, options.zsize, options.smearstep)
global_def.BATCH = False
if options.MPI:
from mpi import mpi_finalize
mpi_finalize()
def main():
arglist = []
for arg in sys.argv:
arglist.append( arg )
progname = os.path.basename( arglist[0] )
usage = progname + " prj_stack volume [begin end step] --CTF --npad=ntimes_padding --list=file --group=ID --snr=SNR --sym=symmetry --verbose=(0|1) --xysize --MPI"
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option("--CTF", action="store_true", default=False, help="apply CTF correction")
parser.add_option("--snr", type="float", default=1.0, help="Signal-to-Noise Ratio" )
parser.add_option("--sym", type="string", default="c1", help="symmetry" )
parser.add_option("--list", type="string", help="file with list of images to be used in the first column" )
parser.add_option("--group", type="int", default=-1, help="perform reconstruction using images for a given group number (group is attribute in the header)" )
parser.add_option("--MPI", action="store_true", default=False, help="use MPI version ")
parser.add_option("--npad", type="int", default=2, help="number of times padding (default 2)" )
parser.add_option("--verbose", type="int", default=0, help="verbose level: 0 no verbose, 1 verbose" )
parser.add_option("--xysize", type="int", default=-1, help="user expected size at xy direction" )
parser.add_option("--zsize", type="int", default=-1, help="user expected size at z direction" )
parser.add_option("--smearstep", type="float", default=0.0, help="Rotational smear step (default 0.0, no smear)" )
parser.add_option("--interpolation_method", type ="string", default="4nn", help="4nn, or tril: nearest neighbor, or trillinear interpolation" )
parser.add_option("--niter", type="int", default=10, help="number of iterations for iterative reconstruction" )
parser.add_option("--upweighted", action="store_true", default=False, help="apply background noise")
parser.add_option("--compensate", action="store_true", default=False, help="compensate in reconstruction")
parser.add_option("--chunk_id", type="int", default=-1, help="reconstruct both odd and even groups of particles")
parser.add_option("--target_window_size", type="int", default=-1, help=" size of the targeted reconstruction ")
(options,args) = parser.parse_args(arglist[1:])
if options.MPI:
from mpi import mpi_init
sys.argv = mpi_init(len(sys.argv), sys.argv)
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
if len(args) == 2:
prj_stack = args[0]
vol_stack = args[1]
nimage = EMUtil.get_image_count( prj_stack )
pid_list = range(0, nimage)
elif len(args) == 5:
prj_stack = args[0]
vol_stack = args[1]
begin = atoi( args[2] )
end = atoi( args[3] )
step = atoi( args[4] )
pid_list = range(begin, end, step)
else:
ERROR("incomplete list of arguments","recon3d_n",1)
exit()
if(options.list and options.group > -1):
ERROR("options group and list cannot be used together","recon3d_n",1)
sys.exit()
from applications import recons3d_n, recons3d_trl_MPI
global_def.BATCH = True
if options.interpolation_method == "4nn":
recons3d_n(prj_stack, pid_list, vol_stack, options.CTF, options.snr, 1, options.npad,\
options.sym, options.list, options.group, options.verbose, options.MPI,options.xysize, options.zsize, options.smearstep, options.upweighted, options.compensate,options.chunk_id)
elif options.interpolation_method == "tril":
if options.MPI is False:
ERROR(" trillinear interpolation reconstruction has MPI version only!")
sys.exit()
recons3d_trl_MPI(prj_stack, pid_list, vol_stack, options.CTF, options.snr, 1, options.npad,\
options.sym, options.verbose, options.niter, options.compensate, options.target_window_size)
else:
ERROR(" Wrong interpolation method. The current options are 4nn, and tril. 4nn is the defalut one. ")
global_def.BATCH = False
if options.MPI:
from mpi import mpi_finalize
mpi_finalize()