def main():
arglist = []
for arg in sys.argv:
arglist.append( arg )
progname = os.path.basename(sys.argv[0])
usage = progname + " stack outdir <maskfile> --ou=outer_radius --delta=angular_bracket --maxit=max_iter --chunk=data_chunk_for_update --center --CTF --snr=SNR --sym=symmetry --function=user_function --MPI"
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--ou", type="float", default=-1, help="outer radius of a circular mask that should encompass the particle< int(nx/2)-1 (set to int(nx/2)-1)")
parser.add_option("--delta", type="float", default=2, help="angular bracket (set to 2)")
parser.add_option("--ts", type="float", default=2, help="shift bracket (set to 2)")
parser.add_option("--center", type="float", default=0, help="-1 - average centering method; 0 - no cetnering of template volume (default), 1 - center the volume using center of gravity")
parser.add_option("--maxit", type="int", default=10, help="maximum number of iterations (set to 10)")
parser.add_option("--chunk", type="float", default=1.0, help="chunk of data after which the 3-D structure will be updated 0<chunk<=1.0 (set to 1.0)")
parser.add_option("--CTF", action="store_true", default=False, help="Consider CTF correction during the alignments")
parser.add_option("--snr", type="float", default=1, help="SNR > 0.0 (set to 1.0)")
parser.add_option("--sym", type="string", default="c1", help="symmetry group (set to c1)")
parser.add_option("--function", type="string", default="ref_ali3d", help="name of the user-supplied reference preparation function")
parser.add_option("--npad", type="int", default= 2, help="padding size for 3D reconstruction")
parser.add_option("--debug", action="store_true", default=False, help="Debug printout")
parser.add_option("--MPI", action="store_true", default=False, help="use MPI version")
parser.add_option("--fourvar", action="store_true", default=False, help="compute Fourier variance")
(options, args) = parser.parse_args(arglist[1:])
if(len(args) < 2 or len(args) > 3):
print "usage: " + usage
print "Please run '" + progname + " -h' for detailed options"
else:
if(len(args) == 2):
mask = None
else:
mask = args[2]
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()
global_def.BATCH = True
if options.fourvar:
from development import nlocal_ali3d_MPI
nlocal_ali3d_MPI(args[0], args[1], mask, options.ou, options.delta, options.ts, options.center, options.maxit,
options.CTF, options.snr, options.sym, options.chunk, options.function, options.fourvar,
options.npad, options.debug)
else:
from applications import local_ali3d
local_ali3d(args[0], args[1], mask, options.ou, options.delta, options.ts, options.center, options.maxit,
options.CTF, options.snr, options.sym, options.chunk, options.function, options.fourvar,
options.npad, options.debug, options.MPI)
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(sys.argv[0])
usage = progname + " stack outdir <maskfile> --ou=outer_radius --delta=angular_bracket --maxit=max_iter --chunk=data_chunk_for_update --center --CTF --snr=SNR --sym=symmetry --function=user_function --MPI"
parser = OptionParser(usage, version=SPARXVERSION)
parser.add_option(
"--ou",
type="float",
default=-1,
help=
"outer radius of a circular mask that should encompass the particle< int(nx/2)-1 (set to int(nx/2)-1)"
)
parser.add_option("--delta",
type="float",
default=2,
help="angular bracket (set to 2)")
parser.add_option("--ts",
type="float",
default=2,
help="shift bracket (set to 2)")
parser.add_option(
"--center",
type="float",
default=0,
help=
"-1 - average centering method; 0 - no cetnering of template volume (default), 1 - center the volume using center of gravity"
)
parser.add_option("--maxit",
type="int",
default=10,
help="maximum number of iterations (set to 10)")
parser.add_option(
"--chunk",
type="float",
default=1.0,
help=
"chunk of data after which the 3-D structure will be updated 0<chunk<=1.0 (set to 1.0)"
)
parser.add_option("--CTF",
action="store_true",
default=False,
help="Consider CTF correction during the alignments")
parser.add_option("--snr",
type="float",
default=1,
help="SNR > 0.0 (set to 1.0)")
parser.add_option("--sym",
type="string",
default="c1",
help="symmetry group (set to c1)")
parser.add_option(
"--function",
type="string",
default="ref_ali3d",
help="name of the user-supplied reference preparation function")
parser.add_option("--npad",
type="int",
default=2,
help="padding size for 3D reconstruction")
parser.add_option("--debug",
action="store_true",
default=False,
help="Debug printout")
parser.add_option("--MPI",
action="store_true",
default=False,
help="use MPI version")
parser.add_option("--fourvar",
action="store_true",
default=False,
help="compute Fourier variance")
parser.add_option("--scipy_minimization",
action="store_true",
default=False,
help="use scipy minimization instead of amoeba")
(options, args) = parser.parse_args(arglist[1:])
if (len(args) < 2 or len(args) > 3):
print("usage: " + usage)
print("Please run '" + progname + " -h' for detailed options")
else:
if (len(args) == 2):
mask = None
else:
mask = args[2]
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()
global_def.BATCH = True
if options.fourvar:
from development import nlocal_ali3d_MPI
nlocal_ali3d_MPI(args[0], args[1], mask, options.ou, options.delta,
options.ts, options.center, options.maxit,
options.CTF, options.snr, options.sym,
options.chunk, options.function, options.fourvar,
options.npad, options.debug)
elif options.scipy_minimization:
if options.MPI:
from applications import local_ali3d_MPI_scipy_minimization
local_ali3d_MPI_scipy_minimization(
args[0], args[1], mask, options.ou, options.delta,
options.ts, options.center, options.maxit, options.CTF,
options.snr, options.sym, options.chunk, options.function,
options.fourvar, options.npad, options.debug)
else:
from applications import local_ali3d
local_ali3d(args[0], args[1], mask, options.ou, options.delta,
options.ts, options.center, options.maxit, options.CTF,
options.snr, options.sym, options.chunk,
options.function, options.fourvar, options.npad,
options.debug, options.MPI)
global_def.BATCH = False
if options.MPI:
from mpi import mpi_finalize
mpi_finalize()