def main():
progname = os.path.basename(sys.argv[0])
usage = progname + " stack outdir --ir --ou --delta --dpsi --lf --hf --rand_seed --maxit --debug --noweights --trials --given --first_zero --weights --MPIGA--pcross --pmut --maxgen --MPI --trials"
parser = OptionParser(usage, version = SPARXVERSION)
parser.add_option("--ir", type="float", default=-1, help="Inner radius of particle (set to 1)")
parser.add_option("--ou", type="float", default=-1, help="Outer radius of particle < int(nx/2)-1")
parser.add_option("--delta", type="float", default=5.0, help="Angle step" )
parser.add_option("--dpsi", type="int", default=1, help="Angle accuracy for sinogram (set to 1)")
parser.add_option("--lf", type="float", default=0.0, help="Filter, minimum frequency (set to 0.0)")
parser.add_option("--hf", type="float", default=0.5, help="Filter, maximum frequency (set to 0.5)")
parser.add_option("--given", action="store_true", default=False, help="Start from given projections orientation (set to False, means start with randomize orientations)")
parser.add_option("--rand_seed", type="int", default=-1, help="Random seed of initial orientations (if set to randomly)")
parser.add_option("--maxit", type="int", default=100, help="Maximum number of iterations ")
parser.add_option("--debug", action="store_true", default=False, help="Help to debug")
parser.add_option("--first_zero", action="store_true", default=False, help="Assign the first projection orientation to 0")
parser.add_option("--noweights", action="store_true", default=False, help="Use Voronoi weighting (by default use weights)")
parser.add_option("--MPI", action="store_true", default=False, help="MPI version")
parser.add_option("--trials", type="int", default=1, help="Number of trials for the MPI version")
parser.add_option("--MPIGA", action="store_true", default=False, help="MPI version (Genetic algorithm)")
parser.add_option("--pcross", type="float", default=0.95, help="Cross-over probability (set to 0.95)")
parser.add_option("--pmut", type="float", default=0.05, help="Mutation probability (set to 0.05)")
parser.add_option("--maxgen", type="int", default=10, help="Maximum number of generations (set to 10)")
(options, args) = parser.parse_args()
if len(args) != 2:
print("usage: " + usage)
print("Please run '" + progname + " -h' for detailed options")
else:
if options.maxit < 1: options.maxit = 1
if options.noweights: weights = False
else: weights = True
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
if options.MPIGA:
from development import cml2_main_mpi
global_def.BATCH = True
cml2_main_mpi(args[0], args[1], options.ir, options.ou, options.delta, options.dpsi,
options.lf, options.hf, options.rand_seed, options.maxit, options.given, options.first_zero,
weights, options.debug, options.maxgen, options.pcross, options.pmut)
global_def.BATCH = False
elif options.MPI:
from mpi import mpi_init
sys.argv = mpi_init(len(sys.argv),sys.argv)
from applications import cml_find_structure_MPI2
global_def.BATCH = True
cml_find_structure_MPI2(args[0], args[1], options.ir, options.ou, options.delta, options.dpsi,
options.lf, options.hf, options.rand_seed, options.maxit, options.given, options.first_zero,
weights, options.debug, options.trials)
global_def.BATCH = False
else:
from applications import cml_find_structure_main
global_def.BATCH = True
cml_find_structure_main(args[0], args[1], options.ir, options.ou, options.delta, options.dpsi,
options.lf, options.hf, options.rand_seed, options.maxit, options.given, options.first_zero,
weights, options.debug, options.trials)
global_def.BATCH = False
if options.MPI:
from mpi import mpi_finalize
mpi_finalize()
def main():
progname = os.path.basename(sys.argv[0])
usage = progname + " stack outdir --ir --ou --delta --dpsi --lf --hf --rand_seed --maxit --debug --noweights --trials --given --first_zero --weights --MPIGA--pcross --pmut --maxgen --MPI --trials"
parser = OptionParser(usage, version = SPARXVERSION)
parser.add_option("--ir", type="float", default=-1, help="Inner radius of particle (set to 1)")
parser.add_option("--ou", type="float", default=-1, help="Outer radius of particle < int(nx/2)-1")
parser.add_option("--delta", type="float", default=5.0, help="Angle step" )
parser.add_option("--dpsi", type="int", default=1, help="Angle accuracy for sinogram (set to 1)")
parser.add_option("--lf", type="float", default=0.0, help="Filter, minimum frequency (set to 0.0)")
parser.add_option("--hf", type="float", default=0.5, help="Filter, maximum frequency (set to 0.5)")
parser.add_option("--given", action="store_true", default=False, help="Start from given projections orientation (set to False, means start with randomize orientations)")
parser.add_option("--rand_seed", type="int", default=-1, help="Random seed of initial orientations (if set to randomly)")
parser.add_option("--maxit", type="int", default=100, help="Maximum number of iterations ")
parser.add_option("--debug", action="store_true", default=False, help="Help to debug")
parser.add_option("--first_zero", action="store_true", default=False, help="Assign the first projection orientation to 0")
parser.add_option("--noweights", action="store_true", default=False, help="Use Voronoi weighting (by default use weights)")
parser.add_option("--MPI", action="store_true", default=False, help="MPI version")
parser.add_option("--trials", type="int", default=1, help="Number of trials for the MPI version")
parser.add_option("--MPIGA", action="store_true", default=False, help="MPI version (Genetic algorithm)")
parser.add_option("--pcross", type="float", default=0.95, help="Cross-over probability (set to 0.95)")
parser.add_option("--pmut", type="float", default=0.05, help="Mutation probability (set to 0.05)")
parser.add_option("--maxgen", type="int", default=10, help="Maximum number of generations (set to 10)")
(options, args) = parser.parse_args()
if len(args) != 2:
print "usage: " + usage
print "Please run '" + progname + " -h' for detailed options"
else:
if options.maxit < 1: options.maxit = 1
if options.noweights: weights = False
else: weights = True
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
if options.MPIGA:
from development import cml2_main_mpi
global_def.BATCH = True
cml2_main_mpi(args[0], args[1], options.ir, options.ou, options.delta, options.dpsi,
options.lf, options.hf, options.rand_seed, options.maxit, options.given, options.first_zero,
weights, options.debug, options.maxgen, options.pcross, options.pmut)
global_def.BATCH = False
elif options.MPI:
from mpi import mpi_init
sys.argv = mpi_init(len(sys.argv),sys.argv)
from applications import cml_find_structure_MPI2
global_def.BATCH = True
cml_find_structure_MPI2(args[0], args[1], options.ir, options.ou, options.delta, options.dpsi,
options.lf, options.hf, options.rand_seed, options.maxit, options.given, options.first_zero,
weights, options.debug, options.trials)
global_def.BATCH = False
else:
from applications import cml_find_structure_main
global_def.BATCH = True
cml_find_structure_main(args[0], args[1], options.ir, options.ou, options.delta, options.dpsi,
options.lf, options.hf, options.rand_seed, options.maxit, options.given, options.first_zero,
weights, options.debug, options.trials)
global_def.BATCH = False
if options.MPI:
from mpi import mpi_finalize
mpi_finalize()