def main():
from optparse import OptionParser
progname = os.path.basename(sys.argv[0])
usage = progname + " filelist outdir --fl=filter_low_value --aa=filter_fall_off --radccc=radius_ccc -repair=repairfile --pca --pcamask --pcanvec --MPI"
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--fl", type="float", default=0.0, help="cut-off frequency of hyperbolic tangent low-pass Fourier filter")
parser.add_option("--aa", type="float", default=0.0, help="fall-off of hyperbolic tangent low-pass Fourier filter")
parser.add_option("--radccc", type="int", default=-1, help="radius for ccc calculation")
parser.add_option("--MPI", action="store_true", default=False, help="use MPI version" )
parser.add_option("--repair", type="string", default="default", help="repair original bootstrap volumes: None or repair file name")
parser.add_option("--pca", action="store_true", default=False, help="run pca" )
parser.add_option("--pcamask", type="string", default=None, help="mask for pca" )
parser.add_option("--pcanvec", type="int", default=2, help="number of eigvectors computed in PCA")
parser.add_option("--n", action="store_true", default=False, help="new")
parser.add_option("--scratch", type="string", default="./", help="scratch directory")
(options, args) = parser.parse_args(sys.argv[1:])
if len(args)<2 :
print "usage: " + usage
print "Please run '" + progname + " -h' for detailed options"
else:
files = args[0:-1]
outdir = args[-1]
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
if options.MPI:
from mpi import mpi_init
sys.argv = mpi_init( len(sys.argv), sys.argv )
arglist = []
for arg in sys.argv:
arglist.append( arg )
global_def.BATCH = True
if(options.n):
from development import var_mpi_new
var_mpi_new( files[0], outdir, options.scratch, options.fl, options.aa, options.radccc, False, False, options.repair, options.pca, options.pcamask, options.pcanvec)
else:
from applications import var_mpi
var_mpi( files, outdir, options.fl, options.aa, options.radccc, options.repair, options.pca, options.pcamask, options.pcanvec)
global_def.BATCH = False
from mpi import mpi_finalize
mpi_finalize()
else:
global_def.BATCH = True
ERROR("Please use MPI version","sxvar",1)
from applications import defvar
defvar( files, outdir, options.fl, options.aa, options.radccc, options.repair, options.pca, options.pcamask, options.pcanvec)
global_def.BATCH = False
def main():
from optparse import OptionParser
progname = os.path.basename(sys.argv[0])
usage = progname + " filelist outdir --fl=filter_low_value --aa=filter_fall_off --radccc=radius_ccc -repair=repairfile --pca --pcamask --pcanvec --MPI"
parser = OptionParser(usage,version=SPARXVERSION)
parser.add_option("--fl", type="float", default=0.0, help="cut-off frequency of hyperbolic tangent low-pass Fourier filter")
parser.add_option("--aa", type="float", default=0.0, help="fall-off of hyperbolic tangent low-pass Fourier filter")
parser.add_option("--radccc", type="int", default=-1, help="radius for ccc calculation")
parser.add_option("--MPI", action="store_true", default=False, help="use MPI version" )
parser.add_option("--repair", type="string", default="default", help="repair original bootstrap volumes: None or repair file name")
parser.add_option("--pca", action="store_true", default=False, help="run pca" )
parser.add_option("--pcamask", type="string", default=None, help="mask for pca" )
parser.add_option("--pcanvec", type="int", default=2, help="number of eigvectors computed in PCA")
parser.add_option("--n", action="store_true", default=False, help="new")
parser.add_option("--scratch", type="string", default="./", help="scratch directory")
(options, args) = parser.parse_args(sys.argv[1:])
if len(args)<2 :
print("usage: " + usage)
print("Please run '" + progname + " -h' for detailed options")
else:
files = args[0:-1]
outdir = args[-1]
if global_def.CACHE_DISABLE:
from utilities import disable_bdb_cache
disable_bdb_cache()
if options.MPI:
from mpi import mpi_init
sys.argv = mpi_init( len(sys.argv), sys.argv )
arglist = []
for arg in sys.argv:
arglist.append( arg )
global_def.BATCH = True
if(options.n):
from development import var_mpi_new
var_mpi_new( files[0], outdir, options.scratch, options.fl, options.aa, options.radccc, False, False, options.repair, options.pca, options.pcamask, options.pcanvec)
else:
from applications import var_mpi
var_mpi( files, outdir, options.fl, options.aa, options.radccc, options.repair, options.pca, options.pcamask, options.pcanvec)
global_def.BATCH = False
from mpi import mpi_finalize
mpi_finalize()
else:
global_def.BATCH = True
ERROR("Please use MPI version","sxvar",1)
from applications import defvar
defvar( files, outdir, options.fl, options.aa, options.radccc, options.repair, options.pca, options.pcamask, options.pcanvec)
global_def.BATCH = False