def get_options(parser):
parser = refinegrains.get_options( parser )
parser.add_argument("-P", "--newparfile", action="store",
dest="newparfile",
type=ImageD11options.ParameterFileType(mode='w'),
help="Name of new parameter file")
parser.add_argument("-v", "--vary", action="append",
dest="varylist", type=str,
default = [ "y_center","z_center",
"tilt_y","tilt_x","tilt_z","wedge",
"t_x","t_y","distance"],
help="Parameters to vary" )
parser.add_argument("-x", "--fiX", action="append",
dest="fixlist", type=str, default = [],
help="Parameters to fix (overrides vary)")
parser.add_argument("-S", "--steps", action="store",
dest="steps", type=int,
default = 1000,
help="Number of simplex iterations")
parser.description = """
Fitgrain should attempt to fit one or more grains to a dataset
using the parameters specified on the command line.
"""
return parser
def get_options(parser):
"""
Command line interface for making a mapping
Add our options to a parser object
"""
parser = ImageD11_file_series.get_options( parser )
parser.add_argument("-p", "--pars", action="store",
dest = "pars", default = None,
type=ImageD11options.ParameterFileType(mode='r'),
help = "ImageD11 parameter file for experiment")
parser.add_argument("-o", "--output", action="store",
dest = "output", default = None,
type=ImageD11options.HdfFileType(mode='r'),
help = "Name of hdf5 output file")
parser.add_argument("-s", "--splinefile", action="store",
dest = "spline", default = None,
type=ImageD11options.SplineFileType(mode='r'),
help = "Name of fit2d spline file for spatial dist")
parser.add_argument("-u", "--ubifile", action="store",
dest = "ubifile", default = None,
type = ImageD11options.UbiFileType(mode='r'),
help = "Name of ubi file (first matrix is used)")
parser.add_argument("-x", "--npixels", action="store", type=int,
dest = "npixels", default = 16,
help = "Number of pixels in reciprocal space map per integer hkl [16]")
parser.add_argument("-i", "--images", action="store", type=int,
dest = "images", default = None,
help = "Number of images to process [all]")
parser.add_argument("-b", "--border", action="store", type=int,
dest = "border", default = 10,
help = "Border around images to allocate space, px [10]")
parser.add_argument("-t", "--saturation", action="store", type=float,
dest = "maxpix", default = None,
help = "Saturation value for excluding pixels")
#parser.add_argument("-t", "--testcolfile", action="store", type="string",
# dest = "testcolfile", default=None,
# help = "A columnfile to test geometry")
parser.add_argument("-c", "--subslice", action="store", type=int,
dest = "subslice", default=1,
help = "Number of omega subslices to repeat images")
parser.add_argument("--maskfilename", action="store", type=str,
dest = "maskfilename", default=None,
help = "Mask image (fit2d style)" )
return parser
def get_options(parser):
parser.add_argument("-p", "--parfile", action="store",
dest="parfile",
type=ImageD11options.ParameterFileType(mode='r'),
help="Name of input parameter file")
parser.add_argument("-u", "--ubifile", action="store",
dest="ubifile",
type=ImageD11options.UbiFileType(mode='r'),
help="Name of ubi file")
parser.add_argument("-U", "--newubifile", action="store",
dest="newubifile",
type=ImageD11options.UbiFileType(mode='w'),
help="Name of new ubi file to output")
parser.add_argument("-f", "--fltfile", action="store",
dest="fltfile",
type=ImageD11options.ColumnFileType(mode='r'),
help="Name of flt file")
parser.add_argument("-F", "--newfltfile", action="store",
dest="newfltfile",
type=ImageD11options.ColumnFileType(mode='w'),
help="Name of flt file containing unindexed peaks")
lattices = ["cubic", "hexagonal", "trigonalH","trigonalP",
"tetragonal", "orthorhombic", "monoclinic_a",
"monoclinic_b","monoclinic_c","triclinic"]
parser.add_argument("-s", "--sym", action="store",
dest="symmetry", # type="choice",
default = "triclinic",
choices = lattices,
help="Lattice symmetry for choosing orientation")
parser.add_argument("-l", "--lattice", action="store",
dest="latticesymmetry", #type="choice",
default = "triclinic",
choices = lattices,
help="Lattice symmetry for choosing orientation from "+
"|".join(lattices))
parser.add_argument("-t", "--tol", action="store",
dest="tol", type=float,
default = 0.25,
help="Tolerance to use in peak assignment, default=%f"%(0.25))
parser.add_argument( "--omega_no_float", action="store_false",
dest = "omega_float",
default = True,
help= "Use exact observed omega values")
parser.add_argument( "--omega_slop", action="store", type=float,
dest = "omega_slop",
default = 0.5,
help= "Omega slop (step) size")
return parser