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