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('-g',
'--gve',
action='store',
type=ImageD11options.GvectorFileType(mode='r'),
dest='gvefilename',
default=None,
help="Filename for g-vectors")
parser.add_argument('-k',
'--ngrains',
action='store',
dest='ngrains',
type=int,
default=1,
help="number of grains to try to find")
parser.add_argument('-o',
'--output',
action='store',
type=ImageD11options.UbiFileType(mode='w'),
default='grains.ubi',
dest='outfile',
help="Name of ubi file to save grains in")
parser = lattice_reduction.get_options(parser)
parser.add_argument('--fft',
action='store_true',
dest='use_fft',
default=False,
help="Use fft to generate lattice vectors [False]")
parser.add_argument('--score_fft',
action='store_true',
dest='score_fft',
default=False,
help="Score fft peaks using fft peaks first [True]")
parser.add_argument(
'--no_sort',
action='store_false',
dest='sort_gve',
default=True,
help="Sorting the gvector by length before indexing [True]")
parser.add_argument('--noisy',
action='store_true',
dest='noisy',
default=False,
help="Print more output")
fft_index_refac.get_options(parser)
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
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):
parser = refinegrains.get_options(parser)
parser.add_argument("-N",
"--notindexed",
action="store",
dest="notindexed",
type=ImageD11options.ColumnFileType(mode='w'),
help="Name of flt file for unindexed peaks")
parser.add_argument("-g",
"--grain",
action="store",
dest="grain",
type=int,
default=None,
help="Which grain to choose")
parser.description = """
Filtergrain should choose the peaks from a filtered
peaks output file according to those which are closest
to a particular grain
"""
return parser
def get_options(parser):
parser.add_argument("-5",
"--hdf5",
action="store",
type=str,
dest="hdf5",
default=None,
help="hdf file containing input image series")
# or, eventually:
# stem, first, last, format, (omegas better be in the headers)
parser.add_argument("-n",
"--stem",
action="store",
type=str,
dest="stem",
default=None,
help="stem name for input image series")
parser.add_argument("-f",
"--first",
action="store",
type=int,
dest="first",
default=None,
help="first number for input image series")
parser.add_argument("-l",
"--last",
action="store",
type=int,
dest="last",
default=None,
help="last number for input image series")
parser.add_argument("--ndigits",
action="store",
type=int,
dest="ndigits",
default=4,
help="Number of digits in file numbering [4]")
parser.add_argument("-P", "--padding", action="store",
choices=["Y","N"],
default="Y", dest="padding",
help="Is the image number to padded Y|N, e.g. "\
"should 1 be 0001 or just 1 in image name, default=Y")
parser.add_argument("-F",
"--format",
action="store",
type=str,
dest="format",
default=".edf",
help="format [.edf] for input image series")
parser.add_argument("-O",
"--flood",
action="store",
type=ImageD11options.ImageFileType(mode='r'),
dest="flood",
default=None,
help="Flood")
parser.add_argument("-d",
"--dark",
action="store",
dest="dark",
default=None,
type=ImageD11options.ImageFileType(mode='r'),
help="Dark image")
parser.add_argument("-S",
"--step",
action="store",
type=float,
dest="OMEGASTEP",
default=None,
help="omega step size")
parser.add_argument("-T",
"--start",
action="store",
type=float,
dest="OMEGA",
default=None,
help="start omega")
parser.add_argument(
"--omega_motor",
action="store",
type=str,
dest="omegamotor",
default="Omega",
help="Header value to use for rotation motor position [Omega]")
parser.add_argument(
"--omega_motor_step",
action="store",
type=str,
dest="omegamotorstep",
default="OmegaStep",
help="Header value to use for rotation width [OmegaStep]")
return parser
def get_options(parser):
""" Add our options to a parser object """
parser.add_argument("-n", "--namestem", action="store",
dest="stem", type=str, default="data",
help="Name of the files up the digits part "+\
"eg mydata in mydata0000.edf" )
parser.add_argument("-F", "--format", action="store",
dest="format",default=".edf", type=str,
help="Image File format, eg edf or bruker or GE or py" )
parser.add_argument("-f", "--first", action="store",
dest="first", default=0, type=int,
help="Number of first file to process, default=0")
parser.add_argument("-l", "--last", action="store",
dest="last", type=int,default =0,
help="Number of last file to process")
parser.add_argument("-o", "--outfile", action="store",
dest="outfile",default="peaks.spt", type=str,
help="Output filename, default=peaks.spt")
parser.add_argument("-d", "--darkfile", action="store",
dest="dark", default=None, type=ImageD11options.ImageFileType(mode='r'),
help="Dark current filename, to be subtracted, default=None")
dod = 0
parser.add_argument("-D", "--darkfileoffset", action="store",
dest="darkoffset", default=dod, type=float,
help=
"Constant to subtract from dark to avoid overflows, default=%d"%(dod))
# s="/data/opid11/inhouse/Frelon2K/spatial2k.spline"
parser.add_argument("-s", "--splinefile", action="store",
dest="spline", default=None, type=ImageD11options.SplineFileType(mode='r'),
help="Spline file for spatial distortion, default=None" )
parser.add_argument("-p", "--perfect_images", action="store",
choices=["Y","N"], default="Y", dest="perfect",
help="Ignore spline Y|N, default=N")
parser.add_argument("-O", "--flood", action="store",
type=ImageD11options.ImageFileType(mode='r'),
default=None, dest="flood",
help="Flood file, default=None")
parser.add_argument("-t", "--threshold", action="append", type=float,
dest="thresholds", default=None,
help="Threshold level, you can have several")
parser.add_argument("--OmegaFromHeader", action="store_false",
dest="OMEGAOVERRIDE", default=False,
help="Read Omega values from headers [default]")
parser.add_argument("--OmegaOverRide", action="store_true",
dest="OMEGAOVERRIDE", default=False,
help="Override Omega values from headers")
parser.add_argument("--singleThread", action="store_true",
dest="oneThread", default=False,
help="Do single threaded processing")
# if you want to do this then instead I think you want
# python -m cProfile -o xx.prof peaksearch.py ...
# python -m pstats xx.prof
# ... sort
# ... stats
# parser.add_argument("--profile", action="store",
# type=ImageD11options.ProfilingFileType,
# dest="profile_file", default=None,
# help="Write profiling information (you will want singleThread too)")
parser.add_argument("-S","--step", action="store",
dest="OMEGASTEP", default=1.0, type=float,
help="Step size in Omega when you have no header info")
parser.add_argument("-T","--start", action="store",
dest="OMEGA", default=0.0, type=float,
help="Start position in Omega when you have no header info")
parser.add_argument("-k","--killfile", action="store",
dest="killfile", default=None,
type=ImageD11options.FileType(),
help="Name of file to create stop the peaksearcher running")
parser.add_argument("--ndigits", action="store", type=int,
dest = "ndigits", default = 4,
help = "Number of digits in file numbering [4]")
parser.add_argument("-P", "--padding", action="store",
choices=["Y","N"], default="Y", dest="padding",
help="Is the image number to padded Y|N, e.g. "\
"should 1 be 0001 or just 1 in image name, default=Y")
parser.add_argument("-m", "--median1D", action="store_true",
default=False, dest="median",
help="Computes the 1D median, writes it to file .bkm and" \
+" subtracts it from image. For liquid background"\
+" on radially transformed images")
parser.add_argument("--monitorcol", action="store", type=str,
dest="monitorcol",
default = None,
help="Header value for incident beam intensity")
parser.add_argument("--monitorval", action="store", type=float,
dest="monitorval",
default = None,
help="Incident beam intensity value to normalise to")
parser.add_argument("--omega_motor", action="store", type=str,
dest = "omegamotor", default = "Omega",
help = "Header value to use for rotation motor position [Omega]")
parser.add_argument("--omega_motor_step", action="store", type=str,
dest = "omegamotorstep", default = "OmegaStep",
help = "Header value to use for rotation width [OmegaStep]")
parser.add_argument("--interlaced", action="store_true",
dest = "interlaced", default = False,
help = "Interlaced DCT scan")
parser.add_argument("--iflip", action="store_true",
dest="iflip", default=False,
help = "Reverse second half of interlaced scan")
return parser
def get_options(parser):
""" add the command line options to parser """
parser.add_argument(
"-n",
"--namestem",
action="store",
type=str,
dest="stem",
help="Name of the files up the digits part, eg mydata in mydata0000.edf"
)
parser.add_argument("-f",
"--first",
action="store",
type=int,
dest="first",
default=0,
help="Number of first file to process, default=0")
parser.add_argument("-l",
"--last",
action="store",
type=int,
dest="last",
default=0,
help="Number of last file to process")
parser.add_argument("-o",
"--outfile",
action="store",
type=ImageD11options.ImageFileType(mode='w'),
dest="outfile",
default="bkg.edf",
help="Output filename, default=bkg.edf")
parser.add_argument("-F",
"--Format",
action="store",
type=str,
dest="format",
default=".edf",
help="File format [edf|bruker]")
parser.add_argument("-s",
"--step",
action="store",
type=int,
dest="step",
default=1,
help="step - every nth image")
parser.add_argument("--ndigits",
action="store",
type=int,
dest="ndigits",
default=4,
help="Number of digits in file numbering [4]")
parser.add_argument(
"-k",
"--kalman-error",
action="store",
type=float,
dest="kalman_error",
default=0,
help="Error value to use Kalman style filter (read noise)")
return parser
def get_options(parser):
""" Add our options to a parser object """
parser.add_argument("-n",
"--nexusfile",
action="store",
dest="nexusfile",
type=str,
default=None,
help="The Nexus file path")
parser.add_argument("-g",
"--group_path",
action="store",
dest="group_path",
type=str,
default=None,
help="Internal NXS path to datasets group")
parser.add_argument("--image_dset",
action="store",
dest="image_dset",
type=str,
default=None,
help="Name of image files dataset")
parser.add_argument("--omega_dset",
action="store",
dest="omega_dset",
type=str,
default=None,
help="Name of omegas dataset")
parser.add_argument("-o",
"--outfile",
action="store",
dest="outfile",
default="peaks.spt",
type=str,
help="Output filename, default=peaks.spt")
parser.add_argument(
"-d",
"--darkfile",
action="store",
dest="dark",
default=None,
type=ImageD11options.ImageFileType(mode='r'),
help="Dark current filename, to be subtracted, default=None")
dod = 0
parser.add_argument(
"-D",
"--darkfileoffset",
action="store",
dest="darkoffset",
default=dod,
type=float,
help="Constant to subtract from dark to avoid overflows, default=%d" %
(dod))
parser.add_argument(
"-s",
"--splinefile",
action="store",
dest="spline",
default=None,
type=ImageD11options.SplineFileType(mode='r'),
help="Spline file for spatial distortion, default=None")
parser.add_argument("-p",
"--perfect_images",
action="store",
choices=["Y", "N"],
default="Y",
dest="perfect",
help="Ignore spline Y|N, default=N")
parser.add_argument("-O",
"--flood",
action="store",
type=ImageD11options.ImageFileType(mode='r'),
default=None,
dest="flood",
help="Flood file, default=None")
parser.add_argument("-t",
"--threshold",
action="append",
type=float,
dest="thresholds",
default=None,
help="Threshold level, you can have several")
parser.add_argument("--singleThread",
action="store_true",
dest="oneThread",
default=False,
help="Do single threaded processing")
parser.add_argument(
"-k",
"--killfile",
action="store",
dest="killfile",
default=None,
type=ImageD11options.FileType(),
help="Name of file to create stop the peaksearcher running")
parser.add_argument("-m", "--median1D", action="store_true",
default=False, dest="median",
help="Computes the 1D median, writes it to file .bkm and" \
+ " subtracts it from image. For liquid background" \
+ " on radially transformed images")
parser.add_argument("--monitorcol",
action="store",
type=str,
dest="monitorcol",
default=None,
help="Header value for incident beam intensity")
parser.add_argument("--monitorval",
action="store",
type=float,
dest="monitorval",
default=None,
help="Incident beam intensity value to normalise to")
parser.add_argument("--interlaced",
action="store_true",
dest="interlaced",
default=False,
help="Interlaced DCT scan")
parser.add_argument("--iflip",
action="store_true",
dest="iflip",
default=False,
help="Reverse second half of interlaced scan")
return parser