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