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src/a/r/arachnid-0.1.7/arachnid/pyspider/defocus.py   arachnid(Download)
 
    group = OptionGroup(parser, "Additional", "Options to customize defocus estimation", group_order=0,  id=__name__)
    group.add_option("",   disable_bin=False,                              help="Disable micrograph decimation")
    group.add_option("",   '--pow-file', output_pow="",                    help="Filename for output power spectra", gui=dict(filetype="save"))
    group.add_option("",   output_roo="",                                  help="Filename for output rotational average", gui=dict(filetype="save"), dependent=False)
    group.add_option("",   output_ctf="",                                  help="Filename for output CTF curve", gui=dict(filetype="save"), dependent=False)
    group.add_option("",   '--small-micrograph-file', output_mic="",       help="Filename for output for decimated micrograph", gui=dict(filetype="save"), dependent=False)

src/a/r/arachnid-0.1.7/arachnid/util/project.py   arachnid(Download)
 
    addgroup = OptionGroup(parser, "Parallel", "Options for parallel processing")
    addgroup.add_option("-w", worker_count=1,  help="Set number of  workers to process files in parallel",  gui=dict(minimum=0), dependent=False)
    addgroup.add_option("-t", thread_count=1,  help="Number of threads per machine, 0 means determine from environment", gui=dict(minimum=0), dependent=False)
    pgroup.add_option_group(addgroup)
 
    shrgroup = OptionGroup(parser, "Metadata", "Files created during workflow")
    shrgroup.add_option("", config_path="cfg",                                     help="Location for configuration scripts", gui=dict(filetype="open"))
    shrgroup.add_option("", linked_files="",                                       help="Location for renamed links - name automatically set based on input", gui=dict(filetype="open"))
    shrgroup.add_option("", micrograph_files="other/mics/mic_00000.dat",          help="Location for micrograph files", gui=dict(filetype="open"))

src/a/r/arachnid-0.1.7/arachnid/app/vicer.py   arachnid(Download)
    from ..core.app.settings import OptionGroup
    group = OptionGroup(parser, "ViCer", "Particle verification with View Classifier or ViCer",  id=__name__)
    group.add_option("", nsamples=1,                help="Number of rotational samples")
    group.add_option("", angle_range=3.0,           help="Angular search range")
    group.add_option("", resolution=40.0,           help="Filter to given resolution - requires apix to be set")
    group.add_option("", disable_rtsq=False,        help="Do not use alignment parameters to rotate projections in 2D")
    group.add_option("", neig=2,                    help="Number of eigen vectors to use", dependent=False)

src/a/r/arachnid-0.1.7/arachnid/pyspider/autorefine.py   arachnid(Download)
    if main_option:        
        bgroup = OptionGroup(parser, "Primary", "Primary options to set for input and output", group_order=0,  id=__name__)
        bgroup.add_option("-i", input_files=[],          help="List of input images or stacks named according to the SPIDER format", required_file=True, gui=dict(filetype="file-list"))
        bgroup.add_option("-o", output="",               help="Base filename for output volume and half volumes, which will be named raw_$output, raw1_$output, raw2_$output", gui=dict(filetype="save"), required_file=True)
        bgroup.add_option("-r", reference="",            help="Filename for reference with the proper pixel size", gui=dict(filetype="open"), required_file=True)
        bgroup.add_option("",   resolution_start=30.0,   help="Starting resolution for the refinement")
        bgroup.add_option("",   num_iterations=10,       help="Maximum number of iterations")

src/a/r/arachnid-0.1.7/arachnid/util/relion_selection.py   arachnid(Download)
    from ..core.app.settings import OptionGroup
    group = OptionGroup(parser, "Relion Selection", "Options to control creation of a relion selection file",  id=__name__)
    group.add_option("-s", class_file="",               help="SPIDER micrograph, class selection file, or comma separated list of classes (e.g. 1,2,3) - if select file does not have proper header, then use `--selection-file filename=id` or `--selection-file filename=id,select`", gui=dict(filetype="open"))
 
    group.add_option("",   selection_file="",               help="SPIDER micrograph selection file - if select file does not have proper header, then use `--selection-file filename=id` or `--selection-file filename=id,select`", gui=dict(filetype="open"))
    group.add_option("-g", good_file="",                    help="SPIDER particle selection file template - if select file does not have proper header, then use `--good-file filename=id` or `--good-file filename=id,select`", gui=dict(filetype="open"))
    group.add_option("",   reindex_file="",                 help="Reindex file for 1) running movie mode on a subset of selected particles in a stack or 2) When generating a relion selection file from a single stack", gui=dict(filetype="open"))
    group.add_option("-p", param_file="",                   help="SPIDER parameters file (Only required when the input is a stack)", gui=dict(filetype="open"))

src/a/r/arachnid-0.1.7/arachnid/pyspider/refine.py   arachnid(Download)
 
        bgroup = OptionGroup(parser, "Primary", "Primary options to set for input and output", group_order=0,  id=__name__)
        bgroup.add_option("-i", input_files=[],          help="List of input images or stacks named according to the SPIDER format", required_file=True, gui=dict(filetype="file-list"))
        bgroup.add_option("-o", output="",               help="Base filename for output volume and half volumes, which will be named raw_$output, raw1_$output, raw2_$output", gui=dict(filetype="save"), required_file=True)
        bgroup.add_option("-r", reference="",            help="Filename for reference with the proper pixel size", gui=dict(filetype="open"), required_file=True)
        bgroup.add_option("-a", alignment="",            help="Filename for the alignment parameters", gui=dict(filetype="open"), required_file=True)
        pgroup.add_option_group(bgroup)
        sgroup = OptionGroup(parser, "Refinement", "Option to change during refinement", group_order=0,  id=__name__)
        sgroup.add_option("",   refine_name=refine_name, help="List of option names to change in each round of refinement, values set in `refine-step`")

src/a/r/arachnid-0.1.7/arachnid/app/lfcpick.py   arachnid(Download)
    #group.add_option("-r", pixel_radius=0,      help="Radius of the expected particle (if default value 0, then overridden by SPIDER params file, --param-file)")
    #group.add_option("",   window=1.0,          help="Size of the output window or multiplicative factor if less than particle diameter (overridden by SPIDER params file, --param-file)")
    group.add_option("",   disk_mult=0.6,       help="Disk smooth kernel size factor", gui=dict(maximum=10.0, minimum=0.01, singleStep=0.1, decimals=2)) #"2:0.1:0.01:10.0"
    group.add_option("",   overlap_mult=1.0,    help="Multiplier for the amount of allowed overlap or inter-particle distance", gui=dict(maximum=10.0, minimum=0.001, singleStep=0.1, decimals=2))
    group.add_option("",   template="",         help="Optional predefined template", gui=dict(filetype="open"))
    group.add_option("",   disable_bin=False,   help="Disable micrograph decimation")
    group.add_option("",   invert=False,        help="Invert the contrast of CCD micrographs")

src/a/r/arachnid-0.1.7/arachnid/app/reconstruct.py   arachnid(Download)
    from ..core.app.settings import OptionGroup
    group = OptionGroup(parser, "Reconstruct", "Reconstruct a volume from an alignment file and particle stacks",  id=__name__)
    group.add_option("",     scale_spi=False,           help="Scale the SPIDER translation (if refinement was done by pySPIDER)")
    group.add_option("",     apix=0.0,                  help="Pixel size for the data")
    group.add_option("-t",   thread_count=1,            help="Number of processes per machine", gui=dict(minimum=0), dependent=False)
    group.add_option("-r",   rand_subset=0,             help="Reconstruct a random subset of the given size", gui=dict(minimum=0), dependent=False)
    group.add_option("",     experimental=False,        help="Test experimental shared memory")

src/a/r/arachnid-0.1.7/arachnid/util/coverage.py   arachnid(Download)
    from ..core.app.settings import OptionGroup
    group = OptionGroup(parser, "Coverage", "Options to control creation of the coverage plot",  id=__name__)
    group.add_option("-p", projection="npstere",    help="Map projection type")
    group.add_option("-d", dpi=300,                 help="Resolution of the image in dots per inch")
    group.add_option("-r", view_resolution=3,       help="Group views into a coarse grid: (2) 15 deg, (3) 7.5 deg ...")
    group.add_option("-a", area_mult=1.0,           help="Cirle area multiplier")
    group.add_option("", disable_mirror=False,      help="Disable mirroring over the equator for counting")

src/a/r/arachnid-0.1.7/arachnid/util/crop.py   arachnid(Download)
    group = OptionGroup(parser, "Cropping", "Options to crop particles from micrographs", id=__name__) #, gui=dict(root=True, stacked="prepComboBox"))
 
    group.add_option("", single_stack=False,       help="Crop all files into a single stack")
    group.add_option("", invert=False,             help="Invert the contrast on the micrograph (usually for raw CCD micrographs)")
    group.add_option("", noise="",                 help="Use specified noise file rather then automatically generate one", gui=dict(filetype="open"))
    group.add_option("", gain_file="",             help="Perform gain correction with given norm image", gui=dict(filetype="open"))
 
    egroup = OptionGroup(parser, "Enhancement", "Enhancement for the windows")
    egroup.add_option("", disable_even=False,       help="Disable forcing windows to be even")

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