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src/a/r/arachnid-0.1.7/arachnid/pyspider/align.py   arachnid(Download)
def setup_options(parser, pgroup=None, main_option=False):
    #Setup options for automatic option parsing
    from ..core.app.settings import setup_options_from_doc, OptionGroup
 
    if pgroup is None: pgroup=parser
    if main_option:
        pgroup.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"))
        pgroup.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)
        pgroup.add_option("-r", reference="",   help="Filename for reference with the proper pixel size", gui=dict(filetype="open"), required_file=True)
        setup_options_from_doc(parser, spider.open_session, group=pgroup)
 
    group = OptionGroup(parser, "Other Parameters", "Options controlling alignment", group_order=0,  id=__name__)
    setup_options_from_doc(parser, 'pj_3q', 'vo_ea', 'ap_sh', classes=spider.Session, group=group)
    pgroup.add_option_group(group)
    if main_option:

src/a/r/arachnid-0.1.7/arachnid/pyspider/resolution.py   arachnid(Download)
def setup_options(parser, pgroup=None, main_option=False):
    #Setup options for automatic option parsing
    from ..core.app.settings import setup_options_from_doc
 
    if main_option:
 
        spider_params.setup_options(parser, pgroup, True)
    setup_options_from_doc(parser, estimate_resolution, 'rf_3', classes=spider.Session, group=pgroup)
    if main_option:
        setup_options_from_doc(parser, spider.open_session, group=pgroup)

src/a/r/arachnid-0.1.7/arachnid/pyspider/reconstruct.py   arachnid(Download)
def setup_options(parser, pgroup=None, main_option=False):
    #Setup options for automatic option parsing
    from ..core.app.settings import setup_options_from_doc, OptionGroup
 
    if main_option:
        pgroup.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"))
        pgroup.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)
        pgroup.add_option("-a", alignment=[],   help="Filename for the alignment parameters", gui=dict(filetype="open"), required_file=True)
 
        setup_options_from_doc(parser, spider.open_session, group=pgroup)
    rgroup.add_option("",   interpolation="Q",                       help="Type of interpolation to use: (Q) quadratic and (FS) Fourier Spline")
    rgroup.add_option("",   boost=False,                             help="Increase the weight on poorly aligned projections")
    setup_options_from_doc(parser, 'bp_cg_3', classes=spider.Session, group=rgroup)
    pgroup.add_option_group(rgroup)
 

src/a/r/arachnid-0.1.7/arachnid/pyspider/mask_volume.py   arachnid(Download)
def setup_options(parser, pgroup=None, main_option=False):
    #Setup options for automatic option parsing
    from ..core.app.settings import setup_options_from_doc, OptionGroup
 
    if main_option:
        pgroup.add_option("-i", input_files=[], help="List of input filenames containing volumes", required_file=True, gui=dict(filetype="file-list"))
        pgroup.add_option("-o", output="",      help="Output filename for masked volume with correct number of digits (e.g. masked_0000.spi)", gui=dict(filetype="save"), required_file=True)
        spider_params.setup_options(parser, pgroup, False)
    mgroup = OptionGroup(parser, "Masking", "Option to control masking",  id=__name__, group_order=0)
    setup_options_from_doc(parser, mask_volume, spherical_mask, tightmask, group=mgroup)
    pgroup.add_option_group(mgroup)
    if main_option:
        setup_options_from_doc(parser, spider.open_session, group=pgroup)
        parser.change_default(thread_count=4, log_level=3)
 

src/a/r/arachnid-0.1.7/arachnid/pyspider/filter_volume.py   arachnid(Download)
def setup_options(parser, pgroup=None, main_option=False):
    #Setup options for automatic option parsing
    from ..core.app.settings import setup_options_from_doc
 
    if main_option:
        pgroup.add_option("-r", resolution=15.0,        help="Resolution to filter the volumes")
        #pgroup.add_option("-g", reg=0.006,              help="Regularization parameter for TVD (4)")
    setup_options_from_doc(parser, filter_volume_lowpass, group=pgroup)
    if main_option:
        setup_options_from_doc(parser, spider.open_session, filter_volume_highpass, group=pgroup)

src/a/r/arachnid-0.1.7/arachnid/pyspider/defocus.py   arachnid(Download)
def setup_options(parser, pgroup=None, main_option=False):
    #Setup options for automatic option parsing
    from ..core.app.settings import setup_options_from_doc, OptionGroup
 
    pgroup.add_option("-i", '--micrograph-files', input_files=[], help="List of input filenames containing micrographs, window stacks or power spectra, e.g. mic_*.mrc ", required_file=True, gui=dict(filetype="open"), regexp=spider_utility.spider_searchpath)
    pgroup.add_option_group(group)
 
    setup_options_from_doc(parser, create_powerspectra, group=pgroup)# classes=spider.Session, for_window_in_micrograph
    if main_option:
        setup_options_from_doc(parser, spider.open_session)

src/a/r/arachnid-0.1.7/arachnid/pyspider/autorefine.py   arachnid(Download)
def setup_options(parser, pgroup=None, main_option=False):
    #Setup options for automatic option parsing
    from ..core.app.settings import OptionGroup, setup_options_from_doc
 
    if main_option:        
        bgroup.add_option("",   restrict_angle=3.0,         help="Angular step size at which to use estimated angular restrictions")
        pgroup.add_option_group(bgroup)
        setup_options_from_doc(parser, spider.open_session, group=pgroup)
        spider_params.setup_options(parser, pgroup, True)
 

src/a/r/arachnid-0.1.7/arachnid/pyspider/refine.py   arachnid(Download)
def setup_options(parser, pgroup=None, main_option=False):
    #Setup options for automatic option parsing
    from ..core.app.settings import OptionGroup, setup_options_from_doc
 
    if main_option:
        sgroup.add_option("",   refine_step=refine_step, help="List of value tuples where each tuple represents a round of refinement and contains a value for each parameter specified in the same order as `refine-name` for each round of refinement; each round is separated with a comma; each value by a colon, e.g. 15,10:0:6:1,8:0:4,1:3:1")
        pgroup.add_option_group(sgroup)
        setup_options_from_doc(parser, spider.open_session, group=pgroup)
        spider_params.setup_options(parser, pgroup, True)
 

src/a/r/arachnid-0.1.7/arachnid/pyspider/enhance_volume.py   arachnid(Download)
def setup_options(parser, pgroup=None, main_option=False):
    #Setup options for automatic option parsing
    from ..core.app.settings import setup_options_from_doc
 
    if main_option:
        pgroup.add_option("-i", input_files=[], help="List of input filenames containing volumes", required_file=True, gui=dict(filetype="file-list"))
        pgroup.add_option("-o", output="",      help="Output filename for filtered/enhanced volume with correct number of digits (e.g. masked_0000.spi)", gui=dict(filetype="save"), required_file=True)
        spider_params.setup_options(parser, pgroup, True)
        pgroup.add_option("-r", resolution=15.0,     help="Resolution to filter the volumes")
        setup_options_from_doc(parser, spider.open_session, group=pgroup)
 
 
    setup_options_from_doc(parser, enhance_volume, group=pgroup)
    parser.change_default(thread_count=4, log_level=3)
 

src/a/r/arachnid-0.1.7/arachnid/pyspider/classify.py   arachnid(Download)
def setup_options(parser, pgroup=None, main_option=False):
    #Setup options for automatic option parsing
 
    if 1 == 1:
        from ..core.app.settings import setup_options_from_doc
        setup_options_from_doc(parser, classify_projections, group=pgroup)

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