def get_valid_opts(self): """return an OptionsList of valid program options""" # terminal, informative options vopts = OPT.OptionList('uber_subject.py options') vopts.add_opt('-help', 0, [], helpstr='show this help') vopts.add_opt('-help_gui', 0, [], helpstr='show help for GUI') vopts.add_opt('-help_todo', 0, [], helpstr='show todo list') vopts.add_opt('-help_howto_program',0,[],helpstr='programming overview') vopts.add_opt('-hist', 0, [], helpstr='show revision history') vopts.add_opt('-show_default_vars',0,[],helpstr='show variable defaults') vopts.add_opt('-show_valid_opts',0,[],helpstr='show all valid options') vopts.add_opt('-ver', 0, [], helpstr='show module version') vopts.add_opt('-verb', 1, [], helpstr='set verbose level') vopts.add_opt('-no_gui', 0, [], helpstr='do not open graphical interface') vopts.add_opt('-qt_opts',-1, [],helpstr='pass the given options to PyQt') vopts.add_opt('-print_script', 0, [], helpstr='print align test script') vopts.add_opt('-save_script', 1, [], helpstr='save align test script') vopts.add_opt('-cvar', -2, [], helpstr='set control variable') vopts.add_opt('-uvar', -2, [], helpstr='set user variable to value') vopts.trailers = 0 # do not allow unknown options return vopts
def get_valid_opts(self): vopts = OL.OptionList('valid opts') # short, terminal arguments vopts.add_opt('-help', 0, [], helpstr='display program help') vopts.add_opt('-help_examples', 0, [], helpstr='display program examples') vopts.add_opt('-hist', 0, [], helpstr='display the modification history') vopts.add_opt('-ver', 0, [], helpstr='display the current version number') # general options vopts.add_opt('-labels', -1, [], helpstr='specify labels to search for') vopts.add_opt('-logfile', 1, [], helpstr='specify input label table log file') vopts.add_opt('-show_all_orig', 0, [], helpstr='show all unranked indices, even if not found') vopts.add_opt('-show_orig', 0, [], helpstr='only show unranked indices') vopts.add_opt('-show_rank', 0, [], helpstr='only show ranked indices') vopts.add_opt('-verb', 1, [], helpstr='set the verbose level (def=1)') vopts.sort() return vopts
def get_valid_opts(self): vopts = OL.OptionList('valid opts') # short, terminal arguments vopts.add_opt('-help', 0, [], helpstr='display program help') vopts.add_opt('-hist', 0, [], helpstr='display the modification history') vopts.add_opt('-ver', 0, [], helpstr='display the current version number') # general options vopts.add_opt('-infiles', -1, [], helpstr='specify input files') vopts.add_opt('-overwrite', 0, [], helpstr='flag to overwrite any existing output files') vopts.add_opt('-prefix', 1, [], helpstr='specify prefix for output files') vopts.add_opt('-verb', 1, [], helpstr='set the verbose level (def=1)') vopts.sort() return vopts
def init_options(self): self.valid_opts = OL.OptionList('valid opts') # terminal options self.valid_opts.add_opt('-help', 0, [], helpstr='display program help') self.valid_opts.add_opt('-help_dot_files', 0, [], helpstr='display help on shell setup files') self.valid_opts.add_opt('-help_rc_files', 0, [], helpstr='display help on shell setup files') self.valid_opts.add_opt('-hist', 0, [], helpstr='display the modification history') self.valid_opts.add_opt('-show_valid_opts', 0, [], helpstr='display all valid options') self.valid_opts.add_opt('-todo', 0, [], helpstr='display the current "todo list"') self.valid_opts.add_opt('-ver', 0, [], helpstr='display the current version number') # action options self.valid_opts.add_opt( '-casematch', 1, [], acplist=['yes', 'no'], helpstr='yes/no: specify case sensitivity in -find_prog') self.valid_opts.add_opt('-check_all', 0, [], helpstr='perform all system checks') self.valid_opts.add_opt('-data_root', 1, [], helpstr='directory to check for class data') self.valid_opts.add_opt('-dot_file_list', 0, [], helpstr='list found dot files') self.valid_opts.add_opt( '-dot_file_pack', 1, [], helpstr='package dot files into given tgz package') self.valid_opts.add_opt('-dot_file_show', 0, [], helpstr='display contents of dot files') self.valid_opts.add_opt( '-exact', 1, [], acplist=['yes', 'no'], helpstr='yes/no: use exact matching in -find_prog') self.valid_opts.add_opt('-find_prog', 1, [], helpstr='search path for *PROG*') self.valid_opts.add_opt('-verb', 1, [], helpstr='set verbosity level (default=1)') return 0
def init_opts(self): global g_help_string self.valid_opts = option_list.OptionList('for input') # short, terminal arguments self.valid_opts.add_opt('-help', 0, [], \ helpstr='display program help') self.valid_opts.add_opt('-hist', 0, [], \ helpstr='display the modification history') self.valid_opts.add_opt('-show_valid_opts', 0, [], \ helpstr='display all valid options') self.valid_opts.add_opt('-ver', 0, [], \ helpstr='display the current version number') # required arguments self.valid_opts.add_opt('-infiles', -1, [], req=1, helpstr='input files (containing BOLD curve)') # optional arguments self.valid_opts.add_opt('-kernel', 1, [], helpstr='response kernel [GAM])') self.valid_opts.add_opt( '-kernel_file', 1, [], helpstr='file for reponse kernel [resp_kernel.1D]') self.valid_opts.add_opt('-mask_dset', 1, [], helpstr='computational mask dataset') self.valid_opts.add_opt('-old', 0, [], helpstr='generate script with old method') self.valid_opts.add_opt('-outdir', 1, [], helpstr='specify output directory') self.valid_opts.add_opt('-prefix', 1, [], helpstr='prefix for deconvolved dataset') self.valid_opts.add_opt('-script', 1, [], req=1, helpstr='output script filename') self.valid_opts.add_opt('-tr', 1, [], helpstr='specify TR for 3dDeconvolve command') self.valid_opts.add_opt( '-tr_nup', 1, [], helpstr='upsample TR factor, e.g. 20 (=2.0/0.1)') self.valid_opts.add_opt( '-verb', 1, [], helpstr='verbose level (0=quiet, 1=default, ...)')
def init_opts(self): global g_help_string self.valid_opts = option_list.OptionList('for input') # short, terminal arguments self.valid_opts.add_opt('-help', 0, [], \ helpstr='display program help') self.valid_opts.add_opt('-hist', 0, [], \ helpstr='display the modification history') self.valid_opts.add_opt('-show_valid_opts', 0, [], \ helpstr='display all valid options') self.valid_opts.add_opt('-ver', 0, [], \ helpstr='display the current version number') # required arguments self.valid_opts.add_opt('-dsets', -1, [], req=1, helpstr='list of input datasets') # optional arguments self.valid_opts.add_opt('-script', 1, [], helpstr='name for output script') self.valid_opts.add_opt( '-verb', 1, [], helpstr='verbose level (0=quiet, 1=default, ...)') self.valid_opts.add_opt('-windows', -1, [], acplist=['axial', 'coronal', 'sagittal'], helpstr='choose afni image windows to display') # corrdinate arguments self.valid_opts.add_opt('-im_size', 2, [], helpstr='image size, in pixels (2 integers)') self.valid_opts.add_opt('-im_xoff', 1, [], helpstr='x-offset for image, in pixels') self.valid_opts.add_opt('-im_yoff', 1, [], helpstr='y-offset for image, in pixels') self.valid_opts.add_opt('-gr_size', 2, [], helpstr='graph size, in pixels (2 integers)') self.valid_opts.add_opt('-gr_xoff', 1, [], helpstr='x-offset for graph, in pixels') self.valid_opts.add_opt('-gr_yoff', 1, [], helpstr='y-offset for graph, in pixels')
def init_options(self): """return an option list instance""" valid_opts = OL.OptionList('valid opts') # short, terminal arguments valid_opts.add_opt('-help', 0, [], helpstr='display program help') valid_opts.add_opt('-hist', 0, [], helpstr='display the modification history') valid_opts.add_opt('-show_valid_opts', 0, [], helpstr='display all valid options') valid_opts.add_opt('-ver', 0, [], helpstr='display the current version number') # general options valid_opts.add_opt('-verb', 1, [], helpstr='set the verbose level (default is 1)') valid_opts.add_opt('-data_choice', 1, [], helpstr='which data to send (motion, motion_norm,...)') valid_opts.add_opt('-dc_params', -2, [], helpstr='set parameters for data_choice processing') valid_opts.add_opt('-extras_on_one_line', 1, [], acplist=['no', 'yes'], helpstr='print sets of data each on only 1 line') valid_opts.add_opt('-serial_port', 1, [], helpstr='serial port filename (e.g. /dev/ttyS0 or COM1)') valid_opts.add_opt('-show_data', 1, [], acplist=['no', 'yes'], helpstr='whether to display received data in terminal') valid_opts.add_opt('-show_comm_times', 0, [], helpstr='display communication times') valid_opts.add_opt('-write_text_data', 1, [], helpstr='write data to text file') # demo options valid_opts.add_opt('-show_demo_data', 1, [], acplist=['no', 'yes'], helpstr='whether to display demo data in terminal') valid_opts.add_opt('-show_demo_gui', 1, [], acplist=['no', 'yes'], helpstr='whether to display demo data in a GUI') valid_opts.add_opt('-swap', 0, [], helpstr='byte-swap numerical reads') valid_opts.add_opt('-tcp_port', 1, [], helpstr='TCP port for incoming connections') return valid_opts
def get_valid_opts(self): """return an OptionsList of valid program options""" # terminal, informative options vopts = OPT.OptionList('uber_subject.py options') vopts.add_opt('-help', 0, [], helpstr='show this help') vopts.add_opt('-help_gui', 0, [], helpstr='show help for GUI') vopts.add_opt('-help_todo', 0, [], helpstr='show todo list') vopts.add_opt('-hist', 0, [], helpstr='show revision history') vopts.add_opt('-show_default_vars', 0, [], helpstr='show variable defaults') vopts.add_opt('-show_valid_opts', 0, [], helpstr='show all valid options') vopts.add_opt('-show_cvar_dict', 0, [], helpstr='show control var dict') vopts.add_opt('-show_uvar_dict', 0, [], helpstr='show user var dictionary') vopts.add_opt('-ver', 0, [], helpstr='show module version') vopts.add_opt('-verb', 1, [], helpstr='set verbose level') vopts.add_opt('-no_gui', 0, [], helpstr='do not open graphical interface') vopts.add_opt('-qt_opts', -1, [], helpstr='pass the given options to PyQt') vopts.add_opt('-print_script', 0, [], helpstr='print align test script') vopts.add_opt('-save_script', 1, [], helpstr='save align test script') vopts.add_opt('-cvar', -2, [], helpstr='set control variable') vopts.add_opt('-uvar', -2, [], helpstr='set user variable to value') vopts.trailers = 0 # do not allow unknown options # add user and control vars directly for dict in [LTT.g_cvar_dict, LTT.g_uvar_dict]: keys = list(dict.keys()) keys.sort() for name in keys: if name == 'verb': continue # already included vopts.add_opt('-' + name, -1, [], helpstr=dict[name]) return vopts
def get_valid_opts(self): vopts = OL.OptionList('valid opts') # short, terminal arguments vopts.add_opt('-help', 0, [], helpstr='display program help') vopts.add_opt('-hist', 0, [], helpstr='display the modification history') vopts.add_opt('-ver', 0, [], helpstr='display the current version number') # general options vopts.add_opt('-infiles', -1, [], helpstr='input text files (from @ss_review_basic)') vopts.add_opt('-overwrite', 0, [], helpstr='allow overwrite for output table file') vopts.add_opt('-report_outliers', -2, [], helpstr='report outlier subjects for test') vopts.add_opt('-report_outliers_fill_style', 1, [], acplist=self.ro_valid_fills, helpstr='how to fill empty (non-outlier) entries') vopts.add_opt('-report_outliers_header_style', 1, [], acplist=self.ro_valid_heads, helpstr='how to format column headers') vopts.add_opt('-separator', 1, [], helpstr="specify field separator (default=':')") vopts.add_opt('-outlier_sep', 1, [], helpstr="output field separator (default=tab)") vopts.add_opt('-showlabs', 0, [], helpstr='show list of labels found') vopts.add_opt('-show_infiles', 0, [], helpstr='make tablefile output start with input files') vopts.add_opt('-show_missing', 0, [], helpstr='show all missing keys') vopts.add_opt('-write_outliers', 1, [], helpstr='file name for outlier table (default=stdout)') vopts.add_opt('-write_table', 1, [], helpstr='file name for output table (dupe for -tablefile)') vopts.add_opt('-tablefile', 1, [], helpstr='file name for output table') vopts.add_opt('-verb', 1, [], helpstr='set the verbose level (def=1)') vopts.sort() return vopts
def get_valid_opts(self): vopts = OPT.OptionList('valid opts') # short, terminal arguments vopts.add_opt('-help', 0, [], helpstr='display program help') vopts.add_opt('-hist', 0, [], helpstr='display the modification history') vopts.add_opt('-show_default_cvars', 0, [], helpstr='show default cvars') vopts.add_opt('-show_default_uvars', 0, [], helpstr='show default uvars') vopts.add_opt('-show_valid_opts', 0, [], helpstr='display all valid options') vopts.add_opt('-ver', 0, [], helpstr='display the current version number') vopts.add_opt('-cvar', -2, [], helpstr='set control variable') vopts.add_opt('-uvar', -2, [], helpstr='set user variable to value') # general options vopts.add_opt('-on_surface', 1, [], acplist=['yes', 'no'], helpstr='work directly on the surface (yes/no)') vopts.add_opt('-print_script', 0, [], helpstr='print script to terminal window') vopts.add_opt('-save_script', 1, [], helpstr='write script to given file') vopts.add_opt('-verb', 1, [], helpstr='set the verbose level (default=1)') return vopts
def init_options(self): self.valid_opts = OL.OptionList('valid opts') # short, terminal arguments self.valid_opts.add_opt('-help', 0, [], \ helpstr='display program help') self.valid_opts.add_opt('-hist', 0, [], \ helpstr='display the modification history') self.valid_opts.add_opt('-show_valid_opts', 0, [],\ helpstr='display all valid options') self.valid_opts.add_opt('-ver', 0, [], \ helpstr='display the current version number') # required parameters self.valid_opts.add_opt('-infile', 1, [], helpstr='read the given 1D file') # general options self.valid_opts.add_opt('-verb', 1, [], helpstr='set the verbose level (default is 1)') return 0
def get_valid_opts(): """return an OptionsList of valid program options""" # terminal, informative options vopts = OPT.OptionList('uber_subject.py options') vopts.add_opt('-help', 0, [], helpstr='show this help') vopts.add_opt('-help_gui', 0, [], helpstr='show help for GUI') vopts.add_opt('-help_howto_program', 0, [], helpstr='help for programming') vopts.add_opt('-help_install', 0, [], helpstr='show install notes') vopts.add_opt('-help_install_nokia', 0, [], helpstr='Nokia install help') vopts.add_opt('-hist', 0, [], helpstr='show revision history') vopts.add_opt('-show_default_vars',0,[],helpstr='show variable defaults') vopts.add_opt('-show_valid_opts',0,[],helpstr='show all valid options') vopts.add_opt('-show_svar_dict',0,[],helpstr='show subject var dictionary') vopts.add_opt('-ver', 0, [], helpstr='show module version') vopts.add_opt('-verb', 1, [], helpstr='set verbose level') vopts.add_opt('-no_gui', 0, [], helpstr='do not open graphical interface') vopts.add_opt('-qt_opts', -1, [], helpstr='pass the given options to PyQt') vopts.add_opt('-print_ap_command',0,[],helpstr='show afni_proc.py script') vopts.add_opt('-save_ap_command',1,[],helpstr='save afni_proc.py script') vopts.add_opt('-exec_ap_command',0,[],helpstr='run afni_proc.py command') vopts.add_opt('-exec_proc_script',0,[],helpstr='run proc script') vopts.add_opt('-cvar', -2, [], helpstr='set control variable to value') vopts.add_opt('-svar', -2, [], helpstr='set subject variable to value') # and add all subject vars directly keys = list(USUBJ.g_svar_dict.keys()) keys.sort() for name in keys: vopts.add_opt('-'+name, -1, [], helpstr=USUBJ.g_svar_dict[name]) vopts.trailers = 0 # do not allow unknown options return vopts
def get_opts(): global g_help_string okopts = option_list.OptionList('for input') okopts.add_opt('-help', 0, [], \ helpstr='display program help') okopts.add_opt('-hist', 0, [], \ helpstr='display the modification history') okopts.add_opt('-show_valid_opts', 0, [], \ helpstr='display all valid options') okopts.add_opt('-ver', 0, [], \ helpstr='display the current version number') okopts.add_opt('-amplitudes', 0, [], \ helpstr='output is in -stim_times_AM1 format') okopts.add_opt('-files', -1, [], req=1, okdash=0, helpstr='set the list of input files') okopts.add_opt('-prefix', 1, [], req=1, \ helpstr='specify the prefix for output files') okopts.add_opt('-tr', 1, [], req=1, \ helpstr='set the TR time, in seconds') okopts.add_opt('-nt', 1, [], req=0, \ helpstr='set the number of TRs per run') okopts.add_opt('-nruns', 1, [], req=0, \ helpstr='set the number of runs') okopts.add_opt('-no_consec', 0, [], \ helpstr='do not allow consecutive events') okopts.add_opt('-offset', 1, [], \ helpstr='specify offset to add to all output times') okopts.add_opt('-run_trs', -1, [], req=0, \ helpstr='specify TRs per run, if they vary') okopts.add_opt('-labels', -1, [], okdash=0, helpstr='add these labels to the file names') okopts.add_opt('-verb', 1, [], \ helpstr='set the verbosity level') okopts.trailers = 1 # process any optlist_ options okopts.check_special_opts(sys.argv) # if argv has only the program name, or user requests help, show it if len(sys.argv) <= 1 or '-help' in sys.argv: print(g_help_string) return if '-hist' in sys.argv: # print history print(g_mst_history) return if '-show_valid_opts' in sys.argv: # show all valid options okopts.show('', 1) return if '-ver' in sys.argv: # print version print(g_mst_version) return opts = option_list.read_options(sys.argv, okopts) return opts
def init_options(self): self.valid_opts = OL.OptionList('valid opts') # short, terminal arguments self.valid_opts.add_opt('-help', 0, [], \ helpstr='display program help') self.valid_opts.add_opt('-help_gui', 0, [], \ helpstr='display program help') self.valid_opts.add_opt('-hist', 0, [], \ helpstr='display the modification history') self.valid_opts.add_opt('-show_valid_opts', 0, [],\ helpstr='display all valid options') self.valid_opts.add_opt('-test', 0, [], \ helpstr='run a basic test with known files') self.valid_opts.add_opt('-test_libs', 0, [], \ helpstr='test for existence of neede python libraries') self.valid_opts.add_opt('-ver', 0, [], \ helpstr='display the current version number') # computational options self.valid_opts.add_opt('-load_xmat', 1, [], helpstr='load the given X-matrix') self.valid_opts.add_opt('-load_1D', 1, [], helpstr='load the given 1D time series') self.valid_opts.add_opt('-choose_cols', 1, [], helpstr='choose X-matrix columns') self.valid_opts.add_opt('-show_col_types', 0, [], helpstr='show the types of columns in the X-matrix') self.valid_opts.add_opt('-show_conds', 0, [], helpstr='show condition numbers from the X-matrix') self.valid_opts.add_opt('-show_cormat', 0, [], helpstr='show the XtX correlation matrix') self.valid_opts.add_opt('-show_cosmat', 0, [], helpstr='show the XtX cosine matrix') self.valid_opts.add_opt('-show_cormat_warnings', 0, [], helpstr='show warnings for the XtX correlation matrix') self.valid_opts.add_opt('-show_cosmat_warnings', 0, [], helpstr='show warnings for the XtX cosine matrix') self.valid_opts.add_opt('-show_fit_betas', 0, [], helpstr='show fit betas of X-matrix to time series') self.valid_opts.add_opt('-show_fit_ts', 0, [], helpstr='show fit time series of X-mat to time series') self.valid_opts.add_opt('-show_xmat', 0, [], helpstr='display info about the given X-matrix') self.valid_opts.add_opt('-show_1D', 0, [], helpstr='display info about the given 1D time series') # general options self.valid_opts.add_opt('-chrono', 0, [], helpstr='process options chronologically') self.valid_opts.add_opt('-cormat_cutoff', 1, [], helpstr='set the correlation matrix warning cutoff') self.valid_opts.add_opt('-cosmat_cutoff', 1, [], helpstr='set the cosine matrix warning cutoff') self.valid_opts.add_opt('-cosmat_motion', 0, [], helpstr='include mot vs base/mot in cosmat warnings') self.valid_opts.add_opt('-verb', 1, [], helpstr='set the verbose level (default is 1)') # GUI options self.valid_opts.add_opt('-no_gui', 0, [], helpstr='do not start the graphical user interface') self.valid_opts.add_opt('-gui_plot_xmat_as_one', 0, [], helpstr='plot Xmat columns on single axis') return 0