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
