def process_options(valid_opts, argv):
"""return status and VarsObject structs of subject and control variables
- given list of valid options, read and process the user options
- if terminal option or -no_gui, return 0 (succesful quit)
return 1 : on success and terminate
0 : on success and continue with GUI
-1 : on error condition
"""
# a quick out
if len(argv) == 0: return 0, None, None, None
# process any optlist_ options
valid_opts.check_special_opts(argv)
# ------------------------------------------------------------
# check for terminal options before processing the rest
if '-help' in sys.argv:
print(g_command_help)
valid_opts.show('', 1, show_count=0)
print(g_help_trailer)
return 1, None, None, None
if '-help_gui' in sys.argv:
print(USUBJ.helpstr_usubj_gui)
return 1, None, None, None
if '-help_howto_program' in sys.argv:
print(USUBJ.helpstr_howto_program)
return 1, None, None, None
if '-help_install' in sys.argv:
print(g_install_str)
return 1, None, None, None
if '-help_install_nokia' in sys.argv:
print(g_install_nokia)
return 1, None, None, None
if '-hist' in sys.argv:
print(USUBJ.g_history)
return 1, None, None, None
if '-show_default_vars' in sys.argv:
USUBJ.g_ctrl_defs.show('default cvars :')
USUBJ.g_subj_defs.show('default svars :')
return 1, None, None, None
if '-show_valid_opts' in sys.argv:
valid_opts.show('', 1)
return 1, None, None, None
if '-show_svar_dict' in sys.argv:
dict = USUBJ.g_svar_dict
keys = list(dict.keys())
keys.sort()
for key in keys:
print(' %-20s : %s' % (key, dict[key]))
return 1, None, None, None
if '-todo' in sys.argv:
print(USUBJ.helpstr_todo)
return 1, None, None, None
if '-ver' in sys.argv:
print('uber_subject.py: version %s' % USUBJ.g_version)
return 1, None, None, None
# ------------------------------------------------------------
# read and process user options (no check for terminal opts)
uopts = OPT.read_options(argv, valid_opts)
if not uopts: return -1, None, None, None
# init subject options struct
svars = VO.VarsObject('subject vars from command line')
cvars = VO.VarsObject('control vars from command line')
guiopts = ['uber_subject.py']
# first set verbose level
val, err = uopts.get_type_opt(int, '-verb')
if val != None and not err: verb = val
else: verb = 1
USUBJ.set_vstr_from_def('cvars', 'verb', ['%d' % verb], cvars)
use_gui = 1 # assume GUI unless we hear otherwise
svar_keys = list(USUBJ.g_svar_dict.keys())
errs = 0
# ------------------------------------------------------------
# first process all setup options (e.g. -anal_type/domain)
# - since they might go via -svar, we must search
for opt in uopts.olist:
# just check for 'rest' here
if opt.name == '-anal_type':
val, err = uopts.get_string_opt('', opt=opt)
if val == None or err: return -1, None, None, None
if val == 'rest':
if verb > 1: print('-- init from rest defaults')
svars.merge(USUBJ.g_rdef_strs)
elif opt.name == '-anal_domain':
val, err = uopts.get_string_opt('', opt=opt)
if val == None or err: return -1, None, None, None
if val == 'surface':
print('** uber_subject.py: not ready for surface analysis')
return -1, None, None, None
elif opt.name == '-svar':
val, err = uopts.get_string_list('', opt=opt)
if val == None or err: return -1, None, None, None
if val[0] == '-anal_type':
if val[1] == 'rest':
if verb > 1: print('-- init from rest defaults')
svars.merge(USUBJ.g_rdef_strs)
elif val[0] == '-anal_domain':
if val[1] == 'surface':
print('** uber_subject.py: not ready for surface analysis')
return -1, None, None, None
# done with analysis init options
# ------------------------------------------------------------
for opt in uopts.olist:
# skip -verb and any terminal option (though they should not be here)
if opt.name == '-help': continue
elif opt.name == '-help_gui': continue
elif opt.name == '-hist': continue
elif opt.name == '-show_valid_opts': continue
elif opt.name == '-todo': continue
elif opt.name == '-ver': continue
elif opt.name == '-verb':
continue
# and skip any pre-setup options ...
elif opt.name == '-anal_type':
continue
elif opt.name == '-anal_domain':
continue
# and skip any post-setup options ...
elif opt.name == '-print_ap_command':
continue
elif opt.name == '-save_ap_command':
continue
elif opt.name == '-exec_ap_command':
continue
elif opt.name == '-exec_proc_script':
continue
vname = opt.name[1:]
# now go after "normal" options
if opt.name == '-no_gui':
use_gui = 0
continue
# get any PyQt4 options
elif opt.name == '-qt_opts':
val, err = uopts.get_string_list('', opt=opt)
if val != None and err: return -1, None, None, None
guiopts.extend(val)
# cvar requires at least 2 parameters, name and value
elif opt.name == '-cvar':
val, err = uopts.get_string_list('', opt=opt)
if val != None and err: return -1, None, None, None
# and set it from the form name = [value_list]
if USUBJ.set_vstr_from_def(
'cvars', val[0], val[1:], cvars, verb=verb, spec=1) < 0:
errs += 1
continue
# svar requires at least 2 parameters, name and value
elif opt.name == '-svar':
val, err = uopts.get_string_list('', opt=opt)
if val == None or err: return -1, None, None, None
# and set it from the form name = [value_list]
if USUBJ.set_vstr_from_def(
'svars', val[0], val[1:], svars, verb=verb, spec=1) < 0:
errs += 1
continue
# go after a direct svar key
elif vname in svar_keys:
val, err = uopts.get_string_list('', opt=opt)
if val == None or err: return -1, None, None, None
if USUBJ.set_vstr_from_def(
'svars', vname, val, svars, verb=verb, spec=1) < 0:
errs += 1
continue
else:
print('** invalid option: %s' % opt.name)
errs += 1
continue
if not errs: # then we can handle any processing options
if uopts.find_opt('-print_ap_command'):
print_ap_command(svars, cvars)
if not errs: # then we can handle any processing options
opt = uopts.find_opt('-save_ap_command')
if opt != None:
val, err = uopts.get_string_opt('', opt=opt)
if val == None or err: return -1, None, None, None
save_ap_command(svars, cvars, val)
if not errs: # then we can handle any processing options
if uopts.find_opt('-exec_ap_command'):
subj = run_ap_command(svars, cvars)
if subj != None and uopts.find_opt('-exec_proc_script'):
subj.exec_proc_script()
if verb > 2: # show applied subject variables
changestr = cvars.changed_attrs_str(USUBJ.g_cdef_strs,
skiplist='name',
showskip=0,
showdel=0)
print('++ applied control variables: %s\n' % changestr)
changestr = svars.changed_attrs_str(USUBJ.g_sdef_strs,
skiplist='name',
showskip=0,
showdel=0)
print('++ applied subject variables: %s\n' % changestr)
if errs: return -1, None, None, None
if use_gui: return 0, svars, cvars, guiopts
else: return 1, svars, cvars, guiopts
- handle NIFTI surf_vol
- append command line to script
0.13 12 Aug, 2019: python3 compatible
"""
g_version = '0.13 (August 12, 2019)'
# ----------------------------------------------------------------------
# global values to apply as defaults
# ----------------------------------------------------------------------
# global definitions of result, control and user defaults
# (as well as string versions of control and user defaults)
# ---- resulting values returned after class actions ----
g_res_defs = VO.VarsObject("slow_surf_clustsim result variables")
g_res_defs.file_proc = '' # file name for process script
g_res_defs.output_proc = '' # output from running proc script
# ---- control variables: process control, not set by user in GUI
g_ctrl_defs = VO.VarsObject("slow_surf_clustsim control defaults")
g_ctrl_defs.verb = 1 # verbose level
g_ctrl_defs.proc_dir = '.' # process dir: holds scripts and result dir
g_ctrl_defs.time_process = 'yes' # run /usr/bin/time on commands?
# rcr - default to 'no'
g_ctrl_defs.on_surface = 'no' # default to starting from the volume
g_ctrl_defs.nsteps = 10
g_ctrl_defs.keepblocks = 10 # number of iteration block outputs to keep
# ---- user variables: process control, alignment inputs and options ----
def process_options(self):
argv = sys.argv
if len(argv) == 0: # non-gui out
print(g_command_help)
return 1
# process any optlist_ options
self.valid_opts.check_special_opts(argv)
# process terminal options without the option_list interface
# (so that errors are not reported)
# if no arguments are given, apply -help
if len(argv) <= 1 or '-help' in argv:
print(g_command_help)
return 1
if '-hist' in argv:
print(CLUST.g_history)
return 1
if '-show_default_cvars' in argv:
CLUST.g_ctrl_defs.show('')
return 1
if '-show_default_uvars' in argv:
CLUST.g_user_defs.show('')
return 1
if '-show_valid_opts' in argv:
self.valid_opts.show('', 1)
return 1
if '-ver' in argv:
print(CLUST.g_version)
return 1
# ============================================================
# read options specified by the user
self.user_opts = OPT.read_options(argv, self.valid_opts)
uopts = self.user_opts # convenience variable
if not uopts: return -1 # error condition
# ------------------------------------------------------------
# init subject options struct
self.cvars = VO.VarsObject('control vars from command line')
self.uvars = VO.VarsObject('user vars from command line')
val, err = uopts.get_type_opt(int, '-verb')
if val != None and not err: self.verb = val
SUBJ.set_var_str_from_def('cvars',
'verb', ['%d' % self.verb],
self.cvars,
defs=CLUST.g_ctrl_defs)
# first process all setup options
errs = 0
for opt in uopts.olist:
# skip -verb (any terminal option should block getting here)
if opt.name == '-verb':
continue
# and skip and post-setup options (print command, save, etc.)
elif opt.name == '-print_script':
continue
elif opt.name == '-save_script':
continue
# now go after "normal" options
elif opt.name == '-on_surface':
val, err = uopts.get_string_list('', opt=opt)
if val == None or err: return -1
if self.cvars.set_var_with_defs(opt.name[1:],
val,
CLUST.g_ctrl_defs,
as_type=1,
oname='cvars',
verb=self.verb) < 0:
errs += 1
continue
# cvar requires at least 2 parameters, name and value
elif opt.name == '-cvar':
val, err = uopts.get_string_list('', opt=opt)
if val == None or err: return -1
# go after verb, in particular
if val[0] == 'verb':
try:
self.verb = int(val[1])
except:
print("** failed to set 'verb' level")
errs += 1
continue
# and set it from the form name = [value_list]
if SUBJ.set_var_str_from_def('cvars',
val[0],
val[1:],
self.cvars,
CLUST.g_ctrl_defs,
verb=self.verb) < 0:
errs += 1
continue
# uvar requires at least 2 parameters, name and value
elif opt.name == '-uvar':
val, err = uopts.get_string_list('', opt=opt)
if val == None or err: return -1
# and set it from the form name = [value_list]
if SUBJ.set_var_str_from_def('uvars',
val[0],
val[1:],
self.uvars,
CLUST.g_user_defs,
verb=self.verb) < 0:
errs += 1
continue
else:
print('** unknown option %s' % opt.name)
errs += 1
if self.verb > 2:
print('-' * 75)
self.uvars.show('post-init uvars', name=0)
self.cvars.show('post-init cvars', name=0)
print('-' * 75)
if errs: return -1
else: return 0 # no error, and continue on return
def __init__(self, parent=None, cvars=None, uvars=None, set_pdir=0):
super(MainWindow, self).__init__(parent)
# ------------------------------
# init main vars structs
self.atest = None # AlignTest class element
self.gvars = VO.VarsObject('uber_subject gui vars')
# init verb and try to update from uvars
self.verb = 1
if uvars != None: # try to update verb from uvars
if uvars.valid('verb'):
try:
self.verb = int(uvars.verb)
except:
print '** UAT Main: bad uvars.verb = %s' % uvars.verb
# initialize the subject variables to defaults, update at the end
self.cvars = USKEL.g_cdef_strs.copy('GUI control vars')
self.uvars = USKEL.g_udef_strs.copy('GUI user vars')
self.set_pdir = set_pdir
# ------------------------------
# L1 - main menubar and layout
self.add_menu_bar()
self.add_tool_bar()
self.add_status_bar()
self.gvars.Wcentral = QtGui.QWidget()
mainlayout = QtGui.QVBoxLayout(self.gvars.Wcentral)
# ------------------------------
# L2 - make top Group Box and Vertical Layout; add to main Layout
self.make_l2_widgets()
# ------------------------------
# L3 - fill m2_vlayout with group boxes
self.make_l3_group_boxes()
# ------------------------------------------------------------
# finish level 2 and then level 1
mainlayout.addWidget(self.gvars.gbox_datasets)
mainlayout.addWidget(self.gvars.m2_scroll)
# ------------------------------
# save this for last to ensure it is all visible
self.gvars.m2_scroll.setWidget(self.gvars.m2_gbox_inputs)
self.gvars.Wcentral.setMinimumSize(350, 400)
self.gvars.Wcentral.setLayout(mainlayout)
self.setCentralWidget(self.gvars.Wcentral)
self.make_extra_widgets()
self.gvars.style = g_styles[g_style_index_def]
# widgets are done, so apply pass subject vars
self.reset_vars(cvars=cvars, uvars=uvars, set_pdir=set_pdir)
# status : 0 = must create script, 1 = have script, ready to execute
# -1 = script failure?
self.status = 0
if self.verb > 1: print '-- finished Single Subject Dialog setup'
def process_options(self):
"""return 1 on valid and exit
0 on valid and continue
-1 on invalid
"""
argv = sys.argv
# a quick out (no help, continue and open GUI)
if len(argv) == 0: return 0
# process any optlist_ options
self.valid_opts.check_special_opts(argv)
# ------------------------------------------------------------
# check for terminal options before processing the rest
if '-help' in argv:
print g_command_help
return 1
if '-help_gui' in argv:
print UALIGN.helpstr_gui
return 1
if '-help_howto_program' in argv:
print UALIGN.helpstr_create_program
return 1
if '-help_todo' in argv:
print UALIGN.helpstr_todo
return 1
if '-hist' in argv:
print UALIGN.g_history
return 1
if '-show_default_vars' in argv:
UALIGN.g_user_defs.show('default uvars :')
return 1
if '-show_valid_opts' in argv:
self.valid_opts.show('', 1)
return 1
if '-ver' in argv:
print 'uber_align_test.py: version %s' % UALIGN.g_version
return 1
# ------------------------------------------------------------
# read and process user options (no check for terminal opts)
self.uopts = OPT.read_options(argv, self.valid_opts)
if not self.uopts: return -1
uopts = self.uopts # convenience
# init subject options struct
self.cvars = VO.VarsObject('control vars from command line')
self.uvars = VO.VarsObject('user vars from command line')
self.guiopts = ['uber_align_test.py']
# first set verbose level
val, err = uopts.get_type_opt(int, '-verb')
if val != None and not err: self.verb = val
else: self.verb = 1
# changed from SUBJ.set_var_str_from_def
self.uvars.set_var_with_defs('verb', ['%d' % self.verb],
UALIGN.g_user_defs,
oname='uvars')
use_gui = 1 # assume GUI unless we hear otherwise
# first process all setup options
errs = 0
for opt in uopts.olist:
# skip -verb (any terminal option should block getting here)
if opt.name == '-verb':
continue
# and skip and post-setup options (print command, save, etc.)
elif opt.name == '-print_script':
continue
elif opt.name == '-save_script':
continue
# now go after "normal" options
if opt.name == '-no_gui':
use_gui = 0
continue
# get any PyQt4 options
elif opt.name == '-qt_opts':
val, err = uopts.get_string_list('', opt=opt)
if val != None and err: return -1
self.guiopts.extend(val)
# cvar requires at least 2 parameters, name and value
elif opt.name == '-cvar':
val, err = uopts.get_string_list('', opt=opt)
if val != None and err: return -1
# and set it from the form name = [value_list]
if self.cvars.set_var_with_defs(val[0],
val[1:],
UALIGN.g_ctrl_defs,
oname='cvars',
verb=self.verb) < 0:
errs += 1
continue
# uvar requires at least 2 parameters, name and value
elif opt.name == '-uvar':
val, err = uopts.get_string_list('', opt=opt)
if val != None and err: return -1
# and set it from the form name = [value_list]
if self.uvars.set_var_with_defs(val[0],
val[1:],
UALIGN.g_user_defs,
oname='uvars',
verb=self.verb) < 0:
errs += 1
continue
if not errs: # then we can handle any processing options
if uopts.find_opt('-print_script'): self.print_script()
if not errs: # then we can handle any processing options
opt = uopts.find_opt('-save_script')
if opt != None:
val, err = uopts.get_string_opt('', opt=opt)
if val != None and not err: self.save_script(val)
if errs: return -1
if use_gui: return 0 # continue and open GUI
else: return 1 # no error, but terminate on return
def process_options(self):
"""return 1 on valid and exit
0 on valid and continue
-1 on invalid
"""
argv = sys.argv
# a quick out (no help, continue and open GUI)
if len(argv) == 0: return 0
# process any optlist_ options
self.valid_opts.check_special_opts(argv)
# ------------------------------------------------------------
# check for terminal options before processing the rest
if '-help' in argv:
print g_command_help
return 1
if '-help_gui' in argv:
print LTT.helpstr_gui
return 1
if '-help_todo' in argv:
print LTT.helpstr_todo
return 1
if '-hist' in argv:
print LTT.g_history
return 1
if '-show_default_vars' in argv:
LTT.g_user_defs.show('default uvars :')
return 1
if '-show_valid_opts' in argv:
self.valid_opts.show('', 1)
return 1
if '-show_cvar_dict' in sys.argv:
dict = LTT.g_cvar_dict
keys = dict.keys()
keys.sort()
for key in keys:
print ' %-20s : %s' % (key, dict[key])
return 1
if '-show_uvar_dict' in sys.argv:
dict = LTT.g_uvar_dict
keys = dict.keys()
keys.sort()
for key in keys:
print ' %-20s : %s' % (key, dict[key])
return 1
if '-ver' in argv:
print 'uber_ttest.py: version %s' % LTT.g_version
return 1
# ------------------------------------------------------------
# read and process user options (no check for terminal opts)
self.uopts = OPT.read_options(argv, self.valid_opts)
if not self.uopts: return -1
uopts = self.uopts # convenience
# init subject options struct
self.cvars = VO.VarsObject('control vars from command line')
self.uvars = VO.VarsObject('user vars from command line')
self.guiopts = ['uber_ttest.py']
# first set verbose level
val, err = uopts.get_type_opt(int, '-verb')
if val != None and not err: self.verb = val
else: self.verb = 1
SUBJ.set_var_str_from_def('cvars', 'verb', ['%d'%self.verb], self.cvars,
defs=LTT.g_ctrl_defs)
use_gui = 1 # assume GUI unless we hear otherwise
cvar_keys = LTT.g_cvar_dict.keys()
uvar_keys = LTT.g_uvar_dict.keys()
# we already processed terminal options
term_opts = ['-help', '-help_gui', '-help_todo',
'-hist', 'show_default_vars', '-ver',
'-show_cvar_dict', '-show_uvar_dict']
# skip post-setup options, to be checked later
post_opts = ['-print_script', '-save_script']
# first process all setup options
errs = 0
for opt in uopts.olist:
# skip -verb (any terminal option should block getting here)
if opt.name in term_opts: continue
# and skip and post-setup options (print command, save, etc.)
if opt.name in post_opts: continue
vname = opt.name[1:]
# now go after "normal" options
if opt.name == '-no_gui':
use_gui = 0
continue
# get any PyQt4 options
elif opt.name == '-qt_opts':
val, err = uopts.get_string_list('', opt=opt)
if val != None and err:
errs += 1
continue
self.guiopts.extend(val)
# cvar requires at least 2 parameters, name and value
elif opt.name == '-cvar':
val, err = uopts.get_string_list('', opt=opt)
if val != None and err:
errs += 1
continue
if self.cvars.set_var_with_defs(val[0], val[1:], LTT.g_ctrl_defs,
oname='cvars', verb=self.verb) < 0:
errs += 1
continue
# uvar requires at least 2 parameters, name and value
elif opt.name == '-uvar':
val, err = uopts.get_string_list('', opt=opt)
if val != None and err:
errs += 1
continue
if self.uvars.set_var_with_defs(val[0], val[1:], LTT.g_user_defs,
oname='uvars', verb=self.verb) < 0:
errs += 1
continue
# maybe this is a control variable key
elif vname in cvar_keys:
val, err = uopts.get_string_list('', opt=opt)
if val == None or err:
errs += 1
continue
if self.cvars.set_var_with_defs(vname, val, LTT.g_ctrl_defs,
oname='cvars', verb=self.verb) < 0:
errs += 1
continue
# maybe this is a user variable key
elif vname in uvar_keys:
val, err = uopts.get_string_list('', opt=opt)
if val == None or err:
errs += 1
continue
if self.uvars.set_var_with_defs(vname, val, LTT.g_user_defs,
oname='uvars', verb=self.verb) < 0:
errs += 1
continue
else:
print '** invalid option: %s' % opt.name
errs += 1
continue
if not errs: # then we can handle any processing options
if uopts.find_opt('-print_script'):
self.print_script()
use_gui = 0
#opt = uopts.find_opt('-save_script')
#if opt != None:
# val, err = uopts.get_string_opt('', opt=opt)
val, err = uopts.get_string_opt('-save_script')
if val != None and not err:
self.save_script(val)
use_gui = 0
if errs: return -1
if use_gui: return 0 # continue and open GUI
else: return 1 # no error, but terminate on return
2.0 28 Dec, 2017: python3 compatible
"""
g_version = '2.0 (December 28, 2017)'
# ----------------------------------------------------------------------
# global definitions
g_prog_list = ['3dttest++', '3dMEMA']
# ----------------------------------------------------------------------
# global definitions of result, control and user defaults
# (as well as string versions of control and user defaults)
# ---- resulting values returned after class actions ----
g_res_defs = VO.VarsObject("uber_ttest result variables")
g_res_defs.file_proc = '' # file name for process script
g_res_defs.output_proc = '' # output from running proc script
# ---- control variables: process control, not set by user in GUI
g_ctrl_defs = VO.VarsObject("uber_ttest control defaults")
g_ctrl_defs.proc_dir = '.' # process dir: holds scripts and result dir
g_ctrl_defs.verb = 1 # verbose level
g_ctrl_defs.copy_scripts = 'yes' # make .orig copies of scripts?
g_ctrl_defs.results_dir = 'test.results' # output directory for results
# control varaible dictionary, for command line options
g_cvar_dict = {
'proc_dir': 'set processing dir to hold scripts',
'verb': 'set verbose level',
