Beispiel #1
0
   def process_options(self):

      # process any optlist_ options
      self.valid_opts.check_special_opts(sys.argv)

      # process terminal options without the option_list interface
      # (so that errors are not reported)

      # if no arguments are given, apply -help
      if len(sys.argv) <= 1 or '-help' in sys.argv:
         print(g_help_string)
         return 0

      if '-hist' in sys.argv:
         print(g_history)
         return 0

      if '-show_valid_opts' in sys.argv:
         self.valid_opts.show('', 1)
         return 0

      if '-ver' in sys.argv:
         print(g_version)
         return 0

      # ============================================================
      # read options specified by the user
      self.user_opts = OL.read_options(sys.argv, self.valid_opts)
      uopts = self.user_opts            # convenience variable
      if not uopts: return 1            # error condition

      # ------------------------------------------------------------
      # process non-chronological options, verb comes first

      val, err = uopts.get_type_opt(int, '-verb')
      if val != None and not err: self.verb = val

      # ------------------------------------------------------------
      # process options sequentially, to make them like a script

      for opt in uopts.olist:

         # main options
         if opt.name == '-infile':
            if self.a1d != None:
               print('** only 1 -infile option allowed')
               return 1
            val, err = uopts.get_string_opt('', opt=opt)
            if val != None and err: return 1
            if self.init_from_file(val): return 1

         # general options

         elif opt.name == '-verb':
            val, err = uopts.get_type_opt(int, '', opt=opt)
            if val != None and err: return 1
            else: self.verb = val
            continue

      return 0
Beispiel #2
0
    def read_opts(self):
        """check for terminal arguments, then read the user options"""

        # process any optlist_ options
        self.valid_opts.check_special_opts(sys.argv)

        # ------------------------------------------------------------
        # check for terminal args in argv (to ignore required args)

        # 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 0

        if '-hist' in sys.argv:
            print g_history
            return 0

        if '-show_valid_opts' in sys.argv:      # show all valid options
            self.valid_opts.show('', 1)
            return 0

        if '-ver' in sys.argv:
            print g_version
            return 0

        # ------------------------------------------------------------
        # now read user options

        self.user_opts = option_list.read_options(sys.argv, self.valid_opts)
        if not self.user_opts: return 1         # error condition

        return None     # normal completion
Beispiel #3
0
   def process_options(self):

      # process any optlist_ options
      self.valid_opts.check_special_opts(sys.argv)

      # process terminal options without the option_list interface
      # (so that errors are not reported)

      # if no arguments are given, apply -help
      if len(sys.argv) <= 1 or '-help' in sys.argv:
         print g_help_string
         return 0

      if '-hist' in sys.argv:
         print g_history
         return 0

      if '-show_valid_opts' in sys.argv:
         self.valid_opts.show('', 1)
         return 0

      if '-ver' in sys.argv:
         print g_version
         return 0

      # ============================================================
      # read options specified by the user
      self.user_opts = OL.read_options(sys.argv, self.valid_opts)
      uopts = self.user_opts            # convenience variable
      if not uopts: return 1            # error condition

      # ------------------------------------------------------------
      # process non-chronological options, verb comes first

      val, err = uopts.get_type_opt(int, '-verb')
      if val != None and not err: self.verb = val

      # ------------------------------------------------------------
      # process options sequentially, to make them like a script

      for opt in uopts.olist:

         # main options
         if opt.name == '-infile':
            if self.a1d != None:
               print '** only 1 -infile option allowed'
               return 1
            val, err = uopts.get_string_opt('', opt=opt)
            if val != None and err: return 1
            if self.init_from_file(val): return 1

         # general options

         elif opt.name == '-verb':
            val, err = uopts.get_type_opt(int, '', opt=opt)
            if val != None and err: return 1
            else: self.verb = val
            continue

      return 0
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
Beispiel #5
0
   def process_options(self):
      """process all options, applying to interfaces where appropriate"""

      # ==================================================
      # first fire up the TCP interface

      self.RTI = RT.RTInterface()
      if not self.RTI: return None

      # and store globally
      global g_RTinterface
      g_RTinterface = self.RTI      # global for signal handler

      # ==================================================
      # gather and process the user options
      self.user_opts = OL.read_options(sys.argv, self.valid_opts)
      uopts = self.user_opts            # for convenience
      if not uopts: return 1

      # process -verb first
      val, err = uopts.get_type_opt(int, '-verb')
      if val != None and not err:
         self.verb = val
         self.RTI.verb = val

      # ==================================================
      # --- serial options ---

      # port first: if set, create SerialInterface
      val, err = uopts.get_string_opt('-serial_port')
      if val != None and not err:
         self.SER = RT.SerialInterface(val, verb=self.verb)
         if not self.SER: return 1

      # ==================================================
      # --- feedback options ---

      val, err = uopts.get_string_opt('-data_choice')
      if val != None and not err: self.data_choice = val

      val, err = uopts.get_type_list(float, '-dc_params')
      if val != None and not err: self.dc_params = val

      # ==================================================
      # --- tcp options ---

      val, err = uopts.get_string_opt('-show_data')
      if val != None and not err:
         if val == 'no': self.RTI.show_data = 0
         else:           self.RTI.show_data = 1

      if uopts.find_opt('-show_comm_times'): self.RTI.show_times = 1
      if uopts.find_opt('-swap'): self.RTI.swap = 1

      val, err = uopts.get_type_opt(int, '-tcp_port')
      if val != None and not err: self.RTI.server_port = val

      # ==================================================
      # --- demo options ---

      val, err = uopts.get_string_opt('-show_demo_data')
      if val != None and not err:
         if val == 'no': self.show_demo_data = 0
         else:           self.show_demo_data = 1

      val, err = uopts.get_string_opt('-show_demo_gui')
      if val != None and not err:
         if val == 'yes': self.set_demo_gui()

      return 0  # so continue and listen
Beispiel #6
0
    def process_options(self):

        # ============================================================
        # read options specified by the user
        self.user_opts = OL.read_options(sys.argv, self.valid_opts)
        uopts = self.user_opts  # convenience variable
        if not uopts: return 1  # error condition

        # ------------------------------------------------------------
        # check -test_libs separately, as we may want to apply -verb

        if '-test_libs' in sys.argv:
            val, err = self.user_opts.get_type_opt(int, '-verb')
            if val == None or err: val = 2
            return self.test_libraries(verb=val)

        # attempting real work, load AM (locally)
        if self.set_afni_xmat(): return 1

        # ------------------------------------------------------------
        # check general options, esp. chrono

        if uopts.find_opt('-chrono'): self.chrono = 1

        # if options are not chronological, process general options now
        # (so -show options are still in order)
        if not self.chrono:

            # general options might affect selection options
            val, err = self.user_opts.get_type_opt(float, '-cormat_cutoff')
            if val != None and not err: self.cormat_cut = val

            val, err = self.user_opts.get_type_opt(float, '-cosmat_cutoff')
            if val != None and not err: self.cosmat_cut = val

            val, err = self.user_opts.get_type_opt(float, '-cosmat_motion')
            if val != None and not err: self.cosmat_motion = 1

            val, err = self.user_opts.get_type_opt(int, '-verb')
            if val != None and not err: self.verb = val

            # selection options
            val, err = uopts.get_string_opt('-load_xmat')
            if val and not err:
                if self.set_xmat(val): return 1

            val, err = uopts.get_string_opt('-load_1D')
            if val and not err:
                if self.set_1D(val): return 1

            val, err = uopts.get_string_opt('-choose_cols')
            if val and not err:
                rstr = self.set_cols_from_string(val)
                if rstr:
                    print "** failed to apply '-choose_cols':\n%s" % rstr
                    return 1

        # ------------------------------------------------------------
        # selection and process options:
        #    process sequentially, to make them like a script

        for opt in uopts.olist:
            # if all options are chronological, check load and general, too
            if self.chrono:
                # selection options
                if opt.name == '-load_xmat':
                    if self.set_xmat(opt.parlist[0]): return 1
                elif opt.name == '-load_1D':
                    if self.set_1D(opt.parlist[0]): return 1
                elif opt.name == '-choose_cols':
                    rstr = self.set_cols_from_string(opt.parlist[0])
                    if rstr:
                        print "** failed to apply '-choose_cols':\n%s" % rstr
                        return 1

                # general options
                elif opt.name == '-cormat_cutoff':
                    val, err = self.user_opts.get_type_opt(float, '', opt=opt)
                    if val != None and err: return 1
                    else: self.cormat_cut = val

                elif opt.name == '-cosmat_cutoff':
                    val, err = self.user_opts.get_type_opt(float, '', opt=opt)
                    if val != None and err: return 1
                    else: self.cosmat_cut = val

                elif opt.name == '-cosmat_motion':
                    self.cosmat_motion = 1

                elif opt.name == '-verb':
                    val, err = self.user_opts.get_type_opt(int, '', opt=opt)
                    if val != None and err: return 1
                    else: self.verb = val

            # 'show' options (allow these to fail?)
            if opt.name == '-show_col_types':
                if self.matX:
                    err, str = self.make_col_type_string()
                    print str
                else:
                    print "** -show_col_types: needs -load_xmat"
            elif opt.name == '-show_conds':
                if self.matX:
                    print self.matX.make_show_conds_str(self.col_list)
                else:
                    print "** -show_conds: needs -load_xmat"
            elif opt.name == '-show_cormat':
                err, str = self.make_cormat_string()
                print '-- Correlation matrix for %s :' % self.fname_mat
                print str
            elif opt.name == '-show_cormat_warnings':
                err, str = self.make_cormat_warnings_string()
                print '-- Correlation matrix warnings for %s :' % self.fname_mat
                print str
            elif opt.name == '-show_cosmat':
                err, str = self.make_cosmat_string()
                print '-- Cosine matrix for %s :' % self.fname_mat
                print str
            elif opt.name == '-show_cosmat_warnings':
                err, str = self.make_cosmat_warnings_string()
                print '-- Cosine matrix warnings for %s :' % self.fname_mat
                print str
            elif opt.name == '-show_fit_betas':
                err, rstr = self.make_matrix_fit_betas_string()
                print rstr
            elif opt.name == '-show_fit_ts':
                err, rstr = self.make_matrix_fit_string()
                print rstr
            elif opt.name == '-show_xmat':
                if self.matX: self.matX.show()
                else: print "** -show_xmat: needs -load_xmat"
            elif opt.name == '-show_1D':
                if self.matX: self.mat1D.show()
                else: print "** -show_1D: needs -load_1D"

            # store gui options in a separate list
            elif opt.name[0:5] == '-gui_':
                self.gui_opts.append(opt)

        # ------------------------------------------------------------
        # process GUI options

        # ------------------------------------------------------------
        # last test before returning
        if uopts.find_opt('-no_gui'): self.use_gui = 0
        else: self.use_gui = 1

        return 0
Beispiel #7
0
   def process_options(self):
      """return  1 on valid and exit
         return  0 on valid and continue
         return -1 on invalid
      """

      argv = sys.argv

      # 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, do default processing
      if '-help' in argv or len(argv) < 2:
         print g_help_string
         return 1

      if '-hist' in argv:
         print g_history
         return 1

      if '-show_valid_opts' in argv:
         self.valid_opts.show('', 1)
         return 1

      if '-ver' in argv:
         print g_version
         return 1

      # ============================================================
      # read options specified by the user
      self.user_opts = OL.read_options(argv, self.valid_opts)
      uopts = self.user_opts            # convenience variable
      if not uopts: return -1           # error condition

      # ------------------------------------------------------------
      # process verb first

      val, err = uopts.get_type_opt(int, '-verb')
      if val != None and not err: self.verb = val

      # ------------------------------------------------------------
      # process options sequentially, to make them like a script
      errs = 0
      for opt in self.user_opts.olist:
         # check for anything to skip
         if opt.name == '-verb': pass

         elif opt.name == '-infiles':
            self.infiles, err = uopts.get_string_list('', opt=opt)
            if self.infiles == None or err:
               print '** failed to read -infiles list'
               errs +=1

            self.parse_infile_names()

         elif opt.name == '-overwrite':
            self.overwrite = 1

         elif opt.name == '-separator':
            self.separator, err = uopts.get_string_opt('', opt=opt)
            if self.separator == None or err:
               print "** bad -tablefile option"
               errs += 1
            if   self.separator == 'tab': self.separator = '\t'
            elif self.separator == 'whitespace': self.separator = 'ws'
            self.seplen = len(self.separator)

         elif opt.name == '-showlabs':
            self.showlabs = 1

         elif opt.name == '-show_missing':
            self.show_missing = 1

         elif opt.name == '-tablefile':
            self.tablefile, err = uopts.get_string_opt('', opt=opt)
            if self.tablefile == None or err:
               print "** bad -tablefile option"
               errs +=1

         else:
            oind = self.user_opts.olist.index(opt)
            print '** unknown option # %d: %s' % (oind+1, opt.name)
            errs += 1
            break

      # allow early and late error returns
      if errs: return -1

      # ------------------------------------------------------------
      # apply any trailing logic

      if len(self.infiles) < 1:
         print '** missing -infiles option'
         errs += 1

      if errs: return -1

      return 0
Beispiel #8
0
    def process_options(self, argv=sys.argv):

        # 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 '-help' in argv or len(argv) < 2:
            print g_help_string
            return 0

        if '-help_rc_files' in argv or '-help_dot_files' in argv:
            print g_help_rc_files
            return 0

        if '-hist' in argv:
            print g_history
            return 0

        if '-show_valid_opts' in argv:
            self.valid_opts.show('', 1)
            return 0

        if '-todo' in argv:
            print g_todo
            return 0

        if '-ver' in argv:
            print g_version
            return 0

        # ============================================================
        # read options specified by the user
        self.user_opts = OL.read_options(argv, self.valid_opts)
        uopts = self.user_opts  # convenience variable
        if not uopts: return 1  # error condition

        # ------------------------------------------------------------
        # process options, go after -verb first

        val, err = uopts.get_type_opt(int, '-verb')
        if val != None and not err: self.verb = val

        for opt in uopts.olist:

            if opt.name == '-casematch':
                if OL.opt_is_yes(opt): self.casematch = 1
                else: self.casematch = 0
                continue

            if opt.name == '-check_all':
                self.act = 1
                self.sys_check = 1
                continue

            if opt.name == '-data_root':
                self.data_root = opt.parlist[0]
                continue

            if opt.name == '-dot_file_list':
                self.dot_file_list = 1
                self.act = 1
                continue

            if opt.name == '-dot_file_pack':
                self.dot_file_pack = opt.parlist[0]
                self.act = 1
                continue

            if opt.name == '-dot_file_show':
                self.dot_file_show = 1
                self.act = 1
                continue

            if opt.name == '-exact':
                if OL.opt_is_yes(opt):
                    self.exact = 1
                    # default of casematching is 1 for this
                    if self.casematch < 0: self.casematch = 1
                else: self.exact = 0
                continue

            if opt.name == '-find_prog':
                self.act = 1
                self.find_prog = opt.parlist[0]
                continue

            # already processing options: just continue

            if opt.name == '-verb': continue

            # an unhandled option
            print '** option %s not yet supported' % opt.name
            return 1

        if not self.act:
            print '** no action option found, please see -help output\n'
            return 1

        return None
Beispiel #9
0
   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 = SUBJ.VarsObject('control vars from command line')
      self.uvars = SUBJ.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
Beispiel #10
0
   def process_options(self):
      """return  1 on valid and exit
         return  0 on valid and continue
         return -1 on invalid
      """

      argv = sys.argv

      # 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, do default processing
      if '-help' in argv or len(argv) < 2:
         print g_help_string
         return 1

      if '-hist' in argv:
         print g_history
         return 1

      if '-show_valid_opts' in argv:
         self.valid_opts.show('', 1)
         return 1

      if '-ver' in argv:
         print g_version
         return 1

      # ============================================================
      # read options specified by the user
      self.user_opts = OL.read_options(argv, self.valid_opts)
      uopts = self.user_opts            # convenience variable
      if not uopts: return -1           # error condition

      # ------------------------------------------------------------
      # process verb first

      val, err = uopts.get_type_opt(int, '-verb')
      if val != None and not err: self.verb = val

      # ------------------------------------------------------------
      # process options sequentially, to make them like a script
      errs = 0
      for opt in self.user_opts.olist:
         # check for anything to skip
         if opt.name == '-verb': pass

         elif opt.name == '-infiles':
            self.infiles, err = uopts.get_string_list('', opt=opt)
            if self.infiles == None or err:
               print '** failed to read -infiles list'
               errs +=1

         elif opt.name == '-overwrite':
            self.overwrite = 1

         elif opt.name == '-prefix':
            val, err = uopts.get_string_opt(opt=opt)
            if val != None and not err: self.prefix = val

      # allow early and late error returns
      if errs: return -1

      # ------------------------------------------------------------
      # apply any trailing logic

      # if here, require input files
      if len(self.infiles) < 1:
         print '** missing -infiles option'
         errs += 1

      # if no -prefix and no -verb, default verb to 2
      if not self.user_opts.find_opt('-verb') and self.prefix == '':
         self.verb = 2

      if errs: return -1

      return 0
Beispiel #11
0
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
Beispiel #12
0
    def process_options(self):
        """return  1 on valid and exit
         return  0 on valid and continue
         return -1 on invalid
      """

        argv = sys.argv

        # 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, do default processing
        if '-help' in argv or len(argv) < 2:
            print(g_help_string)
            return 1

        if '-hist' in argv:
            print(g_history)
            return 1

        if '-show_valid_opts' in argv:
            self.valid_opts.show('', 1)
            return 1

        if '-ver' in argv:
            print(g_version)
            return 1

        # ============================================================
        # read options specified by the user
        self.user_opts = OL.read_options(argv, self.valid_opts)
        uopts = self.user_opts  # convenience variable
        if not uopts: return -1  # error condition

        # ------------------------------------------------------------
        # process verb first

        val, err = uopts.get_type_opt(int, '-verb')
        if val != None and not err: self.verb = val

        # ------------------------------------------------------------
        # process options sequentially, to make them like a script
        errs = 0
        for opt in self.user_opts.olist:
            # check for anything to skip
            if opt.name == '-verb': pass

            elif opt.name == '-infiles':
                self.infiles, err = uopts.get_string_list('', opt=opt)
                if self.infiles == None or err:
                    print('** failed to read -infiles list')
                    errs += 1

                self.parse_infile_names()

            elif opt.name == '-overwrite':
                self.overwrite = 1

            elif opt.name == '-separator':
                self.separator, err = uopts.get_string_opt('', opt=opt)
                if self.separator == None or err:
                    print("** bad -separator option")
                    errs += 1
                if self.separator == 'tab': self.separator = '\t'
                elif self.separator == 'whitespace': self.separator = 'ws'
                self.seplen = len(self.separator)

            elif opt.name == '-outlier_sep':
                self.out_sep, err = uopts.get_string_opt('', opt=opt)
                if self.out_sep == None or err:
                    print("** bad -outlier_sep option")
                    errs += 1
                if self.out_sep == 'tab': self.out_sep = '\t'
                elif self.out_sep == 'comma': self.out_sep = ','
                # 'space' is handled as a special case

            # ------------------------------
            # report outliers
            elif opt.name == '-report_outliers':
                params, err = uopts.get_string_list('', opt=opt)
                if params == None or err:
                    print('** failed to parse -report_outliers %s' % params)
                    errs += 1
                    continue

                if self.add_test_to_outlier_report(params):
                    errs += 1
                    continue

                self.report_outliers = 1

            elif opt.name == '-report_outliers_fill_style':
                self.ro_fill_type, err = uopts.get_string_opt('', opt=opt)
                if self.ro_fill_type is None or err:
                    print("** bad opt: -report_outliers_fill_style %s" \
                          % self.ro_fill_type)
                    errs += 1

            elif opt.name == '-report_outliers_header_style':
                self.ro_head_type, err = uopts.get_string_opt('', opt=opt)
                if self.ro_head_type is None or err:
                    print("** bad opt: -report_outliers_header_style %s" \
                          % self.ro_head_type)
                    errs += 1

            # ------------------------------ outliers end

            elif opt.name == '-showlabs':
                self.showlabs = 1

            elif opt.name == '-show_infiles':
                self.show_infiles = 1

            elif opt.name == '-show_missing':
                self.show_missing = 1

            # try to replace -tablefile with -write_table
            elif opt.name == '-write_table' or opt.name == '-tablefile':
                self.tablefile, err = uopts.get_string_opt('', opt=opt)
                if self.tablefile == None or err:
                    print("** bad %s option" % opt.name)
                    errs += 1

            elif opt.name == '-write_outliers':
                self.ro_tablefile, err = uopts.get_string_opt('', opt=opt)
                if self.ro_tablefile == None or err:
                    print("** bad -write_outliers option")
                    errs += 1

            else:
                oind = self.user_opts.olist.index(opt)
                print('** unknown option # %d: %s' % (oind + 1, opt.name))
                errs += 1
                break

        # allow early and late error returns
        if errs: return -1

        # ------------------------------------------------------------
        # apply any trailing logic

        if len(self.infiles) < 1:
            print('** missing -infiles option')
            errs += 1

        if errs: return -1

        return 0
Beispiel #13
0
    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 = SUBJ.VarsObject("control vars from command line")
        self.uvars = SUBJ.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
Beispiel #14
0
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 = 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 = SUBJ.VarsObject('subject vars from command line')
   cvars = SUBJ.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 = 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
Beispiel #15
0
    def process_options(self):
        """process all options, applying to interfaces where appropriate"""

        # ==================================================
        # first fire up the TCP interface

        self.RTI = RT.RTInterface()
        if not self.RTI: return None

        # and store globally
        global g_RTinterface
        g_RTinterface = self.RTI  # global for signal handler

        # ==================================================
        # gather and process the user options
        self.user_opts = OL.read_options(sys.argv, self.valid_opts)
        uopts = self.user_opts  # for convenience
        if not uopts: return 1

        # process -verb first
        val, err = uopts.get_type_opt(int, '-verb')
        if val != None and not err:
            self.verb = val
            self.RTI.verb = val

        # ==================================================
        # --- serial options ---

        # port first: if set, create SerialInterface
        val, err = uopts.get_string_opt('-serial_port')
        if val != None and not err:
            self.SER = RT.SerialInterface(val, verb=self.verb)
            if not self.SER: return 1

        # ==================================================
        # --- feedback options ---

        val, err = uopts.get_string_opt('-data_choice')
        if val != None and not err: self.data_choice = val

        val, err = uopts.get_type_list(float, '-dc_params')
        if val != None and not err: self.dc_params = val

        # ==================================================
        # --- tcp options ---

        val, err = uopts.get_string_opt('-show_data')
        if val != None and not err:
            if val == 'no': self.RTI.show_data = 0
            else: self.RTI.show_data = 1

        if uopts.find_opt('-show_comm_times'): self.RTI.show_times = 1
        if uopts.find_opt('-swap'): self.RTI.swap = 1

        val, err = uopts.get_type_opt(int, '-tcp_port')
        if val != None and not err: self.RTI.server_port = val

        # ==================================================
        # --- demo options ---

        val, err = uopts.get_string_opt('-show_demo_data')
        if val != None and not err:
            if val == 'no': self.show_demo_data = 0
            else: self.show_demo_data = 1

        val, err = uopts.get_string_opt('-show_demo_gui')
        if val != None and not err:
            if val == 'yes':
                if self.set_demo_gui():
                    print '\n** GUI demo failed, proceeding without GUI...\n'

        return 0  # so continue and listen
Beispiel #16
0
   def process_options(self, argv=sys.argv):

      # 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 '-help' in argv or len(argv) < 2:
         print g_help_string
         return 0

      if '-help_rc_files' in argv or '-help_dot_files' in argv:
         print g_help_rc_files
         return 0

      if '-hist' in argv:
         print g_history
         return 0

      if '-show_valid_opts' in argv:
         self.valid_opts.show('', 1)
         return 0

      if '-todo' in argv:
         print g_todo
         return 0

      if '-ver' in argv:
         print g_version
         return 0

      # ============================================================
      # read options specified by the user
      self.user_opts = OL.read_options(argv, self.valid_opts)
      uopts = self.user_opts            # convenience variable
      if not uopts: return 1            # error condition

      # ------------------------------------------------------------
      # process options, go after -verb first

      val, err = uopts.get_type_opt(int, '-verb')
      if val != None and not err: self.verb = val

      for opt in uopts.olist:

         if opt.name == '-casematch':
            if OL.opt_is_yes(opt): self.casematch = 1
            else:                  self.casematch = 0
            continue

         if opt.name == '-check_all':
            self.act = 1
            self.sys_check = 1
            continue

         if opt.name == '-data_root':
            self.data_root = opt.parlist[0]
            continue

         if opt.name == '-dot_file_list':
            self.dot_file_list = 1
            self.act = 1
            continue

         if opt.name == '-dot_file_pack':
            self.dot_file_pack = opt.parlist[0]
            self.act = 1
            continue

         if opt.name == '-dot_file_show':
            self.dot_file_show = 1
            self.act = 1
            continue

         if opt.name == '-exact':
            if OL.opt_is_yes(opt):
               self.exact = 1
               # default of casematching is 1 for this
               if self.casematch < 0: self.casematch = 1
            else: self.exact = 0
            continue

         if opt.name == '-find_prog':
            self.act = 1
            self.find_prog = opt.parlist[0]
            continue

         # already processing options: just continue

         if opt.name == '-verb': continue

         # an unhandled option
         print '** option %s not yet supported' % opt.name
         return 1

      if not self.act:
         print '** no action option found, please see -help output\n'
         return 1

      return None
Beispiel #17
0
   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 USKEL.helpstr_gui
         return 1

      if '-help_howto_program' in argv:
         print USKEL.helpstr_create_program
         return 1

      if '-help_todo' in argv:
         print USKEL.helpstr_todo
         return 1

      if '-hist' in argv:
         print USKEL.g_history
         return 1

      if '-show_default_vars' in argv:
         USKEL.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_skel.py: version %s' % USKEL.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_skel.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('uvars', 'verb', ['%d'%self.verb], self.uvars,
                                 defs=USKEL.g_user_defs)

      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 SUBJ.set_var_str_from_def('cvars', val[0], val[1:], self.cvars,
                        USKEL.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 and 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,
                        USKEL.g_user_defs, 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
Beispiel #18
0
    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 = SUBJ.VarsObject('control vars from command line')
        self.uvars = SUBJ.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
Beispiel #19
0
   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 = SUBJ.VarsObject('control vars from command line')
      self.uvars = SUBJ.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
Beispiel #20
0
   def process_options(self, argv=sys.argv):

      # 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_help_string
         return 0

      if '-hist' in argv:
         print g_history
         return 0

      if '-show_valid_opts' in argv:
         self.valid_opts.show('', 1)
         return 0

      if '-ver' in argv:
         print g_version
         return 0

      # ============================================================
      # read options specified by the user
      self.user_opts = OL.read_options(argv, self.valid_opts)
      uopts = self.user_opts            # convenience variable
      if not uopts: return 1            # error condition

      # ------------------------------------------------------------
      # require a list of files, at least

      # ------------------------------------------------------------
      # process options, go after -verb first

      val, err = uopts.get_type_opt(int, '-verb')
      if val != None and not err: self.verb = val

      for opt in uopts.olist:

         # main options
         if opt.name == '-AminusB':
            self.comp_dir = opt.name
            continue

         if opt.name == '-BminusA':
            self.comp_dir = opt.name
            continue

         if opt.name == '-command':
            val, err = uopts.get_string_opt('', opt=opt)
            if val == None or err: return 1
            self.command = val
            continue

         if opt.name == '-dsets':
            val, err = uopts.get_string_list('', opt=opt)
            if val == None or err: return 1
            self.dsets.append(val)      # allow multiple such options
            continue

         if opt.name == '-dset_index0_list':
            val, err = uopts.get_string_list('', opt=opt)
            if val == None or err: return 1
            self.index0_list.append(val)      # allow multiple such options
            continue

         if opt.name == '-dset_index1_list':
            val, err = uopts.get_string_list('', opt=opt)
            if val == None or err: return 1
            self.index1_list.append(val)      # allow multiple such options
            continue

         if opt.name == '-factors':
            val, err = uopts.get_type_list(int, '', opt=opt)
            if val == None or err: return 1
            self.factors = val
            continue

         if opt.name == '-keep_dirent_pre':
            self.dent_pre = 1
            continue

         if opt.name == '-options':
            val, err = uopts.get_string_list('', opt=opt)
            if val == None or err: return 1
            self.options = val
            continue

         if opt.name == '-prefix':
            val, err = uopts.get_string_opt('', opt=opt)
            if val == None or err: return 1
            self.prefix = val
            continue

         if opt.name == '-set_labels':
            val, err = uopts.get_string_list('', opt=opt)
            if val == None or err: return 1
            self.lablist = val
            continue

         if opt.name == '-subj_prefix':
            val, err = uopts.get_string_opt('', opt=opt)
            if val == None or err: return 1
            self.subj_prefix = val
            continue

         if opt.name == '-subj_suffix':
            val, err = uopts.get_string_opt('', opt=opt)
            if val == None or err: return 1
            self.subj_suffix = val
            continue

         if opt.name == '-subs_betas':
            val, err = uopts.get_string_list('', opt=opt)
            if val == None or err: return 1
            self.betasubs = val
            continue

         if opt.name == '-subs_tstats':
            val, err = uopts.get_string_list('', opt=opt)
            if val == None or err: return 1
            self.tstatsubs = val
            continue

         if opt.name == '-type':
            val, err = uopts.get_string_opt('', opt=opt)
            if val == None or err: return 1
            self.ttype = val
            continue

         if opt.name == '-verb': continue       # already handled

         if opt.name == '-write_script':
            val, err = uopts.get_string_opt('', opt=opt)
            if val == None or err: return 1
            self.write_script = val
            continue

         # general options

         # an unhandled option
         print '** option %s not yet supported' % opt.name
         return 1

      if self.verb > 2: self.show()

      # process -dset_index_list_0 and _1
      if self.update_dset_lists(): return 1

      return None
Beispiel #21
0
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
Beispiel #22
0
    def process_options(self, argv=sys.argv):

        # 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_help_string
            return 0

        if '-hist' in argv:
            print g_history
            return 0

        if '-show_valid_opts' in argv:
            self.valid_opts.show('', 1)
            return 0

        if '-ver' in argv:
            print g_version
            return 0

        # ============================================================
        # read options specified by the user
        self.user_opts = OL.read_options(argv, self.valid_opts)
        uopts = self.user_opts  # convenience variable
        if not uopts: return 1  # error condition

        # ------------------------------------------------------------
        # require a list of files, at least

        # ------------------------------------------------------------
        # process options, go after -verb first

        val, err = uopts.get_type_opt(int, '-verb')
        if val != None and not err: self.verb = val

        for opt in uopts.olist:

            # main options
            if opt.name == '-AminusB':
                self.comp_dir = opt.name
                continue

            if opt.name == '-BminusA':
                self.comp_dir = opt.name
                continue

            if opt.name == '-command':
                val, err = uopts.get_string_opt('', opt=opt)
                if val == None or err: return 1
                self.command = val
                continue

            if opt.name == '-dsets':
                val, err = uopts.get_string_list('', opt=opt)
                if val == None or err: return 1
                self.dsets.append(val)  # allow multiple such options
                continue

            if opt.name == '-dset_index0_list':
                val, err = uopts.get_string_list('', opt=opt)
                if val == None or err: return 1
                self.index0_list.append(val)  # allow multiple such options
                continue

            if opt.name == '-dset_index1_list':
                val, err = uopts.get_string_list('', opt=opt)
                if val == None or err: return 1
                self.index1_list.append(val)  # allow multiple such options
                continue

            if opt.name == '-factors':
                val, err = uopts.get_type_list(int, '', opt=opt)
                if val == None or err: return 1
                self.factors = val
                continue

            if opt.name == '-keep_dirent_pre':
                self.dent_pre = 1
                continue

            if opt.name == '-options':
                val, err = uopts.get_string_list('', opt=opt)
                if val == None or err: return 1
                self.options = val
                continue

            if opt.name == '-prefix':
                val, err = uopts.get_string_opt('', opt=opt)
                if val == None or err: return 1
                self.prefix = val
                continue

            if opt.name == '-set_labels':
                val, err = uopts.get_string_list('', opt=opt)
                if val == None or err: return 1
                self.lablist = val
                continue

            if opt.name == '-subj_prefix':
                val, err = uopts.get_string_opt('', opt=opt)
                if val == None or err: return 1
                self.subj_prefix = val
                continue

            if opt.name == '-subj_suffix':
                val, err = uopts.get_string_opt('', opt=opt)
                if val == None or err: return 1
                self.subj_suffix = val
                continue

            if opt.name == '-subs_betas':
                val, err = uopts.get_string_list('', opt=opt)
                if val == None or err: return 1
                self.betasubs = val
                continue

            if opt.name == '-subs_tstats':
                val, err = uopts.get_string_list('', opt=opt)
                if val == None or err: return 1
                self.tstatsubs = val
                continue

            if opt.name == '-type':
                val, err = uopts.get_string_opt('', opt=opt)
                if val == None or err: return 1
                self.ttype = val
                continue

            if opt.name == '-verb': continue  # already handled

            if opt.name == '-write_script':
                val, err = uopts.get_string_opt('', opt=opt)
                if val == None or err: return 1
                self.write_script = val
                continue

            # general options

            # an unhandled option
            print '** option %s not yet supported' % opt.name
            return 1

        if self.verb > 2: self.show()

        # process -dset_index_list_0 and _1
        if self.update_dset_lists(): return 1

        return None
Beispiel #23
0
    def process_options(self):
        """return  1 on valid and exit
         return  0 on valid and continue
         return -1 on invalid
      """

        argv = sys.argv

        # 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, do default processing
        if '-help' in argv or len(argv) < 2:
            print g_help_string
            return 1

        if '-hist' in argv:
            print g_history
            return 1

        if '-show_valid_opts' in argv:
            self.valid_opts.show('', 1)
            return 1

        if '-ver' in argv:
            print g_version
            return 1

        # ============================================================
        # read options specified by the user
        self.user_opts = OL.read_options(argv, self.valid_opts)
        uopts = self.user_opts  # convenience variable
        if not uopts: return -1  # error condition

        # ------------------------------------------------------------
        # process verb first

        val, err = uopts.get_type_opt(int, '-verb')
        if val != None and not err: self.verb = val

        # ------------------------------------------------------------
        # process options sequentially, to make them like a script
        errs = 0
        for opt in self.user_opts.olist:
            # check for anything to skip
            if opt.name == '-verb': pass

            elif opt.name == '-infiles':
                self.infiles, err = uopts.get_string_list('', opt=opt)
                if self.infiles == None or err:
                    print '** failed to read -infiles list'
                    errs += 1

            elif opt.name == '-overwrite':
                self.overwrite = 1

            elif opt.name == '-prefix':
                val, err = uopts.get_string_opt(opt=opt)
                if val != None and not err: self.prefix = val

        # allow early and late error returns
        if errs: return -1

        # ------------------------------------------------------------
        # apply any trailing logic

        # if here, require input files
        if len(self.infiles) < 1:
            print '** missing -infiles option'
            errs += 1

        # if no -prefix and no -verb, default verb to 2
        if not self.user_opts.find_opt('-verb') and self.prefix == '':
            self.verb = 2

        if errs: return -1

        return 0
Beispiel #24
0
   def process_options(self):
      """return  1 on valid and exit
         return  0 on valid and continue
         return -1 on invalid
      """

      argv = sys.argv

      # 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, do default processing
      if '-help' in argv or len(argv) < 2:
         print g_help_string
         return 1

      if '-hist' in argv:
         print g_history
         return 1

      if '-show_valid_opts' in argv:
         self.valid_opts.show('', 1)
         return 1

      if '-ver' in argv:
         print g_version
         return 1

      # ============================================================
      # read options specified by the user
      self.user_opts = OL.read_options(argv, self.valid_opts)
      uopts = self.user_opts            # convenience variable
      if not uopts: return -1           # error condition

      # ------------------------------------------------------------
      # process verb first

      val, err = uopts.get_type_opt(int, '-verb')
      if val != None and not err: self.verb = val

      # ------------------------------------------------------------
      # process options sequentially, to make them like a script
      errs = 0
      for opt in self.user_opts.olist:
         # check for anything to skip
         if opt.name == '-verb': pass

         elif opt.name == '-infiles':
            self.infiles, err = uopts.get_string_list('', opt=opt)
            if self.infiles == None or err:
               print '** failed to read -infiles list'
               errs +=1

            self.parse_infile_names()

         elif opt.name == '-overwrite':
            self.overwrite = 1

         elif opt.name == '-separator':
            self.separator, err = uopts.get_string_opt('', opt=opt)
            if self.separator == None or err:
               print "** bad -tablefile option"
               errs += 1
            if   self.separator == 'tab': self.separator = '\t'
            elif self.separator == 'whitespace': self.separator = 'ws'
            self.seplen = len(self.separator)

         elif opt.name == '-showlabs':
            self.showlabs = 1

         elif opt.name == '-tablefile':
            self.tablefile, err = uopts.get_string_opt('', opt=opt)
            if self.tablefile == None or err:
               print "** bad -tablefile option"
               errs +=1

         else:
            oind = self.user_opts.olist.index(opt)
            print '** unknown option # %d: %s' % (oind+1, opt.name)
            errs += 1
            break

      # allow early and late error returns
      if errs: return -1

      # ------------------------------------------------------------
      # apply any trailing logic

      if len(self.infiles) < 1:
         print '** missing -infiles option'
         errs += 1

      if errs: return -1

      return 0
Beispiel #25
0
   def process_options(self):

      # ============================================================
      # read options specified by the user
      self.user_opts = OL.read_options(sys.argv, self.valid_opts)
      uopts = self.user_opts            # convenience variable
      if not uopts: return 1            # error condition

      # ------------------------------------------------------------
      # check -test_libs separately, as we may want to apply -verb

      if '-test_libs' in sys.argv:
         val, err = self.user_opts.get_type_opt(int, '-verb')
         if val == None or err: val = 2
         return self.test_libraries(verb=val)

      # attempting real work, load AM (locally)
      if self.set_afni_xmat(): return 1

      # ------------------------------------------------------------
      # check general options, esp. chrono

      if uopts.find_opt('-chrono'): self.chrono = 1

      # if options are not chronological, process general options now
      # (so -show options are still in order)
      if not self.chrono:

         # general options might affect selection options
         val, err = self.user_opts.get_type_opt(float, '-cormat_cutoff')
         if val != None and not err: self.cormat_cut = val

         val, err = self.user_opts.get_type_opt(float, '-cosmat_cutoff')
         if val != None and not err: self.cosmat_cut = val

         val, err = self.user_opts.get_type_opt(float, '-cosmat_motion')
         if val != None and not err: self.cosmat_motion = 1

         val, err = self.user_opts.get_type_opt(int, '-verb')
         if val != None and not err: self.verb = val

         # selection options
         val, err = uopts.get_string_opt('-load_xmat')
         if val and not err:
            if self.set_xmat(val): return 1

         val, err = uopts.get_string_opt('-load_1D')
         if val and not err:
            if self.set_1D(val): return 1

         val, err = uopts.get_string_opt('-choose_cols')
         if val and not err:
            rstr = self.set_cols_from_string(val)
            if rstr:
               print "** failed to apply '-choose_cols':\n%s" % rstr
               return 1

      # ------------------------------------------------------------
      # selection and process options:
      #    process sequentially, to make them like a script

      for opt in uopts.olist:
         # if all options are chronological, check load and general, too
         if self.chrono:
            # selection options
            if opt.name == '-load_xmat':
               if self.set_xmat(opt.parlist[0]):   return 1
            elif opt.name == '-load_1D':
               if self.set_1D(opt.parlist[0]):     return 1
            elif opt.name == '-choose_cols':
               rstr = self.set_cols_from_string(opt.parlist[0])
               if rstr:
                  print "** failed to apply '-choose_cols':\n%s" % rstr
                  return 1

            # general options
            elif opt.name == '-cormat_cutoff':
               val, err = self.user_opts.get_type_opt(float, '', opt=opt)
               if val != None and err: return 1
               else: self.cormat_cut = val

            elif opt.name == '-cosmat_cutoff':
               val, err = self.user_opts.get_type_opt(float, '', opt=opt)
               if val != None and err: return 1
               else: self.cosmat_cut = val

            elif opt.name == '-cosmat_motion':
               self.cosmat_motion = 1

            elif opt.name == '-verb':
               val, err = self.user_opts.get_type_opt(int, '', opt=opt)
               if val != None and err: return 1
               else: self.verb = val

         # 'show' options (allow these to fail?)
         if opt.name == '-show_col_types':
            if self.matX:
               err, str = self.make_col_type_string()
               print str
            else: print "** -show_col_types: needs -load_xmat"
         elif opt.name == '-show_conds':
            if self.matX: print self.matX.make_show_conds_str(self.col_list)
            else: print "** -show_conds: needs -load_xmat"
         elif opt.name == '-show_cormat':
            err, str = self.make_cormat_string()
            print '-- Correlation matrix for %s :' % self.fname_mat
            print str
Beispiel #26
0
    def process_options(self):
        """return  1 on valid and exit
         return  0 on valid and continue
         return -1 on invalid
      """

        argv = sys.argv

        # 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, do default processing
        if '-help' in argv or len(argv) < 2:
            show_help()
            return 1

        if '-help_examples' in argv:
            print g_help_examples
            return 1

        if '-hist' in argv:
            print g_history
            return 1

        if '-show_valid_opts' in argv:
            self.valid_opts.show('', 1)
            return 1

        if '-ver' in argv:
            print g_version
            return 1

        # ============================================================
        # read options specified by the user
        self.user_opts = OL.read_options(argv, self.valid_opts)
        uopts = self.user_opts  # convenience variable
        if not uopts: return -1  # error condition

        # ------------------------------------------------------------
        # process verb first

        val, err = uopts.get_type_opt(int, '-verb')
        if val != None and not err: self.verb = val

        # ------------------------------------------------------------
        # process options sequentially, to make them like a script
        errs = 0
        for opt in self.user_opts.olist:
            # check for anything to skip
            if opt.name == '-verb': pass

            elif opt.name == '-logfile':
                self.logfile, err = uopts.get_string_opt('', opt=opt)
                if self.logfile == None or err:
                    print '** failed to read -logfile name'
                    errs += 1

            elif opt.name == '-labels':
                self.labels, err = uopts.get_string_list('', opt=opt)
                if self.labels == None or err:
                    print '** option -labels: failed to process option'
                    errs += 1

            elif opt.name == '-show_all_orig':
                pass  # process later

            elif opt.name == '-show_orig':
                self.show_vals = SHOW_ORIG

            elif opt.name == '-show_rank':
                self.show_vals = SHOW_RANK

        if self.user_opts.find_opt('-show_all_orig'):
            if not (self.show_vals & SHOW_ORIG):
                print "** -show_all_orig requires showing orig"
                errs += 1
            self.show_vals |= SHOW_ALL_ORIG

        # allow early and late error returns
        if errs: return -1

        # ------------------------------------------------------------
        ## apply any trailing logic

        if self.logfile == '':
            print '** missing -logfile option'
            errs += 1

        if len(self.labels) < 1:
            print '** missing -labels to search for'
            errs += 1

        if errs: return -1

        return 0