Exemplo n.º 1
0
    def script_analysis_prep(self):
        """return a set of commands to:
            convert pthr_list to zthr_list
            create a dummy time series of lenth itersize (if > 1)
            divide (ceil) niter by itersize (if > 1)
      """

        cmd = SUBJ.comment_section_string('prep: make z-scores, etc.') + '\n'

        cmd += '# make zthr_list (convert p-values to z-scores)\n'        \
               '# (2-tailed computation mirrors athresh() in SurfClust)\n'\
               'set zthr_list = ()\n'                                     \
               'foreach pthr ( $pthr_list )\n'                            \
               '   # convert from p to z (code for N(0,1) is 5)\n'        \
               '   set zthr = `ccalc "cdf2stat(1-$pthr,5,0,0,0)"`\n'      \
               '   set zthr_list = ( $zthr_list $zthr )\n'                \
               'end\n\n'

        cmd += 'echo have p-values: $pthr_list\n' \
               'echo have z-scores: $zthr_list\n\n'

        cmd += '# make a dummy time file of length $itersize for 3dcalc\n' \
               '1deval -num $itersize -expr t > dummy.TRs.$itersize.1D\n\n'

        cmd += '# divide niter by itersize (take ceiling)\n'              \
               '@ niter = ( $niter + $itersize - 1 ) / $itersize\n\n'

        # always create an empty surface, and then an all-1 surface
        cmd += g_make_empty_surf_str

        return cmd
Exemplo n.º 2
0
    def script_set_vars(self):
        """use variables for dataset directories, only
      """

        # init with a section comment
        hdr = SUBJ.comment_section_string('set process variables') + '\n'
        cmd = ''

        # init to nothing
        self.LV.dirA = ''
        self.LV.dirB = ''

        if self.uvars.mask:
            cmd += 'set mask_dset = %s\n\n' \
                   % self.strip_suffix(self.uvars.mask, '.HEAD')

        # set dirA and possibly dirB
        dirs_set = 0
        if not UTIL.is_trivial_dir(self.LV.parent_dirs[0]):
            cmd += 'set dirA = %s\n' % self.LV.parent_dirs[0]
            self.LV.dirA = '$dirA'
            dirs_set = 1

        if len(self.uvars.dsets_B) > 0:
            if not UTIL.is_trivial_dir(self.LV.parent_dirs[1]):
                if self.LV.parent_dirs[0] != self.LV.parent_dirs[1]:
                    cmd += 'set dirB = %s\n' % self.LV.parent_dirs[1]
                    self.LV.dirB = '$dirB'
                    dirs_set = 1
                else:
                    self.LV.dirB = '$dirA'
        if dirs_set: cmd += '\n'

        if cmd: return hdr + cmd
        else: return ''
Exemplo n.º 3
0
   def script_tabulate_areas(self):
      """for each zthr, for each clust file, extract max area"""

      cmd = SUBJ.comment_section_string('extract cluster counts') + '\n'

      cmd += '# tabulate all results for each uncorrected p-threshold\n'  \
             'set maxa_list = ()   # track all max areas\n'               \
             'set failures = ()    # track cluster failures\n'            \
             'foreach pthr ( $pthr_list )\n'                              \
             '   # make note of current file\n'                           \
             '   set zfile = z.max.area.$pthr\n'                          \
             '\n'                                                         \
             '   # create empty file for this p-value\n'                  \
             '   echo -n "" > $zfile\n'                                   \
             '\n'                                                         \
             '   set file_list = ( clust.out.*.$pthr )\n'                 \
             '   echo "-- processing $#file_list files for p = $pthr"\n'  \
             '\n'                                                         \
             '   # process each file, counting through them\n'            \
             '   foreach findex ( `count -digits 1 1 $#file_list` )\n'    \
             '      set file = $file_list[$findex]\n'                     \
             '\n'                                                         \
             '      # print pacifier every 100 files\n'                   \
             '      if ( ! ($findex % 100) ) echo -n .\n'                 \
             '      if ( ! ($findex % 5000) ) echo ""\n'                  \
             '\n'                                                         \
             '      # grab the area field from first (largest) cluster\n' \
             "      set maxa = `awk '$1 == 1 {print $3}' $file`\n"        \
             '\n'                                                         \
             '      # and append it to the max file (if results exist)\n' \
             '      if ( $maxa != "" ) echo $maxa >> $zfile\n'            \
             '\n'                                                         \
             '   end  # file index\n'                                     \
             '\n'                                                         \
             '   # grab the max area for this p-value, and add to list\n' \
             '   # (if the max.area file is not empty for some reason)\n' \
             '   set nlines = `cat $zfile | wc -l`\n'                     \
             '   if ( $nlines != 0 ) then\n'                              \
             '      set maxa = `sort -rn $zfile | head -n 1`\n'           \
             '   else\n'                                                  \
             '      set failures = ( $failures $pthr )\n'                 \
             '      set maxa = 0\n'                                       \
             '   endif\n'                                                 \
             '\n'                                                         \
             '   set maxa_list = ( $maxa_list $maxa )\n'                  \
             '\n'                                                         \
             'end  # pthr\n'                                              \
             '\n'                                                         \
             'echo ""\n'                                                  \
             'echo "p-value thresholds   : $pthr_list"\n'                 \
             'echo "z-score thresholds   : $zthr_list"\n'                 \
             'echo "maximum cluster areas: $maxa_list"\n'                 \
             '\n'                                                         \
             'if ( $#failures ) then\n'                                   \
             '   echo ""\n'                                               \
             '   echo "** no clusters for p = $failures"\n'               \
             'endif\n'                                                    \
             '\n'

      return cmd
Exemplo n.º 4
0
    def script_tabulate_areas(self):
        """for each zthr, for each clust file, extract max area"""

        cmd = SUBJ.comment_section_string('extract cluster counts') + '\n'

        cmd += '# tabulate all results for each uncorrected p-threshold\n'  \
               'set maxa_list = ()   # track all max areas\n'               \
               'set failures = ()    # track cluster failures\n'            \
               'foreach pthr ( $pthr_list )\n'                              \
               '   # make note of current file\n'                           \
               '   set zfile = z.max.area.$pthr\n'                          \
               '\n'                                                         \
               '   # create empty file for this p-value\n'                  \
               '   echo -n "" > $zfile\n'                                   \
               '\n'                                                         \
               '   set file_list = ( clust.out.*.$pthr )\n'                 \
               '   echo "-- processing $#file_list files for p = $pthr"\n'  \
               '\n'                                                         \
               '   # process each file, counting through them\n'            \
               '   foreach findex ( `count -digits 1 1 $#file_list` )\n'    \
               '      set file = $file_list[$findex]\n'                     \
               '\n'                                                         \
               '      # print pacifier every 100 files\n'                   \
               '      if ( ! ($findex % 100) ) echo -n .\n'                 \
               '      if ( ! ($findex % 5000) ) echo ""\n'                  \
               '\n'                                                         \
               '      # grab the area field from first (largest) cluster\n' \
               "      set maxa = `awk '$1 == 1 {print $3}' $file`\n"        \
               '\n'                                                         \
               '      # and append it to the max file (if results exist)\n' \
               '      if ( $maxa != "" ) echo $maxa >> $zfile\n'            \
               '\n'                                                         \
               '   end  # file index\n'                                     \
               '\n'                                                         \
               '   # grab the max area for this p-value, and add to list\n' \
               '   # (if the max.area file is not empty for some reason)\n' \
               '   set nlines = `cat $zfile | wc -l`\n'                     \
               '   if ( $nlines != 0 ) then\n'                              \
               '      set maxa = `sort -rn $zfile | head -n 1`\n'           \
               '   else\n'                                                  \
               '      set failures = ( $failures $pthr )\n'                 \
               '      set maxa = 0\n'                                       \
               '   endif\n'                                                 \
               '\n'                                                         \
               '   set maxa_list = ( $maxa_list $maxa )\n'                  \
               '\n'                                                         \
               'end  # pthr\n'                                              \
               '\n'                                                         \
               'echo ""\n'                                                  \
               'echo "p-value thresholds   : $pthr_list"\n'                 \
               'echo "z-score thresholds   : $zthr_list"\n'                 \
               'echo "maximum cluster areas: $maxa_list"\n'                 \
               '\n'                                                         \
               'if ( $#failures ) then\n'                                   \
               '   echo ""\n'                                               \
               '   echo "** no clusters for p = $failures"\n'               \
               'endif\n'                                                    \
               '\n'

        return cmd
Exemplo n.º 5
0
   def script_set_vars(self):
      """use variables for dataset directories, only
      """

      # init with a section comment
      hdr = SUBJ.comment_section_string('set process variables') + '\n'
      cmd = ''

      # init to nothing
      self.LV.dirA = ''
      self.LV.dirB = ''

      if self.uvars.mask:
         cmd += 'set mask_dset = %s\n\n' \
                % self.strip_suffix(self.uvars.mask, '.HEAD')

      # set dirA and possibly dirB
      dirs_set = 0
      if not UTIL.is_trivial_dir(self.LV.parent_dirs[0]):
         cmd += 'set dirA = %s\n' % self.LV.parent_dirs[0]
         self.LV.dirA = '$dirA'
         dirs_set = 1

      if len(self.uvars.dsets_B) > 0:
         if not UTIL.is_trivial_dir(self.LV.parent_dirs[1]):
            if self.LV.parent_dirs[0] != self.LV.parent_dirs[1]:
               cmd += 'set dirB = %s\n' % self.LV.parent_dirs[1]
               self.LV.dirB = '$dirB'
               dirs_set = 1
            else: self.LV.dirB = '$dirA'
      if dirs_set: cmd += '\n'

      if cmd: return hdr + cmd
      else:   return ''
    def script_analysis_prep(self):
        """return a set of commands to:
            convert pthr_list to zthr_list
            create a dummy time series of lenth itersize (if > 1)
            divide (ceil) niter by itersize (if > 1)
      """

        cmd = SUBJ.comment_section_string("prep: make z-scores, etc.") + "\n"

        cmd += (
            "# make zthr_list (convert p-values to z-scores)\n"
            "# (2-tailed computation mirrors athresh() in SurfClust)\n"
            "set zthr_list = ()\n"
            "foreach pthr ( $pthr_list )\n"
            "   # convert from p to z (code for N(0,1) is 5)\n"
            '   set zthr = `ccalc "cdf2stat(1-$pthr,5,0,0,0)"`\n'
            "   set zthr_list = ( $zthr_list $zthr )\n"
            "end\n\n"
        )

        cmd += "echo have p-values: $pthr_list\n" "echo have z-scores: $zthr_list\n\n"

        cmd += (
            "# make a dummy time file of length $itersize for 3dcalc\n"
            "1deval -num $itersize -expr t > dummy.TRs.$itersize.1D\n\n"
        )

        cmd += "# divide niter by itersize (take ceiling)\n" "@ niter = ( $niter + $itersize - 1 ) / $itersize\n\n"

        # always create an empty surface, and then an all-1 surface
        cmd += g_make_empty_surf_str

        return cmd
Exemplo n.º 7
0
    def script_set_vars(self):
        """use variables for inputs (anat, epi, epi_base) and for
         options (cost_main, cost_list, align_opts)
      """

        # init with a section comment
        cmd = SUBJ.comment_section_string('set processing variables') + '\n'

        # maybe init with top_dir
        if not self.LV.is_trivial_dir('top_dir'):
            cmd += '# top data directory\n' \
                   'set top_dir = %s\n\n' % self.LV.top_dir

        # anat and epi might use top_dir
        if self.LV.is_trivial_dir('top_dir'):
            astr = self.uvars.anat
            estr = self.uvars.epi
        else:
            astr = '$top_dir/%s' % self.LV.short_names[0][0]
            estr = '$top_dir/%s' % self.LV.short_names[0][1]

        # if we are aligning centers, set center_base variable (maybe w/top_dir)
        if self.uvars.align_centers == 'yes':
            if self.LV.is_trivial_dir('top_dir'): cstr = self.uvars.center_base
            else:
                cdir = UTIL.child_dir_name(self.LV.top_dir,
                                           self.uvars.center_base)
                if cdir == self.uvars.center_base: cstr = cdir
                else: cstr = '$top_dir/%s' % cdir
            ccmd = 'set center_base = %s\n' % cstr
        else:
            ccmd = ''

        # now set variables for inputs, possibly including center_base
        cmd += '# input dataset options (ebase is EPI index)\n'           \
               'set in_anat     = %s\n'                                   \
               'set in_epi      = %s\n'                                   \
               'set in_ebase    = %d\n'                                   \
               '%s'                                                       \
               '\n'                                                       \
               % (astr, estr, self.uvars.epi_base, ccmd)

        # note whether to use multi_cost
        cmd += '# main options\n' \
               'set cost_main = %s\n' % self.uvars.cost_list[0]
        if len(self.uvars.cost_list) > 1:
            cmd += 'set cost_list = ( %s )\n' % ' '.join(
                self.uvars.cost_list[1:])
        cmd += '\n'

        # possibly add align_opts list variable
        cmd += self.make_align_opts_str()

        return cmd
Exemplo n.º 8
0
   def script_set_vars(self):
      """use variables for inputs (anat, epi, epi_base) and for
         options (cost_main, cost_list, align_opts)
      """

      # init with a section comment
      cmd = SUBJ.comment_section_string('set processing variables') + '\n'

      # maybe init with top_dir
      if not self.LV.is_trivial_dir('top_dir'):
         cmd += '# top data directory\n' \
                'set top_dir = %s\n\n' % self.LV.top_dir

      # anat and epi might use top_dir
      if self.LV.is_trivial_dir('top_dir'):
         astr = self.uvars.anat
         estr = self.uvars.epi
      else:
         astr = '$top_dir/%s' % self.LV.short_names[0][0]
         estr = '$top_dir/%s' % self.LV.short_names[0][1]

      # if we are aligning centers, set center_base variable (maybe w/top_dir)
      if self.uvars.align_centers == 'yes':
         if self.LV.is_trivial_dir('top_dir'): cstr = self.uvars.center_base
         else:
            cdir = UTIL.child_dir_name(self.LV.top_dir, self.uvars.center_base)
            if cdir == self.uvars.center_base: cstr = cdir
            else: cstr = '$top_dir/%s' % cdir
         ccmd = 'set center_base = %s\n' % cstr
      else: ccmd = ''

      # now set variables for inputs, possibly including center_base
      cmd += '# input dataset options (ebase is EPI index)\n'           \
             'set in_anat     = %s\n'                                   \
             'set in_epi      = %s\n'                                   \
             'set in_ebase    = %d\n'                                   \
             '%s'                                                       \
             '\n'                                                       \
             % (astr, estr, self.uvars.epi_base, ccmd)

      # note whether to use multi_cost
      cmd += '# main options\n' \
             'set cost_main = %s\n' % self.uvars.cost_list[0]
      if len(self.uvars.cost_list) > 1:
         cmd += 'set cost_list = ( %s )\n' % ' '.join(self.uvars.cost_list[1:])
      cmd += '\n'

      # possibly add align_opts list variable
      cmd += self.make_align_opts_str()

      return cmd
Exemplo n.º 9
0
   def script_main(self):
      """write command with prefix, datasets and extra options
      """
      
      cmd = SUBJ.comment_section_string('process the data') + '\n'

      if self.uvars.program == '3dttest++':
         cmd += self.script_ttest()
      elif self.uvars.program == '3dMEMA':
         cmd += self.script_MEMA()
      else:
         self.errors.append('** bad program name: %s' % self.uvars.program)
         return ''

      return UTIL.add_line_wrappers(cmd)
Exemplo n.º 10
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    def script_main(self):
        """write command with prefix, datasets and extra options
      """

        cmd = SUBJ.comment_section_string('process the data') + '\n'

        if self.uvars.program == '3dttest++':
            cmd += self.script_ttest()
        elif self.uvars.program == '3dMEMA':
            cmd += self.script_MEMA()
        else:
            self.errors.append('** bad program name: %s' % self.uvars.program)
            return ''

        return UTIL.add_line_wrappers(cmd)
Exemplo n.º 11
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    def script_copy_data(self):
        """these commands only vary based on results_dir"""

        cmd = SUBJ.comment_section_string('copy data') + '\n'

        if self.uvars.is_trivial_dir('results_dir'): rdir = '.'
        else: rdir = '$results_dir'

        cmd += '# copy dataset to processing directory\n'         \
               '3dbucket -prefix %s/anat $in_anat\n'              \
               '3dbucket -prefix %s/epi $in_epi"[$in_ebase]"\n'   \
               '\n' % (rdir, rdir)

        if rdir != '.':
            cmd += '# enter the processing directory\n'    \
                   'cd %s\n\n' % rdir

        return cmd
Exemplo n.º 12
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   def script_copy_data(self):
      """these commands only vary based on results_dir"""

      cmd = SUBJ.comment_section_string('copy data') + '\n'

      if self.uvars.is_trivial_dir('results_dir'): rdir = '.'
      else:                                        rdir = '$results_dir'

      cmd += '# copy dataset to processing directory\n'         \
             '3dbucket -prefix %s/anat $in_anat\n'              \
             '3dbucket -prefix %s/epi $in_epi"[$in_ebase]"\n'   \
             '\n' % (rdir, rdir)

      if rdir != '.':
         cmd += '# enter the processing directory\n'    \
                'cd %s\n\n' % rdir

      return cmd
Exemplo n.º 13
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   def script_align_centers(self):
      """if align_centers should be run, deoblique both and align with
         center_base (probably TT_N27+tlrc)

         note: these commands should be fixed, since the dataset names are
      """

      if self.uvars.align_centers != 'yes': return ''

      cmd = SUBJ.comment_section_string('align centers') + '\n'

      cmd += '# since altering grid, remove any oblique transformation\n'    \
             '3drefit -deoblique anat+orig epi+orig\n'                       \
             '\n'                                                            \
             '# align volume centers (we do not trust spatial locations)\n'  \
             '@Align_Centers -no_cp -base $center_base -dset anat+orig\n'    \
             '@Align_Centers -no_cp -base $center_base -dset epi+orig\n\n'   \

      return cmd
Exemplo n.º 14
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    def script_align_centers(self):
        """if align_centers should be run, deoblique both and align with
         center_base (probably TT_N27+tlrc)

         note: these commands should be fixed, since the dataset names are
      """

        if self.uvars.align_centers != 'yes': return ''

        cmd = SUBJ.comment_section_string('align centers') + '\n'

        cmd += '# since altering grid, remove any oblique transformation\n'    \
               '3drefit -deoblique anat+orig epi+orig\n'                       \
               '\n'                                                            \
               '# align volume centers (we do not trust spatial locations)\n'  \
               '@Align_Centers -no_cp -base $center_base -dset anat+orig\n'    \
               '@Align_Centers -no_cp -base $center_base -dset epi+orig\n\n'   \

        return cmd
Exemplo n.º 15
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    def script_align_datasets(self):
        """actually run align_epi_anat.py

         only current option is -mult_cost, everything else is via variables
      """

        if len(self.uvars.cost_list) > 1: mstr = ' -multi_cost $cost_list'
        else: mstr = ''

        cmd = SUBJ.comment_section_string('align data') + '\n'

        cmd += \
         '# test alignment, using variables set above\n'          \
         'align_epi_anat.py -anat anat+orig -epi epi+orig '       \
                           '-epi_base $in_ebase \\\n'             \
         '                  -cost $cost_main%s $align_opts\n'     \
         '\n' % mstr

        return cmd
Exemplo n.º 16
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   def script_align_datasets(self):
      """actually run align_epi_anat.py

         only current option is -mult_cost, everything else is via variables
      """

      if len(self.uvars.cost_list) > 1: mstr = ' -multi_cost $cost_list'
      else:                             mstr = ''

      cmd = SUBJ.comment_section_string('align data') + '\n'

      cmd += \
       '# test alignment, using variables set above\n'          \
       'align_epi_anat.py -anat anat+orig -epi epi+orig '       \
                         '-epi_base $in_ebase \\\n'             \
       '                  -cost $cost_main%s $align_opts\n'     \
       '\n' % mstr

      return cmd
Exemplo n.º 17
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   def script_results_dir(self):

      # if no results dir, just put everything here
      if self.uvars.is_trivial_dir('results_dir'): return ''

      cmd  = SUBJ.comment_section_string('test and create results dir') + '\n'

      cmd += '# note directory for results\n'           \
             'set results_dir = %s\n\n' % self.uvars.results_dir

      cmd += '# make sure it does not yet exist\n'      \
             'if ( -e $results_dir ) then\n'            \
             '    echo "** results dir \'$results_dir\' already exists"\n'  \
             '    exit\n'                               \
             'endif\n\n'

      cmd += '# create results directory, where the work will be done\n' \
             'mkdir $results_dir\n\n'

      return cmd
Exemplo n.º 18
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    def script_results_dir(self):

        # if no results dir, just put everything here
        if self.uvars.is_trivial_dir('results_dir'): return ''

        cmd = SUBJ.comment_section_string('test and create results dir') + '\n'

        cmd += '# note directory for results\n'           \
               'set results_dir = %s\n\n' % self.uvars.results_dir

        cmd += '# make sure it does not yet exist\n'      \
               'if ( -e $results_dir ) then\n'            \
               '    echo "** results dir \'$results_dir\' already exists"\n'  \
               '    exit\n'                               \
               'endif\n\n'

        cmd += '# create results directory, where the work will be done\n' \
               'mkdir $results_dir\n\n'

        return cmd
    def script_results_dir(self):

        # if no results dir, just put everything here
        if self.uvars.is_trivial_dir("results_dir"):
            return ""

        cmd = SUBJ.comment_section_string("test, create and enter results dir") + "\n"

        cmd += "# note directory for results\n" "set results_dir = %s\n\n" % self.uvars.results_dir

        cmd += (
            "# make sure it does not yet exist\n"
            "if ( -e $results_dir ) then\n"
            "    echo \"** results dir '$results_dir' already exists\"\n"
            "    exit\n"
            "endif\n\n"
        )

        cmd += "# create and enter results directory\n" "mkdir $results_dir\n" "cd $results_dir\n\n"

        return cmd
Exemplo n.º 20
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   def script_analysis_prep(self):
      """return a set of commands to:
            convert pthr_list to zthr_list
            create a dummy time series of lenth itersize (if > 1)
            divide (ceil) niter by itersize (if > 1)
      """

      cmd  = SUBJ.comment_section_string('prep: make z-scores, etc.') + '\n'

      cmd += '# make zthr_list (convert p-values to z-scores)\n'        \
             '# (2-tailed computation mirrors athresh() in SurfClust)\n'\
             'set zthr_list = ()\n'                                     \
             'foreach pthr ( $pthr_list )\n'                            \
             '   # convert from p to z (code for N(0,1) is 5)\n'        \
             '   set zthr = `ccalc "cdf2stat(1-$pthr,5,0,0,0)"`\n'      \
             '   set zthr_list = ( $zthr_list $zthr )\n'                \
             'end\n\n'

      cmd += 'echo have p-values: $pthr_list\n' \
             'echo have z-scores: $zthr_list\n\n'

      cmd += '# make a dummy time file of length $itersize for 3dcalc\n' \
             '1deval -num $itersize -expr t > dummy.TRs.$itersize.1D\n\n'

      cmd += '# divide niter by itersize (take ceiling)\n'              \
             '@ niter = ( $niter + $itersize - 1 ) / $itersize\n\n'

      # always create an empty surface, and then an all-1 surface
      cmd += g_make_empty_surf_str
      if self.LV.val('smask'):
         cmd += '# make an all-1 masked surface for 3dmaskave\n' \
                '3dcalc -a $empty_surf -b $surf_mask'            \
                ' -expr "bool(b)" -prefix all_1.gii\n\n'
      else: 
         cmd += '# make an all-1 surface for 3dmaskave\n' \
             '3dcalc -a $empty_surf -expr 1 -prefix all_1.gii\n\n'

      return cmd
Exemplo n.º 21
0
    def script_set_vars(self):
        """use variables for inputs (anat, epi, epi_base) and for
         options (cost_main, cost_list, align_opts)
      """

        U = self.uvars  # for convenience

        # init with a section comment
        cmd = SUBJ.comment_section_string('set processing variables') + '\n'

        # maybe init with top_dir
        if not self.LV.is_trivial_dir('top_dir'):
            cmd += '# top data directory\n' \
                   'set top_dir = %s\n\n' % self.LV.top_dir

        # surf_vol and vol_mask might use top_dir
        if self.LV.is_trivial_dir('top_dir'):
            # if self.cvars.val('on_surface') != 'yes': self.LV.svol  = U.surf_vol
            #
            # rcr - fix this, surf_vol should not be needed if only on surface
            #       (for getting the node count, avoid SurfMeasures or any other
            #       program that uses -sv)
            self.LV.svol = U.surf_vol
            self.LV.svset = BASE.afni_name(self.LV.svol)
            self.LV.vmask = U.vol_mask
            self.LV.vmset = BASE.afni_name(U.vol_mask)
            self.LV.spec = U.spec_file
            if self.uvars.surf_mask != '':
                self.LV.smset = BASE.afni_name(self.uvars.surf_mask)
                self.LV.smask = self.LV.smset.real_input()
        else:
            self.LV.svol = '$top_dir/%s' % self.LV.short_names[0][0]
            self.LV.svset = BASE.afni_name(self.LV.svol)
            self.LV.spec = '$top_dir/%s' % self.LV.short_names[0][1]
            if self.cvars.val('on_surface') == 'yes':
                if self.uvars.surf_mask != '':
                    self.LV.smask = '$top_dir/%s' % self.LV.short_names[0][2]
                    self.LV.smset = BASE.afni_name(self.LV.smask)
            else:
                self.LV.vmask = '$top_dir/%s' % self.LV.short_names[0][2]
                self.LV.vmset = BASE.afni_name(self.LV.vmask)

        cmd += '# input datasets and surface specification file\n'         \
               '# (absolute paths are used since inputs are not copied)\n' \
               'set surf_vol    = %s\n'   \
               'set spec_file   = %s\n' % (self.LV.svol, self.LV.spec)

        if self.cvars.val('on_surface') != 'yes':
            cmd += 'set vol_mask    = %s\n' % self.LV.vmask

        if self.LV.val('smask'):
            cmd += 'set surf_mask   = %s\n' % self.LV.smask

        # as a list, these might come is as strings or floats, be generic
        plist = ['%s' % p for p in U.pthr_list]
        cmd += '\n'                                       \
               '# iterations and blur/clust parameters\n' \
               'set niter       = %d\n'                   \
               'set itersize    = %d\n'                   \
               'set pthr_list   = ( %s )\n\n'             \
               'set blur        = %g\n'                   \
               'set rmm         = %g\n\n'                 \
               % (U.niter, U.itersize, ' '.join(plist), U.blur, U.rmm)

        cmd += '# surface mapping parameters\n'   \
               'set surfA       = %s\n'           \
               'set surfB       = %s\n'           \
               'set map_func    = %s\n'           \
               'set nsteps      = %d\n\n'         \
               % (U.surfA, U.surfB, U.map_func, self.cvars.nsteps)

        if self.cvars.keepblocks > 0:
            cmd += '# note how many blocks to keep output datasets for\n' \
                   'set keepblocks  = %d\n\n' % self.cvars.keepblocks

        if self.cvars.time_process:
            cmd += "# prepare to possibly time programs (/usr/bin/time or '')\n" \
                   "set time_str    = /usr/bin/time \n\n"
            self.LV.time_str = '$time_str \\\n'
        else:
            self.LV.time_str = ''

        return cmd
    def script_set_vars(self):
        """use variables for inputs (anat, epi, epi_base) and for
         options (cost_main, cost_list, align_opts)
      """

        U = self.uvars  # for convenience

        # init with a section comment
        cmd = SUBJ.comment_section_string("set processing variables") + "\n"

        # maybe init with top_dir
        if not self.LV.is_trivial_dir("top_dir"):
            cmd += "# top data directory\n" "set top_dir = %s\n\n" % self.LV.top_dir

        # surf_vol and vol_mask might use top_dir
        if self.LV.is_trivial_dir("top_dir"):
            # if self.cvars.val('on_surface') != 'yes': self.LV.svol  = U.surf_vol
            #
            # rcr - fix this, surf_vol should not be needed if only on surface
            #       (for getting the node count, avoid SurfMeasures or any other
            #       program that uses -sv)
            self.LV.svol = U.surf_vol
            self.LV.svset = BASE.afni_name(self.LV.svol)
            self.LV.vmask = U.vol_mask
            self.LV.spec = U.spec_file
        else:
            self.LV.svol = "$top_dir/%s" % self.LV.short_names[0][0]
            self.LV.svset = BASE.afni_name(self.LV.svol)
            self.LV.spec = "$top_dir/%s" % self.LV.short_names[0][1]
            if self.cvars.val("on_surface") != "yes":
                self.LV.vmask = "$top_dir/%s" % self.LV.short_names[0][2]

        cmd += (
            "# input datasets and surface specification file\n"
            "# (absolute paths are used since inputs are not copied)\n"
            "set surf_vol    = %s\n"
            "set spec_file   = %s\n" % (self.LV.svol, self.LV.spec)
        )

        if self.cvars.val("on_surface") != "yes":
            cmd += "set vol_mask    = %s\n" % self.LV.vmask

        # as a list, these might come is as strings or floats, be generic
        plist = ["%s" % p for p in U.pthr_list]
        cmd += (
            "\n"
            "# iterations and blur/clust parameters\n"
            "set niter       = %d\n"
            "set itersize    = %d\n"
            "set pthr_list   = ( %s )\n\n"
            "set blur        = %g\n"
            "set rmm         = %g\n\n" % (U.niter, U.itersize, " ".join(plist), U.blur, U.rmm)
        )

        cmd += (
            "# surface mapping parameters\n"
            "set surfA       = %s\n"
            "set surfB       = %s\n"
            "set map_func    = %s\n"
            "set nsteps      = %d\n\n" % (U.surfA, U.surfB, U.map_func, self.cvars.nsteps)
        )

        if self.cvars.keepblocks > 0:
            cmd += (
                "# note how many blocks to keep output datasets for\n"
                "set keepblocks  = %d\n\n" % self.cvars.keepblocks
            )

        if self.cvars.time_process:
            cmd += "# prepare to possibly time programs (/usr/bin/time or '')\n" "set time_str    = /usr/bin/time \n\n"
            self.LV.time_str = "$time_str \\\n"
        else:
            self.LV.time_str = ""

        return cmd