コード例 #1
0
ファイル: gen_ss_review_table.py プロジェクト: ccraddock/afni
   def parse_infile_names(self):
      """try to get subject and possibly group names from infiles

         fill self.snames and self.gnames, if possible

         1. get SID
            - if files look like out.ss_review.SID.txt, that is a good start
            - else, look for varying part of filename
         2. get GID
            - replace SID in infile names and for varying group name
      """

      rv, slist = UTIL.list_minus_pref_suf(self.infiles,'out.ss_review.','.txt')
      if rv < 0: return
      if rv > 0:
         if self.verb > 1: print '++ trying to get SID from glob form'
         slist = UTIL.list_minus_glob_form(self.infiles, strip='dir')
      else:
         if self.verb > 1: print "++ have SIDs from 'out.ss_reiview' form"

      if len(slist) == 0:
         if self.verb > 1: print "-- empty SID list"
         return

      # make sure names are unique and not empty
      if not UTIL.vals_are_unique(slist):
         if self.verb > 1: print '-- SIDs not detected: not unique'
         return
      minlen = min([len(ss) for ss in slist])
      if minlen < 1:
         if self.verb > 1: print '-- SIDs not detected: some would be empty'
         return

      # we have a subject list
      self.snames = slist

      # now go for GID, start by replacing SIDs in infiles
      newfiles = [fname.replace(slist[ind], 'SUBJ') for ind, fname in
                        enumerate(self.infiles)]

      if UTIL.vals_are_constant(newfiles):
         print '-- no groups detected from filenames'
         return

      # okay, try to make a group list
      glist = UTIL.list_minus_glob_form(newfiles)

      # cannot have dirs in result
      for gid in glist:
         if gid.find('/') >= 0:
            if self.verb>1: print '-- no GIDs, dirs vary in multiple places'
            return

      minlen = min([len(ss) for ss in glist])
      if minlen < 1:
         if self.verb > 1: print '-- GIDs not detected: some would be empty'
         return

      if self.verb > 1: print "++ have GIDs from infiles"
      self.gnames = glist
コード例 #2
0
   def parse_infile_names(self):
      """try to get subject and possibly group names from infiles

         fill self.snames and self.gnames, if possible

         1. get SID
            - if files look like out.ss_review.SID.txt, that is a good start
            - else, look for varying part of filename
         2. get GID
            - replace SID in infile names and for varying group name
      """

      rv, slist = UTIL.list_minus_pref_suf(self.infiles,'out.ss_review.','.txt')
      if rv < 0: return
      if rv > 0:
         if self.verb > 1: print '++ trying to get SID from glob form'
         slist = UTIL.list_minus_glob_form(self.infiles, strip='dir')
      else:
         if self.verb > 1: print "++ have SIDs from 'out.ss_reiview' form"

      if len(slist) == 0:
         if self.verb > 1: print "-- empty SID list"
         return

      # make sure names are unique and not empty
      if not UTIL.vals_are_unique(slist):
         if self.verb > 1: print '-- SIDs not detected: not unique'
         return
      minlen = min([len(ss) for ss in slist])
      if minlen < 1:
         if self.verb > 1: print '-- SIDs not detected: some would be empty'
         return

      # we have a subject list
      self.snames = slist

      # now go for GID, start by replacing SIDs in infiles
      newfiles = [fname.replace(slist[ind], 'SUBJ') for ind, fname in
                        enumerate(self.infiles)]

      if UTIL.vals_are_constant(newfiles):
         print '-- no groups detected from filenames'
         return

      # okay, try to make a group list
      glist = UTIL.list_minus_glob_form(newfiles)

      # cannot have dirs in result
      for gid in glist:
         if gid.find('/') >= 0:
            if self.verb>1: print '-- no GIDs, dirs vary in multiple places'
            return

      minlen = min([len(ss) for ss in glist])
      if minlen < 1:
         if self.verb > 1: print '-- GIDs not detected: some would be empty'
         return

      if self.verb > 1: print "++ have GIDs from infiles"
      self.gnames = glist
コード例 #3
0
    def set_ids_from_dsets(self, prefix='', suffix='', hpad=0, tpad=0, dpre=0):
        """use the varying part of the dataset names for subject IDs

         If hpad > 0 or tpad > 0, expand into the head or tail of the dsets.
         If prefix or suffix is passed, apply them.

         return 0 on success, 1 on error
      """

        if hpad < 0 or tpad < 0:
            print('** set_ids_from_dsets: will not apply negative padding')
            return 1

        # try filenames without paths, first
        dlist = [s.dset.split('/')[-1] for s in self.subjects]
        if UTIL.vals_are_constant(dlist):
            print('** constant dataset names (%s)' % dlist[0])
            print('   trying directories...')
            dlist = [s.dset for s in self.subjects]

        slist = UTIL.list_minus_glob_form(dlist,
                                          hpad,
                                          tpad,
                                          keep_dent_pre=dpre)

        # in the case of diretories, check for success
        # (maybe we can try to skip past them, that might be okay)
        for index in range(len(slist)):
            if '/' in slist[index]:
                posn = slist[index].rfind('/')
                slist[index] = slist[index][posn + 1:]
                if len(slist[index]) < 1:
                    print(
                        '** failed to extract subject IDs from directory list')
                    print('   (directories do not vary at single level)')
                    return 1

        if len(slist) != len(self.subjects):
            print('** failed to set SIDs from dset names\n'        \
                  '   dsets = %s\n'                                \
                  '   slist = %s' % (dlist, slist))
            return 1

        if not UTIL.vals_are_unique(slist):
            print('** cannot set IDs from dsets, labels not unique: %s' %
                  slist)
            print('-- labels come from dsets: %s' % dlist)
            return 1

        for ind, subj in enumerate(self.subjects):
            subj.sid = '%s%s%s' % (prefix, slist[ind], suffix)

        return 0
コード例 #4
0
ファイル: lib_subjects.py プロジェクト: pmolfese/afni
   def set_ids_from_dsets(self, prefix='', suffix='', hpad=0, tpad=0, dpre=0):
      """use the varying part of the dataset names for subject IDs

         If hpad > 0 or tpad > 0, expand into the head or tail of the dsets.
         If prefix or suffix is passed, apply them.

         return 0 on success, 1 on error
      """

      if hpad < 0 or tpad < 0:
         print '** set_ids_from_dsets: will not apply negative padding'
         return 1

      # try filenames without paths, first
      dlist = [s.dset.split('/')[-1] for s in self.subjects]
      if UTIL.vals_are_constant(dlist):
         print '** constant dataset names (%s)' % dlist[0]
         print '   trying directories...'
         dlist = [s.dset for s in self.subjects]

      slist = UTIL.list_minus_glob_form(dlist, hpad, tpad, keep_dent_pre=dpre)

      # in the case of diretories, check for success
      # (maybe we can try to skip past them, that might be okay)
      for index in range(len(slist)):
         if '/' in slist[index]:
            posn = slist[index].rfind('/')
            slist[index] = slist[index][posn+1:]
            if len(slist[index]) < 1:
               print '** failed to extract subject IDs from directory list'
               print '   (directories do not vary at single level)'
               return 1

      if len(slist) != len(self.subjects):
         print '** failed to set SIDs from dset names\n'        \
               '   dsets = %s\n'                                \
               '   slist = %s' % (dlist, slist)
         return 1

      if not UTIL.vals_are_unique(slist):
         print '** cannot set IDs from dsets, labels not unique: %s' % slist
         print '-- labels come from dsets: %s' % dlist
         return 1

      for ind, subj in enumerate(self.subjects):
         subj.sid = '%s%s%s' % (prefix, slist[ind], suffix)

      return 0