swe_select.m

function varargout = swe_select(varargin)
  % File selector
  % This is a copy of swe_select but able to handle CIfTI files as well.
  % FORMAT [t,sts] = swe_select(n,typ,mesg,sel,wd,filt,frames)
  % n      - number of files [Default: Inf]
  %          A single value or a range.  e.g.
  %          1       - select one file
  %          Inf     - select any number of files
  %          [1 Inf] - select 1 to Inf files
  %          [0 1]   - select 0 or 1 files
  %          [10 12] - select from 10 to 12 files
  % typ    - file type [Default: 'any']
  %          'any'   - all files
  %          'image' - Image files (".img" and ".nii")
  %                    Note that it gives the option to select individuals
  %                    volumes of the images.
  %          'mesh'  - Surface mesh files (".gii")
  %          'xml'   - XML files
  %          'mat'   - MATLAB .mat files or .txt files (assumed to contain
  %                    ASCII representation of a 2D-numeric array)
  %          'batch' - SPM batch files (.m or .mat)
  %          'dir'   - select a directory
  %          Other strings act as a filter to regexp. This means that
  %          e.g. DCM*.mat files should have a typ of '^DCM.*\.mat$'
  % mesg   - a prompt [Default: 'Select files...']
  % sel    - list of already selected files [Default: {}]
  % wd     - directory to start off in [Default: pwd]
  % filt   - value for user-editable filter [Default: '.*']
  % frames - image frame numbers to include [Default: '1']
  %
  % t      - selected files
  % sts    - status (1 means OK, 0 means window quit)
  %
  % FORMAT [files,dirs] = swe_select('List',direc,filt)
  % Return files matching the filter 'filt' and directories within 'direc'
  % direc  - directory to search [Default: pwd]
  % filt   - filter to select files with regexp, e.g. '^w.*\.img$' [Default: '.*']
  %
  % files  - files matching 'filt' in directory 'direc'
  % dirs   - subdirectories of 'direc'
  %
  % FORMAT [files,dirs] = swe_select('ExtList',direc,filt,frames)
  % As above, but for selecting frames of 4D NIfTI files
  % frames - vector of frames to select (defaults to 1, if not specified).
  %          If the frame number is Inf, all frames for the matching images
  %          are listed.
  %
  % FORMAT [files,dirs] = swe_select('FPList',direc,filt)
  % FORMAT [files,dirs] = swe_select('ExtFPList',direc,filt,frames)
  % As above, but return files with full paths (i.e. prefixes 'direc' to each)
  %
  % FORMAT [files,dirs] = swe_select('FPListRec',direc,filt)
  % FORMAT [files,dirs] = swe_select('ExtFPListRec',direc,filt,frames)
  % As above, but return files with full paths (i.e. prefixes 'direc' to each)
  % and search through sub directories recursively.
  %
  % FORMAT [dirs] = swe_select('List',direc,'dir',filt)
  % FORMAT [dirs] = swe_select('FPList',direc,'dir',filt)
  % FORMAT [dirs] = swe_select('FPListRec',direc,'dir',filt)
  % Return directory names matching filter 'filt' within 'direc'
  %__________________________________________________________________________
  % Copyright (C) 2005-2015 Wellcome Trust Centre for Neuroimaging
  % John Ashburner
  % Modified by Bryan Guillaume
  % Version Info:  $Format:%ci$ $Format:%h$


  % For developers:
  %--------------------------------------------------------------------------
  % FORMAT cpath = swe_select('CPath',path,cwd)
  % Canonicalise paths: prepend cwd to relative paths, process '..' & '.'
  % directories embedded in path.
  % path   - string matrix containing path name
  % cwd    - current working directory [Default: '.']
  % cpath  - canonicalised paths, in same format as input path argument
  %
  % FORMAT [t,ind] = swe_select('Filter',files,typ,filt,frames)
  % Filter the list of files (cell or char array) in the same way as the
  % GUI would do. There is an additional typ 'extimage' which will match
  % images with frame specifications, too. Also, there is a typ 'extdir',
  % which will match canonicalised directory names. The 'frames' argument
  % is currently ignored, i.e. image files will not be filtered out if
  % their frame numbers do not match.
  % t returns the filtered list (cell or char array, depending on input),
  % ind an index array, such that t = files{ind}, or t = files(ind,:).
  %
  % FORMAT swe_select('PrevDirs',dir)
  % Add directory dir to list of previous directories.
  % FORMAT dirs = swe_select('PrevDirs')
  % Retrieve list of previous directories.
  %
  % FORMAT files = swe_select('Expand',files)
  % Return a list of image filenames with appended frame numbers.

  persistent isInitSelect;
  if isempty(isInitSelect)
      isInitSelect = true;
      swe_select('init');
      if nargin == 1 && strcmpi(varargin{1},'init'), return; end
  end

  %-Commands that are not passed to cfg_getfile
  local_cmds = {'regfilter', 'init', 'expand'};

  if nargin && ischar(varargin{1}) && any(strcmpi(varargin{1},local_cmds))
      switch lower(varargin{1})
          case 'init'
              if ~isdeployed && ~exist('cfg_getfile','file')
                  addpath(fullfile(spm('dir'),'matlabbatch'));
              end
              swe_select('regfilter');
              swe_select('prevdirs',spm('Dir'));

          case 'regfilter'
              % Regexp based filters without special handlers
              cfg_getfile('regfilter', 'mesh',  {'\.gii$'});
              cfg_getfile('regfilter', 'gifti', {'\.gii$'});
              cfg_getfile('regfilter', 'nifti', {'\.nii$','\.img$'});
              % Filter for 3D images that handles frame expansion
              frames = cfg_entry;
              frames.name    = 'Frames';
              frames.tag     = 'frames';
              frames.strtype = 'n';
              frames.num     = [1 Inf];
              frames.val     = {1};
              cfg_getfile('regfilter', 'image',...
                  {'.*\.nii(,\d+){0,2}$','.*\.img(,\d+){0,2}$'},...
                  false, @swe_select_image, {frames});

          case 'expand'
              varargout{1} = swe_select_expand(varargin{2});
              if ischar(varargin{2}), varargout{1} = char(varargout{1}); end
      end
  else
      needchar = false;
      % cfg_getfile expects cellstr arguments for multi-line strings
      if nargin > 1 && ischar(varargin{1}) && ...
              ismember(lower(varargin{1}),{'filter','cpath'}) && ischar(varargin{2})
          varargin{2} = cellstr(varargin{2});
          needchar = true;
      elseif nargin > 0 && ischar(varargin{1}) && ...
              ismember(lower(varargin{1}),{'extlist','extfplist','extfplistrec'})
          varargin{1} = varargin{1}(4:end);
          if nargin > 3
              varargin{5} = struct('frames', varargin{4});
          else
              varargin{5} = struct('frames', Inf);
          end
          varargin{4} = varargin{3};
          varargin{3} = 'image';
      elseif nargin > 6 && isnumeric(varargin{1})
          varargin{7} = struct('frames', varargin{7});
      end

      [t, sts] = cfg_getfile(varargin{:});

      % cfg_getfile returns cellstr arrays, convert to char arrays
      if nargin > 0 && ischar(varargin{1})
          switch lower(varargin{1})
              case {'filter','cpath'}
                  if needchar
                      t = char(t);
                  end
              case {'list','fplist','extlist','extfplist','fplistrec','extfplistrec'}
                  t = char(t);
                  sts = char(sts);
          end
      else
          t = char(t);
      end

      varargout{1} = t;
      if nargout > 1
          varargout{2} = sts;
      end
  end


  %==========================================================================
  % FUNCTION varargout = swe_select_image(cmd, varargin)
  %==========================================================================
  function varargout = swe_select_image(cmd, varargin)
  % Implements extended filtering for NIfTI images (including 3D frame
  % selection)
  switch lower(cmd)
      case 'list'
          dr     = varargin{1};
          files  = varargin{2};
          prms   = varargin{3};
          frames = prms.frames;
          ii = cell(1,numel(files));
          if numel(frames)==1 && isnan(frames)
              [ii{:}] = deal(1);
          elseif numel(frames)~=1 || frames(1)~=1
              % if domsg
              %     msg(ob,['Reading headers of ' num2str(numel(f)) ' images...']);
              % end
              for i=1:numel(files)
                  try
                      n = swe_select_get_nbframes(fullfile(dr,files{i}));
                      d4 = (1:n)';
                  catch
                      d4 = 1;
                  end
                  if all(isfinite(frames))
                      ii{i} = intersect(d4, frames(:))';
                  else
                      ii{i} = d4(:)';
                  end
              end
          elseif numel(frames)==1 && frames(1)==1
              [ii{:}] = deal(1);
          end

          % if domsg
          %     msg(ob,['Listing ' num2str(numel(f)) ' files...']);
          % end

          % Combine filename and frame number(s)
          nii      = cellfun(@numel, ii);
          cfiles   = cell(sum(nii),1);
          fi       = cell(numel(files),1);
          for k = 1:numel(fi)
              fi{k} = k*ones(1,nii(k));
          end
          ii = [ii{:}];
          fi = [fi{:}]';
          if numel(frames)==1 && isnan(frames)
              cfiles = files;
          else
              for i=1:numel(cfiles)
                  cfiles{i} = sprintf('%s,%d', files{fi(i)}, ii(i));
              end
          end
          varargout{1} = cfiles;
          varargout{2} = fi;
      case 'filter'
          % Do not filter for frame numbers
          varargout{1} = varargin{1};
          varargout{2} = 1:numel(varargout{1});
  end

  %==========================================================================
  % FUNCTION ofiles = swe_select_expand(ifiles)
  %==========================================================================
  function ofiles = swe_select_expand(ifiles)
  ifiles = cellstr(ifiles);
  ofiles = {};
  for i=1:numel(ifiles)
      [p,f,e,n] = spm_fileparts(ifiles{i});
      if ~isempty(n)
          ofiles = [ofiles; ifiles{i}];
      else
          n = swe_select_get_nbframes(ifiles{i});
          vfiles = cell(n,1);
          for j=1:n
              vfiles{j} = [ifiles{i} ',' num2str(j)];
          end
          ofiles = [ofiles; vfiles];
      end
  end


  %==========================================================================
  % FUNCTION n = swe_select_get_nbframes(file)
  %==========================================================================
  function n = swe_select_get_nbframes(file)
    file_ext = swe_get_file_extension(file);
    isCifti  = strcmpi(file_ext,'.dtseries.nii') ||  strcmpi(file_ext,'.dscalar.nii');
    if isCifti
      ciftiObject = swe_cifti(file);
      n = ciftiObject.dat.dim(5);
    else
      N   = nifti(file);
      dim = [N.dat.dim 1 1 1 1 1];
      n   = dim(4);
    end