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# find_brainstorm_files

## (Toolbox/find_brainstorm_files.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    [DataDir,DataPopup,Leader] = find_brainstorm_files(Type,DirPath,hf);

### Help Text

    FIND_BRAINSTORM_FILES - Find BrainStorm subjects or study files, create Menu
     function [DataDir,DataPopup,Leader] = find_brainstorm_files(Type,DirPath,hf);
     Type is either
      "studies"
      "subjects"
      "tri" or "tess" for tessellation files
      "data"
      "results"
      "anatomy" (subjectimage files)
      "headmodel"
      "ctf"
      "neuromag"
      "besa"
      "neuroscan"
      "gis image"
     If no DirPath is given or is null, searches the
      folders located in Users.STUDIES or Users.SUBJECTS;
      otherwise searches subfolders of DirPath.
     Returns cell array DataDir of referentially qualified directory names.
     Returns character array DataPopup with '|' separators needed for
      the uicontrol popup.
     Leader is such that fullfile(Leader,DataDir{i}) gives fully qualified name.

     If hf is given, and type is 'studies' or 'subjects', then a menubar is created
      in the given figure.

     If Type is not 'studies' or 'subjects', then Type is assumed to be a specific
      filename. The Users.STUDIES and Users.SUBJECTS are searched for exactly this
      name, and the fully qualified filename is returned.

     Run find_brainstorm_structure to get all files associated with name

### Cross-Reference Information

This function calls

    find_brainstorm_structure          C:\BrainStorm_2001\Toolbox\find_brainstorm_structure.m
    find_subdir                        C:\BrainStorm_2001\Toolbox\find_subdir.m
    get_user_directory                 C:\BrainStorm_2001\Toolbox\get_user_directory.m

This function is called by

    data_manager                       C:\BrainStorm_2001\Toolbox\data_manager.m
    dataplot_cb                        C:\BrainStorm_2001\Toolbox\dataplot_cb.m
    file_selection_win                 C:\BrainStorm_2001\Toolbox\file_selection_win.m
    headmodeler_gui                    C:\BrainStorm_2001\Toolbox\headmodeler_gui.m
    importdata                         C:\BrainStorm_2001\Toolbox\importdata.m
    load_brainstorm_file               C:\BrainStorm_2001\Toolbox\load_brainstorm_file.m
    subject_editor                     C:\BrainStorm_2001\Toolbox\subject_editor.m
    tessellation_handler               C:\BrainStorm_2001\Toolbox\tessellation_handler.m

### Listing of function C:\BrainStorm_2001\Toolbox\find_brainstorm_files.m

    function [DataDir,DataPopup,Leader] = find_brainstorm_files(Type,DirPath,hf);
    %FIND_BRAINSTORM_FILES - Find BrainStorm subjects or study files, create Menu
    % function [DataDir,DataPopup,Leader] = find_brainstorm_files(Type,DirPath,hf);
    % Type is either
    %  "studies"
    %  "subjects"
    %  "tri" or "tess" for tessellation files
    %  "data"
    %  "results"
    %  "anatomy" (subjectimage files)
    %  "headmodel"
    %  "ctf"
    %  "neuromag"
    %  "besa"
    %  "neuroscan"
    %  "gis image"
    % If no DirPath is given or is null, searches the
    %  folders located in Users.STUDIES or Users.SUBJECTS;
    %  otherwise searches subfolders of DirPath.
    % Returns cell array DataDir of referentially qualified directory names.
    % Returns character array DataPopup with '|' separators needed for
    %  the uicontrol popup.
    % Leader is such that fullfile(Leader,DataDir{i}) gives fully qualified name.
    %
    % If hf is given, and type is 'studies' or 'subjects', then a menubar is created
    %  in the given figure.
    %
    % If Type is not 'studies' or 'subjects', then Type is assumed to be a specific
    %  filename. The Users.STUDIES and Users.SUBJECTS are searched for exactly this
    %  name, and the fully qualified filename is returned.
    %
    % Run find_brainstorm_structure to get all files associated with name

    %<autobegin> ---------------------- 12-Oct-2004 01:11:14 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Utility - General
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\find_subdir.m
    %   toolbox\get_user_directory.m
    %
    % At Check-in: $Author: Mosher $  $Revision: 29 $  $Date: 10/11/04 11:32p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 23-Sep-2004
    %
    % Principal Investigators and Developers:
    % ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
    %    University of Southern California, Los Angeles, CA
    % ** John C. Mosher, PhD, Biophysics Group,
    %    Los Alamos National Laboratory, Los Alamos, NM
    % ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
    %    CNRS, Hopital de la Salpetriere, Paris, France
    %
    % See BrainStorm website at http://neuroimage.usc.edu for further information.
    %
    % Copyright (c) 2004 BrainStorm by the University of Southern California
    % This software distributed  under the terms of the GNU General Public License
    % as published by the Free Software Foundation. Further details on the GPL
    % license can be found at http://www.gnu.org/copyleft/gpl.html .
    %
    % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
    % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
    % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
    % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
    % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
    %<autoend> ------------------------ 12-Oct-2004 01:11:14 -----------------------

    % /---Script Authors--------------------------------------\
    % |  *** John C. Mosher, Ph.D.                            |
    % |  Biophysics Group                                    |
    % |                                                       |
    % |  *** Sylvain Baillet, Ph.D.                           |
    % |  Cognitive Neuroscience & Brain Imaging Laboratory    |
    % |  CNRS UPR640 - LENA                                   |
    % |  Hopital de la Salpetriere, Paris, France             |
    % |  sylvain.baillet@chups.jussieu.fr                     |
    % \-------------------------------------------------------/

    % Date of creation: January 1999
    %
    % Script History -------------------------------------------------------------------------------------
    % 06-Jun-1999     upgraded to bring out prefixes of the flagfiles
    % 16-Jun-1999     modified to handle null returns on find files
    % 26-Oct-1999     modified to handle specific filenames.
    % 06-Nov-1999     modified to give REFERENTIAL file names, referenced to
    % ...........     Users.STUDIES or .SUBJECTS.  Used local variable Leader to distinguish
    % 08-Apr-2002 SB  added 'headmodel' file type
    % 16-Apr-2002 SB  gathered all file types in a shorter switchyard to keep file search general.
    % ...........     and removed all reference to platform dependency.
    % 29-Apr-2002 SB  Fixed typo in Header.
    % ...........     Fixed search for general type of files (see 'otherwise' case on Type below).
    % 24-May-2002 SB  Added 'tess' file type.
    % ........... SB  Secured subdir search.
    % ........... SB  Come back to original folder rather than stay in last visited folder
    % 27-May-2002 SB  Search for TESS files does not return associated VERTCONN and TRICONN files anymore
    % 11-Jun-2002 JCM If DirPath is empty, set it to '.' (the current directory), also minor comments
    %                 fixes.
    % 09-Jul-2002 SB  Updated comments with all available file types
    % 23-Jul-2002 SB  Added Neuromag and CTF file types (find_*_data.m are now obsolete and are deleted from Toolbox)
    % 02-Sep-2002 SB  Return to original folder when no file was found.
    % 31-Oct-2002 JCM referential names should not begin with \, so ensured DirPath ends in a filesep
    % 03-Jun-2003 SB  Added the 'results' file type
    % 15-May-2004 JCM Added Pantazis "dsgl" modification for file type extension
    % 17-May-2004 JCM Added Pantazis "dfs" modification
    % 20-Jul-2004 DB  Added GIS and MESH formats
    % 08-Oct-2004 DP  Changed EGI format
    % ---------------------------------------------------------------------------------------------------

    OrigFolder = pwd;

    files = [];

    if(~exist('Type')),
       DataDir = [];
       DataPopup = [];
       msgbox('FIND_BRAINSTORM_FILES, Must give Type of Studies or Subjects','Error','Modal');
       return
    end

    if(~exist('DirPath','var')), % user gave no input
       DirPath = []; % default
    end

    if(~exist('hf','var')), % user gave no figure
       hf = []; % set to empty
    end

    if(isempty(DirPath)),
       DirPath = '.'; % current directory
    end

    Users = get_user_directory;% the User directory information

    Extension = '.mat'; % default extension, unless overridden below
    switch lower(deblank(Type))
       case 'studies'
          FileString = 'brainstormstudy'; % File filter for the dir command
          %DirPath = Users.STUDIES; % Root directory for this file type.
       case 'subjects'
          FileString = 'brainstormsubject';
          %DirPath = Users.SUBJECTS;
       case 'tri'
          FileString = '';
          %DirPath = Users.SUBJECTS;
          Extension = '.tri';
       case 'mesh'
          FileString = '';
          %DirPath = Users.SUBJECTS;
          Extension = '.mesh';
       case 'dsgl'
          FileString = '';
          %DirPath = Users.SUBJECTS;
          Extension = '.dsgl';
       case 'dfs'
          FileString = '';
          %DirPath = Users.SUBJECTS;
          Extension = '.dfs';
       case 'tess'
          FileString = 'tess';
          FileStringFilter = {'vertconn','triconn'}; % don't return files with names that include both FileString and either of the FileStringFilter strings
       case 'results'
          FileString = 'results';
       case 'data'
          FileString = 'data';
          FileStringFilter = {'results'}; % don't return files with names that include both FileString and either of the FileStringFilter strings
       case 'anatomy'
          FileString = 'subjectimage';
          %DirPath = Users.STUDIES;
       case 'headmodel'
          FileString = 'headmodel';
          %DirPath = Users.STUDIES;

          % below are system files that we seek, where the type is a System name from
          %  {'magnes','ctf','neuromag','neuroscan','egi','prn','raw'}
          % See importdata routine and the "create" switchyard case for valid
          % Systems

       case 'magnes'
         % unknown at this time
          FileString = ''; % No specific string in file name
          Extension = '.magnes'; % extension is specific
       case 'besa'
           % BESA ASCII file format
           FileString = ''; % No specific string in file name
           Extension = '.avr'; % extension is specific
       case 'ctf'
          FileString = ''; % No specific string in file name
          Extension = '.ds'; % extension is specific
       case 'neuromag'
          FileString = ''; % No specific string in file name
          Extension = '.fif';  % extension is specific
       case 'neuroscan'
          % Neuroscan binary EEG format
          FileString = ''; % No specific string in file name
          Extension = '.avg'; % extension is specific
       case 'egi'
          % unknown at this time
          FileString = ''; % No specific string in file name
          Extension = '.raw'; % extension is specific
       case 'prn'
          % unknown at this time
          FileString = ''; % No specific string in file name
          Extension = '.prn'; % extension is specific
       case 'raw'
          FileString = ''; % No specific string in file name
          Extension = '.raw'; % extension is specific
      case 'gis image' % GIS MRI format -> see [http://brainvisa.info]
          FileString = ''; % No specific string in file name
          Extension = '.ima'; % extension is specific

      otherwise % try handling as a default case
          FileString = Type;
          Extension = '';
    end

    % we need DirPath to end in a file separator, in order to cleanly remove
    if(~strcmp(DirPath(end),filesep)),
       DirPath(end+1) = filesep;
    end

    Leader = DirPath; % prefix on the file names

    FileList = dir(fullfile(DirPath,sprintf('*%s*%s',FileString,Extension)));
    [subdirs] = find_subdir(DirPath); % Looking for all subfolders within current folder - recursive search

    dirinit = pwd;
    % Now browse every folder and look for files of requested type
    for k=1:length(subdirs)
       cd(subdirs{k})
       nFileList = dir(fullfile(subdirs{k},sprintf('*%s*%s',FileString,Extension))); % New file list
       subdirs{k} = strrep(subdirs{k},[DirPath],''); % Make subdirs names relative to root folder
       for kk = 1:length(nFileList)
          nFileList(kk).name = fullfile(subdirs{k},nFileList(kk).name);
       end
       FileList(end+1:end+length(nFileList)) = nFileList; % Add study files to the list
       cd(dirinit)
    end

    if exist('FileStringFilter','var') % Filter out  some file names that contain string FileStringFilter.
       iok = []; % Indices of the filenames that does not contain FileStringFilter
       for k=1:length(FileList)
          for filt = 1:length(FileStringFilter)
             if ~isempty(strfind(FileList(k).name,FileStringFilter{filt}))
                iFlag = 1;
             end
          end
          if ~exist('iFlag','var')
             iok = [iok,k]; % Keep this file
          end

          clear('iFlag')

       end

       FileList = FileList(iok);

    end

    try % Secured file search
       cd(DirPath)
    catch
       try
          cd(fullfile(Users.STUDIES,DirPath))
       catch
          cd(fullfile(Users.SUBJECTS,DirPath))
       end
    end

    if(isempty(FileList)), % there are no files to process
       % there ain't nothing to process
       DataDir = [];
       DataPopup = [];
       cd(OrigFolder) % Go back to original calling folder
       return
    else
       FileList = {FileList.name};
    end

    %Leader = deblank(lower(Leader)); % reduced sensitivity
    if(~strcmp(Leader(end),filesep)),
       % does not end in a file separator, add one
       Leader(end+1) = filesep;
    end

    % 11/6/99 remove the Leader to make a referential list
    filess = FileList;
    %FileList = strrep(FileList,fullfile(Users.STUDIES,Leader),'');
    FileList = strrep(FileList,Leader,'');

    DataPopup = char(FileList{:});
    DataDir = FileList;

    % switch lower(deblank(computer))
    % case 'pcwin'
    %     %ndx = findstr(char(FileList),sprintf('\n'));
    %     ndx = strmatch(FileList,sprintf('\n'));
    %     % the popup button needs these separated by '|'.
    %     DataPopup = FileList; % map the character array
    %     if ~isempty(ndx)
    %         DataPopup(ndx(1:(end-1))) = '|'; % replace all but the last linefeed
    %         DataPopup(ndx(end)) = []; % remove the last linefeed
    %         % need convenient cell array. string is already terminated with linefeed
    %         DataDir = cell(1,length(ndx)); % null entries
    %         ndx = [0 ndx];  %prepend zero
    %
    %         % scan through the string, parsing by EOL
    %         for i = 1:(length(ndx)-1),
    %             temp = FileList([(ndx(i)+1):(ndx(i+1)-1)]);
    %             DataDir{i} = temp;
    %         end
    %     else
    %         DataDir = DataPopup;
    %     end
    %
    % otherwise
    %     ndx = 1:length(FileList);
    %     DataPopup = FileList; % map the character array
    %     for k = 1:length(FileList)
    %         %[path,name,ext,ver] = fileparts(filess{k});
    %         %tmp = strrep(filess{k},path,'');
    %         %DataDir{k} = strrep(tmp,FileList{k},'');
    %         DataDir{k} = FileList{k};
    %     end
    % end

    if(~isempty(hf)), % user wants pull down menu of files
       switch lower(deblank(Type))
          case 'studies'

             hu = findobj(hf,'Tag','UimenuBSTStudy');
             if(~isempty(hu)), % existing menu
                delete(hu);
             end
             hu = uimenu(hf,'Label','BrainStorm Study','Tag','UimenuBSTStudy');

             for i = 1:length(DataDir),
                uimenu(hu,'Label',DataDir{i},'Callback',...
                   sprintf('taskbar_userdata(find_brainstorm_structure(''%s''));',DataDir{i}));
             end
             if(0), % 11/4/99 JCM we don't need this
                uimenu(hu,'Label','Refresh Studies','Callback',...
                   sprintf('find_brainstorm_files(''studies'',[],%.0f);',hf),...
                   'Separator','On','Position',length(DataDir)+1);
             end

          case 'subjects'

             hu = findobj(hf,'Tag','UimenuBSTSubject');
             if(~isempty(hu)), % no menu
                delete(hu);
             end
             hu = uimenu(hf,'Label','BrainStorm Subject','Tag','UimenuBSTSubject','Position',11);

             for i = 1:length(DataDir),
                uimenu(hu,'Label',DataDir{i},'Callback',...
                   sprintf('taskbar_userdata(find_brainstorm_structure(''%s''));',DataDir{i}));
             end
             if(0), % 11/4/99 JCM we don't need this
                uimenu(hu,'Label','Refresh Subjects','Callback',...
                   sprintf('find_brainstorm_files(''subjects'',[],%.0f);',hf),...
                   'Separator','On','Position',length(DataDir)+1);
             end

          otherwise
             % do nothing, we were looking for a file
       end
    end

    cd(OrigFolder) % Go back to original calling folder

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