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# browse_study_folder

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

### Function Synopsis

    FileList = browse_study_folder(dir_name);

### Help Text

    BROWSE_STUDY_FOLDER - Find all *brainstormstudy.mat files in a directory tree
     function FileList = browse_study_folder(dir_name);
     Finds all studies in DIR_NAME and its subfolders
      and stores the related information in FILELIST, a cell array of structures.
     dir_name must be an absolute directory name

     FILELIST is a "dir" structure, plus the following features:
      name is referential to include the dir_name, not just the name
      Subject has subfields Name and SubjectFile, the namestring and the referential
       filename for each study file
      display is a prettyprint display of the name

### Cross-Reference Information

This function calls

    bst_message_window                 C:\BrainStorm_2001\Toolbox\bst_message_window.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
    database_manager                   C:\BrainStorm_2001\Toolbox\database_manager.m
    get_user_directory                 C:\BrainStorm_2001\Toolbox\get_user_directory.m
    make_default_database              C:\BrainStorm_2001\Toolbox\make_default_database.m
    study_editor                       C:\BrainStorm_2001\Toolbox\study_editor.m

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

    function FileList = browse_study_folder(dir_name);
    %BROWSE_STUDY_FOLDER - Find all *brainstormstudy.mat files in a directory tree
    % function FileList = browse_study_folder(dir_name);
    % Finds all studies in DIR_NAME and its subfolders
    %  and stores the related information in FILELIST, a cell array of structures.
    % dir_name must be an absolute directory name
    %
    % FILELIST is a "dir" structure, plus the following features:
    %  name is referential to include the dir_name, not just the name
    %  Subject has subfields Name and SubjectFile, the namestring and the referential
    %   filename for each study file
    %  display is a prettyprint display of the name

    %<autobegin> ---------------------- 14-Jun-2004 17:09:50 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Database Management
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\bst_message_window.m
    %   toolbox\find_subdir.m
    %   toolbox\get_user_directory.m
    %
    % At Check-in: $Author: Mosher $  $Revision: 20 $  $Date: 6/14/04 3:37p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 14-Jun-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> ------------------------ 14-Jun-2004 17:09:50 -----------------------

    % /---Script Author--------------------------------------\
    % |                                                      |
    % | *** Sylvain Baillet, Ph.D.                           |
    % | Cognitive Neuroscience & Brain Imaging Laboratory    |
    % | CNRS UPR640 - LENA                                   |
    % | Hopital de la Salpetriere, Paris, France             |
    % | sylvain.baillet@chups.jussieu.fr                     |
    % |                                                      |
    % |  *** John C. Mosher, Ph.D.                           |
    % |  Biophysics Group                                    |
    % \------------------------------------------------------/
    %
    % Date of creation: February 2002
    %---------------------------------------------------------------------------------------------------------------------------

    % Script History
    %
    % JCM 25-Mar-2002 Cosmetic changes to strings, using %-s format
    % SB  05-Apr-2002 Cosmetic changes to FileList.display for improved layout in listbox
    % JCM 09-May-2002 handling filesep case at end of dir_name, adding n/a to keep deblank controlled
    % JCM 04-Jun-2002 auto comments, cleaning, switched error message to bst_message_window
    % SB  23-Jul-2002 Added StudyName field to FileList output and changed .name to .StudyFile
    % SB  30-Jul-2002 Changed FileList.Display to display only the name of the Study folder and not
    %                 the very name of the brainstormstudy file, asuuming there is only a single study file
    %                 per study folder.
    % SB  01-Aug-2002 Sanity check on StudyName:
    %                 Added ischar test on Name of Study. If ~ischar, Name is set to 'N/A' by default
    % -----------------------------------------------------

    if(~strcmp(dir_name(end),filesep)), % doesn't end in a file separation
       % since this is optional in windows, add it for a cleaner
       %  FileList name below that does not begin with a filesep
       dir_name(end+1) = filesep;
       % CHEAT: does this work in Unix too? A valid directory name in Windows
       %  optionally ends with a file separation parameter.
    end

    Users = get_user_directory;

    if ~exist(dir_name,'dir')
        FileList = [];
        bst_message_window('wrap',...
           [dir_name, ' is not a valid directory on this platform. ',...
              'Please reselect a valid database.']);
        return
    end

    % Looking for all subfolders within the study folder - recursive search
    [subdirs] = find_subdir(dir_name); % alternative to genpath
    % All names include the dir_name

    % go first to the dir_name requested
    cd(dir_name)

    % Look for study files in current folder
    FileList = dir('*brainstormstudy*.mat');

    if length(FileList) > 1 % multiple studyfiles were found in this folder
        % Display warning
        errordlg(...
            {sprintf('Multiple BrainStormStudy files were found in %s.',dir_name),...
                sprintf('Please organize %s so that there is a single BrainStormStudyFile per Study folder.',...
                Users.STUDIES)...
            },'Problem with DataBase Organization')
        return
    end

    % Now browse every folder and look for study files
    for k=1:length(subdirs)
        cd(subdirs{k})
        nFileList = dir('*brainstormstudy*.mat');
        subdirs{k} = strrep(subdirs{k},[dir_name],'');
        if length(nFileList) > 1 % multiple studyfiles were found in this folder
            % Display warning
            errordlg(...
                {sprintf('Multiple BrainStormStudy files were found in %s.',subdirs{k}),...
                    sprintf('Please organize %s so that there is a single BrainStormStudyFile per Study folder.',...
                    Users.STUDIES)...
                },'Problem with DataBase Organization')
            return
        end
        % Make subdirs names relative to the study 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
    end

    % Change .name field to .StudyFile to make this more explicit
    if(length(FileList)), % are there any files?
       for i = 1:length(FileList),
          FileList(i).StudyFile = FileList(i).name;
       end
       % remove old field
       FileList = rmfield(FileList,'name');
    else
     % don't matter, there are no files
    end

    % back to where we started
    cd(dir_name)

    % make a pretty print line for each brainstormstudy
    for k = 1:length(FileList)
        try
            warnlevel = warning;
            warning off;
            load(FileList(k).StudyFile,'Name','BrainStormSubject');
            warning(warnlevel);

            % Older study files with this variable not defined
            if ~exist('Name','var') % Older Study File
                Name = 'N/A';
            end
            FileList(k).StudyName = Name;

            Subj = load(fullfile(Users.SUBJECTS,BrainStormSubject),'Name');
            FileList(k).Subject.Name = Subj.Name;
            FileList(k).Subject.SubjectFile = BrainStormSubject;
        catch
            FileList(k).Subject.Name = 'File not found';
            FileList(k).Subject.SubjectFile = '';
            Subj.Name ='N/A';
            Name = 'N/A';
        end

        [StudyDirName{k},file,ext] = fileparts(FileList(k).StudyFile);
        FileList(k).StudyFolder = StudyDirName{k};

        if ~isempty(Name)
            if ~ischar(Name)
                StudyName{k} = 'N/A';
            else
                StudyName{k} = Name;
            end
        else
            StudyName{k} = 'N/A'; % if all names blank, the deblank below causes crash
        end
        if ~isempty(Subj.Name)
            SubjectName{k} = Subj.Name;
        else
            SubjectName{k} = 'N/A';
        end
    end

    if(length(FileList)), % the list may have been empty
       % Now improve the layout of the final .display field
       StudyDirName = deblank(char(StudyDirName)); % Pad all names to same character length
       StudyName = deblank(char(StudyName));
       SubjectName = deblank(char(SubjectName));

       fmtstr = sprintf('%%-%ds | %%-%ds | %%-%ds',...
          size(StudyDirName,2),size(StudyName,2),size(SubjectName,2));

       for k = 1:length(FileList)
          FileList(k).display = sprintf(fmtstr,...
             strrep(StudyDirName(k,:),' ','.'),strrep(StudyName(k,:),' ','.'),strrep(SubjectName(k,:),' ','.'));
       end
    end

Produced by color_mat2html, a customized BrainStorm 2.0 (Alpha) version of mat2html on Tue Nov 2 16:17:59 2004
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