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# find_brainstorm_structure

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

### Function Synopsis

    StudySubject = find_brainstorm_structure(Fname);

### Help Text

    FIND_BRAINSTORM_STRUCTURE - Find all of the available files with a subject or study
     function StudySubject = find_brainstorm_structure(Fname);
     function StudySubject = find_brainstorm_structure(fname);
     fname must contain either "brainstormstudy.mat" or "brainstormsubject.mat"
     fname is assumed to be referentially qualified only, no fully qualified names allowed.
     If a study file, then program attempts to find the corresponding
      subject information as well, Study.BrainStormSubject
     Note that StudySubject.Data and StudySubject.Results are returned always as cell
      arrays for possible multiple files.

### Cross-Reference Information

This function calls

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

This function is called by

    bst_sourceimaging                  C:\BrainStorm_2001\Toolbox\bst_sourceimaging.m
    data_selector_cb                   C:\BrainStorm_2001\Toolbox\data_selector_cb.m
    dataplot_cb                        C:\BrainStorm_2001\Toolbox\dataplot_cb.m
    find_brainstorm_files              C:\BrainStorm_2001\Toolbox\find_brainstorm_files.m
    parametric_estimation              C:\BrainStorm_2001\Toolbox\parametric_estimation.m
    sourceimaging                      C:\BrainStorm_2001\Toolbox\sourceimaging.m

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

    function StudySubject = find_brainstorm_structure(Fname);
    %FIND_BRAINSTORM_STRUCTURE - Find all of the available files with a subject or study
    % function StudySubject = find_brainstorm_structure(Fname);
    % function StudySubject = find_brainstorm_structure(fname);
    % fname must contain either "brainstormstudy.mat" or "brainstormsubject.mat"
    % fname is assumed to be referentially qualified only, no fully qualified names allowed.
    % If a study file, then program attempts to find the corresponding
    %  subject information as well, Study.BrainStormSubject
    % Note that StudySubject.Data and StudySubject.Results are returned always as cell
    %  arrays for possible multiple files.

    %<autobegin> ---------------------- 09-Jul-2004 22:17:05 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Utility - General
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\get_user_directory.m
    %   toolbox\load_brainstorm_file.m
    %
    % Subfunctions in this file, in order of occurrence in file:
    %   k = findstrc(s1,c1);
    %   [subdirs] = find_subdir(dirname);
    %
    % At Check-in: $Author: Mosher $  $Revision: 17 $  $Date: 7/09/04 8:42p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 09-Jul-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> ------------------------ 09-Jul-2004 22:17:05 -----------------------

    % 11/6/99 JCM adjust to handle referential filenames
    % 12/2/99 JCM further adjusting
    % 01-May-2002 JCM force everything lowercase for pattern matching

    % keywords
    SUBJECT = 'brainstormsubject.mat';
    STUDY =   'brainstormstudy.mat';

    % Fname is the original spelling of the name,
    %  fname is the lower case version

    fname = deblank((Fname)); % reduced sensitivity in pattern matching: removed because causes too many pbs under Linux
    SUBJECT = deblank((SUBJECT));
    STUDY = deblank((STUDY));

    % now figure out which keyword this is
    iSuffix = findstr(fname,SUBJECT);
    if(~isempty(iSuffix)), % found a subject match
       SUFFIX = SUBJECT;
    else % not a match
       iSuffix = findstr(fname,STUDY);
       if(isempty(iSuffix)), % not a match either
          % don't know what this is
          msgbox(sprintf('FIND_BRAINSTORM_STRUCTURE: Invalid StudySubject File: %s',fname),'Error','modal');
          return
       end
       SUFFIX = STUDY;
    end

    User = get_user_directory; % the default user directories, remove from filenames for referential calls
    %User.STUDIES = lower(User.STUDIES); % for case insensitivity
    %User.SUBJECTS = lower(User.SUBJECTS);

    % so now SUFFIX is set to SUBJECT or STUDY
    PREFIX = fname(1:(iSuffix-1)); % the prefix before the keyword. Used to search for other names
    % remove the database location,if already attached
    PREFIX = strrep(PREFIX,(User.STUDIES),'');
    PREFIX = strrep(PREFIX,(User.SUBJECTS),'');

    % define the structure. Note that these are key names as well. The corresponding filename
    %  must contain these names (filenames are assumed case insensitive. On unix, they should be lowercase).
    StudySubject = struct(...
       'Subject',[],...
       'Study',[],...
       'SubjectImage',[],...
       'SubjectTess',[],...
       'SubjectTriConn',[],...
       'SubjectVertConn',[],...
       'Channel',[],...
       'HeadModel',[],...
       'Data',[],...
       'Results',[]);

    % now process according to which case

    if(strcmp(SUFFIX,SUBJECT)),
       % this one is easy, since the info is loaded in the subject file
       % It's redundant to load into StudySubject, but it is handy.

       % load up some of the pre-determined information in the brainstormstudy file
       StudySubject.Subject = Fname;
       tempbsstudy = load_brainstorm_file(fullfile(User.SUBJECTS,Fname));
       if ~isfield(tempbsstudy,'Tesselation')
           tempbsstudy.Tesselation = [];
       end
       StudySubject.SubjectTess = tempbsstudy.Tesselation; % use the preset tesselation
       if ~isfield(tempbsstudy,'Anatomy')
           tempbsstudy.Anatomy = [];
       end
       StudySubject.SubjectImage = tempbsstudy.Anatomy; % FIX: What is anatomy vs SubjectImage?

    elseif(strcmp(SUFFIX,STUDY)),

       % this one is harder, we have to look for possibly lots of files
       Leader = deblank((fullfile(User.STUDIES,PREFIX))); % precedes all names

       switch computer
       case 'PCWIN'
          % find all Matlab .mat files in the same directory with the same prefix
          [s,files] = dos(sprintf('dir %s /s /b',sprintf('%s',[Leader,'*.mat'])));
          % files is a string array of fully qualified file names

          ndx = findstr(files,char(10));
          Files = cell(1,length(ndx));
          ndx = [0 ndx];  %prepend zero
          % scan through the string, parsing by EOL
          for i = 1:(length(ndx)-1),
             temp = files([(ndx(i)+1):(ndx(i+1)-1)]);
             %temp = lower(temp); % for case insensitivity
             % remove the user directory for portability
             temp = strrep((temp),(User.STUDIES),'');
             Files{i} = temp;
          end
       otherwise
          [path,name,ext,ver] = fileparts(Leader);
          filess = what(path);
          filess = filess.mat;
          i=0;
          for k = 1:length(filess)
             if findstr(filess{k},name)
                i = i+1;
                Files{i} = (fullfile(path,filess{k}));
                Files{i} = strrep(Files{i},(User.STUDIES),'');
             end
          end
       end % other cases were rejected above

       % So now Files is a cell array of all potential names with the same prefix
       % Match them up

       % the fieldnames contain the flag strings for the filenames
       Names = lower(fieldnames(StudySubject)); % get all of the names into a cell array
       oNames = (fieldnames(StudySubject)); % Field names are case-sensitive in BrainStorm
       for i = 1:length(Names),
          % use local function below
          k = findstrc(deblank((Names{i})),(Files)); % local function, any matches?
          if(any(k)), % we have a match

             switch deblank((Names{i}))
             case 'study'
                % do nothing, handled elsewhere
             case 'subject'
                % do nothing, handled elsewhere
             case 'data'
                % first remove any that have the word 'results' in them
                kndx = find(k); % valid data file
                k1 = findstrc('results',(Files(kndx)));
                k1ndx = find(k1==0); % subindex of names without 'results'
                % collect all applicable into cell structure
                StudySubject = setfield(StudySubject,'Data',Files(kndx(k1ndx)));
             case 'results'
                % collect all applicable into cell structure
                StudySubject = setfield(StudySubject,'Results',Files(find(k)));
             case {'tess' ,'image'}
                % do nothing, loaded in subject editor
             otherwise
                % collect first one into string
                StudySubject = setfield(StudySubject,oNames{i},Files{min(find(k))});
             end

          end
       end

       % now clean up

       StudySubject.Study = Fname;
       % can we find the subject for this one?
       Study = load(fullfile(User.STUDIES,StudySubject.Study));
       StudySubject.Subject = Study.BrainStormSubject;
       if(~isempty(StudySubject.Subject)), % non-empty name
          if(exist(fullfile(User.SUBJECTS,StudySubject.Subject),'file')==2)
             % get the subject information with recursive call to this routine
             tempSubject = feval(mfilename,StudySubject.Subject);
             Names = fieldnames(tempSubject); % extract the names
             for i = 1:length(Names),
                temp = getfield(tempSubject,Names{i});
                if(~isempty(temp)),
                   % information returned for subject, avoids overwriting study information
                   StudySubject = setfield(StudySubject,Names{i},temp);
                end
             end
          else
             % FIX: doesn't appear to be a valid filename, help the user append a subject name
          end
       else
          % Subject name is empty, FIX: help the user
       end

    end % "case switch" looking for subject or study data

    return

    %-----------------------------------------------------------------------
    function k = findstrc(s1,c1);
    % return vector k with 0 or 1 to indicate if string s1 is found in the strings of
    %  cell array c1

    k = zeros(1,length(c1));

    for i = 1:length(c1),
       if(~isempty(findstr(s1,c1{i}))),
          k(i) = 1;
       end
    end

    %-----------------------------------------------------------------------
    function [subdirs] = find_subdir(dirname);
    %function [subdirs] = find_subdir(dirname);
    % Find all the subdirectories within dirname and
    % return them is the cell array subdirs

    cd(dirname)
    D = dir(dirname);
    for i = 1:length(D),
       if findstr(D(i).name,'..'),
          D(i).isdir = logical(0);  % don't want it
       end
    end
    D = D([D.isdir]);

    subdirs = {D.name};
    if ~isempty(subdirs)
       for k = 1:length(subdirs)
          sub_subdirs{k} = fullfile(dirname,subdirs{k});
       end
       subdirs  = sub_subdirs;
    else
       sub_subdirs = [];
    end

    for d = 1:length(D)
       sub_subdirs = find_subdir(fullfile(dirname,D(d).name));

       while 0%~isempty(sub_subdirs)
          subdirs = [subdirs,sub_subdirs];
          for k = 1:length(sub_subdirs)
             sub_subdirs = find_subdir(fullfile(dirname,sub_subdirs));
          end
       end

       subdirs = [subdirs,sub_subdirs];

    end
    disp('')

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