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# rap_music_parameters

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

### Function Synopsis

    varargout = rap_music_parameters(varargin)

### Help Text

    RAP_MUSIC_PARAMETERS - Application M-file for rap_music_parameters.fig
     function varargout = rap_music_parameters(varargin)
        FIG = RAP_MUSIC_PARAMETERS launch rap_music_parameters GUI.
        RAP_MUSIC_PARAMETERS('callback_name', ...) invoke the named callback.

### Cross-Reference Information

This function calls

    bst_color_scheme                   C:\BrainStorm_2001\Toolbox\bst_color_scheme.m
    bst_layout                         C:\BrainStorm_2001\Toolbox\bst_layout.m
    bst_message_window                 C:\BrainStorm_2001\Toolbox\bst_message_window.m
    bst_static_taskbar                 C:\BrainStorm_2001\Toolbox\bst_static_taskbar.m
    dataplot_cb                        C:\BrainStorm_2001\Toolbox\dataplot_cb.m
    get_user_directory                 C:\BrainStorm_2001\Toolbox\get_user_directory.m
    rapmusic_gui                       C:\BrainStorm_2001\Toolbox\rapmusic_gui.m
    save_fieldnames                    C:\BrainStorm_2001\Toolbox\save_fieldnames.m

This function is called by

    bst_static_taskbar                 C:\BrainStorm_2001\Toolbox\bst_static_taskbar.m
    dataplot_cb                        C:\BrainStorm_2001\Toolbox\dataplot_cb.m
    parametric_estimation              C:\BrainStorm_2001\Toolbox\parametric_estimation.m

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

    function varargout = rap_music_parameters(varargin)
    %RAP_MUSIC_PARAMETERS - Application M-file for rap_music_parameters.fig
    % function varargout = rap_music_parameters(varargin)
    %    FIG = RAP_MUSIC_PARAMETERS launch rap_music_parameters GUI.
    %    RAP_MUSIC_PARAMETERS('callback_name', ...) invoke the named callback.

    %<autobegin> ---------------------- 08-Jun-2004 15:12:54 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Inverse Modeling
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\bst_color_scheme.m
    %   toolbox\bst_layout.m
    %   toolbox\bst_message_window.m
    %   toolbox\bst_static_taskbar.m
    %   toolbox\dataplot_cb.m
    %   toolbox\get_user_directory.m
    %   toolbox\rapmusic_gui.m
    %
    % Subfunctions in this file, in order of occurrence in file:
    %   load_parameters(hf,StudySubject,GUI); % called from parametric_estimation
    %   varargout = pushbutton_execute_Callback(h, eventdata, handles, varargin)
    %   varargout = PopupReg_Callback(h, eventdata, handles, varargin)
    %   varargout = PopupReg_ButtonDownFcn(h, eventdata, handles, varargin)
    %   varargout = EditReg_Callback(h, eventdata, handles, varargin)
    %   varargout = CheckboxColumnNorm_Callback(h, eventdata, handles, varargin)
    %   varargout = pushbutton_quit_Callback(h, eventdata, handles, varargin)
    %   varargout = slider_threshold_Callback(h, eventdata, handles, varargin)
    %   varargout = edit_threshold_Callback(h, eventdata, handles, varargin)
    %   varargout = CurrentDipole_Callback(h, eventdata, handles, varargin)
    %   varargout = popup_cd_headmodel_Callback(h, eventdata, handles, varargin)
    %   varargout = CurrentDipole2_Callback(h, eventdata, handles, varargin)
    %   varargout = popup_cd2_headmodel_Callback(h, eventdata, handles, varargin)
    %   varargout = Multipole_Callback(h, eventdata, handles, varargin)
    %   varargout = popup_cme_headmodel_Callback(h, eventdata, handles, varargin)
    %   varargout = Multipole2_Callback(h, eventdata, handles, varargin)
    %   varargout = popup_cme2_headmodel_Callback(h, eventdata, handles, varargin)
    %   varargout = HeadModel_Directory_Callback(h, eventdata, handles, varargin)
    %   varargout = pushbutton_help_Callback(h, eventdata, handles, varargin)
    %   varargout = popup_cd_headmodel_ButtonDownFcn(h, eventdata, handles, varargin)
    %   varargout = popup_cd2_headmodel_ButtonDownFcn(h, eventdata, handles, varargin)
    %   varargout = popup_cme_headmodel_ButtonDownFcn(h, eventdata, handles, varargin)
    %   varargout = popup_cme2_headmodel_ButtonDownFcn(h, eventdata, handles, varargin)
    %   varargout = menu_quit_Callback(h, eventdata, handles, varargin)
    %   varargout = menu_help_correlation_Callback(h, eventdata, handles, varargin)
    %   varargout = Untitled_5_Callback(h, eventdata, handles, varargin)
    %   varargout = checkbox_interactive_graphs_Callback(h, eventdata, handles, varargin)
    %   varargout = checkbox_final_graphs_Callback(h, eventdata, handles, varargin)
    %
    % Application data and their calls in this file:
    %   'GUI'
    %   'HeadModelNames'
    %   'HeadModelRefNames'
    %   'StudySubject'
    %   'TileType'
    %
    %   setappdata(fig,'GUI',GUI);
    %   setappdata(fig,'HeadModelNames',HeadModelNames);
    %   setappdata(fig,'HeadModelRefNames',HeadModelRefNames);
    %   setappdata(fig,'StudySubject',StudySubject);
    %   setappdata(fig,'TileType','D');
    %
    %   GUI = getappdata(fig,'GUI');
    %   HeadModelRefNames = getappdata(fig,'HeadModelRefNames');
    %   RESULTS = getappdata(fig,'RESULTS');
    %   StudySubject = getappdata(fig,'StudySubject');
    %   fname = getappdata(fig,'RESULTS');
    %
    % Figure Files opened by this function:
    %   mfilename
    %
    %   Format of strings below: Type:Style:Tag, "String", CallBack Type and Call
    %   <automatic> callback is <Tag>_Callback by Matlab default
    %
    % Callbacks by figure rap_music_parameters.fig
    %   uicontrol:checkbox:checkbox_final_graphs "Final" uses Callback for <automatic>
    %   uicontrol:checkbox:checkbox_interactive_graphs "Interactive" uses Callback for <automatic>
    %   uicontrol:checkbox:CheckboxColumnNorm "Column Normalization" uses Callback for <automatic>
    %   uicontrol:checkbox:CurrentDipole "Current Dipoles" uses Callback for <automatic>
    %   uicontrol:checkbox:CurrentDipole2 "Synchronous Pairs of Dipoles" uses Callback for <automatic>
    %   uicontrol:checkbox:Multipole "1st-order Multipoles" uses Callback for <automatic>
    %   uicontrol:checkbox:Multipole2 "Synchronous Pairs of Multipoles" uses Callback for <automatic>
    %   uicontrol:edit:edit_threshold "0.95" uses Callback for <automatic>
    %   uicontrol:edit:EditReg "100" uses Callback for <automatic>
    %   uicontrol:edit:HeadModel_Directory "Head Model Directory" uses Callback for <automatic>
    %   uicontrol:popupmenu:popup_cd2_headmodel "Popup Menu" uses ButtonDownFcn for <automatic>
    %   uicontrol:popupmenu:popup_cd2_headmodel "Popup Menu" uses Callback for <automatic>
    %   uicontrol:popupmenu:popup_cd_headmodel "Popup Menu" uses ButtonDownFcn for <automatic>
    %   uicontrol:popupmenu:popup_cd_headmodel "Popup Menu" uses Callback for <automatic>
    %   uicontrol:popupmenu:popup_cme2_headmodel "Popup Menu" uses ButtonDownFcn for <automatic>
    %   uicontrol:popupmenu:popup_cme2_headmodel "Popup Menu" uses Callback for <automatic>
    %   uicontrol:popupmenu:popup_cme_headmodel "Popup Menu" uses ButtonDownFcn for <automatic>
    %   uicontrol:popupmenu:popup_cme_headmodel "Popup Menu" uses Callback for <automatic>
    %   uicontrol:popupmenu:PopupReg "Regularization . . ." uses ButtonDownFcn for <automatic>
    %   uicontrol:popupmenu:PopupReg "Regularization . . ." uses Callback for <automatic>
    %   uicontrol:pushbutton:pushbutton_execute "Execute" uses Callback for <automatic>
    %   uicontrol:slider:slider_threshold "" uses Callback for <automatic>
    %   uimenu::menu_help_correlation "" uses Callback for <automatic>
    %   uimenu::menu_quit "" uses Callback for <automatic>
    %   uimenu::Untitled_5 "" uses Callback for <automatic>
    %
    % At Check-in: $Author: Mosher $  $Revision: 29 $  $Date: 6/08/04 1:39p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 28-May-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> ------------------------ 08-Jun-2004 15:12:54 -----------------------

    % ---------------- change history --------------------
    %
    % JCM 31-Oct-2002  handled popup error when no headmodel exists
    % SB  11-Jul-2003  make it fit as a layout tile and modified access to current data set
    %                  (do not use .CurrentData anymore)
    % ---------------------------------------------------------

    % Last Modified by GUIDE v2.0 17-Nov-2003 09:17:09

    if nargin == 0  % LAUNCH GUI

        fig = openfig(mfilename,'new');

        % Generate a structure of handles to pass to callbacks, and store it.
        handles = guihandles(fig);
        guidata(fig, handles);

        if nargout > 0
            varargout{1} = fig;
        end

       % custom creations begin here
       bst_color_scheme(fig); % apply standard colorings
       setappdata(fig,'TileType','D');
       bst_layout('align',fig)
       set(fig,'visible','on')

    elseif ischar(varargin{1}) % INVOKE NAMED SUBFUNCTION OR CALLBACK

        try
            if (nargout)
                [varargout{1:nargout}] = feval(varargin{:}); % FEVAL switchyard
            else
                feval(varargin{:}); % FEVAL switchyard
            end
        catch
            disp(lasterr);
        end

    end

    % ----------------------- Local Functions ---------------------------
    % ------------------ INITIALIZE THE GUI WITH RAP MUSIC PARAMETERS -------
    function load_parameters(hf,StudySubject,GUI); % called from parametric_estimation

    handles = guidata(hf); % get the handles for this figure
    fig = handles.RAPMUSICparameters; % convenient figure handle

    % copy in the sent data
    setappdata(fig,'StudySubject',StudySubject);
    setappdata(fig,'GUI',GUI);

    User = get_user_directory; % where everything is stored

    % The head models are stored with the data set
    % what is the referential path for the head models
    refpath = fileparts(GUI.StudySubject.Study);%User.CurrentData.DataFile); SB

    % what is the full path name to the head models
    fullpath = fileparts(fullfile(User.STUDIES,GUI.StudySubject.Study));%User.CurrentData.DataFile)); SB

    % now get all of the headmodel filenames in that directory
    HeadModelNames = dir(fullfile(fullpath,'*headmodelVolGrid*.mat'));
    % SB 20-Nov-2002 / Look only for scan grid headmodels.

    if isempty(HeadModelNames) % No such headmodel available
        errordlg({'No volume scan grid headmodel available',...
                'Please compute one with the HeadModeling tool'...
            })
    end

    HeadModelNames = {HeadModelNames.name}; % convert to cell array of names
    % now make all names also referential
    HeadModelRefNames = HeadModelNames; % initialize
    for i= 1:length(HeadModelRefNames),
       HeadModelRefNames{i} = fullfile(refpath,HeadModelNames{i});
    end

    % HeadModelNames will be good for display, HeadModelRefNames for load
    setappdata(fig,'HeadModelNames',HeadModelNames); % store
    setappdata(fig,'HeadModelRefNames',HeadModelRefNames); % store

    % Now load the popups with the head model names
    % SourceOrder -1 is for dipoles, SourceOrder 1 is for multipoles

    SourceOrder = zeros(length(HeadModelRefNames),1); % for each head model
    for i= 1:length(HeadModelRefNames),
       temp = load(fullfile(User.STUDIES,HeadModelRefNames{i}),'SourceOrder');
       SourceOrder(i) = temp.SourceOrder;
    end

    % setup the dipole and multipole popups
    % First initialize the source model checkboxes

    Tags = {'CurrentDipole'}; % unique tag identifiers
    for i = 1:length(Tags),
       eval(sprintf('ht = handles.%s;',Tags{i}));
       set(ht,'Val',1); % set default on
    end

    Tags = {'CurrentDipole2','Multipole','Multipole2'}; % unique tag identifiers
    for i = 1:length(Tags),
       eval(sprintf('ht = handles.%s;',Tags{i}));
       set(ht,'Val',0); % set default off
    end

    % now setup popups and checkboxes based on identified head models
    % cd is current dipole, cme is current multipole, suffix 2 indicates synchronous pair
    Tags = {'cd','cd2','cme','cme2'}; % unique tag identifiers
    TagCheckBox = {'CurrentDipole','CurrentDipole2','Multipole','Multipole2'}; % checkboxes
    TagOrder = [-1 -1 1 1]; % source order, one-to-one with Tags
    for i = 1:length(Tags),
       % create temporary handle to the appropriate popup
       eval(sprintf('ht = handles.popup_%s_headmodel;',Tags{i}));
       eval(sprintf('hc = handles.%s;',TagCheckBox{i})); % corresponding checkbox
       tmpndx = find(SourceOrder == TagOrder(i)); % appropriate headmodel
       if(length(tmpndx)), % there are such head models built
          set(ht,'Val',1,'String',HeadModelNames(tmpndx),'enable','on');
          set(hc,'enable','on');
       else
          set(ht,'Val',1,'String','None','enable','off');
          set(hc,'Val',0,'enable','off'); % disable checkbox
       end
    end

    set(handles.HeadModel_Directory,'String',refpath); % information for user

    % initialize the regularization models
    % The Literal Strings are not important, but the ordering is
    RegStrings = {'Regularization . . .','Truncated Condition','Truncated Energy',...
          'Tikhonov Condition','None'};
    % initialze to Tikhonov Regularization
    set(handles.PopupReg,'Val',4,'String',RegStrings);
    set(handles.EditReg,'String','10'); % default regularization

    % In MMII, we need each head model to have the source order put into
    %  the Params structure, rather than the separater Order parameter of
    %  BST 2000. As an interim, CHEAT by manually guessing this parameter
    %  setting it into each head model, if it's not there.

    if(0),% deprecated, head model tool now does
       for i= 1:length(HeadModelRefNames),
          FullName = fullfile(User.STUDIES,HeadModelRefNames{i});
          L = load(FullName,'Param');
          LName = fieldnames(L.Param);
          if(isempty(strmatch('Order',LName))), % Order is missing
             HeadModel = load(FullName); % load the whole thing
             DIM = size(HeadModel.Gain{1},2)/size(HeadModel.GridLoc{1},2);
             switch DIM
             case 1
                Order = -1; % constrained dipoles
             case 3
                Order = -1; % unconstrained dipoles
             case 12
                Order = 1; % unconstrained multipoles
             otherwise
                Order = input(sprintf('Dim is %.0f, what order is this: '));
             end
             for i = 1:length(HeadModel.Param),
                HeadModel.Param(i).Order = Order;
             end
             save_fieldnames(HeadModel,FullName); % save back
          end % if no order present
       end
    end

    % ---------------------  The Callbacks ------------------------------

    % ----------- EXECUTE THE RAP MUSIC FUNCTION ------------------------
    function varargout = pushbutton_execute_Callback(h, eventdata, handles, varargin)
    % Execute RAP MUSIC by gathering the data and calling
    % collect the data
    fig = handles.RAPMUSICparameters; % convenient tag
    bst_fig = bst_message_window; % get handle to the message window
    arrow_fig = [fig;bst_fig]; % figures to show busy mouse

    set(arrow_fig,'pointer','watch'); % busy mouse

    StudySubject = getappdata(fig,'StudySubject');
    GUI = getappdata(fig,'GUI');
    User = get_user_directory;

    refpath = get(handles.HeadModel_Directory,'String');
    % refpath to add to the headmodel names

    % now set the Orders to search by checking which flags are set
    GUI.Order = []; % set to none first
    GUI.OrderHeadModel = [];

    % the order in which GUI.Order is loaded determines the order in
    %  which the source models will be sequenced. Should look like
    %  GUI from top to bottom.

    if(get(handles.CurrentDipole,'Value')),
       GUI.Order = [GUI.Order -1]; % add the current dipole order
       TheseStr = get(handles.popup_cd_headmodel,'string');
       GUI.OrderHeadModel{end+1} = ...
          fullfile(refpath,TheseStr{get(handles.popup_cd_headmodel,'val')});
    end
    if(get(handles.Multipole,'Value')),
       GUI.Order = [GUI.Order 1]; % add the current multipole order
       TheseStr = get(handles.popup_cme_headmodel,'string');
       GUI.OrderHeadModel{end+1} = ...
          fullfile(refpath,TheseStr{get(handles.popup_cme_headmodel,'val')});
    end
    if(get(handles.CurrentDipole2,'Value')),
       GUI.Order = [GUI.Order 2]; % add the 2 synchronous current dipole order
       TheseStr = get(handles.popup_cd2_headmodel,'string');
       GUI.OrderHeadModel{end+1} = ...
          fullfile(refpath,TheseStr{get(handles.popup_cd2_headmodel,'val')});
    end
    if(get(handles.Multipole2,'Value')),
       GUI.Order = [GUI.Order 4]; % add the 2 synchronous multipole order
       TheseStr = get(handles.popup_cme2_headmodel,'string');
       GUI.OrderHeadModel{end+1} = ...
          fullfile(refpath,TheseStr{get(handles.popup_cme2_headmodel,'val')});
    end
    % Orders 0 and 3 are for magnetic dipole and pairs of mag dipoles

    if(isempty(GUI.Order)), % user didn't check anything
       bst_message_window('You must select a starting model order');
       set(arrow_fig,'pointer','arrow'); % normal mouse
       return
    end

    GUI.Corr = get(handles.slider_threshold,'Value');

    Val = get(handles.PopupReg,'Value'); % which regularization
    switch Val
    case 1
       bst_message_window('You must select a regularization technique');
       set(arrow_fig,'pointer','arrow'); % normal mouse
       return
    case 2
       % truncated svd
       GUI.Condition = str2num(get(handles.EditReg,'String'));
       GUI.Energy = [];
       GUI.Tikhonov = [];
    case 3
       % energy svd
       GUI.Condition = [];
       GUI.Energy = str2num(get(handles.EditReg,'String'));
       GUI.Tikhonov = [];
    case 4
       % Tikhonov Condition normalization
       GUI.Condition = [];
       GUI.Energy = [];
       GUI.Tikhonov = str2num(get(handles.EditReg,'String'));
    case 5
       % none
       GUI.Condition = [];
       GUI.Energy = [];
       GUI.Tikhonov = [];
    end

    GUI.Column_norm = get(handles.CheckboxColumnNorm,'Value'); % 0 is no, 1 is yes

    % now hash together a results name
    [PATH,NAME,EXT,VER] = fileparts(strrep(GUI.DataName,User.STUDIES,''));
    c = clock;
    NAME = strrep(NAME,'data','results'); % replace
    newname = fullfile(PATH,[NAME sprintf('_%02.0f%02.0f',c(4:5)) EXT VER]);
    i = 0;
    while(exist(newname,'file')),
       i = i+1; % subtract another minute
       c(5) = mod(c(5) - 1,60);
       newname = fullfile(PATH,[NAME sprintf('_%02.0f%02.0f',c(4),c(5)) EXT VER]);
    end
    GUI.Results = newname;

    more off % let the text flow freely

    %For displaying graphics
    if get(handles.checkbox_interactive_graphs,'val'),
       GUI.DisplayGraphics = 1; % display during the analysis
    else
       GUI.DisplayGraphics = 0; % don't
    end

    if get(handles.checkbox_final_graphs,'val'),
       % when done, launch the MRI tool to view the results
       GUI.FinalDisplayGraphics = 1;
    else
       GUI.FinalDisplayGraphics = 0; % don't
    end

    [PATH,NAME,EXT,VER] = fileparts(StudySubject.SubjectTess);

    TessRap = fullfile(PATH,[[NAME '_rap'] EXT VER]); % possible tesselation file
    if(exist(TessRap,'file')), % there is a reduce one for rap
       StudySubject.SubjectTess = TessRap; % map it in
    end

    rapmusic_gui(StudySubject,GUI);

    % Now update result file list in STATIC_TASKBAR and load last result file into Viewer if open
    %[fname,ResultsPopDown] = bst_static_taskbar('GET','RESULTS');
    fig = findobj(get(0,'children'),'flat','tag','static_taskbar');
    fname = getappdata(fig,'RESULTS');
    [tmp,h] = bst_static_taskbar('GET','RESULTS');
    fname{end+1} = GUI.Results;
    bst_static_taskbar('SET','RESULTS',fname);
    set(h,'Value',length(fname))
    bst_static_taskbar('popupmenu_RESULTS_Callback',h, [],guihandles(fig), []);

    val = get(h,'val'); % where are we in the popup
    RESULTS = getappdata(fig,'RESULTS');

    global DATAPLOT
    if ~ishandle(DATAPLOT) % Viewer is not active
        % Load last result file into viewer
        bst_message_window('wrap',...
            {'Loading new results into Viewer',' '});
        tmp = bst_static_taskbar('GET','RESULTS');
        Users = get_user_directory;
        if ~isempty(tmp)
            dataplot_cb('loadfile',tmp);
        end
    end

    set(arrow_fig,'pointer','arrow'); % normal mouse

    % --------------------------------------------------------------------
    function varargout = PopupReg_Callback(h, eventdata, handles, varargin)
    % change the regularization technique and set a default parameter for each
    Val = get(h,'Val');
    switch Val
    case 1
       % Calls for Regularization
       set(handles.EditReg,'String','','Tooltipstring',...
          'Variable parameter dependent on method');
    case 2
       % Truncated Condition
       set(handles.EditReg,'String','10','Tooltipstring',...
          'Condition number');
    case 3
       % Truncated Energy
       set(handles.EditReg,'String','0.98','Tooltipstring',...
          'Percentage energy');
    case 4
       % Tikhonov Condition
       set(handles.EditReg,'String','10','Tooltipstring',...
          'Relative regularization level');
    case 5
       % None
       set(handles.EditReg,'String','','Tooltipstring',...
          '');
    end

    % --------------------------------------------------------------------
    function varargout = PopupReg_ButtonDownFcn(h, eventdata, handles, varargin)
    % Give help on the regularization method
    Val = get(h,'Val');
    switch Val
    case 1
       bst_message_window(' ');
       msg_str = ['Left-click to select a regularization method, then right ',...
             'click on the method for more help.'];
       bst_message_window('wrap',msg_str);

    case 2
       msg_str = ['Truncate the SVD of the forward model at the smallest singular ',...
             'value which still yields the desired condition. Condition is the ',...
             'largest singular value divided by the smallest. Condition of 100 ',...
             'is good for quality SNR, 10 for poorer.'];
       bst_message_window(' ');
       bst_message_window('wrap',msg_str);

    case 3
       msg_str = ['Square each singular value and sum, which equals the total ',...
             'sum square of all data in the matrix. Truncate the SVD at the ',...
             'singular value whos sum is at least the percentage desired. ',...
             'Select percentage based on plausible signal energy.'];
       bst_message_window(' ');
       bst_message_window('wrap',msg_str);

    case 4
       msg_str = ['When the singular value is equal to the Tikhonov parameter, ',...
             'the contribution of that component is suppressed from the inverse ',...
             'by a factor of 1/2, the "knee." Smaller singular values are ',...
             'therefore progressively suppressed as compared to truncation. ',...
             'The parameter here sets the knee as a condition number relative ',...
             'to the first singular value, i.e. 100 means set the knee at the ',...
             '1/100th of the largest singular value.'];
       bst_message_window(' ');
       bst_message_window('wrap',msg_str);

    case 5
       msg_str = ['No regularization will be applied, other than to truncate ',...
             'any forward model at the numeric rank of the matrix. In double ',...
             'precision, this truncation can be equivalent to a condition of',...
             'of about 1e16 and is extremely numerically sensitive. ',...
             'The use of "none" is recommended only for ',...
             'simulated noiseless data. Even in this case, it may be better ',...
             'to use a truncated condition of 1e8 rather than to be so dependent ',...
             'on double precision noise floors.'];
       bst_message_window(' ');
       bst_message_window('wrap',msg_str);
    end

    % --------------------------------------------------------------------
    function varargout = EditReg_Callback(h, eventdata, handles, varargin)
    % parameter, no callback

    % --------------------------------------------------------------------
    function varargout = CheckboxColumnNorm_Callback(h, eventdata, handles, varargin)
    set(h,'val',0,'enable','off','tooltipstring','Disabled in this version');
    bst_message_window('Column normalization turned off in this version');

    % --------------------------------------------------------------------
    function varargout = pushbutton_quit_Callback(h, eventdata, handles, varargin)
    close(handles.RAPMUSICparameters)

    % --------------------------------------------------------------------
    function varargout = slider_threshold_Callback(h, eventdata, handles, varargin)
    Val = get(h,'Val');
    % sanity check
    Val = max(0,Val);
    Val = min(1,Val);
    set(handles.edit_threshold,'String',sprintf('%01.2f',Val));

    % --------------------------------------------------------------------
    function varargout = edit_threshold_Callback(h, eventdata, handles, varargin)
    Val = str2num(get(h,'String'));
    if(~isempty(Val)),
       % sanity check
       Val = max(0,Val);
       Val = min(1,Val);
       set(handles.slider_threshold,'Val',Val);
    else
       % invalid input by user
       Val = get(handles.slider_threshold,'Val'); % get the slider value
    end

    % set the formatted display of the string
    set(handles.edit_threshold,'String',sprintf('%01.2f',Val));

    % --------------------------------------------------------------------
    function varargout = CurrentDipole_Callback(h, eventdata, handles, varargin)
    % Checkbox

    % --------------------------------------------------------------------
    function varargout = popup_cd_headmodel_Callback(h, eventdata, handles, varargin)
    % changed head model
    % make sure corresponding box is checked
    set(handles.CurrentDipole,'Val',1);

    % --------------------------------------------------------------------
    function varargout = CurrentDipole2_Callback(h, eventdata, handles, varargin)
    % Checkbox

    % --------------------------------------------------------------------
    function varargout = popup_cd2_headmodel_Callback(h, eventdata, handles, varargin)
    % changed head model
    % make sure corresponding box is checked
    set(handles.CurrentDipole2,'Val',1);

    % --------------------------------------------------------------------
    function varargout = Multipole_Callback(h, eventdata, handles, varargin)
    % Checkbox

    % --------------------------------------------------------------------
    function varargout = popup_cme_headmodel_Callback(h, eventdata, handles, varargin)
    % changed head model
    % make sure corresponding box is checked
    set(handles.Multipole,'Val',1);

    % --------------------------------------------------------------------
    function varargout = Multipole2_Callback(h, eventdata, handles, varargin)
    % Checkbox

    % --------------------------------------------------------------------
    function varargout = popup_cme2_headmodel_Callback(h, eventdata, handles, varargin)
    % changed head model
    % make sure corresponding box is checked
    set(handles.Multipole2,'Val',1);

    % --------------------------------------------------------------------
    function varargout = HeadModel_Directory_Callback(h, eventdata, handles, varargin)
    % a inactive edit window, used as inactive for visual purposes

    % --------------------------------------------------------------------
    function varargout = pushbutton_help_Callback(h, eventdata, handles, varargin)

    msg_str = ['DRAFT Help: Right click on each regularization method displayed to ',...
          'read more about each technique. Correlation threshold is . ',...
          'Regularization Methods are: .',...
          'Source Models are: .'];

    bst_message_window('wrap',msg_str)

    % ----------- Right Click operations on the head models ----------------
    % --------------------------------------------------------------------
    function varargout = popup_cd_headmodel_ButtonDownFcn(h, eventdata, handles, varargin)
    % show user some stats about this particular head model
    fig = handles.RAPMUSICparameters; % convenient handle
    HeadModelRefNames = getappdata(fig,'HeadModelRefNames'); % referential names
    User = get_user_directory;

    refpath = get(handles.HeadModel_Directory,'String');
    % refpath to add to the headmodel names

    Val = get(h,'Val'); % which name is displayed
    TheseStr = get(h,'String'); % strings in this popup

    fname = fullfile(User.STUDIES,refpath,TheseStr{Val});
    [FullPath,NameOnly] = fileparts(fname); % informational

    % let's obtain the names and size of grid
    L1 = load(fname,'HeadModelName','HeadModelType','GridName','GridLoc','SourceOrder');

    SourceType = {'Current Dipole','Magnetic Dipole','Current Multipole'};

    % display to the message window
    bst_message_window({'',sprintf('Database: %s',FullPath),...
          sprintf('Filename: %s',NameOnly),...
          sprintf('Head Model: %s, Source Type: %s',...
          L1.HeadModelName,SourceType{L1.SourceOrder+2}),...
          sprintf('Type of Grid: %s',L1.HeadModelType),...
          sprintf('Name of Grid: %s',L1.GridName{1}),...
          sprintf('Size of Grid: %.0f locations',size(L1.GridLoc{1},2))});

    % --------------------------------------------------------------------
    function varargout = popup_cd2_headmodel_ButtonDownFcn(h, eventdata, handles, varargin)
    % simply use cd version
    popup_cd_headmodel_ButtonDownFcn(h, eventdata, handles, varargin);

    % --------------------------------------------------------------------
    function varargout = popup_cme_headmodel_ButtonDownFcn(h, eventdata, handles, varargin)
    % simply use cd version
    popup_cd_headmodel_ButtonDownFcn(h, eventdata, handles, varargin);

    % --------------------------------------------------------------------
    function varargout = popup_cme2_headmodel_ButtonDownFcn(h, eventdata, handles, varargin)
    % simply use cd version
    popup_cd_headmodel_ButtonDownFcn(h, eventdata, handles, varargin);

    % --------------------------------------------------------------------
    function varargout = menu_quit_Callback(h, eventdata, handles, varargin)

    % --------------------------------------------------------------------
    function varargout = menu_help_correlation_Callback(h, eventdata, handles, varargin)

    % --------------------------------------------------------------------
    function varargout = Untitled_5_Callback(h, eventdata, handles, varargin)

    % --------------------------------------------------------------------
    function varargout = checkbox_interactive_graphs_Callback(h, eventdata, handles, varargin)
    % if on, wants interactive graphs during the run

    % --------------------------------------------------------------------
    function varargout = checkbox_final_graphs_Callback(h, eventdata, handles, varargin)
    % if on, wants final display graphs

Produced by color_mat2html, a customized BrainStorm 2.0 (Alpha) version of mat2html on Tue Oct 12 12:05:14 2004
Cross-Directory links are: ON