spm_mf_box.m

toolbox for spm 5 for data, model free analysis

function varargout=spm_mf_box(varargin)
%
% mfBox - The model-free toolbox for SPM
%
% spm_mf_box is the main GUI window function.
% Call this with SPM in the path, or directly from SPM.
%
% Copyright by Peter Gruber and Fabian J. Theis
% Signal Processing & Information Theory group
% Institute of Biophysics, University of Regensburg, Germany
% Homepage: http://research.fabian.theis.name
%           http://www-aglang.uni-regensburg.de
%
% This file is free software, subject to the 
% GNU GENERAL PUBLIC LICENSE, see gpl.txt


% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',mfilename, ...
    'gui_Singleton',gui_Singleton, ...
    'gui_OpeningFcn',@spm_mf_box_OpeningFcn, ...
    'gui_OutputFcn',@spm_mf_box_OutputFcn, ...
    'gui_LayoutFcn',[], ...
    'gui_Callback',[]);
if (nargin&&(ischar(varargin{1})))
    gui_State.gui_Callback = str2func(varargin{1});
end

if (nargout)
    [varargout{1:nargout}] = gui_mainfcn(gui_State,varargin{:});
else
    gui_mainfcn(gui_State,varargin{:});
end
% End initialization code - DO NOT EDIT

% --- redraw all diagrams
function handles=redraw_all(handles)

set(handles.comp_pos,'Position',get(handles.comp_pos,'Position')); % fix for brokeness without java
set(handles.time_pos,'Position',get(handles.time_pos,'Position'));

vt = floor(get(handles.time_pos,'Value'));
vc = floor(get(handles.comp_pos,'Value'));
set(handles.time_pos,'Value',vt)
set(handles.comp_pos,'Value',vc)
mt = floor(get(handles.time_pos,'Max'));
mc = floor(get(handles.comp_pos,'Max'));
contents = get(handles.plot_type,'String');
if (isempty(contents)), t = '';
else t = contents{get(handles.plot_type,'Value')};
end
set(handles.time,'String',sprintf('%2d/%2d',vt,mt));
if (~isempty(handles.permutation)), vc = handles.permutation(vc); end
if ((strcmp(t,'Post-processed Data'))&&(isfield(handles.mfbss.ppS,'tag')))
    c = handles.mfbss.ppS.tag;
    set(handles.comp,'String',c{vc});
else
    set(handles.comp,'String',sprintf('%2d/%2d',vc,mc));
end

[st,re] = getdisplayopts(handles.display_opts);

if (isfield(handles,'lastplotstate')), oldplot = handles.lastplotstate;
else oldplot = {[0,0],'none',1};
end

S = []; A = []; position = []; markings = {}; plotvol = {};
if (strcmp(t,'Original Data'))
    if (~strcmp(oldplot{2},t))
        plotvol = {handles.sequence.private(vt) []};
    elseif (oldplot{1}(2)~=vt)
        [handles.private,position] = mfbox_databackend('getposition', ...
            handles.private);
        plotvol = {handles.sequence.private(vt)};
    end
    if (~isempty(handles.mfbss.reference))
        g = mfbox_mkgrid(size(handles.mfbss.bg))';
        mg = [[1;1;1],size(handles.mfbss.bg)'];
        g = g(:,handles.mfbss.reference);
        l = sum(handles.mfbss.reference(:));
        markings{1} = {[g,mg] [ones(l,1)*0.5;0;1] [0.5,1,0.5]'};
    end
elseif ((strcmp(t,'Processed Data'))||(strcmp(t,'Post-processed Data'))|| ...
    (strcmp(t,'Preprocessing'))||(strcmp(t,'Mask')))
    plotvol = {handles.private};
    if (~strcmp(oldplot{2},t))
        plotvol{2} = [];
        oldplot{1} = [0,0];
    end
    if ((strcmp(t,'Processed Data'))||(strcmp(t,'Post-processed Data')))
        if (strcmp(t,'Processed Data')),
            S = handles.mfbss.S.dat;
            m = handles.mfbss.S.map;
            mask = handles.mfbss.S.mask;
        else
            S = handles.mfbss.ppS.dat;
            m = handles.mfbss.ppS.map;
            mask = handles.mfbss.ppS.mask;
        end

        if (m(vt,vc)>0)
            S = S(:,m(vt,vc));
            sc = st*std(S(:));
            if (re), S = S-mean(S(:)); end
            ls = (S<-sc); us = (S>sc);
            g = handles.mfbss.grid(:,mask);
            mS = abs(S(:))>=(max(abs(S(:)))-eps);
            maxp = g(:,mS);
            if (numel(maxp))
                position = maxp(:,1);
            else
                position = g(:,ceil(size(g,2)/2));
            end
            S = S(ls|us);
            mg = [[1;1;1],size(handles.mfbss.bg)'];
            markings{1} = {[g(:,us),mg] [S(S>0);0;1] [1,0,0]'};
            markings{2} = {[g(:,ls),mg] [-S(S<0);0;1] [0,0,1]'};
            if (~isempty(handles.mfbss.reference))
                g = mfbox_mkgrid(size(handles.mfbss.bg))';
                g = g(:,handles.mfbss.reference);
                l = sum(handles.mfbss.reference(:));
                markings{3} = {[g,mg] [ones(l,1)*0.5;0;1] [0.5,1,0.5]'};
            end
        end
        if (strcmp(t,'Processed Data'))
            if (size(handles.mfbss.A,2)~=0), A = handles.mfbss.A; end
        else
            if (size(handles.mfbss.ppA,2)~=0), A = handles.mfbss.ppA; end
        end
    elseif ((strcmp(t,'Preprocessing'))||(strcmp(t,'Mask')))
        if (oldplot{1}(2)~=vt)
            [handles.private,position] = mfbox_databackend('getposition', ...
                handles.private);
            if (strcmp(t,'Preprocessing'))
                if (isstruct(handles.mfbss.X))
                    c = reshape(mfbox_databackend('getdata', ...
                        handles.mfbss.X,vt),[],1);
                else
                    s = size(handles.mfbss.X);
                    c = reshape(handles.mfbss.X,[],s(end));
                    c = c(:,vt);
                end
                sgr = size(handles.mfbss.grid);
                sbg = size(handles.mfbss.bg);
                g = mat2cell(min(repmat(sbg',1,sgr(2)), ...
                    max(ones(sgr),round(handles.mfbss.grid))), ...
                    ones(1,sgr(1)),sgr(2));
                xm = handles.mfbss.mask(sub2ind(sbg,g{:}));
                c = c(xm);
                gr = handles.mfbss.grid(:,xm);
                mg = [[1;1;1],sbg'];
                markings{1} = {[gr(:,c>0),mg] [c(c>0);0;1] [1,0.5,0]'};
                markings{2} = {[gr(:,c<0),mg] [-c(c<0);0;1] [0,0.5,1]'};
            else
                l = sum(handles.mfbss.mask(:));
                if (l~=0)
                    g = mfbox_mkgrid(size(handles.mfbss.mask))';
                    mg = [[1;1;1],size(handles.mfbss.mask)'];
                    markings{1} = {[g(:,handles.mfbss.mask(:)),mg] ...
                        [ones(l,1)*0.75;0;1] [1,1,1]'};
                end
            end
        end
        cla(handles.timecourse); cla(handles.cross);
        cla(handles.miscplot); cla(handles.histogram);
    else
        cla(handles.timecourse); cla(handles.cross);
        cla(handles.miscplot); cla(handles.histogram);
        return;
    end
end

handles.lastplotstate = {[vt,vc] t {st,re}};

if ((~isempty(plotvol))||(~isempty(markings)))
    handles.private = mfbox_databackend('redraw',handles.private, ...
        plotvol,markings,position);
end

if (~isempty(A))
    tc = A(:,vc);
    ma = max(tc(:));
    mi = min(tc(:));
    if (~isempty(handles.mfbss.design))
        ds = size(handles.mfbss.design);
        colors = repmat([1,0,0;0,1,0;0,0,1;1,1,0;1,0,1;0,1,1],ceil(ds(2)/6),1);
        de = reshape(handles.mfbss.design*colors(1:ds(2),:),1,ds(1),3);
        de = 0.5*((de-min(de(:)))/(max(de(:))-min(de(:))));
        image([handles.mfbss.timeline(1),handles.mfbss.timeline(end)],[mi,ma],1-de, ...
            'Parent',handles.timecourse);
        set(handles.timecourse,'NextPlot','add','YDir','normal');
    end
    p = plot(handles.timecourse,handles.mfbss.timeline,A);
    set(p,'Color',[0.7;0.7;0.7],'LineWidth',2,'LineStyle','-.');
    set(handles.timecourse,'NextPlot','add');
    if (isfield(handles,'mytc'))
        p = plot(handles.timecourse,handles.mfbss.timeline, ...
            A(:,handles.permutation(handles.mytc)));
        set(p,'Color',[1;0.2;0.2],'LineWidth',2,'LineStyle','-');
        set(handles.timecourse,'NextPlot','add');
        handles = rmfield(handles,'mytc');
    end
    p = plot(handles.timecourse,handles.mfbss.timeline,real(tc));
    set(p,'Color',[0;0;0],'LineWidth',3);
    set(handles.timecourse,'NextPlot','replace','YLim', ...
        [mi,ma]+[-1,1]*(ma-mi)/2);
else
    cla(handles.timecourse);
end

if (~isempty(S)), hist(handles.histogram,real(S),100);
else cla(handles.histogram);
end

ct = [];
rel = struct();
if (strcmp(t,'Processed Data'))
    if (isfield(handles.mfbss,'reliability')), rel = handles.mfbss.reliability; end
    if (isfield(handles.mfbss,'crosstalk')), ct = handles.mfbss.crosstalk; end
elseif (strcmp(t,'Post-processed Data'))
    if (isfield(handles.mfbss,'ppreliability')), rel = handles.mfbss.ppreliability; end
    if (isfield(handles.mfbss,'ppcrosstalk')), ct = handles.mfbss.ppcrosstalk; end
else
    cla(handles.cross); cla(handles.miscplot);
    return
end

if (size(ct,1)~=0)
    u = triu(ct); l = tril(ct); lp = size(ct,1);
    t = reshape(u(:)*[1,0,0]+l(:)*[0,0,1],[lp,lp,3])+repmat(eye(lp),[1,1,3]);
    t(vc,:,2) = 0.2; t(:,vc,2) = 0.2;
    image(t,'Parent',handles.cross,'ButtonDownFcn',{@cross_event_handler,handles});
    set(handles.cross,'YDir','reverse')
else
    cla(handles.cross);
end

r = cell2mat(struct2cell(rel));
if (size(r,1)~=0)
    b = bar(handles.miscplot,r(:,vc));
    set(b,'Horizontal','on','FaceColor',[0.5;0.5;0.5]);
    set(handles.miscplot,'XLim',[0,1],'YTick',1:size(r,1),'YTickLabel',fieldnames(rel));
else
    cla(handles.miscplot);
end


% ---
function cross_event_handler(src,eventdata,h)

p = get(h.cross,'CurrentPoint'); p = p(1,1:2);
h.mytc = round(p);
if (~isempty(h.permutation))
    h.mytc(1) = find(h.permutation==h.mytc(1));
    h.mytc(2) = find(h.permutation==h.mytc(2));
end
if (h.mytc(1)==h.mytc(2)), set(h.comp_pos,'Value',h.mytc(1)); end
h = redraw_all(h);


% --- identifies button to activate, fills in appropriate drop down boxes
function handles=reset_views(handles,varargin)

nSeq = handles.sequence.timesteps;
if (isstruct(handles.mfbss.X)), nX = handles.mfbss.X.timesteps;
else, nX = size(handles.mfbss.X,ndims(handles.mfbss.X));
end
[nT,nA] = size(handles.mfbss.A);
[npT,nP] = size(handles.mfbss.ppA);

buttons = struct('import_data',1,'save_res',0,'load_res',1,'import_ref',0, ...
    'import_des',0,'import_bg',0,'design_clear',0,'reference_clear',0, ...
    'export_data',0,'export_result',0,'plot_ic_wo',0, ...
    'run',0,'clear_post',0,'run_pre',0,'run_post',0,'plot',0, ...
    'keeppre',0,'run_estimate',0,'load_params',1,'save_params',1, ...
    'modify_params',0,'export_mask',0,'export_congraph',0, ...
    'export_ics',0,'export_ic',0,'export_cross',0,'compare_ics',0, ...
    'plot_connectiongraph',0);
plot_types = {};
display_opts = {};
sort_comps = {'No sort'};
keeppre = 0;

if (nSeq>0)
    plot_types = cat(1,plot_types,{'Original Data'});
    buttons.run = 1;
    buttons.run_pre = 1;
    buttons.run_estimate = 1;
    buttons.modify_params = 1;
    buttons.import_bg = 1;
    buttons.import_ref = 1;
    buttons.import_des = 1;
end
if (nX>0)
    plot_types = cat(1,plot_types,{'Mask'});
    plot_types = cat(1,plot_types,{'Preprocessing'});
    buttons.run_estimate = 1;
    buttons.save_res = 1;
    buttons.run = 1;
    buttons.export_data = 1;
    buttons.export_mask = 1;
    buttons.modify_params = 1;
    buttons.import_bg = 1;
    buttons.import_ref = 1;
    buttons.import_des = 1;
    keeppre = 1;
end
if ((nX>0)&&(nSeq>0))
    buttons.keeppre = 1;
end
if (~isempty(handles.mfbss.reference))
    buttons.reference_clear = 1;
end
if (~isempty(handles.mfbss.design))
    buttons.design_clear = 1;
end
if (nA>0)
    plot_types = cat(1,plot_types,{'Processed Data'});
    display_opts = {'>3 std, 0 centered','>2 std, 0 centered','>1 std, 0 centered', ...
        '0 centered','>3 std, mean centered','>2 std, mean centered','>1 std, mean centered', ...
        'mean centered'};
    buttons.save_res = 1;
    buttons.run_post = 1;
    buttons.export_result = 1;
    buttons.export_ics = 1;
    buttons.export_congraph = 1;
    buttons.plot = 1;
    buttons.plot_ic_wo = 1;
    buttons.export_ic = 1;
    buttons.compare_ics = 1;
    if (isfield(handles.mfbss,'extraplot'))
        buttons.plot_connectiongraph = 1;
    end
    t = fieldnames(handles.mfbss.reliability);
    for i=1:length(t), sort_comps = cat(1,sort_comps,{['Sort by ' t{i}]}); end
end
if (nP>0)
    plot_types = cat(1,plot_types,{'Post-processed Data'});
    display_opts = {'>3 std, 0 centered','>2 std, 0 centered','>1 std, 0 centered', ...
        '0 centered','>3 std, mean centered','>2 std, mean centered','>1 std, mean centered', ...
        'mean centered'};
    buttons.clear_post = 1;
end

if (isempty(plot_types)), plot_types = {'No data'}; end
if (isempty(display_opts)), display_opts = {'No data'}; end

plot_type = length(plot_types);
display_opt = 1;
sort_comp = 1;
for i=2:2:nargin
    switch varargin{i-1}
        case 'plot_type'
            plot_type = min(plot_type,varargin{i});
        case 'display_opt'
            display_opt = varargin{i};
        case 'sort_comp'
            sort_comp = varargin{i};
    end
end
switch plot_types{plot_type}
    case 'Original Data'
        time_max = nSeq+0.01;
        comp_max = 1.001;
    case 'Mask'
        time_max = 1.001;
        comp_max = 1.001;
    case 'Preprocessing'
        time_max = nX+0.01;
        comp_max = 1.001;
    case 'Processed Data'
        time_max = nT+0.01;
        comp_max = nA+0.01;
    case 'Post-processed Data'
        time_max = npT+0.01;
        comp_max = nP+0.01;
    otherwise
        time_max = 1.001;
        comp_max = 1.001;
end
set(handles.plot_type,'Value',plot_type,'String',plot_types);
set(handles.display_opts,'Value',display_opt,'String',display_opts);
set(handles.sort_comp,'Value',sort_comp,'String',sort_comps);
if (sort_comp==1), handles.permutation = 1:nA;
else [d,handles.permutation] = sort(-handles.mfbss.reliability.(sort_comps{sort_comp}));
end
set(handles.time_pos,'Min',1,'Max',time_max,'Value',1, ...