spm_mf_box.m

toolbox for spm 5 for data, model free analysis

if (strcmp(v,'No sort'))
    handles.permutation = 1:size(handles.mfbss.A,2);
else
    [d,handles.permutation] = sort(-handles.mfbss.reliability.(v(9:end)));
end

set(handles.time_pos,'Value',1);
set(handles.comp_pos,'Value',1);
handles = redraw_all(handles);

guidata(hObject,handles);

% --- Executes on selection change in display_opts.
function display_opts_Callback(hObject,eventdata,handles)

handles = redraw_all(handles);

guidata(hObject,handles);

% --- Executes during object creation, after setting all properties.
function sort_comp_CreateFcn(hObject,eventdata,handles)

if (ispc&&(isequal(get(hObject,'BackgroundColor'),get(0,'defaultUicontrolBackgroundColor'))))
    set(hObject,'BackgroundColor','white');
end

% --- Executes during object creation, after setting all properties.
function display_opts_CreateFcn(hObject,eventdata,handles)

if (ispc&&(isequal(get(hObject,'BackgroundColor'),get(0,'defaultUicontrolBackgroundColor'))))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on selection change in algo_preprocess.
function algo_preprocess_Callback(hObject,eventdata,handles)


% --- Executes during object creation, after setting all properties.
function algo_preprocess_CreateFcn(hObject,eventdata,handles)

if (ispc&&(isequal(get(hObject,'BackgroundColor'),get(0,'defaultUicontrolBackgroundColor'))))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on selection change in algo_reliability.
function algo_reliability_Callback(hObject,eventdata,handles)


function algo_reliability_CreateFcn(hObject,eventdata,handles)

if (ispc&&(isequal(get(hObject,'BackgroundColor'),get(0,'defaultUicontrolBackgroundColor'))))
    set(hObject,'BackgroundColor','white');
end


function algo_postprocess_Callback(hObject,eventdata,handles)

% --- Executes during object creation, after setting all properties.
function algo_postprocess_CreateFcn(hObject,eventdata,handles)

if (ispc&&(isequal(get(hObject,'BackgroundColor'),get(0,'defaultUicontrolBackgroundColor'))))
    set(hObject,'BackgroundColor','white');
end

% --- Executes on button press in export_mask.
function export_mask_Callback(hObject,eventdata,handles)

mfbox_databackend('export_mask',handles.private,handles.mfbss.mask);

guidata(hObject,handles);


% --- Executes on button press in export_result.
function export_result_Callback(hObject,eventdata,handles)

contents = get(handles.plot_type,'String');
if (isempty(contents)), t = '';
else t = contents{get(handles.plot_type,'Value')};
end
vt = get(handles.time_pos,'Value');
vc = get(handles.comp_pos,'Value');
if (~isempty(handles.permutation)), vc = handles.permutation(vc); end

d = zeros(size(handles.mfbss.bg));
if (strcmp(t,'Processed Data'))
    sgr = size(handles.mfbss.grid);
    sm = size(handles.mfbss.mask);
    g = mat2cell(min(repmat(sm',1,sgr(2)),max(ones(sgr), ...
        round(handles.mfbss.grid))),ones(1,sgr(1)),sgr(2));
    d(unique(sub2ind(sm,g{:}))) = handles.mfbss.S.dat(:,handles.mfbss.S.map(vt,vc));
else
    sgr = size(handles.mfbss.grid);
    sm = size(handles.mfbss.mask);
    g = mat2cell(min(repmat(sm',1,sgr(2)),max(ones(sgr), ...
        round(handles.mfbss.grid))),ones(1,sgr(1)),sgr(2));
    d(unique(sub2ind(sm,g{:}))) = handles.mfbss.ppS.dat(:,handles.mfbss.ppS.map(vt,vc));
end

if (isempty(handles.filenames)), handles.filenames = char(ones(1,0)*' '); end

handles.filenames = mfbox_databackend('export_result', ...
    handles.private,d,handles.filenames(1,:));

guidata(hObject,handles);


% --- Executes on button press in run_estimate.
function run_estimate_Callback(hObject,eventdata,handles)

if ((get(handles.keeppre,'Value')==0)||(isempty(handles.mfbss.X))||(isstruct(handles.mfbss.X)))
    if (isstruct(handles.mfbss.X))
        X = handles.mfbss.X;
        mask = handles.mfbss.mask;
    else
        X = handles.sequence;
        mask = true(X.dim);
    end
    mm = sum(mask(:));
    s = [X.dim,X.timesteps];
    C = zeros(X.timesteps);
    m = zeros(1,X.timesteps);
    Y = zeros(sum(mask(:)),s(end));
    for i=1:X.timesteps
        ly = reshape(mfbox_databackend('getdata',X,i),[],1);
        Y(:,i) = ly(mask,:);
    end
    for i=1:X.timesteps
        for j=(i+1):X.timesteps
            v = Y(:,[i,j]);
            if (i==(j-1))
                C(i,i) = sum(v(:,1).^2);
                m(i) = sum(v(:,1));
            end
            C(i,j) = v(:,1)'*v(:,2);
            C(j,i) = C(i,j);
            if ((i==(j-1))&&(j==X.timesteps))
                C(j,j) = sum(v(:,2).^2);
                m(j) = sum(v(:,2));
            end
        end
    end
    m = m/mm;
    C = C/(mm-1)-m'*m;
else
    mm = sum(handles.mfbss.mask(:));
    X = single(handles.mfbss.X);
    s = size(X);
    X = reshape(X,prod(s(1:(end-1))),s(end));
    sgr = size(handles.mfbss.grid);
    sm = size(handles.mfbss.mask);
    g = mat2cell(min(repmat(sm',1,sgr(2)),max(ones(sgr), ...
        round(handles.mfbss.grid))),ones(1,sgr(1)),sgr(2));
    mask = handles.mfbss.mask(sub2ind(sm,g{:}));
    if (any(~mask)), X = X(mask,:); end
    C = double(cov(X));
end
[E,D] = eig(C);
D = -sort(-diag(D));
mdlcomp = max(min(mfbox_getmdl(D,mm),s(end)),1);

v = fieldnames(handles.mfbss.params);
for i=1:length(v)
    if (isfield(handles.mfbss.params.(v{i}),'numComponents'))
        handles.mfbss.params.(v{i}).numComponents = mdlcomp;
    end
end

guidata(hObject,handles);


% --- Executes on button press in export_ic.
function export_ic_Callback(hObject, eventdata, handles)

vt = get(handles.time_pos,'Value');
vc = get(handles.comp_pos,'Value');
if (~isempty(handles.permutation)), vc = handles.permutation(vc); end
contents = get(handles.plot_type,'String');
if (isempty(contents)), return;
else t = contents{get(handles.plot_type,'Value')};
end
[st,re] = getdisplayopts(handles.display_opts);

[f,d] = uiputfile('*.svg','Select output file ...');
if (isempty(f)), return; end
tmpfile = fullfile(d,f);

prgs = mfbox_progress([],'title','Plot','string','Generating plot','progress',[1,4]);
drawnow;

[bg,handles.private] = mfbox_databackend('getbg',handles.private);
[atlas,handles.private] = mfbox_databackend('getatlas',handles.private);

mfbox_progress(prgs,'string','Generating plot','progress',[2,4]);

name = '';
if (strcmp(t,'Processed Data'))
    tc = handles.mfbss.A(:,vc)';
    [ic,handles.private] = mfbox_databackend('getic',handles.private, ...
        handles.mfbss.S.dat(:,handles.mfbss.S.map(vt,vc)), ...
        handles.mfbss.grid(:,handles.mfbss.S.mask),handles.mfbss.mask);
else
    tc = handles.mfbss.ppA(:,vc)';
    [ic,handles.private] = mfbox_databackend('getic',handles.private, ...
        handles.mfbss.ppS.dat(:,handles.mfbss.ppS.map(vt,vc)), ...
        handles.mfbss.grid(:,handles.mfbss.ppS.mask),handles.mfbss.mask);
    if (isfield(handles.mfbss.ppS,'tag')), name = handles.mfbss.ppS.tag{vc}; end
end

mfbox_progress(prgs,'string','Generating plot','progress',[3,4]);

mfbox_progress(prgs,'close',[]);

tc = {tc,handles.mfbss.timeline};
if (~isempty(handles.mfbss.design))
    sd = size(handles.mfbss.design);
    for i=1:sd(2)
        tc{2+i} = interp1(linspace(handles.mfbss.timeline(1),handles.mfbss.timeline(end),sd(1)), ...
            handles.mfbss.design(:,i),handles.mfbss.timeline)';
    end
end

f = fopen(tmpfile,'w');
dat = mfbox_plotic(ic,tc, ...
    sprintf('%s analysis component %d %s',handles.mfbss.name,vc,name), ...
    {st,re},bg,atlas,1);
fwrite(f,dat,'char');
fclose(f);

guidata(hObject,handles);


% --- Executes on button press in plot.
function plot_Callback(hObject,eventdata,handles)

vt = get(handles.time_pos,'Value');
vc = get(handles.comp_pos,'Value');
if (~isempty(handles.permutation)), vc = handles.permutation(vc); end
contents = get(handles.plot_type,'String');
if (isempty(contents)), return;
else t = contents{get(handles.plot_type,'Value')};
end
[st,re] = getdisplayopts(handles.display_opts);

prgs = mfbox_progress([],'title','Plot','string','Generating plot','progress',[1,4]);
drawnow;

[bg,handles.private] = mfbox_databackend('getbg',handles.private);
[atlas,handles.private] = mfbox_databackend('getatlas',handles.private);

mfbox_progress(prgs,'string','Generating plot','progress',[2,4]);

aviplot = false;
name = '';
map = [];
if (strcmp(t,'Processed Data'))
    map = handles.mfbss.S.map(:,vc);
    cs = unique(map)';
else
    map = handles.mfbss.ppS.map(:,vc);
    cs = unique(map)';
end
ic = {};
if (length(cs)>1)
    a = questdlg(sprintf( ...
        'Generate Movie from all frames in this component?\n'), ...
        'Movie','Yes','No','Yes');
    if (strcmp(a,'Yes')), aviplot = true; end
end
if (~aviplot)
    if (strcmp(t,'Processed Data'))
        cs = handles.mfbss.S.map(vt,vc);
    else
        cs = handles.mfbss.ppS.map(vt,vc);
    end
end
for comp=cs
    if (strcmp(t,'Processed Data'))
        tc = handles.mfbss.A(:,vc)';
        cic = handles.mfbss.S.dat(:,comp);
        if (~all(cic(:)==0))
            [ic{end+1},handles.private] = mfbox_databackend('getic',handles.private, ...
                cic,handles.mfbss.grid(:,handles.mfbss.S.mask),handles.mfbss.mask);
        end
    else
        tc = handles.mfbss.ppA(:,vc)';
        cic = handles.mfbss.ppS.dat(:,comp);
        if (~all(cic(:)==0))
            [ic{end+1},handles.private] = mfbox_databackend('getic',handles.private, ...
                cic,handles.mfbss.grid(:,handles.mfbss.ppS.mask),handles.mfbss.mask);
        end
        if (isfield(handles.mfbss.ppS,'tag')), name = handles.mfbss.ppS.tag{vc}; end
    end
end

mfbox_progress(prgs,'string','Generating plot','progress',[3,4]);

mfbox_progress(prgs,'close',[]);

tc = {tc,handles.mfbss.timeline};
if (~isempty(handles.mfbss.design))
    sd = size(handles.mfbss.design);
    for i=1:sd(2)
        tc{2+i} = interp1(linspace(handles.mfbss.timeline(1),handles.mfbss.timeline(end),sd(1)), ...
            handles.mfbss.design(:,i),handles.mfbss.timeline)';
    end
end
if (aviplot)
    p = cell(1,length(ic));
    fh = 0;
    for i=1:length(ic)
        mtc = tc(1:2);
        mtc{3} = map==cs(i);
        p{i} = mfbox_plotic(ic{i},mtc, ...
            sprintf('%s analysis component %d %s',handles.mfbss.name,vc,name), ...
            {st,re},bg,atlas,{fh,2});
        fh = p{i};
        M(i) = getframe(fh);
    end
    close(fh);
    figure;
    run = true;
    while (run)
        movie(M,5,1);
        a = questdlg(sprintf('Repeat or save?\n'), ...
            'Movie','Yes','Save','No','Yes');
        run = strcmp(a,'Yes');
        if (strcmp(a,'Save'))
            [f,d] = uiputfile('*.avi','Select output file ...');
            if (isempty(f)), return; end
            tmpfile = fullfile(d,f);
            movie2avi(M,tmpfile);
            run = false;
        end
    end
else
    mfbox_plotic(ic{1},tc, ...
        sprintf('%s analysis component %d %s',handles.mfbss.name,vc,name), ...
        {st,re},bg,atlas,2);
end

guidata(hObject,handles);


% --- Executes on button press in keeppre.
function keeppre_Callback(hObject,eventdata,handles)

if (get(hObject,'Value')==1)
    set(handles.algo_preprocess,'Enable','off');
    set(handles.run_pre,'Enable','off');
else
    set(handles.algo_preprocess,'Enable','on');
    set(handles.run_pre,'Enable','on');
end


% --- Executes on button press in compare_ics.
function compare_ics_Callback(hObject,eventdata,handles)

mfbox_tool_compare_run(handles.mfbss);


% --- Executes on button press in open_help.
function open_help_Callback(hObject,eventdata,handles)

mfd = fileparts(which('spm_mf_box'));
dirs = {fullfile(mfd,'doc','html'),'/usr/local/share/mfbox/html','/usr/share/mfbox/html'};

r = true; i = 1;
while (r&&(i<=length(dirs)))
    d = dirs{i};
    f = fullfile(d,'index.html');
    if (exist(f))
        r = false;
        web(sprintf('file://%s',f),'-helpbrowser');
    end
    i = i+1;
end


% --- Executes on button press in load_params.
function load_params_Callback(hObject,eventdata,handles)

nSeq = handles.sequence.timesteps;

p = {'name','params','rel_name','rel_params','pos_name','pos_params'};
pp = {'pre_name','pre_params'};

[mfbss,handles.params_filename] = mfbox_databackend('load_params', ...