bfm_plot_brainlv.m

绝对经典,老外制作的功能强大的matlab实现PLS_TOOBOX

    %
    if isempty(cluster_info)
       cluster_idx = newcoords;
    else
       cluster_idx = cluster_info.data{1}.idx;
    end

    if isequal(newcoords, cluster_idx)
       non_cluster_coords = [];
    else
       [tmp cluster_coords] = intersect(newcoords,cluster_idx);
       non_cluster_coords = ones(1,length(newcoords));
       non_cluster_coords(cluster_coords) = 0;
       non_cluster_coords = find(non_cluster_coords);
    end

    if (no_background_image),
       non_brain_region_color_idx = size(cmap,1);
       img = zeros(1,rows*cols*slices) + non_brain_region_color_idx;

       disp_blv(non_cluster_coords) = brain_region_color_idx;

       img(newcoords) = disp_blv;
       img = reshape(img,[rows cols 1 slices]); 
    else
       max_bg = max(bg_img(:));
       min_bg = min(bg_img(:));
       img = (bg_img - min_bg) / (max_bg - min_bg) * 100;

       disp_blv(non_cluster_coords) = img(newcoords(non_cluster_coords));

       if exist('lower_idx','var') & ~isempty(lower_idx)
          img(newcoords(lower_idx)) = disp_blv(lower_idx);
       end

       if exist('upper_idx','var') & ~isempty(upper_idx)
          img(newcoords(upper_idx)) = disp_blv(upper_idx);
       end
    end;

    blv = reshape(img,[rows*cols,slices]);

    %  rotate image
    %
    for i=1:num_slices
        tmp=reshape(blv(:,i),img_width,img_height);
        tmp=rot90(tmp,mod(rot_amount,4));
        blv(:,i)=tmp(:);
    end

    % save a cornor of the last slice as the background intensity
    %
    bg_intensity = blv(1, num_slices);

    %  calculate how many slices to display for each row and column
    %  it's an algorithm from montage which will layout the slice
    %  in near square
    %
    if dims(1) > dims(2)
        siz = [dims(1), dims(2), dims(4)];
    else
        siz = [dims(2), dims(1), dims(4)];
    end

    cols_disp = sqrt(prod(siz))/siz(2);
    rows_disp = siz(3)/cols_disp;
    if (ceil(cols_disp)-cols_disp) < (ceil(rows_disp)-rows_disp),
        cols_disp = ceil(cols_disp); rows_disp = ceil(siz(3)/cols_disp);
    else
        rows_disp = ceil(rows_disp); cols_disp = ceil(siz(3)/rows_disp);
    end

    max_slice = rows_disp * cols_disp;
    rest_slices = max_slice - num_slices;
    empty_slices = -1 * ones(1,rest_slices);
    slice_idx = [slice_idx, empty_slices];

    % for empty slice (27-30), filled them with background intensity
    %
    blv_filled = [blv, ...
	bg_intensity * ...
	ones(img_height*img_width,rows_disp*cols_disp-num_slices)];

    blv_disp = [];
    for(row = 0:rows_disp-1)

        % take 'cols_disp' amount of slices from blv_filled
        % and put into blv_row
        %
        blv_row = blv_filled(:,[row*cols_disp+1:row*cols_disp+cols_disp]);

        % reshape the slice to integrate the whole row together
        %
        blv_row = reshape(blv_row, [img_height, img_width*cols_disp]);

        blv_disp = [blv_disp; blv_row];

    end

    blv_disp = reshape(blv_disp, [rows_disp*img_height, cols_disp*img_width]);

%%    h_img = image(blv_disp,'CDataMapping','scaled');
%    h_img = image(blv_disp);

    if update
       h_img = findobj(gcf,'tag','BLVImg');
       set(h_img,'CData',blv_disp);
    else
       h_img = image(blv_disp); 
    end

    set(h_img,'Tag','BLVImg');
    colormap(cmap);

    num_plus = repmat({'+ '},1,rows_disp);
    for i = 0:rows_disp-1
        num_plus{i+1} = [num2str(i*cols_disp) num_plus{i+1}];
    end

    set(gca,'tickdir','out','ticklength',[0.001 0.001]);
    set(gca,'xtick',[img_width/2:img_width:img_width*cols_disp]);
    set(gca,'xticklabel',[1:cols_disp]);
    set(gca,'ytick',[img_height/2:img_height:img_height*rows_disp]);
    set(gca,'yticklabel',num_plus);

    if (new_fig)
        create_colorbar(colorbar_hdl, cbar_map, min_blv, max_blv);
        return;
    end

    if grp_idx				% called from datamatcorrs plot
       set(h_img,'ButtonDownFcn','bfm_plot_datamatcorrs(''SelectPixel'')');
    else
       set(h_img,'ButtonDownFcn','bfm_result_ui(''SelectPixel'')');
    end

    create_colorbar(colorbar_hdl, cbar_map, min_blv, max_blv );


    %  save the attributes of the current image
    %
    if ~isappdata(gcf, 'VoxelSize')
       setappdata(gcf,'Dims',dims);
       setappdata(gcf,'VoxelSize',voxel_size);
       setappdata(gcf,'Origin',origin);
       setappdata(gcf,'orient_pattern', []);
    end

    setappdata(gcf,'SliceIdx',slice_idx);
    setappdata(gcf,'ImgHeight',img_height);
    setappdata(gcf,'ImgWidth',img_width);
    setappdata(gcf,'RowsDisp',rows_disp);
    setappdata(gcf,'ColsDisp',cols_disp);
    setappdata(gcf,'ImgRotateFlg',1);
    setappdata(gcf,'NumLVs',num_lv);
%    setappdata(gcf,'BLVData',brainlv);

    if ~isappdata(gcf,'origin_coords')
       setappdata(gcf,'origin_coords',origin_coords);
    end

    if ~isappdata(gcf,'BLVCoords')
       setappdata(gcf,'BLVCoords',newcoords);
    end

    setappdata(gcf,'BLVThreshold',thresh);
    setappdata(gcf,'RotateAmount',rot_amount);
    setappdata(gcf,'BLVDisplay',blv);

    %  in order to use function like 'cluster' etc. created by fMRI
    %
    if ~isappdata(gcf, 'STDims') | ~isappdata(gcf, 'STVoxelSize') ...
	| ~isappdata(gcf, 'STOrigin')
       setappdata(gcf,'STDims',dims);
       setappdata(gcf,'STVoxelSize',voxel_size);
       setappdata(gcf,'STOrigin',origin);
    end

    setappdata(gcf,'WinSize',1);

    if ViewBootstrapRatio
        setappdata(gcf,'BSThreshold',thresh);

       if ~isappdata(gcf, 'BSRatioCoords')
          setappdata(gcf,'BSRatioCoords',newcoords);
       end
    end

    if ~isempty(behav_idx)			% called from datamatcorrs plot
        setappdata(gcf,'NumBehav',num_behav);
    end

    %  save background to img
    %
    setappdata(gcf,'cmap',cmap);
    
    return;					%  bfm_plot_brainlv


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%   Convert the indexed matrix back into the original matrix
%
%   Usage [outmat]=unmapblv(inmat, coords, siz)
%
%   I (inmat): indexed matrix
%   I (coords): index
%   I (siz): size of original matrix
%   O (outmat): original matrix
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function [outmat] = unmapblv(inmat, coords, siz)

    [r c]=size(inmat);
    outmat=zeros(r,siz);

    for i=1:r;
        outmat(i,coords)=inmat(i,:);
    end

    return;					% unmapblv


%-------------------------------------------------------------------------
%
function [cmap] = set_colormap(max_value, min_value, thresh)
%
%   set the display colormap based on the max/min display values and 
%   the threshold setting.
%
%   The upper colors are coming from the entries of [140:239] of the 
%   255 jet colormap, and the lower colors are from the entries of 
%   [1:100] of the colormap.
%

   cmap = [];

   range_interval = max_value - min_value;
   upper_interval = max_value - thresh;
   lower_interval = abs(min_value) - thresh;
   
   %  colormap entries for the upper range values, using the
   %  entries of [140:239] from the 255 jet colormap
   %
   num_upper_colors = 0;
   if (upper_interval > 0)
      num_upper_colors = round(upper_interval / range_interval * 255); 
      cmap_size = round(255 * num_upper_colors/100);
      first_color_idx = round(140 / 255 * cmap_size);
      last_color_idx = first_color_idx + num_upper_colors - 1;
      uppermap = jet(cmap_size);
      upper_colors = uppermap(first_color_idx:last_color_idx,:);
   end;
   
   %  colormap entries for the lower range values, using the 
   %  entries of [1:100] from the 255 jet colormap
   %
   num_lower_colors = 0;
   if (lower_interval > 0)  
      num_lower_colors = round(lower_interval / range_interval * 255); 
      cmap_size = round(255 * num_lower_colors/100);
      first_color_idx = 1;
      last_color_idx = num_lower_colors;
      lowermap = jet(cmap_size);
      lower_colors = lowermap(first_color_idx:last_color_idx,:);
   end;
   
   ignore_pts = [num_lower_colors+1:255-num_upper_colors];

   if isempty(ignore_pts), return; end;

   cmap = zeros(256,3);
   cmap(1:255,:) = jet(255);
   
   if (num_lower_colors > 0),
     cmap(1:num_lower_colors,:) = lower_colors;
   end;
   if (num_upper_colors > 0),
     cmap(ignore_pts(end)+1:255,:) = upper_colors;
   end;
   
   cmap(ignore_pts,:) = ones(length(ignore_pts),3) * 140/255;
   cmap(256,:) = [1 1 1];
   
   return; 					% set_colormap


%--------------------------------------------------------------------------
function [range, bar_data] = create_colorbar(axes_hdl,cmap,min_range,max_range)

   tick_steps = (max_range - min_range) / (size(cmap,1) - 1);
   y_range = [min_range:tick_steps:max_range];
   range = [max_range:-tick_steps:min_range];
   
   axes(axes_hdl);
   img_h = image([0,1],[min_range max_range],[1:size(cmap,1)]');

   %  use true colour for the colour bar to make sure change of colormap
   %  won't affect it
   %
   bar_data = get(img_h,'CData');
   len = length(bar_data);
   cdata = zeros(len,1,3);
   for i=1:len,
     cdata(i,1,:) = cmap(bar_data(i),:);
   end;
   set(img_h,'CData',cdata);

   %  setup the axes property
%   set(axes_hdl, 'XTick',[],'XLim',[0 1], ...
%            'YLim',[min_range max_range], ...
%	    'YDir','normal', ...
%            'YAxisLocation','right');
   set(axes_hdl, 'XTick',[], ...
            'YLim',[min_range max_range], ...
	    'YDir','normal', ...
            'YAxisLocation','right');

   return;