pet_plot_datamatcorrs.m

绝对经典,老外制作的功能强大的matlab实现PLS_TOOBOX

         pls_contrasts(i).name = sprintf('Contrast #%d',i);
         pls_contrasts(i).value = helmert_contrasts(:,i)';
      end;
   else
      try
         load(contrast_file);
      catch 
         msg = sprintf('ERROR: Cannot open contrast file "%s".',contrast_file); 
         set(findobj(gcf,'Tag','MessageLine'),'String',msg);
         return;
      end;
   end;

   contrast_fig = pls_input_contrast_ui(pls_contrasts,conditions,1);

   link_info.hdl = gcbf;
   link_info.name = 'ContrastFigHdl';
   setappdata(contrast_fig,'LinkFigureInfo',link_info);
   setappdata(gcbf,'ContrastFigHdl',contrast_fig);

   return;					% OpenContrastWindow


%-------------------------------------------------------------------------
%
function plot_bs_ratio(PLSresultFile,lv_idx,slice_idx,thresh,range,new_fig)
%
  if (new_fig)
     bg_img = getappdata(gcbf,'BackgroundImg');
     rot_amount = getappdata(gcbf,'RotateAmount');
  else
     bg_img = getappdata(gcf,'BackgroundImg');
     rot_amount = getappdata(gcf,'RotateAmount');
  end;

%  load(PLSresultFile,'boot_result','dims','st_win_size','st_coords', ...
%		     'st_voxel_size','st_origin');
  load(PLSresultFile,'boot_result','dims','st_win_size','st_coords', ...
		     'st_voxel_size','st_origin');
  bs_ratio = boot_result.compare;

  if ~exist('slice_idx','var')
     slice_idx = [1:slices];
  end
  num_slices = length(slice_idx);

  num_lv = size(bs_ratio,2);

  min_ratio = min(bs_ratio(:,lv_idx));
  max_ratio = max(bs_ratio(:,lv_idx));
  if ~exist('range','var') | isempty(range)
     if (abs(min_ratio) > abs(max_ratio)),
       max_ratio = abs(min_ratio);
     else
       min_ratio = -1 * max_ratio;
     end
     range = [min_ratio max_ratio];
  else
     min_ratio = range(1);
     max_ratio = range(2);
  end

  if ~exist('thresh','var') | isempty(thresh)
     thresh = (abs(max_ratio) + abs(min_ratio)) / 6;
  end

  h = findobj(gcf,'Tag','BSThreshold');  set(h,'String',num2str(thresh));
  h = findobj(gcf,'Tag','MaxRatio');   set(h,'String',num2str(max_ratio));
  h = findobj(gcf,'Tag','MinRatio');   set(h,'String',num2str(min_ratio));

  win_size = st_win_size;

  if (mod(rot_amount,2) == 0)
    img_height = dims(1);		  % rows
    img_width  = dims(2);
  else
    img_height = dims(2);		  % rows - after 90 or 270 rotation
    img_width  = dims(1);
  end;

  mont_height = win_size * img_height;
  mont_width = num_slices * img_width;


  %  construct the bootstrap ratio images
  %
  ratio_imgs = zeros(win_size*img_height,mont_width);
  first_rows = 1; last_rows = img_height;
  for i=1:win_size,
     bsr = bs_ratio(i:win_size:end,lv_idx);

     [img,cmap,cbar] = fmri_plot_brainlv(bsr,st_coords,dims,slice_idx, ...
                                    thresh,range,rot_amount,bg_img);
     ratio_imgs(first_rows:last_rows,:) = reshape(img,[img_height, mont_width]);
     first_rows = last_rows + 1; last_rows = first_rows + img_height - 1;
  end;

  %  display the images
  %
  if (new_fig)
      [axes_hdl,colorbar_hdl] = create_new_blv_figure;
  else
      axes_hdl = getappdata(gcf,'BlvAxes');
%      colorbar_hdl = getappdata(gcf,'Colorbar');
  end;

  axes(axes_hdl);
  h_img = image(ratio_imgs);
  set(h_img,'Tag','BLVImg');
  colormap(cmap);

  set(gca,'tickdir','out','ticklength',[0.001 0.001]);
  set(gca,'xlabel',text('String','Slice','FontSize',10,'Interpreter','none'));
  set(gca,'xtick',[img_width/2:img_width:mont_width]);
  set(gca,'xticklabel',slice_idx);
  set(gca,'ylabel',text('String','Lag','FontSize',10,'Interpreter','none'));
  set(gca,'ytick',[img_height/2:img_height:mont_height]);
  set(gca,'yticklabel',[0:win_size-1]);

  if (new_fig)
%     pet_create_colorbar(colorbar_hdl,cbar,min_ratio,max_ratio);
     return;
  end;

  set(h_img,'ButtonDownFcn','pet_plot_datamatcorrs(''SelectPixel'')');
%  pet_create_colorbar( colorbar_hdl, cbar, min_ratio, max_ratio );


  %  save the attributes of the current image
  %
  setappdata(gcf,'Dims',dims);
  setappdata(gcf,'VoxelSize',st_voxel_size);
  setappdata(gcf,'Origin',st_origin);
  setappdata(gcf,'WinSize',win_size);
  setappdata(gcf,'SliceIdx',slice_idx);
  setappdata(gcf,'ImgHeight',img_height);
  setappdata(gcf,'ImgWidth',img_width);
  setappdata(gcf,'ImgRotateFlg',1);
  setappdata(gcf,'NumLVs',num_lv);
  setappdata(gcf,'BSRatio',bs_ratio);
  setappdata(gcf,'BSRatioCoords',st_coords);
  setappdata(gcf,'BSThreshold',thresh);
  setappdata(gcf,'RotateAmount',rot_amount);

  return;					% plot_bs_ratio

%-------------------------------------------------------------------------
%
function SaveResultToIMG(is_disp)
%

  h = findobj(gcf,'Tag','ResultFile'); PLSresultFile = get(h,'Userdata');

  try 				% load the dimension info of the st_datamat
     load(PLSresultFile,'dims'),
  catch
     msg =sprintf('ERROR: Cannot load the PET result file "%s".',PLSresultFile);
     set(findobj(gcf,'Tag','MessageLine'),'String',msg);
     return;
  end;

  h = findobj(gcf,'Tag','LVIndexEdit');  lv_idx = get(h,'Userdata');
  curr_lv_idx = getappdata(gcf,'CurrLVIdx');
  if (lv_idx ~= curr_lv_idx),
     lv_idx = curr_lv_idx;
     set(h,'String',num2str(lv_idx));
  end;

  h = findobj(gcf,'Tag','GroupIndexEdit');  grp_idx = get(h,'Userdata');
  curr_grp_idx = getappdata(gcf,'CurrGroupIdx');
  if (grp_idx ~= curr_grp_idx),
     grp_idx = curr_grp_idx;
     set(h,'String',num2str(grp_idx));
  end;

  h = findobj(gcf,'Tag','BehavIndexEdit');  behav_idx = get(h,'Userdata');
  curr_behav_idx = getappdata(gcf,'CurrBehavIdx');
  if (behav_idx ~= curr_behav_idx),
     behav_idx = curr_behav_idx;
     set(h,'String',num2str(behav_idx));
  end;

  old_pointer = get(gcf,'Pointer');
  fig_hdl = gcf;
  set(fig_hdl,'Pointer','watch');

  if 1 % (getappdata(gcf,'ViewBootstrapRatio') == 0),	% save brain lv
     thresh = getappdata(gcf,'BLVThreshold');
     if is_disp
        create_brainlv_disp(PLSresultFile,lv_idx,thresh,grp_idx,behav_idx);
     else
        create_brainlv_img(PLSresultFile,lv_idx,thresh,grp_idx,behav_idx);
     end

  else							% save bootstrap ratio
     thresh_ratio = getappdata(gcf,'BSThreshold');
     create_bs_ratio_img(PLSresultFile,lv_idx,thresh_ratio);
  end;

  set(fig_hdl,'Pointer',old_pointer);

  return;					% SaveResultToIMG


%--------------------------------------------------------------------------
function create_brainlv_disp(PLSresultFile,lv_idx,thresh_ratio,grp_idx,behav_idx);

  %  get the output IMG filename first  
  %
  [pn fn] = fileparts(PLSresultFile);
  resultfile_prefix = fn(1:end-9);

  image_fn = sprintf('%sPETdatcorr_disp_grp%d_cond%d_beh%d.img',resultfile_prefix,grp_idx,lv_idx,behav_idx);

  [filename, pathname] = uiputfile(image_fn,'Datamat Correlation IMG file');

  img_file = [pathname, filesep, filename];

  if isequal(filename,0)
      return;
  end;

  %  load the result file
  %
  load(PLSresultFile,'dims','newcoords','voxel_size','origin');

  dims = dims([1 2 4]);

  blv = getappdata(gcbf,'BLVData');
  brainlv = blv{grp_idx, behav_idx};

  %  save background to img
  %
  brainlv = brainlv(:,lv_idx);


   bs = getappdata(gcbf,'BSRatio');
   h = findobj(gcf,'Tag','BSLVIndexEdit'); bs_lv_idx = str2num(get(h,'String'));
   h = findobj(gcf,'Tag','BSThreshold'); bs_thresh = str2num(get(h,'String'));
   bs = bs(:, bs_lv_idx);
   bs_strong = zeros(size(bs));
   bs_idx = [find(bs <=- bs_thresh); find(bs >= bs_thresh)];
   bs_strong(bs_idx) = 1;
   brainlv = brainlv .* bs_strong;


  bg_img = getappdata(gcf,'BackgroundImg');
  cmap = getappdata(gcf,'cmap');
  num_blv_colors = 25;
  brain_region_color_idx = 51;
  first_lower_color_idx = 101;
  first_upper_color_idx = 126;
  h = findobj(gcf,'Tag','MaxValue'); max_blv = str2num(get(h,'String'));
  h = findobj(gcf,'Tag','MinValue'); min_blv = str2num(get(h,'String'));
  too_large = find(brainlv > max_blv); brainlv(too_large) = max_blv;
  too_small = find(brainlv < min_blv); brainlv(too_small) = min_blv;

  % Create the image slices in which voxels are set to be within certain range
  %
  lower_interval = (abs(min_blv) - thresh_ratio) / (num_blv_colors-1);
  upper_interval = (max_blv - thresh_ratio) / (num_blv_colors-1);

  blv = zeros(1,length(newcoords)) + brain_region_color_idx;
  lower_idx = find(brainlv <= -thresh_ratio);
  blv_offset = brainlv(lower_idx) - min_blv; 
  lower_color_idx = round(blv_offset/lower_interval)+first_lower_color_idx;
  blv(lower_idx) = lower_color_idx;

  upper_idx = find(brainlv >= thresh_ratio);
  blv_offset = max_blv - brainlv(upper_idx); 
  upper_color_idx = num_blv_colors - round(blv_offset/upper_interval);
  upper_color_idx = upper_color_idx + first_upper_color_idx - 1;
  blv(upper_idx) = upper_color_idx;

  if isempty(bg_img)
     non_brain_region_color_idx = size(cmap,1);
     img = zeros(1,dims(1)*dims(2)*dims(3)) + non_brain_region_color_idx;
     img(newcoords) = blv;
     img = reshape(img,dims); 
  else
     max_bg = max(bg_img(:));
     min_bg = min(bg_img(:));
     img = (bg_img - min_bg) / (max_bg - min_bg) * 100;
     img(newcoords(lower_idx)) = blv(lower_idx);
     img(newcoords(upper_idx)) = blv(upper_idx);
     img = reshape(img,dims); 
  end

%  img = zeros(dims);

%  blv = brainlv(1,lv_idx); 
%  blv(abs(blv) < thresh_ratio) = 0;

%  img(newcoords) = blv;

  descrip = sprintf('DatamatCorrelation from %s, Group: %d, Condition: %d, Behavior: %d, Threshold: %8.5f', ...
		PLSresultFile,grp_idx,lv_idx,behav_idx,thresh_ratio);
  rri_write_img(filename,img,0,dims,voxel_size,16,origin,descrip);

  %  save background to img
  %
  [tmp filename] = fileparts(filename);
  save(filename,'cmap');

  return;					% create_brainlv_disp


%--------------------------------------------------------------------------
function create_brainlv_img(PLSresultFile,lv_idx,thresh_ratio,grp_idx,behav_idx);

  %  get the output IMG filename first  
  %
  [pn fn] = fileparts(PLSresultFile);
  resultfile_prefix = fn(1:end-9);

  image_fn = sprintf('%sPETdatcorr_grp%d_cond%d_beh%d.img',resultfile_prefix,grp_idx,lv_idx,behav_idx);

  [filename, pathname] = uiputfile(image_fn,'Datamat Correlation IMG file');

  img_file = [pathname, filesep, filename];

  if isequal(filename,0)
      return;
  end;

  %  load the result file
  %
  load(PLSresultFile,'dims','newcoords','voxel_size','origin');

  dims = dims([1 2 4]);
  img = zeros(dims);

  blv = getappdata(gcbf,'BLVData');
  brainlv = blv{grp_idx, behav_idx};

  blv = brainlv(:,lv_idx); 


   bs = getappdata(gcbf,'BSRatio');
   h = findobj(gcf,'Tag','BSLVIndexEdit'); bs_lv_idx = str2num(get(h,'String'));
   h = findobj(gcf,'Tag','BSThreshold'); bs_thresh = str2num(get(h,'String'));
   bs = bs(:, bs_lv_idx);
   bs_strong = zeros(size(bs));
   bs_idx = [find(bs <=- bs_thresh); find(bs >= bs_thresh)];
   bs_strong(bs_idx) = 1;
   blv = blv .* bs_strong;


  blv(abs(blv) < thresh_ratio) = 0;

  img(newcoords) = blv;

  descrip = sprintf('DatamatCorrelation from %s, Group: %d, Condition: %d, Behavior: %d, Threshold: %8.5f', ...
		PLSresultFile,grp_idx,lv_idx,behav_idx,thresh_ratio);
  rri_write_img(filename,img,0,dims,voxel_size,16,origin,descrip);

  return;					% create_brainlv_img


%--------------------------------------------------------------------------
function create_bs_ratio_img(PLSresultFile,lv_idx,thresh_ratio);

  %  get the output IMG filename first  
  %
  [pn fn] = fileparts(PLSresultFile);
  resultfile_prefix = fn(1:end-9);
  image_fn = [resultfile_prefix, 'PETbsr.img'];

  [filename, pathname] = uiputfile(image_fn,'Bootstrap Result IMG file');

  img_file = [pathname, filesep, filename];

  if isequal(filename,0)
      return;
  end;

  %  load the result file
  %
  load(PLSresultFile,'boot_result','dims','newcoords','voxel_size','origin');

  bs_ratio = boot_result.compare;

  dims = dims([1 2 4]);
  img = zeros(dims);

  bsr = bs_ratio(1,lv_idx); 
  bsr(abs(bsr) < thresh_ratio) = 0;

  img(newcoords) = bsr;

  descrip = sprintf('Bootstrap Ratio from %s, LV: %d, Threshold: %8.5f', ...
				           PLSresultFile,lv_idx,thresh_ratio);
  rri_write_img(filename,img,0,dims,voxel_size,16,origin,descrip);

  return;					% create_bs_ratio_img


%--------------------------------------------------------------------------
function [st_filename] = get_st_datamat_filename(DatamatFileList,with_path)
%
%   INPUT:
%       DatamatFileList - vector of cell structure, each element contains
%                         the full path of a session file.
%       with_path - whether including path in the constructed the filename
%                   of the st_datamat. 
%		    with_path = 0 : no path 
%		    with_path = 1 : including path
%
  num_files = length(DatamatFileList);
  st_filename = cell(1,num_files);

  for i=1:num_files,
     load( DatamatFileList{i} );
     if with_path,
       st_filename{i} = sprintf('%s/%s_st_datamat.mat', ...
                     session_info.pls_data_path, session_info.datamat_prefix);
     else
       st_filename{i} = sprintf('%s_st_datamat.mat', ...
                                                 session_info.datamat_prefix);
     end;
  end;

  return;					% get_st_datamat_name


%--------------------------------------------------------------------------
%
function ToggleView(view_state)

   if ~exist('view_state','var') | isempty(view_state),
      view_state = ~(getappdata(gcf,'ViewBootstrapRatio'));
   end;

   if (view_state == 0)			% view brain lv
      setappdata(gcf,'ViewBootstrapRatio',0);
      bs_visibility = 'off';
   else					% view bootstrap ratio
      setappdata(gcf,'ViewBootstrapRatio',1);
      bs_visibility = 'on';
   end;

   %  set visibility of the bootstrap fields
   %
   set(findobj(gcf,'Tag','BSLVIndexLabel'),'enable',bs_visibility);
   set(findobj(gcf,'Tag','BSLVIndexEdit'),'enable',bs_visibility);
   set(findobj(gcf,'Tag','BSLVNumberLabel'),'enable',bs_visib