Merge pull request #80 from roemervandermeij/partialrevertfix6c5d55e

Partially revert a previous revert

ft_electrodeplacement.m

@@ -357,8 +357,7 @@
     opt.handlesfigure = h;
     opt.handlesmarker = [];
     opt.quit          = false;
-    opt.ana           = dat; % this will be clipped
-    opt.org           = dat; % this will remain unclipped
+    opt.ana           = dat;
     opt.update        = [1 1 1];
     opt.init          = true;
     opt.tag           = 'ik';
@@ -456,7 +455,7 @@ function cb_redraw(h, eventdata)
 str1 = sprintf('voxel %d, index [%d %d %d]', sub2ind(mri.dim(1:3), xi, yi, zi), opt.ijk);
 
 if opt.init
-  ft_plot_ortho(opt.ana, 'transform', eye(4), 'location', opt.ijk, 'style', 'subplot', 'parents', [h1 h2 h3], 'update', opt.update, 'doscale', false);
+  ft_plot_ortho(opt.ana, 'transform', eye(4), 'location', opt.ijk, 'style', 'subplot', 'parents', [h1 h2 h3], 'update', opt.update, 'doscale', false,'clim', opt.clim);
 
   opt.anahandles = findobj(opt.handlesfigure, 'type', 'surface')';
   parenttag = get(opt.anahandles,'parent');
@@ -473,7 +472,7 @@ function cb_redraw(h, eventdata)
   opt.axis([1 3 5]) = 0.5;
   opt.axis([2 4 6]) = size(opt.ana) + 0.5;
 else
-  ft_plot_ortho(opt.ana, 'transform', eye(4), 'location', opt.ijk, 'style', 'subplot', 'surfhandle', opt.anahandles, 'update', opt.update, 'doscale', false);
+  ft_plot_ortho(opt.ana, 'transform', eye(4), 'location', opt.ijk, 'style', 'subplot', 'surfhandle', opt.anahandles, 'update', opt.update, 'doscale', false,'clim', opt.clim);
 
   if all(round([xi yi zi])<=mri.dim) && all(round([xi yi zi])>0)
     fprintf('==================================================================================\n');
@@ -955,11 +954,6 @@ function cb_minslider(h4, eventdata)
 h = getparent(h4);
 opt = getappdata(h, 'opt');
 opt.clim(1) = newlim;
-% re-apply the clipping to the original anatomy
-opt.ana = opt.org;
-opt.ana(opt.ana<opt.clim(1)) = opt.clim(1);
-opt.ana(opt.ana>opt.clim(2)) = opt.clim(2);
-opt.ana = opt.ana/(opt.clim(2)-opt.clim(1));
 fprintf('contrast limits updated to [%.03f %.03f]\n', opt.clim);
 setappdata(h, 'opt', opt);
 cb_redraw(h);
@@ -973,11 +967,6 @@ function cb_maxslider(h5, eventdata)
 h = getparent(h5);
 opt = getappdata(h, 'opt');
 opt.clim(2) = newlim;
-% re-apply the clipping to the original anatomy
-opt.ana = opt.org;
-opt.ana(opt.ana<opt.clim(1)) = opt.clim(1);
-opt.ana(opt.ana>opt.clim(2)) = opt.clim(2);
-opt.ana = opt.ana/(opt.clim(2)-opt.clim(1));
 fprintf('contrast limits updated to [%.03f %.03f]\n', opt.clim);
 setappdata(h, 'opt', opt);
 cb_redraw(h);

ft_volumerealign.m

@@ -326,7 +326,7 @@
       case 'ortho'
         % start building the figure
         h = figure;
-        set(h, 'color', [1 1 1]);
+        %set(h, 'color', [1 1 1]);
         set(h, 'visible', 'on');
 
         % axes settings
@@ -405,6 +405,36 @@
         markerlabel = {};
         markercolor = {};
 
+        % determine clim if empty (setting to [0 1] could be done at the top, but not sure yet if it interacts with the other visualizations -roevdmei)
+        if isempty(cfg.clim)
+          cfg.clim = [min(dat(:)) min([.5 max(dat(:))])]; % 
+        end
+
+        % intensity range sliders
+        h45text = uicontrol('Style', 'text',...
+          'String','Intensity',...
+          'Units', 'normalized', ...
+          'Position',[2*h1size(1)+0.03 h3size(2)+0.03 h1size(1)/4 0.04],...
+          'HandleVisibility','on');
+
+        h4 = uicontrol('Style', 'slider', ...
+          'Parent', h, ...
+          'Min', 0, 'Max', 1, ...
+          'Value', cfg.clim(1), ...
+          'Units', 'normalized', ...
+          'Position', [2*h1size(1)+0.02 0.10+h3size(2)/3 0.05 h3size(2)/2], ...
+          'Callback', @cb_minslider);
+
+        h5 = uicontrol('Style', 'slider', ...
+          'Parent', h, ...
+          'Min', 0, 'Max', 1, ...
+          'Value', cfg.clim(2), ...
+          'Units', 'normalized', ...
+          'Position', [2*h1size(1)+0.07 0.10+h3size(2)/3 0.05 h3size(2)/2], ...
+          'Callback', @cb_maxslider);
+
+
+        % instructions to the user
         fprintf(strcat(...
           '1. To change the slice viewed in one plane, either:\n',...
           '   a. click (left mouse) in the image on a different plane. Eg, to view a more\n',...
@@ -431,7 +461,7 @@
         opt.handlesaxes   = [h1 h2 h3];
         opt.handlesfigure = h;
         opt.quit          = false;
-        opt.ana           = dat;
+        opt.ana           = dat; 
         opt.update        = [1 1 1];
         opt.init          = true;
         opt.tag           = 'ik';
@@ -1495,3 +1525,33 @@ function cb_cleanup(h, eventdata)
 if ~isempty(eventdata.Modifier)
   key = [eventdata.Modifier{1} '+' key];
 end
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% SUBFUNCTION
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function cb_minslider(h4, eventdata)
+
+newlim = get(h4, 'value');
+h = getparent(h4);
+opt = getappdata(h, 'opt');
+opt.clim(1) = newlim;
+fprintf('contrast limits updated to [%.03f %.03f]\n', opt.clim);
+setappdata(h, 'opt', opt);
+cb_redraw(h);
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% SUBFUNCTION
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function cb_maxslider(h5, eventdata)
+
+newlim = get(h5, 'value');
+h = getparent(h5);
+opt = getappdata(h, 'opt');
+opt.clim(2) = newlim;
+fprintf('contrast limits updated to [%.03f %.03f]\n', opt.clim);
+setappdata(h, 'opt', opt);
+cb_redraw(h);
+
+
+

plotting/ft_plot_ortho.m

@@ -74,11 +74,6 @@
   dat = cast(dat, 'double');
 end
 
-if ~isempty(clim)
-  % clip the data between the color limits
-  dat(dat<clim(1)) = clim(1);
-  dat(dat>clim(2)) = clim(2);
-end
 
 % determine the orientation key-value pair
 keys = varargin(sellist(1:2:end));
@@ -158,13 +153,13 @@
       hold on
     end
 
-    varargin{sel+1} = ori(1,:);
+    varargin{2*sel} = ori(1,:);
     hx = ft_plot_slice(dat, varargin{:});
 
-    varargin{sel+1} = ori(2,:);
+    varargin{2*sel} = ori(2,:);
     hy = ft_plot_slice(dat, varargin{:});
 
-    varargin{sel+1} = ori(3,:);
+    varargin{2*sel} = ori(3,:);
     hz = ft_plot_slice(dat, varargin{:});
     axis equal; axis tight; axis off;axis vis3d
     view(3);

plotting/ft_plot_slice.m

@@ -23,7 +23,7 @@
 %   'interpmethod' = string specifying the method for the interpolation, see INTERPN (default = 'nearest')
 %   'style'        = string, 'flat' or '3D'
 %   'colormap'     = string, see COLORMAP
-%   'colorlim'     = 1x2 vector specifying the min and max for the colorscale
+%   'clim'         = 1x2 vector specifying the min and max for the colorscale
 %
 % See also FT_PLOT_ORTHO, FT_PLOT_MONTAGE, FT_SOURCEPLOT