Image3DIsosurface: add support for label images (through the regionIsosurfaces method)

Author: dlegland

ImageM/+imagem/+actions/+view/Image3DIsosurface.m

@@ -37,17 +37,19 @@ function run(obj, frame) %#ok<INUSL>
 
         % get handle to current doc
         doc = currentDoc(frame);
+        img = doc.Image;
 
         % check image size
-        img = doc.Image;
         if size(img, 3) == 1
             return;
         end
 
         % creates a new dialog, and populates it with some fields
         gd = imagem.gui.GenericDialog('3D Isosurface');
 
-        addNumericField(gd, 'Isosurface Value', 50, 2);
+        if ~isLabelImage(img)
+            addNumericField(gd, 'Isosurface Value', 50, 2);
+        end
         addNumericField(gd, 'Smoothing Radius (voxels)', 2, 0);
         addCheckBox(gd, 'Reverse Z-axis', false);
         addCheckBox(gd, 'Rotate Ox', false);
@@ -59,7 +61,10 @@ function run(obj, frame) %#ok<INUSL>
             return;
         end
 
-        isosurfaceValue = getNextNumber(gd);
+        % parse user inputs
+        if ~isLabelImage(img)
+            isosurfaceValue = getNextNumber(gd);
+        end
         smoothRadius    = getNextNumber(gd);
         reverseZAxis    = getNextBoolean(gd);
         rotateXAxis     = getNextBoolean(gd);
@@ -70,27 +75,40 @@ function run(obj, frame) %#ok<INUSL>
             img = rotate90(img, 'x', 1);
         end
 
-        if smoothRadius > 0
-            disp('% smoothing...');
-            siz = floor(smoothRadius * 2) + 1;
-            img = gaussianFilter(img, siz, smoothRadius);
-        end
-
-        
-        % eventually rotate image around X-axis
-        if rotateXAxis
-            img = flip(rotate90(img, 'x', 1), 2);
-        end
-        
-        % create figure 
+        % create figure
         hf = figure(); hold on;
         set(hf, 'renderer', 'opengl');
-        isosurface(img, isosurfaceValue);
+
+        if ~isLabelImage(img)
+            % smooth grayscale / intensities
+            if smoothRadius > 0
+                disp('% smoothing...');
+                siz = floor(smoothRadius * 2) + 1;
+                img = gaussianFilter(img, siz, smoothRadius);
+            end
+            
+            % compute isosurface of grayscale/intensity values
+            isosurface(img, isosurfaceValue);
+            
+        else
+            % For label images, call the specific regionIsosurfaces
+            [meshes, labels] = regionIsosurfaces(img, 'smoothRadius', smoothRadius);
+            
+            % display each mesh with color specified by colormap of doc
+            colors = doc.ColorMap;
+            for iLabel = 1:length(meshes)
+                label = labels(iLabel);
+                p = patch(meshes{iLabel});
+                color = colors(label, :);
+                set(p, 'FaceColor', color, 'LineStyle', 'none');
+            end
+        end
 
         % setup display
         axis equal;
         axis(physicalExtent(img));
         axis('vis3d'); view(3);
+        set(hf, 'Name', sprintf('%s-isosurface', img.Name));
         light;
 
         if rotateXAxis || reverseZAxis
@@ -110,8 +128,11 @@ function run(obj, frame) %#ok<INUSL>
         end
 
         % add history
-%         string = sprintf('showOrthoSlices(%s, [%d %d %d]);\n', doc.Tag, pos);
-        string = sprintf('isosurface(%s, %g);\n', doc.Tag, isosurfaceValue);
+        if ~isLabelImage(img)
+            string = sprintf('isosurface(%s, %g);\n', doc.Tag, isosurfaceValue);
+        else
+            string = sprintf('%% isosurface of label image %s\n', doc.Tag);
+        end
         addToHistory(frame, string);
     end
 

ImageM/+imagem/+app/ImageDoc.m

@@ -27,6 +27,8 @@
     % Display range info are managed within the ImageViewer class.
 
     % Look-up table (colormap) used for displaying the image. 
+    % Uses 256 values for grayscale/intensity images, and label number for
+    % label images.
     % If empty -> no lut
     ColorMap = [];
 

ImageM/+imagem/+app/ImagemDoc.m

@@ -7,11 +7,11 @@
 %   ImagemDoc
 %
 %   See also
-%
+%     ImageDoc, TableDoc
 
 % ------
 % Author: David Legland
-% e-mail: david.legland@inra.fr
+% e-mail: david.legland@inrae.fr
 % Created: 2011-10-22,    using Matlab 7.9.0.529 (R2009b)
 % Copyright 2011 INRA - Cepia Software Platform.