Greatly improve the performance of plotting and responsiveness of plots.

We now plot the cell many contours as a single patch object relying
on the special low-level syntax of patch.

src/@deproj/deproj.m

@@ -31,6 +31,9 @@ classdef deproj
         % Returns the faces and vertices of a deproj collection.
         [ V, F ] = to_vertices_and_faces( obj )
         
+        % Returns the cells boundary polygons as 3 matrices padded by NaNs.
+        [ X, Y, Z ] = to_matrices( obj )
+
         %% Generate figures.
         
         % Figure with the local tissue orientation for a collection of epicells.

src/@deproj/plot_values_contour.m

@@ -5,22 +5,24 @@ function hts = plot_values_contour( obj, values, ax )
 %   obj: a deproj object, with N epicells.
 %   values - a N x 1 array with values to use for coloring.
 %   ax - the axes to plot in.
-% 
+%
 % OUTPUT:
-%   a N x 1 array of handles to the cell polygon objects.
-    
+%   the handle to the cells patch object.
+
     epicells = obj.epicells;
     boundaries = { epicells.boundary };
-    n_objects = numel( boundaries );    
-    hts = NaN( n_objects, 1 );
-    
+
+    n_objects = numel( boundaries );
     if n_objects > 1000, lw = 1; else, lw = 2; end
-    
-    for i = 1 :  n_objects
 
-        p = boundaries{ i };
-        val = values( i );
-        hts(i ) = patch( ax, p(:,1), p(:,2), p(:,3), val, ...
-            'LineWidth', lw );
-    end
+    [ X, Y, Z ] = obj.to_matrices();
+    hts = patch( ...
+        'XData', X, ...
+        'YData', Y, ...
+        'ZData', Z, ...
+        'FaceVertexCData', values, ...
+        'FaceColor', 'flat', ...
+        'LineWidth', lw, ...
+        'Parent', ax );
+
 end

src/@deproj/to_matrices.m

+function [ X, Y, Z ] = to_matrices( obj )
+%TO_MATRICES Returns the cells boundary polygons as 3 matrices padded by NaNs.
+
+    n_obj = numel( obj.epicells );
+    
+    boundaries = { obj.epicells.boundary }';
+    n_points = cellfun( @(c) size(c,1), boundaries );
+    max_n_poins = max( n_points );
+    
+    % 1 column per polygon.
+    X = zeros( max_n_poins + 1, n_obj );
+    Y = zeros( max_n_poins + 1, n_obj );
+    Z = zeros( max_n_poins + 1, n_obj );
+    
+    for i = 1 : n_obj
+        
+        P = boundaries{ i };
+        np = n_points(i);
+        X( 1 : np, i ) = P( : , 1 );
+        Y( 1 : np, i ) = P( : , 2 );
+        Z( 1 : np, i ) = P( : , 3 );
+    
+        X( np + 1 : end, i ) = P( 1 , 1 );
+        Y( np + 1 : end, i ) = P( 1 , 2 );
+        Z( np + 1 : end, i ) = P( 1 , 3 );
+
+    end
+
+end
+