Apply the same performance tweak to the ellipse plot.

We plot all ellipses as single patch, but this time we color the
vertices. A bit different, but still very instructive. It also turns
out it works very well. Also simplifies and shortens the code.

src/@deproj/deproj.m

@@ -64,7 +64,7 @@ classdef deproj
         hts = plot_values_contour( obj, values, ax )
         
         % Plot the tissue with cells as ellipses, colored by the specified values.
-        hts = plot_values_ellipse( obj, values, cmap, ax, min_val_col, max_val_col )
+        hts = plot_values_ellipse( obj, values, ax )
                 
     end
     

src/@deproj/figure_cell_elongation.m

@@ -10,13 +10,13 @@ function [ hf, ax1, ax2 ] = figure_cell_elongation( obj, scale_bar_length )
     %% Direction.
     
     ax1 = subplot( 2, 1, 1 );
-    cmap1 = 'hsv';
-    colormap( cmap1 )
+    colormap( 'hsv' )
     hold on
     axis equal
     
     values1 = rad2deg( [ obj.epicells.proj_direction ]' );
-    obj.plot_values_ellipse( values1, cmap1, ax1, -90, 90 );
+    obj.plot_values_ellipse( values1, ax1 );
+    set( ax1, 'CLim', [ -90 90 ] )
 
     axis( ax1, 'off' )
     colorbar( ax1 )
@@ -31,8 +31,9 @@ function [ hf, ax1, ax2 ] = figure_cell_elongation( obj, scale_bar_length )
     axis equal
     
     values2 = [ obj.epicells.eccentricity ]';
-    cmap2 = 'parula';
-    obj.plot_values_ellipse( values2, cmap2, ax2, 0, 1 );
+    obj.plot_values_ellipse( values2, ax2 );
+    set( ax2, 'CLim', [ 0 1 ] )
+    colormap(ax2, 'parula' );
 
     axis( ax2, 'off' )
     colorbar( ax2 )
@@ -42,8 +43,7 @@ function [ hf, ax1, ax2 ] = figure_cell_elongation( obj, scale_bar_length )
     
     
     add_plot_scalebar(  obj, scale_bar_length, ax2 );
-
-
+    linkaxes( [ ax1 ax2 ] )
 
 end
 

src/@deproj/plot_values_ellipse.m

-function hts = plot_values_ellipse( obj, values, cmap, ax, min_val_col, max_val_col )
+function hts = plot_values_ellipse( obj, values, ax )
 %PLOT_VALUES_ELLIPSE Plot the tissue with cells as ellipses, colored by the specified values.
 %
 % INPUTS:
@@ -7,64 +7,53 @@ function hts = plot_values_ellipse( obj, values, cmap, ax, min_val_col, max_val_
 %
 %   values - a N x 1 array with values to use for coloring.
 %
-%   cmap - the color-map to use for coloring. Optional, default value id
-% the parula colormap.
-%
 %   ax - the axes to plot in. Optional, default is current axes.
 %
-%   min_val_col - min value to generate color. Optional, default is the
-% minimal value of the specified values.
-%
-%   max_val_col - max value to generate color. Optional, default is the
-% maximal value of the specified values.
-%   
 % OUTPUT:
 %
-%   a 2N x 1 array of handles to the ellipse and major-axis line objects.
+%   the handle to the ellipse patch object.
 %
 
     epicells = obj.epicells;
     n_objects = numel( epicells );
-    hts = NaN( 2 * n_objects, 1 );
-
-    minv = min( values );
-    maxv = max( values );
     
-    if nargin < 3
-        cmap = 'parula';
-    end
     if nargin < 4
         ax = gca;
     end
-    if nargin < 5
-        min_val_col = minv;
-    end
-    if nargin < 6
-        max_val_col = maxv;
-    end
-       
-    colors = colormap( ax, cmap );
+    
+    n_points = 21;
+    X = zeros( n_points + 2, n_objects );
+    Y = zeros( n_points + 2, n_objects );
+    Z = zeros( n_points + 2, n_objects );
+    V = zeros( ( n_points + 2 ) * n_objects, 1 );
     
     if n_objects > 1000, lw = 1; else, lw = 2; end
 
-    idx = @(v) 1 + round( (v - min_val_col)/(max_val_col - min_val_col)  * ( size( colors, 1 ) - 1 ) );
+    index = 1;
+    mid = ceil( n_points / 2 );
     for i = 1 :  n_objects
 
         o = epicells( i );
-        h1 =  o.plot_ellipse_3d( 23, ax );
-        h2 =  o.plot_ellipse_3d( 3, ax );
+        p = o.get_ellipse_points( n_points );        
+        xp = p( :, 1 );
+        yp = p( :, 2 );
+        zp = p( :, 3 );
+        
+        X( 1 : n_points + 2, i ) = [ xp ; xp( mid ) ];
+        Y( 1 : n_points + 2, i ) = [ yp ; yp( mid ) ];
+        Z( 1 : n_points + 2, i ) = [ zp ; zp( mid ) ];
+        V( index : index + n_points + 1 ) = values( i );
+        index = index + n_points + 2;
 
-        hts( 2 * i - 1 ) =  h1;
-        hts( 2 * i ) =  h2;
-        val = values( i );
-        j = idx( val );
-        j = max( [ 1 j ] );
-        j = min( [ size( colors, 1 ) j ] );
-        set( [ h1 h2 ], ...
-            'Color', colors( j, : ), ...
-            'LineWidth', lw )
     end
     
-    set( ax, 'CLim', [ min_val_col max_val_col ] )
-    
+    hts = patch( ...
+        'XData', X, ...
+        'YData', Y, ...
+        'ZData', Z, ...
+        'FaceVertexCData', V, ...
+        'EdgeColor', 'flat', ...
+        'FaceColor', 'none', ...
+        'LineWidth', lw, ...
+        'Parent', ax );
 end