Plotting routines relying on the new epicell class.

src/add_plot_euler_alpha.m

+function hts = add_plot_euler_alpha( ax, epicells )
+%ADD_PLOT_EULER_ALPHA Add the tissue plot colored with the 1st euler angle.
+    
+    angles = vertcat( epicells.euler_angles );
+    alphas = rad2deg( angles( :, 1 ) );
+    
+    % Wrap back to 0 - 180º.
+    neg_alphas = alphas < 0;
+    alphas( neg_alphas ) = 180 + alphas( neg_alphas );
+
+    hts = add_plot_variable( ax, { epicells.boundary }, alphas );
+end
+

src/add_plot_euler_beta.m

+function hts = add_plot_euler_beta( ax, epicells )
+%ADD_PLOT_EULER_BETA Add the tissue plot colored with the 2nd euler angle.
+    
+    angles = vertcat( epicells.euler_angles );
+    betas = rad2deg( angles( :, 2 ) );
+    
+    % Wrap back to 0 - 90º.
+    large_betas = betas > 90;
+    betas( large_betas ) = 180 - betas( large_betas );
+
+    hts = add_plot_variable( ax, { epicells.boundary }, betas );
+end
+

src/add_plot_euler_gamma.m

+function hts = add_plot_euler_gamma( ax, epicells )
+%ADD_PLOT_EULER_GAMMA Add the tissue plot colored with the 3rd euler angle.
+    
+    angles = vertcat( epicells.euler_angles );
+    gammas = rad2deg( angles( :, 3 ) );
+    hts = add_plot_variable( ax, { epicells.boundary }, gammas );
+end
+

src/add_plot_id.m

+function hts = add_plot_id( epicells, ax )
+%ADD_PLOT_ID Add the epicell ids to the specified plot axes.
+
+    n_objects = numel( epicells );
+    hts = NaN( n_objects, 1 );
+    
+    for i = 1 :  n_objects
+        o = objects( i );
+        hts(i ) = text( ax,  o.center(1), o.center(2), o.center(3) + 0.5, num2str( o.id ), ...
+            'HorizontalAlignment', 'center', ...
+            'VerticalAlignment', 'middle' );
+    end
+end
+

src/add_plot_scalebar.m

+function [ hsb, ht ] = add_plot_scalebar( ax, epicells, length, units )
+%ADD_PLOT_SCALEBAR Add a scale-bar to the plot.
+%   We used the collection of epicells to determine a sensible position.
+
+    POS_RATIO = 0.10; % of width to position the bar
+    THICKNESS_RATIO = 0.02;
+
+    p = vertcat( epicells.boundary );
+    minp = double( min( p ) );
+    maxp = double( max( p ) );
+    rangep = maxp - minp;
+    
+    xpos = minp(1) + POS_RATIO * rangep( 1 );
+    ypos = minp(2) - POS_RATIO * rangep( 2 );
+    
+    thickness = THICKNESS_RATIO * rangep( 2 );
+    
+    xs = [
+        xpos            % 1
+        xpos            % 2
+        xpos + length   % 3
+        xpos + length   % 4
+        xpos + length   % 5
+        xpos + length   % 6
+        xpos            % 7
+        xpos            % 8    
+        ];
+
+    ys = [
+        ypos                        % 1
+        ypos + 0.25 * thickness     % 2
+        ypos + 0.25 * thickness     % 3
+        ypos                        % 4
+        ypos +  thickness           % 5
+        ypos + 0.75 * thickness     % 6
+        ypos + 0.75 * thickness     % 7
+        ypos +  thickness           % 8
+        ];
+    
+    zs = repmat( maxp(3), 8, 1 );
+    
+    hsb = patch( ax, xs, ys, zs, 'k' );
+    ht = text( mean(xs), min(ys), mean(zs), ...
+        sprintf('%.0f %s', length, units ), ...
+        'HorizontalAlignment', 'center', ...
+        'VerticalAlignment', 'top' );
+    
+end
+

src/add_plot_variable.m

+function hts = add_plot_variable( ax, boundaries, values )
+%ADD_PLOT_VARIABLE Plots the boundaries as patches, colored by the specified values.
+    
+    n_objects = numel( boundaries );
+    hts = NaN( n_objects, 1 );
+    
+    for i = 1 :  n_objects
+
+        p = boundaries{ i };
+        val = values( i );
+        hts(i ) = patch( ax, p(:,1), p(:,2), p(:,3), val, ...
+            'LineWidth', 2 );
+    end
+end

src/plot_fit_plane.m

+function [ hf, ax1, ax2, ax3 ] = plot_fit_plane( epicells )
+%PLOT_FIT_PLANE Figure with the local plan orientation for a collection of epicells.
+
+    hf = figure( 'Position', [ 1204 20 600 1000 ] );
+    
+    ax1 = subplot( 3, 1, 1 );
+    hold on
+    axis equal
+    add_plot_euler_alpha( ax1, epicells );
+    colormap( ax1, 'hsv' )
+    colorbar(ax1)
+
+    ax2 = subplot( 3, 1, 2 );
+    hold on
+    axis equal
+    add_plot_euler_beta( ax2, epicells );
+    colorbar(ax2)
+
+    ax3 = subplot( 3, 1, 3 );
+    hold on
+    axis equal
+    add_plot_euler_gamma( ax3, epicells );
+    colormap( ax3, 'hsv' )
+    colorbar(ax3)   
+    
+    add_plot_scalebar( ax3,  epicells, 10, 'µm' );
+    linkaxes( [ ax3 ax2 ax1 ] )
+    
+    axis( ax1, 'off' )
+    axis( ax2, 'off' )
+    axis( ax3, 'off' )
+    
+    title( ax1, 'Orientation of plane (º)', ...
+        'FontWeight', 'normal' )
+    title( ax2, 'Slope of plane (º)' , ...
+        'FontWeight', 'normal' )
+    title( ax3, 'Cell main orientation in plane (º)' , ...
+        'FontWeight', 'normal' )
+
+end
+