Externalize curvature calculation and put the right units.

src/@deproj/compute_curvatures.m

+function [ curvMean, curvGauss, curvK1, curvK2 ] = compute_curvatures( H, object_scale, pixel_size, voxel_depth, invert_z )
+%COMPUTE_CURVATURES Compute local curvature from the smoothed height-map.
+% Ref: http://users.vcnet.com/simonp/curvature.pdf
+    
+
+    if nargin < 5
+        invert_z = false;
+    end
+    if nargin < 4
+        voxel_depth = 1;
+    end
+    if nargin < 3
+        pixel_size = 1;
+    end
+
+    if nargin >= 2 && ~isnan( object_scale) && ~isempty( object_scale )
+        % We need to smooth the height-map over the scale of several cells.
+        Hs = imgaussfilt( H, 3 * object_scale );
+    else
+        Hs = H;
+    end
+    % Physical units.
+    Hs = Hs * voxel_depth;
+    
+    if invert_z
+        Hs = -Hs;
+    end
+    
+    [ Hx , Hy  ] = gradient( Hs, pixel_size );
+    [ Hxx, Hxy ] = gradient( Hx, pixel_size );
+    [  ~ , Hyy ] = gradient( Hy, pixel_size );
+    
+    % Gaussian curvature.
+    Nk = ( 1. + Hx .^ 2 + Hy .^ 2 );
+    curvGauss = ( Hxx .* Hyy - Hxy .^ 2 ) ./ ( Nk .^ 2 );
+    
+    % Mean curvature.
+    Dk1 = ( 1. + Hx .^ 2 ) .* Hyy;
+    Dk2 = ( 1. + Hy .^ 2 ) .* Hxx;
+    Dk3 = - 2. * Hx .* Hy .* Hxy;
+    curvMean = ( Dk1 + Dk2 + Dk3 ) ./ ( 2 * Nk .^ 1.5 );
+    
+    % Principle curvatures.
+    curvK1 = curvMean + sqrt( curvMean .* curvMean - curvGauss );
+    curvK2 = curvMean - sqrt( curvMean .* curvMean - curvGauss );
+    
+end
+

src/@deproj/deproj.m

@@ -87,6 +87,10 @@ classdef deproj
         
         % Returns the seismic colormap.
         cmap = cmap_seismic();
+        
+        % Compute local curvature from the smoothed height-map.
+        [ curvMean, curvGauss, curvK1, curvK2 ] = compute_curvatures( H, object_scale, pixel_size, voxel_depth, invert_z )
+
     end
     
     %% Private static methods: utilities.

src/@deproj/from_heightmap.m

@@ -139,28 +139,12 @@ function obj = from_heightmap( ...
     % Ref: http://users.vcnet.com/simonp/curvature.pdf
     
     fprintf('Compuing tissue local curvature.\n' )
-    
-    % We need to smooth the height-map over the scale of several cells.
-    Hs2 = imgaussfilt( Hs1, 3 * object_scale );
-    
-    if invert_z
-        Hs2 = -Hs2;
-    end
-    
-    [ Hx , Hy  ] = gradient( Hs2 );
-    [ Hxx, Hxy ] = gradient( Hx );
-    [  ~ , Hyy ] = gradient( Hy );
-    % Gaussian curvature.
-    Nk = ( 1. + Hx .^ 2 + Hy .^ 2 );
-    curvGauss = ( Hxx .* Hyy - Hxy .^ 2 ) ./ ( Nk .^ 2 );
-    % Mean curvature.
-    Dk1 = ( 1. + Hx .^ 2 ) .* Hyy;
-    Dk2 = ( 1. + Hy .^ 2 ) .* Hxx;
-    Dk3 = - 2. * Hx .* Hy .* Hxy;
-    curvMean = ( Dk1 + Dk2 + Dk3 ) ./ ( 2 * Nk .^ 1.5 );
-    % Principle curvatures.
-    curvK1 = curvMean + sqrt( curvMean .* curvMean - curvGauss );
-    curvK2 = curvMean - sqrt( curvMean .* curvMean - curvGauss );
+    [ curvMean, curvGauss, curvK1, curvK2 ] = deproj.compute_curvatures( ...
+        Hs1, ...
+        object_scale, ...
+        pixel_size, ...
+        voxel_depth, ...
+        invert_z );
     
     %% Create epicell instances.
     

src/@deproj/plot_curvatures.m

@@ -43,7 +43,8 @@ function [ hf, ax1, ax2, ax3 ] = plot_curvatures( obj, scale_bar_length )
     colormap( ax1, cmap )
     colormap( ax2, cmap )
     colormap( ax3, cmap )
-    colorbar(ax3, 'Location', 'EastOutside' )
+    c = colorbar(ax3, 'Location', 'EastOutside' );
+    c.Label.String = sprintf('Curvature (1/%s)', obj.units );
     
     add_plot_scalebar( obj, scale_bar_length, ax3 );