Use the mesh to specify the Z position in the from_bellaiche import.

src/@deproj/from_bellaiche.m

@@ -3,7 +3,7 @@ function obj = from_bellaiche( ...
     frame, ...
     sides, ...
     vertices, ...
-    voxel_depth, ...
+    mesh_file_path, ...
     units )
 %FROM_BELLAICHE Returns a deproj object built from the results of the tool
 %from Yohannes Bellaiche lab.
@@ -13,6 +13,17 @@ function obj = from_bellaiche( ...
     width = frame.imageSize( 1 );
     pixel_size = frame.scale1D;
     
+    %% Read the mesh file.
+    
+    fprintf('Loading and processing the tissue mesh file.\n' )
+    tic
+    
+    V = deproj.ply_read( mesh_file_path );
+    si = scatteredInterpolant( V(:,1), V(:,2), V(:,3), 'linear', 'nearest' );
+    
+    fprintf('Loaded %d vertices in %.1f seconds.\n', size(V, 1), toc )
+    
+    
     %% Build the junction graph.
     
     tic
@@ -25,23 +36,22 @@ function obj = from_bellaiche( ...
     
     node_table = table();
     jxy = vertices.XYs;
-    % TODO
-    jz = zeros( size( jxy, 1 ), 1 );    
+
+    jz = si( jxy );
     node_table.Centroid = [ jxy jz ];
     node_table.ID = vertices.numbers;
     
     junction_graph = graph( edge_table, node_table, 'omitselfloops' );
     
     fprintf('Built the junction graph with %d nodes and %d edges in %.1f seconds.\n', ...
-         junction_graph.numnodes, junction_graph.numedges, toc )
-    
+        junction_graph.numnodes, junction_graph.numedges, toc )
     
     %% Convert YB structure to epicells.
-
-    fprintf('Converting to objects.\n' )
-    tic
     
     n_cells = numel( cells.contour_indices );
+
+    fprintf('Computing morphological descriptors of %d objects.\n', n_cells-1 )
+    tic
     
     % We don't go for the first one, which contains the contour of the tissue.
     % Get boundary.
@@ -57,8 +67,8 @@ function obj = from_bellaiche( ...
         P = deproj.find_countour( P );
         P = P * pixel_size;
         
-        % TODO
-        z = zeros( numel(x), 1 );
+        % Get Z from the mesh.
+        z = si( P );
         boundary = [ P z ];
         
         % Get the junction ids.
@@ -70,8 +80,10 @@ function obj = from_bellaiche( ...
         
     end
     
+    fprintf('Done in %.1f seconds.\n', toc )
+    
     obj = deproj( epicells, junction_graph, units );
     
-
+    
 end