diff --git a/RunExample.m b/RunExample.m
index e317d9b80138323251b46d5c5b71b09b853f5454..d39626755a2c41447a40002fe9cadc4c383396c8 100755
--- a/RunExample.m
+++ b/RunExample.m
@@ -135,32 +135,17 @@ max_z = max( z_junction );
z_junction = max_z - z_junction;
junction_graph.Nodes.Centroid = [ junction_graph.Nodes.Centroid z_junction ];
-for i = 1 : n_objects
+for i = 1 : n_objects
objects( i ).boundary( :, 3 ) = max_z - objects( i ).boundary( :, 3 );
objects( i ).center( 3 ) = max_z - objects( i ).center( 3 );
end
-%% Compute object de-projected area.
+%% Create epicell instances.
-for i = 1 : n_objects
-
+epicells = repmat( epicell, n_objects, 1 );
+for i = 1 : n_objects
o = objects( i );
-
- [ area, uncorr_area ] = area3d( o );
- [ perim, uncorr_perim ] = perimeter3d( o );
- [ f, E ] = fit_ellipse( o );
-
- objects( i ).id = i;
- objects( i ).area = area;
- objects( i ).perimeter = perim;
- objects( i ).euler_angles = E;
- objects( i ).ellipse_fit = f;
-
- uncorr = struct();
- uncorr.area = uncorr_area;
- uncorr.perimeter = uncorr_perim;
- objects( i ).uncorr = uncorr;
-
+ epicells( i ) = epicell( o.boundary, o.junctions, i );
end
@@ -200,7 +185,7 @@ axis equal
for i = 1 : n_objects
- o = objects( i );
+ o = epicells( i );
P = o.boundary;
% err = o.perimeter / o.uncorr.perimeter - 1;
diff --git a/src/area3d.m b/src/area3d.m
deleted file mode 100644
index b47b52d9e7cf91b781d68a7eeba94ebf5d52dd40..0000000000000000000000000000000000000000
--- a/src/area3d.m
+++ /dev/null
@@ -1,40 +0,0 @@
-function [ area, uncorr_area ] = area3d( o )
-%AREA3D Computes the area of the object.
-
- %% Deprojected 3D version.
-
- % Put all vertex coordinates with respect to center.
- p = centered_points( o );
-
- n_vertices = size( p, 1 );
-
- % Build small triangles.
- index = [ 2 : n_vertices 1 ];
- p1 = p;
- p2 = p( index, : );
-
- % Cross product.
- cp = cross( p1, p2 );
-
- % Norm of each vector.
- vn = euclidean_norm( cp );
-
- % Positive area.
- area_triangle = abs( vn );
-
- % Total positive area.
- area = sum( area_triangle ) / 2;
-
- %% 2D area.
-
- uncorr_area = polyarea( o.boundary(:,1), o.boundary(:,2) );
-
-
- %% Subfunction.
-
- function n = euclidean_norm( v )
- n = sqrt( sum( v .* v, ndims( v ) ) );
- end
-
-end
-
diff --git a/src/centered_points.m b/src/centered_points.m
deleted file mode 100644
index 29f7cbb4f38b34478203ebdac208766e1c5302c8..0000000000000000000000000000000000000000
--- a/src/centered_points.m
+++ /dev/null
@@ -1,12 +0,0 @@
-function p = centered_points( o )
-%CENTERED_POINTS Returns the 3D coordinates of the object bounds, with
-%respect to its center.
-
- p = o.boundary;
- n_vertices = size( p ,1 );
- center = mean( p );
- center = repmat( center, [ n_vertices, 1 ] );
- p = p - center;
-
-end
-
diff --git a/src/epicell.m b/src/epicell.m
new file mode 100644
index 0000000000000000000000000000000000000000..c353d9d0f4fa4ea5f38b750d581e057b0fc067ba
--- /dev/null
+++ b/src/epicell.m
@@ -0,0 +1,110 @@
+classdef epicell
+ %EPICELL Data class that store data resulting from tissue cell segmentation.
+
+ % Immutable class: all properties are read-only.
+ properties (SetAccess = private)
+ boundary
+ center
+ junction_ids
+ area
+ perimeter
+ euler_angles
+ ellipse_fit
+ uncorrected_area
+ uncorrected_perimeter
+ id
+ end
+
+ methods
+ function obj = epicell( boundary, junction_ids, id )
+ %EPICELL Construct an epicell from a N x 3 list of points.
+
+ if nargin == 0
+ return
+ end
+
+ % Base properties.
+ obj.boundary = boundary;
+ obj.junction_ids = junction_ids;
+ obj.id = id;
+ obj.center = mean( boundary );
+
+ % Morphological descriptors.
+ p = epicell.centered_points( boundary );
+ [ obj.area, obj.uncorrected_area ] = epicell.area3d( p );
+ [ obj.perimeter, obj.uncorrected_perimeter ] = epicell.perimeter3d( p );
+ obj.euler_angles = epicell.fit_plane( p );
+ obj.ellipse_fit = fit_ellipse( p, obj.euler_angles );
+ end
+ end
+
+ %% Static methods: compute final properties value.
+ methods ( Access = private, Hidden = true, Static = true )
+
+ function p = centered_points( p )
+ %CENTERED_POINTS Returns the 3D coordinates of the object bounds, with
+ %respect to its center.
+ n_vertices = size( p ,1 );
+ center = mean( p );
+ center = repmat( center, [ n_vertices, 1 ] );
+ p = double( p - center );
+ end
+
+ function [ area, uncorr_area ] = area3d( p )
+ %AREA3D Computes the area of the object.
+
+ n_vertices = size( p, 1 );
+
+ % Build small triangles.
+ index = [ 2 : n_vertices 1 ];
+ p1 = p;
+ p2 = p( index, : );
+
+ % Cross product.
+ cp = cross( p1, p2 );
+
+ % Norm of each vector.
+ vn = euclidean_norm( cp );
+
+ % Positive area.
+ area_triangle = abs( vn );
+
+ % Total positive area.
+ area = sum( area_triangle ) / 2;
+
+ % 2D area.
+ uncorr_area = polyarea( p(:,1), p(:,2) );
+
+ function n = euclidean_norm( v )
+ n = sqrt( sum( v .* v, ndims( v ) ) );
+ end
+
+ end
+
+ function [ perim, uncorr_perim ] = perimeter3d( p )
+ %PERIMETER3D Perimeter of a closed N-dimensional polygon.
+
+ perim = compute_perim( p );
+ uncorr_perim = compute_perim( p( : , 1:2 ) );
+
+ function l_perim = compute_perim( p )
+ % p can be a N x d matrix, with d being the dimensionality.
+
+ p2 = [ p ; p( 1, : ) ];
+ p_diff = diff( p2 );
+
+ p_diff_2 = p_diff .* p_diff;
+ p_diff_2_sum = sum( p_diff_2, 2 );
+ sls = sqrt( p_diff_2_sum );
+ l_perim = sum( sls );
+ end
+ end
+
+ function E = fit_plane( p )
+ % Fit a plane to these points.
+ [ ~, ~, v ] = svd( p );
+ E = rot2eulerZXZ( v );
+ end
+ end
+end
+
diff --git a/src/fit_ellipse.m b/src/fit_ellipse.m
index 2922dccd7f713476af12580c0a5b6e85c38c6f5d..4b60f7a5bf09a4856f04c98cb920403e558162fd 100644
--- a/src/fit_ellipse.m
+++ b/src/fit_ellipse.m
@@ -1,4 +1,4 @@
-function [ f, E ] = fit_ellipse( o )
+function f = fit_ellipse( p, E )
%FIT_ELLIPSE Fit a 2D ellipse to the 3D points.
% The fit requires the Euler angles of the plane fitted through the
% opints, so that we can project them on this plane. We then make a 2D
@@ -8,11 +8,12 @@ function [ f, E ] = fit_ellipse( o )
% Greatly inspired from
% https://stackoverflow.com/questions/29051168/data-fitting-an-ellipse-in-3d-space
- p = double( centered_points( o ) );
-
% Fit a plane to these points.
- [ ~, ~, v ] = svd( p );
- E = rot2eulerZXZ( v );
+ if nargin < 2
+ [ ~, ~, v ] = svd( p );
+ else
+ v = euleurZXZ2rot( E );
+ end
% Rotate the points into the principal axes frame.
p = p * v;
diff --git a/src/perimeter3d.m b/src/perimeter3d.m
deleted file mode 100644
index d026425f54ba2841f3759b3484957ea29542cfd1..0000000000000000000000000000000000000000
--- a/src/perimeter3d.m
+++ /dev/null
@@ -1,23 +0,0 @@
-function [ perim, uncorr_perim ] = perimeter3d( o )
-%PERIMETER3D Perimeter of a closed N-dimensional polygon.
-
- perim = compute_perim( o.boundary );
- uncorr_perim = compute_perim( o.boundary( : , 1:2 ) );
-
- %% Subfunction
-
- function l_perim = compute_perim( p )
- % p can be a N x d matrix, with d being the dimensionality.
-
- p2 = [ p ; p( 1, : ) ];
- p_diff = diff( p2 );
-
- p_diff_2 = p_diff .* p_diff;
- p_diff_2_sum = sum( p_diff_2, 2 );
- sls = sqrt( p_diff_2_sum );
- l_perim = sum( sls );
-
- end
-
-end
-