imMeasures/imInscribedCircle.m: takes into account spatial calibration

Author: dlegland

matImage/imMeasures/imInscribedCircle.m

@@ -1,11 +1,18 @@
 function [circle, labels] = imInscribedCircle(lbl, varargin)
-%IMINSCRIBEDCIRCLE Maximal circle inscribed in a particle
+% Maximal circle inscribed in a region.
 %
 %   CIRC = imInscribedCircle(IMG)
 %   Computes the maximal circle inscribed in a given particle, or
 %   around each labeled particle in the input image.
 %
-%   CIRC = imInscribedCircle(IMG, LABELS)
+%   CIRC = imInscribedCircle(IMG, SPACING)
+%   CIRC = imInscribedCircle(IMG, SPACING, ORIGIN)
+%   Takes into account the spatical calibration to compute the results in
+%   physical units. Both SPACING and ORIGIN are 1-by-2 row vectors, that
+%   correspond to the spacing between pixels and to the position of the
+%   first pixel, respectively.
+%
+%   CIRC = imInscribedCircle(..., LABELS)
 %   Specify the labels for which the inscribed circle needs to be computed.
 %   The result is a N-by-3 array with as many rows as the number of labels.
 %
@@ -15,15 +22,15 @@
 %     img = imFillHoles(imread('circles.png'));
 %     imshow(img); hold on;
 %     circ = imInscribedCircle(img);
-%     drawCircle(circ, 'linewidth', 2)
+%     drawCircle(circ, 'LineWidth', 2)
 %
 %   % Compute and display the equivalent ellipses of several particles
 %     img = imread('rice.png');
 %     img2 = img - imopen(img, ones(30, 30));
 %     lbl = bwlabel(img2 > 50, 4);
 %     circles = imInscribedCircle(lbl);
 %     imshow(img); hold on;
-%     drawCircle(circles, 'linewidth', 2, 'color', 'g');
+%     drawCircle(circles, 'LineWidth', 2, 'Color', 'g');
 %
 %   See also
 %     drawCircle, imEnclosingCircle, imInertiaEllipse, imInscribedBall
@@ -35,6 +42,27 @@
 % Created: 2012-07-08,    using Matlab 7.9.0.529 (R2009b)
 % Copyright 2012 INRA - Cepia Software Platform.
 
+%% Process input arguments
+
+% default values
+spacing = [1 1];
+origin  = [1 1];
+calib   = false;
+
+% extract spacing
+if ~isempty(varargin) && sum(size(varargin{1}) == [1 2]) == 2
+    spacing = varargin{1};
+    varargin(1) = [];
+    calib = true;
+    origin = [0 0];
+end
+
+% extract origin
+if ~isempty(varargin) && sum(size(varargin{1}) == [1 2]) == 2
+    origin = varargin{1};
+    varargin(1) = [];
+end
+
 % check if labels are specified
 labels = [];
 if ~isempty(varargin) && size(varargin{1}, 2) == 1
@@ -47,12 +75,15 @@
 end
 nLabels = length(labels);
 
+
+%% Main processing
+
 % allocate memory for result
 circle = zeros(nLabels, 3);
 
 for iLabel = 1:nLabels
     % compute distance map
-    distMap = imDistanceMap(lbl==iLabel);
+    distMap = imDistanceMap(lbl==labels(iLabel));
 
     % find value and position of the maximum
     maxi = max(distMap(:));    
@@ -61,3 +92,8 @@
     circle(iLabel,:) = [xc yc maxi];
 end
 
+% apply spatial calibration
+if calib
+    circle(:,1:2) = bsxfun(@plus, bsxfun(@times, circle(:,1:2) - 1, spacing), origin);
+    circle(:,3) = circle(:,3) * spacing(1);
+end

tests/imMeasures/test_imInscribedCircle.m

@@ -0,0 +1,83 @@
+function tests = test_imInscribedCircle
+% Test suite for the file imInscribedCircle.
+%
+%   Test suite for the file imInscribedCircle
+%
+%   Example
+%   test_imInscribedCircle
+%
+%   See also
+%     imInscribedCircle
+
+% ------
+% Author: David Legland
+% e-mail: [email protected]
+% Created: 2021-01-11,    using Matlab 9.8.0.1323502 (R2020a)
+% Copyright 2021 INRAE - BIA-BIBS.
+
+tests = functiontests(localfunctions);
+
+function test_SimpleRect(testCase) %#ok<*DEFNU>
+% Test call of function without argument.
+
+img = zeros(100, 100, 'uint8');
+img(30:60, 20:80) = 1;
+
+circle = imInscribedCircle(img);
+
+assertEqual(testCase, size(circle), [1 3]);
+assertEqual(testCase, circle(3), 16, 'AbsTol', 0.01);
+
+
+function test_MultiLabels(testCase) %#ok<*DEFNU>
+% Test call of function without argument.
+
+img = [ ...
+    0 0 0 0 0 0 0 0 0 0 0; ...
+    0 1 1 1 0 4 4 4 4 4 0; ...
+    0 1 1 1 0 4 4 4 4 4 0; ...
+    0 1 1 1 0 4 4 4 4 4 0; ...
+    0 0 0 0 0 0 0 0 0 0 0; ...
+    0 6 6 6 6 6 6 6 6 6 0; ...
+    0 6 6 6 6 6 6 6 6 6 0; ...
+    0 6 6 6 6 6 6 6 6 6 0; ...
+    0 6 6 6 6 6 6 6 6 6 0; ...
+    0 6 6 6 6 6 6 6 6 6 0; ...
+    0 6 6 6 6 6 6 6 6 6 0; ...
+    0 6 6 6 6 6 6 6 6 6 0; ...
+    0 6 6 6 6 6 6 6 6 6 0; ...
+    0 6 6 6 6 6 6 6 6 6 0; ...
+    0 6 6 6 6 6 6 6 6 6 0; ...
+    0 0 0 0 0 0 0 0 0 0 0] ; ...
+
+[circles, labels] = imInscribedCircle(img);
+
+assertEqual(testCase, size(circles), [3 3]);
+assertEqual(testCase, length(labels), 3);
+
+expRadius = [2 2 5]';
+assertEqual(testCase, circles(:,3), expRadius, 'AbsTol', 0.01);
+
+
+function test_LabelsTouchingImageBorder(testCase) %#ok<*DEFNU>
+% Test call of function without argument.
+
+img = [ ...
+    1 1 1 0 4 4 4 4 4; ...
+    1 1 1 0 4 4 4 4 4; ...
+    1 1 1 0 4 4 4 4 4; ...
+    0 0 0 0 0 0 0 0 0; ...
+    6 6 6 6 6 6 6 6 6; ...
+    6 6 6 6 6 6 6 6 6; ...
+    6 6 6 6 6 6 6 6 6; ...
+    6 6 6 6 6 6 6 6 6; ...
+    6 6 6 6 6 6 6 6 6] ; ...
+
+[circles, labels] = imInscribedCircle(img);
+
+assertEqual(testCase, size(circles), [3 3]);
+assertEqual(testCase, length(labels), 3);
+
+expRadius = [3 3 5]';
+assertEqual(testCase, circles(:,3), expRadius, 'AbsTol', 0.01);
+