add regionIsosurfaces.m

src/@Image/isosurface.m

@@ -1,8 +1,8 @@
 function varargout = isosurface(obj, isovalue, varargin)
-% Isosurface generation of a 3D image.
+% Generate isosurface of a 3D image.
 %
 %   isosurface(IMG, ISOVALUE)
-%   Computes isosurface from image data ans the specified isovalue. 
+%   Computes isosurface from image data and the specified isovalue. 
 %   The functions simply consists in a wrapper to the "isosurface" function
 %   from Matlab.
 %
@@ -15,14 +15,16 @@
 
 % ------
 % Author: David Legland
-% e-mail: david.legland@inra.fr
+% e-mail: david.legland@inrae.fr
 % Created: 2010-12-16,    using Matlab 7.9.0.529 (R2009b)
 % Copyright 2010 INRA - Cepia Software Platform.
 
+% retrieve voxel coordinates in physical space
 x = getX(obj);
 y = getY(obj);
 z = getZ(obj);
 
+% permute data to comply with Matlab orientation
 v = permute(obj.Data(:,:,:,1,1), [2 1 3]);
 
 if nargout == 0

src/@Image/regionIsosurfaces.m

@@ -0,0 +1,129 @@
+function [res, labels] = regionIsosurfaces(obj, varargin)
+% Generate isosurface of each region within a label image.
+%
+%   MESHES = regionIsosurfaces(LBL)
+%   Computes isosurfaces of each region within the label image LBL.
+%   
+%
+%   Example
+%     markers = Image.true([50 50 50]);
+%     n = 100;
+%     rng(10);
+%     seeds = randi(50, [n 3]);
+%     for i = 1:n
+%         markers(seeds(i,1), seeds(i,2), seeds(i,3)) = false;
+%     end
+%     wat = watershed(distanceMap(markers), 6);
+%     wat2 = killBorders(wat);
+%     figure; hold on; axis equal; 
+%     regionIsosurfaces(wat2, 'smoothRadius', 2, 'LineStyle', 'none');
+%     view(3), light;
+%
+%   See also
+%     isosurface, gt
+%
+
+% ------
+% Author: David Legland
+% e-mail: [email protected]
+% INRAE - BIA Research Unit - BIBS Platform (Nantes)
+% Created: 2021-02-22,    using Matlab 9.8.0.1323502 (R2020a)
+% Copyright 2021 INRAE.
+
+
+%% Input arguiment processing
+
+% check if labels are specified
+labels = [];
+if ~isempty(varargin) && size(varargin{1}, 2) == 1
+    labels = varargin{1};
+    varargin(1) = [];
+end
+
+% extract the set of labels, without the background
+if isempty(labels)
+    labels = findRegionLabels(obj);
+end
+nLabels = length(labels);
+
+% parse other options
+smoothRadius = 0; 
+siz = 0;
+if ~isempty(varargin) && strcmpi(varargin{1}, 'smoothRadius')
+    smoothRadius = varargin{2};
+    if isscalar(smoothRadius)
+        smoothRadius = smoothRadius([1 1 1]);
+    end
+    siz = floor(smoothRadius * 2) + 1;
+    varargin(1:2) = [];
+end
+
+
+%% Preprocessing
+
+% retrieve voxel coordinates in physical space
+% (common to all labels)
+x = getX(obj);
+y = getY(obj);
+z = getZ(obj);
+
+% permute data to comply with Matlab orientation
+v = permute(obj.Data(:,:,:,1,1), [2 1 3]);
+
+% allocate memory for labels
+meshes = cell(1, nLabels);
+
+
+%% Isosurface computation
+
+% iterate over regions to generate isosurfaces
+for iLabel = 1:nLabels
+    label = labels(iLabel);
+
+    vol = double(v == label);
+    % optional smoothing
+    if smoothRadius > 0
+        vol = filterData(vol, siz, smoothRadius);
+    end
+
+    meshes{iLabel} = isosurface(x, y, z, vol, 0.5);
+end
+
+
+%% Finalization
+
+if nargout == 0
+    % display isosurfaces
+    for i = 1:nLabels
+        patch(meshes{i}, varargin{:});
+    end
+
+else
+    % return computed mesh list
+    res = meshes;
+end
+end
+
+%% Utility function
+function data = filterData(data, kernelSize, sigma)
+% process each direction
+for i = 1:3
+    % compute spatial reference
+    refSize = (kernelSize(i) - 1) / 2;
+    s0 = floor(refSize);
+    s1 = ceil(refSize);
+    lx = -s0:s1;
+
+    % compute normalized kernel
+    sigma2 = 2*sigma(i).^2;
+    kernel = exp(-(lx.^2 / sigma2));
+    kernel = kernel / sum(kernel);
+
+    % reshape the kernel such as it is elongated in the i-th direction
+    newDim = [ones(1, i-1) kernelSize(i) ones(1, 3-i)];
+    kernel = reshape(kernel, newDim);
+
+    % apply filtering along one direction
+    data = imfilter(data, kernel, 'replicate');
+end
+end