[feat] drop image proc toolbox dep. self-implement volgrow,shrink,clo…

…se,open

deislands2d.m

@@ -26,11 +26,11 @@
 
 cleanimg = zeros(size(img));
 if (sum(img(:)))
-    img = imclose(img, strel('disk', 3));
+    img = volclose(img, 1, true(5, 5));
     islands = bwislands(img);
 end
 
-if (length(islands))
+if (~isempty(islands))
     % remove small islands of the foreground
     maxblock = -1;
     maxblockid = -1;

fillholes3d.m

@@ -1,4 +1,4 @@
-function resimg = fillholes3d(img, maxgap)
+function resimg = fillholes3d(img, maxgap, varargin)
 %
 % resimg=fillholes3d(img,maxgap)
 %
@@ -18,19 +18,41 @@
 % -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
 %
 
-if (maxgap)
-    resimg = imclose(img, strel(ones(maxgap, maxgap, maxgap)));
+if (nargin > 1 && maxgap)
+    resimg = volclose(img, maxgap);
 else
     resimg = img;
 end
 
-if (isoctavemesh)
-    if (~exist('bwfill'))
-        error('you need to install octave-image toolbox first');
-    end
-    for i = 1:size(resimg, 3)
-        resimg(:, :, i) = bwfill(resimg(:, :, i), 'holes');
-    end
+% if (exist('imfill', 'file'))
+%     resimg = imfill(resimg, 'holes');
+%     return;
+% end
+
+newimg = ones(size(resimg) + 2);
+
+oldimg = zeros(size(newimg));
+if (ndims(resimg) == 3)
+    oldimg(2:end - 1, 2:end - 1, 2:end - 1) = resimg;
+    newimg(2:end - 1, 2:end - 1, 2:end - 1) = 0;
 else
-    resimg = imfill(resimg, 'holes');
+    oldimg(2:end - 1, 2:end - 1) = resimg;
+    newimg(2:end - 1, 2:end - 1) = 0;
+end
+
+newsum = sum(newimg(:));
+oldsum = -1;
+
+while (newsum ~= oldsum)
+    newimg = (volgrow(newimg, 1, varargin{:}) & ~(oldimg > 0));
+    oldsum = newsum;
+    newsum = sum(newimg(:));
 end
+
+if (ndims(resimg) == 3)
+    resimg = newimg(2:end - 1, 2:end - 1, 2:end - 1);
+else
+    resimg = newimg(2:end - 1, 2:end - 1);
+end
+
+resimg = double(~resimg);

thickenbinvol.m

@@ -1,4 +1,4 @@
-function vol = thickenbinvol(vol, layer)
+function vol = thickenbinvol(varargin)
 %
 % vol=thickenbinvol(vol,layer)
 %
@@ -19,16 +19,4 @@
 % -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
 %
 
-dim = size(vol);
-dxy = dim(1) * dim(2);
-fulllen = prod(dim);
-
-offs = [1, -1, dim(1), -dim(1), dxy, -dxy];
-for i = 1:layer
-    idx = find(vol);
-    for j = 1:6
-        idxnew = idx + offs(j);
-        idxnew = idxnew(find(idxnew > 0 & idxnew < fulllen));
-        vol(idxnew) = 1;
-    end
-end
+vol = volgrow(varargin{:});

thinbinvol.m

@@ -1,6 +1,6 @@
-function vol = thinbinvol(vol, layer, nobd)
+function vol = thinbinvol(varargin)
 %
-% vol=thinbinvol(vol,layer,nobd)
+% vol=thinbinvol(vol,layer,mask)
 %
 % thinning a binary volume by a given pixel width
 % this is similar to bwmorph(vol,'thin',n) except
@@ -21,29 +21,4 @@
 % -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
 %
 
-dim = size(vol);
-dxy = dim(1) * dim(2);
-fulllen = prod(dim);
-
-if (nargin < 3)
-    nobd = 0;
-end
-
-if (nobd == 1)
-    bdmask = vol;
-    if (ndims(vol) == 2)
-        bdmask(2:end - 1, 2:end - 1) = 0;
-    elseif (ndims(vol) == 3)
-        bdmask(2:end - 1, 2:end - 1, 2:end - 1) = 0;
-    end
-end
-
-for i = 1:layer
-    idx = find(~vol);
-    idxnew = [idx + 1; idx - 1; idx + dim(1); idx - dim(1); idx + dxy; idx - dxy];
-    idxnew = idxnew(find(idxnew > 0 & idxnew < fulllen));
-    vol(idxnew) = 0;
-    if (nobd)
-        vol = vol | bdmask;
-    end
-end
+vol = volshrink(varargin{:});

volclose.m

@@ -0,0 +1,26 @@
+function newvol = volclose(varargin)
+%
+% vol = volclose(vol, layer, mask)
+%
+% close a binary volume by applying layer-counter of growth operation
+% followed by layer-count of shrinkage operation
+%
+% author: Qianqian Fang, <q.fang at neu.edu>
+%
+% input:
+%     vol: a volumetric binary image
+%     layer: number of iterations for the thickenining
+%     mask: (optional) a 3D neighborhood mask
+%
+% output:
+%     vol: the volume image after closing
+%
+% -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
+%
+
+if (isempty(varargin))
+    error('must provide a volume');
+end
+
+newvol = volgrow(varargin{:});
+newvol = volshrink(newvol, varargin{2:end});

volgrow.m

@@ -0,0 +1,43 @@
+function newvol = volgrow(vol, layer, mask)
+%
+% vol = volgrow(vol, layer, mask)
+%
+% thickening a binary image or volume by a given pixel width
+% this is similar to bwmorph(vol,'thicken',3) except
+% this does it in both 2d and 3d
+%
+% author: Qianqian Fang, <q.fang at neu.edu>
+%
+% input:
+%     vol: a volumetric binary image
+%     layer: number of iterations for the thickenining
+%     mask: (optional) a 3D neighborhood mask
+%
+% output:
+%     vol: the volume image after the thickening
+%
+% -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
+%
+
+if (nargin < 2)
+    layer = 1;
+end
+
+if (nargin < 3)
+    if (ndims(vol) == 3)
+        mask = zeros(3, 3, 3);
+        mask(2, 2, :) = 1;
+        mask(:, 2, 2) = 1;
+        mask(2, :, 2) = 1;
+    else
+        mask = [0 1 0; 1 1 1; 0 1 0];
+    end
+end
+
+newvol = vol;
+
+for i = 1:layer
+    newvol = (convn(newvol, mask, 'same') > 0);
+end
+
+newvol = double(newvol);

volopen.m

@@ -0,0 +1,26 @@
+function newvol = volopen(varargin)
+%
+% vol = volopen(vol, layer, mask)
+%
+% open a binary volume by applying layer-counter of shrink operation
+% followed by layer-count of growth operation
+%
+% author: Qianqian Fang, <q.fang at neu.edu>
+%
+% input:
+%     vol: a volumetric binary image
+%     layer: number of iterations for the thickenining
+%     mask: (optional) a 3D neighborhood mask
+%
+% output:
+%     vol: the volume image after opening
+%
+% -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
+%
+
+if (isempty(varargin))
+    error('must provide a volume');
+end
+
+newvol = volshrink(varargin{:});
+newvol = volgrow(newvol, varargin{2:end});

volshrink.m

@@ -0,0 +1,44 @@
+function newvol = volshrink(vol, layer, mask)
+%
+% vol = volshrink(vol, layer, mask)
+%
+% thinning a binary image or volume by a given pixel width
+% this is similar to bwmorph(vol,'thin',3) except
+% this does it in both 2d and 3d
+%
+% author: Qianqian Fang, <q.fang at neu.edu>
+%
+% input:
+%     vol: a volumetric binary image
+%     layer: number of iterations for the thickenining
+%     mask: (optional) a 3D neighborhood mask
+%
+% output:
+%     vol: the volume image after the thinning operations
+%
+% -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
+%
+
+if (nargin < 2)
+    layer = 1;
+end
+
+if (nargin < 3)
+    if (ndims(vol) == 3)
+        mask = zeros(3, 3, 3);
+        mask(2, 2, :) = 1;
+        mask(:, 2, 2) = 1;
+        mask(2, :, 2) = 1;
+    else
+        mask = [0 1 0; 1 1 1; 0 1 0];
+    end
+end
+
+totalmask = sum(mask(:));
+newvol = vol;
+
+for i = 1:layer
+    newvol = (convn(logical(newvol), logical(mask), 'same') == totalmask);
+end
+
+newvol = double(newvol);