From e37057a123e537ccdf26122054dd5b74a1c28f29 Mon Sep 17 00:00:00 2001
From: Qianqian Fang <fangqq@gmail.com>
Date: Wed, 18 Dec 2024 18:01:37 -0500
Subject: [PATCH] [feat] allow fillholes3d to perform floodfill

---
 fillholes3d.m | 41 +++++++++++++++++++++++++++++++----------
 1 file changed, 31 insertions(+), 10 deletions(-)

diff --git a/fillholes3d.m b/fillholes3d.m
index 53a1af1..6b1fc7a 100644
--- a/fillholes3d.m
+++ b/fillholes3d.m
@@ -1,14 +1,17 @@
 function resimg = fillholes3d(img, maxgap, varargin)
 %
-% resimg=fillholes3d(img,maxgap)
+% resimg=fillholes3d(img,maxgap,mask)
 %
 % close a 3D image with the speicified gap size and then fill the holes
 %
 % author: Qianqian Fang, <q.fang at neu.edu>
 %
 % input:
-%    img: a 3D binary image
-%    maxgap: maximum gap size for image closing
+%    img: a 2D or 3D binary image
+%    maxgap: if is a scalar, specify maximum gap size for image closing
+%            if a pair of coordinates, specify the seed position for
+%            floodfill
+%    mask: (optional) neighborhood structure element for floodfilling
 %
 % output:
 %    resimg: the image free of holes
@@ -18,18 +21,22 @@
 % -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
 %
 
-if (nargin > 1 && maxgap)
+if (nargin > 1 && numel(maxgap) == 1)
     resimg = volclose(img, maxgap);
 else
     resimg = img;
 end
 
-% if (exist('imfill', 'file'))
-%     resimg = imfill(resimg, 'holes');
-%     return;
-% end
+if (exist('imfill', 'file'))
+    resimg = imfill(resimg, 'holes');
+    return
+end
 
-newimg = ones(size(resimg) + 2);
+if (nargin > 1 && numel(maxgap) > 1)
+    newimg = zeros(size(resimg) + 2);
+else
+    newimg = ones(size(resimg) + 2);
+end
 
 oldimg = zeros(size(newimg));
 if (ndims(resimg) == 3)
@@ -40,6 +47,16 @@
     newimg(2:end - 1, 2:end - 1) = 0;
 end
 
+isseeded = false;
+if (nargin > 1 && numel(maxgap) > 1)
+    if (size(maxgap, 2) == 3)
+        newimg(sub2ind(size(newimg), maxgap(:, 1) + 1, maxgap(:, 2) + 1, maxgap(:, 3) + 1)) = 1;
+    else
+        newimg(sub2ind(size(newimg), maxgap(:, 1) + 1, maxgap(:, 2) + 1)) = 1;
+    end
+    isseeded = true;
+end
+
 newsum = sum(newimg(:));
 oldsum = -1;
 
@@ -55,4 +72,8 @@
     resimg = newimg(2:end - 1, 2:end - 1);
 end
 
-resimg = double(~resimg);
+if (~isseeded)
+    resimg = double(~resimg);
+else
+    resimg = double(resimg);
+end