filter_function.m

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% filter_function.m is a helper function for interate.m. To run snakes
% (active contours) with GUI see below. To go to the meat of the code, see
% interate.m
%
% To run it with GUI
%   1. Type guide on the matlab prompt.
%   2. Click on "Go to Existing GUI"
%   3. Select the snk.fig file in the same directory as this file
%   4. Click the green arrow at the top to launch the GUI
%
%   Once the GUI has been launched, you can use snakes by
%   1. Click on "New Image" and load an input image. Samples image are
%   provided.
%   2. Set the smoothing parameter "sigma" or leave it at its default value
%   and click "Filter". This will smooth the image.
%   3. As soon as you click "Filter", cross hairs would appear and using
%   them and left click of you mouse you can pick initial contour location
%   on the image. A red circle would appead everywhere you click and in
%   most cases you should click all the way around the object you want to
%   segement. The last point must be picked using a right-click in order to
%   stop matlab for asking for more points.
%   4. Set the various snake parameters (relative weights of energy terms
%   in the snake objective function) or leave them with their default value
%   and click "Iterate" button. The snake would appear and move as it
%   converges to its low energy state.
%
% Copyright (c) Ritwik Kumar, Harvard University 2010
%               www.seas.harvard.edu/~rkkumar
%
% This code implements Snakes: Active Contour Models by Kass, Witkin and
% Terzopolous incorporating Eline, Eedge and Eterm energy factors. See the
% included report and the paper to learn more.
%
% If you find this useful, also look at Radon-Like Features based
% segmentation in  the following paper:
% Ritwik Kumar, Amelio V. Reina & Hanspeter Pfister, Radon-Like Features 
% and their Application to Connectomics, IEEE Computer Society Workshop %
% on Mathematical Methods in Biomedical Image Analysis (MMBIA) 2010
% http://seas.harvard.edu/~rkkumar
% Its code is also available on MATLAB Central
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function [smth] = filter_function(image, sigma)
% This function smooths the image with a Gaussian filter of width sigma

smask = fspecial('gaussian', ceil(3*sigma), sigma);
smth = filter2(smask, image, 'same');