%% Rebecca Paz
%% BME 4201
%% Homework #2

clc; clear all; close all;

% matrix = [20 20 20 10 10 10 10 10 10; 20 20 20 20 20 20 20 20 10; 20 20 20 10 10 10 10 20 10; 20 20 10 10 10 10 10 20 10; 20 10 10 10 10 10 10 20 10; 10 10 10 10 20 10 10 20 10; 10 10 10 10 10 10 10 10 10; 20 10 20 20 10 10 10 20 20; 20 10 10 20 10 10 20 10 20];
maska = [-1 -1 0; -1 0 1; 0 1 1];
maskb = [0 -1 -1; 1 0 -1; 1 1 0];
maskc = [-1 -1 -1; 2 2 2; -1 -1 -1];
maskd = [-1 2 -1; -1 2 -1; -1 2 -1];
maske = [-1 -1 -1; -1 8 -1; -1 -1 -1];
maskf = ones(3, 3);
maskg = [-1 0 1; -1 0 1; -1 0 1];
maskh = [0 -1 0; -1 4 -1; 0 -1 0];

a = imread('BRAIN8-bit.tif');

imga = imfilter(a, maska, 'conv', 'same');
imgb = imfilter(a, maskb, 'conv', 'same');
imgc = imfilter(a, maskc, 'conv', 'same');
imgd = imfilter(a, maskd, 'conv', 'same');
imge = imfilter(a, maske, 'conv', 'same');
imgf = imfilter(a, maskf, 'conv', 'same');
imgg = imfilter(a, maskg, 'conv', 'same');
imgh = imfilter(a, maskh, 'conv', 'same');

imwrite(imga,'FilterA.tiff','TIFF');
imwrite(imgb,'FilterB.tiff','TIFF');
imwrite(imgc,'FilterC.tiff','TIFF');
imwrite(imgd,'FilterD.tiff','TIFF');
imwrite(imge,'FilterE.tiff','TIFF');
imwrite(imgf,'FilterF.tiff','TIFF');
imwrite(imgg,'FilterG.tiff','TIFF');
imwrite(imgh,'FilterH.tiff','TIFF');

ininoise = imnoise(a,'gaussian',0,0.000001);

x = size(ininoise,1);   y = size(ininoise,2);

noiseimage = zeros(x+2,y+2);
imgnew = zeros(size(ininoise));

for r = 1:x
	noiseimage(r+1,2:y+1) = ininoise(r,:);
end

for r = 1:x
	for c = 1:y
		imgnew(r, c) = mean2(noiseimage(r:r+2,c:c+2));
	end
end

fspav = fspecial('average');

autoimg = imfilter(ininoise, fspav, 'conv', 'same');

imwrite(autoimg,'AutoFiltered.tiff','TIFF');