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% Math 336 - Image Processing - Laboratory 6
%
% Image Morphology (Part 2):
% Use morphological operations to filter the images of the cells.
%
% Marty Kandes
% Computational Science Research Center / Department of Physics
% San Diego State University
% Fall 2008
% -------------------------------------------------------------------------
clear all; close all; clc;                   % Clear Matlab workspace.
F = imread('normal.tiff');                   % Read in the image of normal cells
G = imread('cancer.tiff');                   % Read in the image of cancer cells.
imwrite(F,'normalrgb.jpg','jpg');            % Write color images to jpg files. 
imwrite(G,'cancerrgb.jpg','jpg');            %
F = rgb2gray(F);                             % Convert normal image to grayscale.
G = rgb2gray(G);                             % Convert cancer image to grayscale.
figure;                                      % Open new figure.
imshow(F);                                   % Display normal cell grayscale image.
imwrite(F,'normalgray.jpg','jpg');           % Write normal cell grayscale image to file.
figure;                                      % Open new figure.
imshow(G);                                   % Display cancerous cell binary image.
imwrite(G,'cancergray.jpg','jpg');           % Write cancerous cell binary image to file.
F = im2bw(F,graythresh(F));                  % Convert grayscale normal to binary image.
G = im2bw(G,graythresh(G));                  % Convert grayscale cancer to binary image.
F = ~F;                                      % Invert binary image of normal cells.
G = ~G;                                      % Invert binary image of cancerous cells.
figure;                                      % Open new figure.
imshow(F);                                   % Display normal cell binary image.
imwrite(F,'normalbinary.jpg','jpg');         % Write normal cell binary image to file.
figure;                                      % Open new figure.
imshow(G);                                   % Display cancerous cell binary image.
imwrite(G,'cancerbinary.jpg','jpg');         % Write cancerous cell binary image to file.
M = 5; N = 5;                                % Set dimensions of the structure element.
SE = ones(M,N);                              % Build square structure element.
AP = [3,3];                                  % Set active point of the SE.
H = mfilter(F,SE,AP,'binary','close');       % Apply morphological filter.
H = mfilter(H,SE,AP,'binary','open');        % Apply morphological filter.
figure;                                      % Open new figure.
imshow(H);                                   % Display filtered binary image.
imwrite(H,'normalbinaryfiltered.jpg','jpg'); % Write filtered binary image to file.
M = 3; N = 3;                                % Set dimensions of the structure element.
SE = ones(M,N);                              % Build square structure element.
AP = [2,2];                                  % Set active point of the SE.
I = mfilter(G,SE,AP,'binary','close');       % Apply morphological filter.
I = mfilter(I,SE,AP,'binary','open');        % Apply morphological filter.
figure;                                      % Open new figure.
imshow(I);                                   % Display filtered binary image.
imwrite(I,'cancerbinaryfiltered.jpg','jpg'); % Write filtered binary image to file.
M = 3; N = 3;                                % Set dimensions of the structure element.
SE = ones(M,N);                              % Build square structure element.
AP = [2,2];                                  % Set active point of the SE.
H = H - merode(H,SE,AP,'binary');            % Compute boundary extraction;
I = I - merode(I,SE,AP,'binary');            %
figure;                                      %
imshow(H);                                   %
figure;                                      %
imshow(I);                                   %
imwrite(H,'normalbinarybound.jpg','jpg');    % Write boundary image to file.
imwrite(I,'cancerbinarybound.jpg','jpg');    % Write boundary image to file.
F = imread('normal.tiff');                   % Read in the image of normal cells
G = imread('cancer.tiff');                   % Read in the image of cancer cells.
F = rgb2gray(F);                             % Convert normal image to grayscale.
G = rgb2gray(G);                             % Convert cancer image to grayscale.
F = edge(F,'sobel');                         % Apply sobel filter.
G = edge(G,'sobel');                         % Apply sobel filter.
imwrite(F,'normalsobel.jpg','jpg');          % Write sobel image to file.
imwrite(G,'cancersobel.jpg','jpg');          % Write sobel image to file.
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