From: Greg Burri <greg.burri@gmail.com>
Date: Thu, 19 Mar 2015 15:42:32 +0000 (+0100)
Subject: Add of MATLAB tests.
X-Git-Url: http://git.euphorik.ch/index.cgi?a=commitdiff_plain;h=67471e7dc44204d2847f895228749d9bf236749e;p=malaria.git

Add of MATLAB tests.
---

67471e7dc44204d2847f895228749d9bf236749e
diff --git a/src/loadImg.m b/src/loadImg.m
new file mode 100644
index 0000000..5397aca
--- /dev/null
+++ b/src/loadImg.m
@@ -0,0 +1,10 @@
+function [img, gt] = loadImg(name, num)
+
+    imagesFolder = '../imgs_corrMK';
+    groundTruthFolder = '../gt';
+    filename = [name, '-', num, '.png'];
+    
+    img = imread([imagesFolder, '/', name, '/', filename]);
+    gt = imread([groundTruthFolder, '/', name, '/', filename]) ./ 255;
+end
+
diff --git a/src/main.m b/src/main.m
new file mode 100644
index 0000000..0ba3187
--- /dev/null
+++ b/src/main.m
@@ -0,0 +1,139 @@
+% Load the image and its ground truth.
+imageFolder = '1305121398';
+imageNumber = '0001';
+[img, gt] = loadImg(imageFolder, imageNumber);
+
+% Resample the image and its ground truth.
+img = imresize(img, 0.2);
+gt = imresize(img, 0.2);
+
+% Crop the image (for testing).
+% img = img(1:300, 1:300, :);
+
+% Image properties.
+[h, w, d] = size(img); % height, width, depth
+
+%% To gray.
+img = rgb2hsv(img);
+imgGray = zeros(h, w);
+
+for i = 1:h
+    for j = 1:w
+        h = img(i, j, 1);
+        s = img(i, j, 2);
+        v = img(i, j, 3);
+        imgGray(i, j) = v;
+%         
+%         if (h > 0.861 || h < 0.042) && s > 0.05 && v < 0.85
+%             imgGray(i, j) = 255 * v;
+%         else
+%             imgGray(i, j) = 0;
+%         end
+    end
+end
+
+
+%% Normalization.
+minimum = min(min(imgGray));
+maximum = max(max(imgGray));
+imgGrayNorm = uint8(255 * (imgGray - minimum) / (maximum - minimum));
+
+
+%% Morphologic transformation
+
+% Top-hat transformation (p 673).
+% Try to do some shading correction
+a = imgGrayNorm - mmopen(imgGrayNorm, mmsedisk(40));
+
+% Area opening to flatten the cells.
+b = mmareaopen(a, 200);
+
+% Threshold the image to segment cells.
+c = mmcmp(uint8(0), '<=', b, '<=', uint8(45));
+
+% Smooth the cells and remove little holes.
+d = mmopen(c, mmsedisk(2, '2D', 'OCTAGON'));
+
+% Distance of each cell pixel to its border.
+e1 = mmdist(d, mmsebox, 'EUCLIDEAN');
+e2 = mmregmax(e1); % Regional maxima,default SE is a 3x3 cross.
+e  = mmdil(e2); % Dilation by a 3x3 cross.
+
+% Watershed.
+f = mmneg(e1);
+fs = mmsurf(f);
+g = mmcwatershed(f, e, mmsebox);
+
+% Cell separation.
+h = mmintersec(c, mmneg(g));
+
+% Removing the cells touching the border and too small cells.
+i = mmopen(mmedgeoff(h), mmsedisk(3));
+
+% Create the border of each cell. 
+j = mmgradm(i);
+
+figure('Position', [100 100 1000 800])
+colormap(gray);
+
+subplot(2, 2, 1); 
+imagesc(imgGrayNorm);
+title([imageFolder, '-', imageNumber]);
+
+subplot(2, 2, 2);
+imagesc(a);
+title('a');
+
+subplot(2, 2, 3);
+imagesc(b);
+title('b');
+
+subplot(2, 2, 4);
+imagesc(c);
+title('c');
+
+figure('Position', [100 100 1000 800])
+colormap(gray);
+
+subplot(2, 2, 1);
+imagesc(d);
+title('d');
+
+subplot(2, 2, 2);
+imagesc(mmsurf(e1));
+title('Surface of e1');
+
+subplot(2, 2, 3);
+imagesc(i);
+title('i');
+
+subplot(2, 2, 4);
+mmshow(imgGrayNorm, j);
+title('Original + j');
+
+
+
+% figure('Position', [100 100 1000 800])
+% colormap(gray);
+% 
+% subplot(2, 2, 1);
+% imagesc(f);
+% title('f');
+% 
+% subplot(2, 2, 2);
+% imagesc(fs);
+% title('fs');
+
+
+
+
+
+
+% image(imfuse(img, gt, 'blend'));
+% colormap('HSV')
+% image(gt);
+% colormap([0 0 0; 1 1 1]);
+
+% disp('Some tests ...');
+
+