From: Greg Burri <greg.burri@gmail.com>
Date: Thu, 30 Apr 2015 22:09:44 +0000 (+0200)
Subject: Add the main script and a test script about the hue component.
X-Git-Url: http://git.euphorik.ch/index.cgi?a=commitdiff_plain;h=c9ed8d104a62abf86629a17b4ba89c04019a5036;p=malaria.git

Add the main script and a test script about the hue component.
---

diff --git a/src/DetectionOfParasites.m b/src/DetectionOfParasites.m
index 9dca5c4..8d3b2be 100644
--- a/src/DetectionOfParasites.m
+++ b/src/DetectionOfParasites.m
@@ -5,8 +5,6 @@
 %  THS: Parasites of all types and WBC (mask).
 %  c: Typical red cell radius [px].
 function [THS, c] = DetectionOfParasites(imgRGB)
-
-    imwrite(imgRGB, '../output/imgRGB.png')
     
     %% Extracting of H, S and V components
     imgHSV = rgb2hsv(imgRGB);
@@ -32,7 +30,7 @@ function [THS, c] = DetectionOfParasites(imgRGB)
     imwrite(imgFiltered{1}, '../output/imgHFiltered.png');
     imwrite(imgFiltered{2}, '../output/imgSFiltered.png');
     imwrite(imgFiltered{3}, '../output/imgVFiltered.png');
-    
+        
     % Shading correction with a Top-hat transformation (p. 673).
     % Not in the article -> disable for the moment, not needed.
     % imgHFiltered = mmopenth(imgHFiltered, mmsedisk(80, '2D', 'OCTAGON'));
diff --git a/src/Main.m b/src/Main.m
new file mode 100644
index 0000000..f5dd0a4
--- /dev/null
+++ b/src/Main.m
@@ -0,0 +1,33 @@
+%% Parameters
+
+mkdir('../output') % Just in case the 'output' directory doesn't exist.
+
+% Hue is unusable for '1305121398'/'0001'
+% imageFolder = '1305121398'; % 1.
+% imageFolder = '1307210661'; % 2.
+% imageFolder = '1401063467'; % 3.
+% imageFolder = '1405022890'; % 4.
+imageFolder = '1409191647'; % 9.
+% imageFolder = '1412151257'; % 10.
+
+imageNumber = '0004';
+
+scaleFactor = 0.6;
+
+% Load the image and its ground truth.
+[imgRGB, gt] = loadImg(imageFolder, imageNumber);
+
+% Resample the image and its ground truth.
+imgRGBResampled = imresize(imgRGB, scaleFactor);
+gtResampled = imresize(gt, scaleFactor);
+
+imwrite(imgRGBResampled, '../output/imgRGB.png')
+imwrite(gtResampled, '../output/gt.png')
+
+[THS, c] = DetectionOfParasites(imgRGBResampled);
+[WBC] = DetectionOfWhiteCells(THS, c);
+[Shizonts] = DetectionOfSchizonts(THS, c);
+
+infectedRedCells = THS - WBC - Shizonts;
+imwrite(infectedRedCells, '../output/infectedRedCells.png')
+
diff --git a/src/THue.m b/src/THue.m
new file mode 100644
index 0000000..996f816
--- /dev/null
+++ b/src/THue.m
@@ -0,0 +1,47 @@
+%% THue.m
+
+%% Init
+clear
+close all
+
+%% Data
+% RGB = imread ('/Users/michel.kocher/michel/Data/Movable/imgs_corrMK/Gamma/1412151257-Gamma-0.8-0002.png');
+
+RGB = imread('../imgs_corrMK/Gamma/1412151257-Gamma-0.8-0002.png');
+
+%% HSV
+HSV = rgb2hsv (RGB);
+H = HSV (:, :, 1);
+S = HSV (:, :, 2);
+Bin = linspace (0, 1, 200);
+[Count] = hist (H(:), Bin);
+
+
+%% Compute by hands of Hue
+
+% Normalized in [0..1]. From : http://en.wikipedia.org/wiki/Hue
+hue = @(r, g, b) atan2(sqrt(3.0) * (g - b), 2.0 * r - g - b) / (2.0 * pi);
+i = 20;
+j = 20;
+r = double(RGB(i,j,1)) / 255 * 2 * pi;
+g = double(RGB(i,j,2)) / 255 * 2 * pi;
+b = double(RGB(i,j,3)) / 255 * 2 * pi;
+fprintf('r: %d, g: %d, b: %d\n', double(RGB(i,j,1)) / 255, double(RGB(i,j,2)) / 255, double(RGB(i,j,3)) / 255);
+fprintf('Hue by hand: %0.5f\n', hue(r, g, b));
+fprintf('Hue by ''rgb2hsv'' : %0.5f\n', H(i, j));
+
+%% Display
+figure('Position', [100 100 1600 800])
+ax (1) = subplot (2, 2, 1);
+imshow (RGB), title ('RGB')
+ax (2) = subplot (2, 2 ,2);
+imshow (H, []), title ('Hue')
+subplot (2, 2, 3)
+bar (Bin, log10(Count+1)), axis square, axis tight, title ('hist(Hue), log space')
+ax (3) = subplot (2, 2, 4);
+imshow (S, []), title ('Saturation')
+
+linkaxes (ax)
+
+%% Print 2 file
+% print ('-f1', '-dpng', 'THue.png')
\ No newline at end of file
diff --git a/src/loadImg.m b/src/loadImg.m
index 1db3a64..c985597 100644
--- a/src/loadImg.m
+++ b/src/loadImg.m
@@ -1,10 +1,20 @@
+% Load the image and the ground-truth from the given foldername and suffix.
+% If the ground-truth isn't found then it is put to white.
 function [img, gt] = loadImg(name, num)
 
     imagesFolder = '../imgs_corrMK';
     groundTruthFolder = '../gt';
     filename = [name, '-', num, '.png'];
+    filepath_img = [imagesFolder, '/', name, '/', filename];
+    filepath_gt = [groundTruthFolder, '/', name, '/', filename];
     
-    img = imread([imagesFolder, '/', name, '/', filename]);
-    gt = imread([groundTruthFolder, '/', name, '/', filename]);
+    img = imread(filepath_img);
+    
+    try
+        gt = imread(filepath_gt);
+    catch exception
+        fprintf('Can''t load the ground-truth : %s\n', exception.message)
+        gt = ones(size(img));
+    end        
 end