* Use 'mmlabel' to detect schizonts instead of a complex code involving reconstructions.

* Use of a regional minimum for the saturation component.

diff --git a/src/DetectionOfParasites.m b/src/DetectionOfParasites.m
index 8d3b2be..830f484 100644 (file)
--- a/src/DetectionOfParasites.m
+++ b/src/DetectionOfParasites.m
@@ -23,14 +23,16 @@ function [THS, c] = DetectionOfParasites(imgRGB)
 
     % p. 136: median filter to smooth the noise and 
     % area closing to enhance the bright objects and make flatter, darker and cleaner the image background.
-    imgFiltered{1} = mmareaclose(medfilt2(imgH, [5, 5]), 400); % Hue.
-    imgFiltered{2} = mmareaclose(medfilt2(imgS, [5, 5]), 400); % Saturation.
-    imgFiltered{3} = mmareaclose(medfilt2(imgV, [5, 5]), 400); % Value.
+    medianFilterWindow = [5, 5];
+    imgFiltered{1} = mmareaclose(medfilt2(imgH, medianFilterWindow), 200); % Hue.
+    % We use an opening fot the saturation because the parasites are darker than the rest of the image.
+    imgFiltered{2} = mmareaopen(medfilt2(imgS, medianFilterWindow), 200); % Saturation.
+    imgFiltered{3} = mmareaclose(medfilt2(imgV, medianFilterWindow), 200); % Value.
     
     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'));
@@ -47,7 +49,7 @@ function [THS, c] = DetectionOfParasites(imgRGB)
 
     sizeDistribution = zeros(redCellMaxSize, 1);
     parfor k = 1:redCellMaxSize 
-        SE = mmsedisk(k, '2D', 'OCTAGON'); % TODO : tester avec 'euclidean'
+        SE = mmsedisk(k, '2D', 'OCTAGON'); % 'EUCLIDEAN' is more precise.
         imgOpened = mmopen(imgFiltered{2}, SE);
         A = funVolume(imgOpened);
         N = 1 - A / volImg;
@@ -70,11 +72,15 @@ function [THS, c] = DetectionOfParasites(imgRGB)
     %% Regional extrema
     % The size of the SE (c) must be equal to the size of red cells (see granulometry below).
 
-    regionalMaxSE = mmsedisk(c, '2D', 'OCTAGON');
+    regionalExtremumSE = mmsedisk(c, '2D', 'OCTAGON');
 
+    % The functions 'mmregmax' and 'mmregmin' are very time consuming!
     parfor i = 1:3
-        % This operation is very time consuming!
-        M{i} = mmregmax(imgFiltered{i}, regionalMaxSE);
+        if i == 2
+            M{i} = mmregmin(imgFiltered{i}, regionalExtremumSE); % Special case for the saturation component.
+        else
+            M{i} = mmregmax(imgFiltered{i}, regionalExtremumSE);
+        end
     end
 
     nucleiSE = mmsedisk(nucleiRadius, '2D', 'OCTAGON');
@@ -85,7 +91,7 @@ function [THS, c] = DetectionOfParasites(imgRGB)
     muS = funVolume(uint8(MHS) .* imgFiltered{2}) / volumeMHS;
 
     TH = im2bw(imgFiltered{1}, double(muH) / 255);
-    TS = im2bw(imgFiltered{2}, double(muS) / 255);    
+    TS = ~im2bw(imgFiltered{2}, double(muS) / 255);    
     
     THS = TH & TS;
 

diff --git a/src/DetectionOfSchizonts.m b/src/DetectionOfSchizonts.m
index e16327d..c2b53ee 100644 (file)
--- a/src/DetectionOfSchizonts.m
+++ b/src/DetectionOfSchizonts.m
@@ -8,21 +8,18 @@ function [schizonts] = DetectionOfSchizonts(THS, c)
     
     %% Extract all sets.
     sets = {};
+    labelizedTHS = mmlabel(THS, mmsedisk(1, '2D', 'OCTAGON')); % We choose a SE which is not a point to fill side-by-side areas.
+    
     n = 1;
-    remainingTHS = THS;
-    marker = false(size(THS));    
     while 1
-        [i, j] = find(remainingTHS, 1);    
-        if ~isempty(i)
-            marker(i, j) = 1;
-            sets{n} = mminfrec(marker, remainingTHS); %#ok<AGROW> % Reconstruction by dilation. 
-            remainingTHS = remainingTHS & ~sets{n};
-            n = n + 1;
-            marker(i, j) = 0;
+        set = labelizedTHS == n;
+        if any(any(set))
+            sets{n} = set;
         else
             break
         end
-    end
+        n = n + 1;
+    end    
     
     %% Check the Hausdorff distance between each set combination by dilation.
     for i = 1:length(sets)

diff --git a/src/Main.m b/src/Main.m
index f5dd0a4..a7f6ca5 100644 (file)
--- a/src/Main.m
+++ b/src/Main.m
@@ -1,5 +1,6 @@
 %% Parameters
 
+delete('../output')
 mkdir('../output') % Just in case the 'output' directory doesn't exist.
 
 % Hue is unusable for '1305121398'/'0001'
@@ -7,10 +8,10 @@ mkdir('../output') % Just in case the 'output' directory doesn't exist.
 % imageFolder = '1307210661'; % 2.
 % imageFolder = '1401063467'; % 3.
 % imageFolder = '1405022890'; % 4.
-imageFolder = '1409191647'; % 9.
-% imageFolder = '1412151257'; % 10.
+% imageFolder = '1409191647'; % 9.
+imageFolder = '1412151257'; % 10. (Gamma)
 
-imageNumber = '0004';
+imageNumber = 'Gamma-0.8-0002';
 
 scaleFactor = 0.6;
 
@@ -24,10 +25,21 @@ gtResampled = imresize(gt, scaleFactor);
 imwrite(imgRGBResampled, '../output/imgRGB.png')
 imwrite(gtResampled, '../output/gt.png')
 
+disp('1) Detection of parasites ...')
 [THS, c] = DetectionOfParasites(imgRGBResampled);
+
+disp('2) Detection of white cells ...')
 [WBC] = DetectionOfWhiteCells(THS, c);
-[Shizonts] = DetectionOfSchizonts(THS, c);
 
-infectedRedCells = THS - WBC - Shizonts;
-imwrite(infectedRedCells, '../output/infectedRedCells.png')
+disp('3) Detection of schizonts ...')
+[schizonts] = DetectionOfSchizonts(THS, c);
+
+disp('Segmentation of red cells ...')
+SegmentationOfRedCells();
+
+% infectedRedCells = THS - WBC - schizonts;
+% imwrite(infectedRedCells, '../output/infectedRedCells.png')
+
+
+disp('Finished')
 

diff --git a/src/SegmentationOfRedCells.m b/src/SegmentationOfRedCells.m
index fe6292b..4a86c1b 100644 (file)
--- a/src/SegmentationOfRedCells.m
+++ b/src/SegmentationOfRedCells.m
@@ -1 +1,4 @@
-function 
\ No newline at end of file
+function [] = DetectionOfSchizonts()
+
+
+end
\ No newline at end of file