From 20705acd23212f557b714364b959a602dd1fd3e9 Mon Sep 17 00:00:00 2001
From: Greg Burri <greg.burri@gmail.com>
Date: Fri, 1 May 2015 16:35:47 +0200
Subject: [PATCH] Add a connectivity parameter when identifying the schizonts.

---
 src/DetectionOfSchizonts.m | 38 +++++++++++++++++++++++++++++---------
 1 file changed, 29 insertions(+), 9 deletions(-)

diff --git a/src/DetectionOfSchizonts.m b/src/DetectionOfSchizonts.m
index c2b53ee..823d9c5 100644
--- a/src/DetectionOfSchizonts.m
+++ b/src/DetectionOfSchizonts.m
@@ -2,7 +2,8 @@
 %  THS:
 %  c: (TODO: should be the average red cell size)
 function [schizonts] = DetectionOfSchizonts(THS, c)    
-
+    
+    schizontsConnectivityMin = 3; % Minimum cluster size when detecting schizonts.
     redCellsSE = mmsedisk(c, '2D', 'OCTAGON');    
     schizonts = zeros(size(THS), 'uint8');    
     
@@ -20,25 +21,44 @@ function [schizonts] = DetectionOfSchizonts(THS, c)
         end
         n = n + 1;
     end    
+        
+    %% Check the Hausdorff distance between each set combination by dilation -> create a graph by populate 'adjacencyMatrix'.
+    adjacencyMatrix = spalloc(length(sets), length(sets), 500);
+    addedSet = zeros(length(sets));
     
-    %% Check the Hausdorff distance between each set combination by dilation.
     for i = 1:length(sets)
         setA = sets{i};
-        if isempty(setA)
-            continue
-        end
         dilatedSetA = mmdil(setA, redCellsSE);
         for j = 1:length(sets)
             setB = sets{j};
-            if isequal(setB, setA) || isempty(setB)
+            if isequal(setB, setA) || addedSet(j)
                 continue
             end
             if (dilatedSetA & setB) == setB % If B is a subset of A -> there are both in a Hausdorff distance of 2*c.
-                schizonts = schizonts | setA | setB;
-                sets{i} = [];
-                sets{j} = [];
+                adjacencyMatrix(i, j) = 1;
+                adjacencyMatrix(j, i) = 1;
+                addedSet(i) = 1;
             end
         end
+    end
+    
+    %% Fill 'schizonts' by testing the connectivity of each cluster set.
+    [~, C] = graphconncomp(adjacencyMatrix, 'Directed', false, 'Weak', true);
+    n = 1;    
+    while 1
+        relatedSets = C == n;
+        if ~any(relatedSets)
+            break
+        end
+        if sum(relatedSets) >= schizontsConnectivityMin
+            for i = find(relatedSets)
+                if ~isempty(sets{i})
+                    schizonts = schizonts | sets{i};
+                    sets{i} = [];                    
+                end
+            end
+        end
+        n = n + 1;
     end    
     
     imwrite(schizonts, '../output/schizonts.png')
-- 
2.45.2