From 785a7ea4885e87d76f0b1fb1c715230a08389558 Mon Sep 17 00:00:00 2001
From: Greg Burri <greg.burri@gmail.com>
Date: Wed, 23 Dec 2015 12:29:51 +0100
Subject: [PATCH] Change the way the parasites are detected.

---
 Parasitemia/Parasitemia/Config.fs           |  4 ++--
 Parasitemia/Parasitemia/ParasitesMarker2.fs | 14 +++++++++++---
 Parasitemia/Parasitemia/Program.fs          |  4 ++--
 3 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/Parasitemia/Parasitemia/Config.fs b/Parasitemia/Parasitemia/Config.fs
index 3e3a06c..5cf392c 100644
--- a/Parasitemia/Parasitemia/Config.fs
+++ b/Parasitemia/Parasitemia/Config.fs
@@ -23,11 +23,11 @@ type Parameters = {
     maxDarkStainRatio: float
 
     stainArea: float // Factor of a RBC area. 0.5 means the half of RBC area.
-    stainLevel: float // [0, 1]
+    stainLevel: float // [0, 2]
     maxStainRatio: float // [0, 1]
 
     infectionArea: float // Factor of a RBC area. 0.5 means the half of RBC area.
-    infectionLevel: float // [0, 1]
+    infectionLevel: float // [0, 2]
     parasitePixelsRequired: int
 
     standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation
diff --git a/Parasitemia/Parasitemia/ParasitesMarker2.fs b/Parasitemia/Parasitemia/ParasitesMarker2.fs
index 6afef44..42645b4 100644
--- a/Parasitemia/Parasitemia/ParasitesMarker2.fs
+++ b/Parasitemia/Parasitemia/ParasitesMarker2.fs
@@ -1,6 +1,7 @@
 module ParasitesMarker2
 
 open System.Drawing
+open System.Linq
 
 open Emgu.CV
 open Emgu.CV.Structure
@@ -30,7 +31,7 @@ let find (filteredGreen: Image<Gray, byte>) (filteredGreenFloat: Image<Gray, flo
     let darkStain = d_fg.Cmp(median_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
     darkStain._And(filteredGreenWithoutInfection.Cmp(median_fg, CvEnum.CmpType.LessThan))
 
-    let marker (img: Image<Gray, byte>) (closed: Image<Gray, byte>) (threshold: float) : Image<Gray, byte> =
+    let marker (img: Image<Gray, byte>) (closed: Image<Gray, byte>) (level: float) : Image<Gray, byte> =
         let diff = closed - img
 
         let min = ref [| 0. |]
@@ -40,8 +41,15 @@ let find (filteredGreen: Image<Gray, byte>) (filteredGreenFloat: Image<Gray, flo
         diff.MinMax(min, max, minLocation, maxLocation)
         let max = (!max).[0]
 
-        let limitThreshold = 0.1
-        let valueThreshold = (*if max < limitThreshold * (median_bg - median_fg) then max / 2. else *) max * threshold
+        let threshold = 0.2 * max
+        let diff' = diff - threshold
+
+        let m = MathNet.Numerics.Statistics.StreamingStatistics.Mean(seq {
+                for m in ImgTools.findMaxima diff' do
+                    let p = m.First()
+                    yield diff'.Data.[p.Y, p.X, 0] |> float }) + threshold
+
+        let valueThreshold = m * level
 
         diff._ThresholdBinary(Gray(valueThreshold), Gray(255.))
         diff
diff --git a/Parasitemia/Parasitemia/Program.fs b/Parasitemia/Parasitemia/Program.fs
index 781d9ad..25c707d 100644
--- a/Parasitemia/Parasitemia/Program.fs
+++ b/Parasitemia/Parasitemia/Program.fs
@@ -73,11 +73,11 @@ let main args =
                 maxDarkStainRatio = 0.1
 
                 infectionArea = 0.012 // 1.2 %
-                infectionLevel = 0.2
+                infectionLevel = 0.85
                 parasitePixelsRequired = 1
 
                 stainArea = 0.08
-                stainLevel = 0.1
+                stainLevel = 0.85
                 maxStainRatio = 0.12 // 12 %
 
                 standardDeviationMaxRatio = 0.55
-- 
2.43.0