X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FParasitesMarker.fs;h=b89caa68c02760b2dc4af0af0be28b48d4d12a1a;hp=e3c3ca2b3c8e17c2ddf8f5b381192a3c3bb41fe2;hb=2d712781def419c9acc98368f7102b19b064f16d;hpb=828e126c88524d3dc123abc966a132532aed118b

diff --git a/Parasitemia/ParasitemiaCore/ParasitesMarker.fs b/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
index e3c3ca2..b89caa6 100644
--- a/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
+++ b/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
@@ -7,53 +7,60 @@ open Emgu.CV
 open Emgu.CV.Structure
 
 open Utils
+open Histogram
+open Otsu
+open Morpho
+open ImgTools
 
-type Result = {
-    darkStain: Image<Gray, byte> // Colored pixel, it's independent of the size of the areas. It corresponds to white cells, schizontes, gametocytes, throphozoites.
-    nucleus: Image<Gray, byte> // Parasite nucleus. It may contain some debris. It shouldn't contain thrombocytes or larger elements.
-    cytoplasm: Image<Gray, byte> } // Parasite cytoplasm.
+type Result =
+    {
+        darkStain : Image<Gray, byte> // Colored pixel, it's independent of the size of the areas. It corresponds to white cells, schizontes, gametocytes, throphozoites.
+        nucleus : Image<Gray, byte> // Parasite nucleus. It may contain some debris. It shouldn't contain thrombocytes or larger elements.
+        parasite : Image<Gray, byte> // The whole parasites.
+    }
 
-let find (img: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
+let find (img : Image<Gray, float32>) (config : Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
 
-    let imgFilteredParasite = ImgTools.gaussianFilter img config.LPFStandardDeviationParasite
-
-    let filteredGreenWithoutNucleus = imgFilteredParasite.Copy()
-    ImgTools.areaCloseF filteredGreenWithoutNucleus (roundInt config.RBCRadius.NucleusArea)
+    let imgWithoutNucleus = img.Copy ()
+    areaCloseF imgWithoutNucleus (roundInt config.RBCRadius.NucleusArea)
 
     let darkStain =
         // We use the filtered image to find the dark stain.
         let _, mean_fg, mean_bg =
-            let hist = ImgTools.histogramImg filteredGreenWithoutNucleus 300
-            ImgTools.otsu hist
-        filteredGreenWithoutNucleus.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel + (float mean_fg), CvEnum.CmpType.LessThan)
+            let hist = histogramImg imgWithoutNucleus 300
+            otsu hist
+        imgWithoutNucleus.Cmp (float mean_fg - config.Parameters.darkStainLevel * float (mean_bg - mean_fg), CvEnum.CmpType.LessThan)
 
-    let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
-        let diff = img.Copy()
-        diff._Mul(level)
-        CvInvoke.Subtract(closed, diff, diff)
-        diff._ThresholdBinary(Gray(0.0), Gray(255.))
-        diff.Convert<Gray, byte>()
+    let marker (img : Image<Gray, float32>) (closed : Image<Gray, float32>) (level : float) : Image<Gray, byte> =
+        let diff = img.Copy ()
+        diff._Mul level
+        CvInvoke.Subtract (closed, diff, diff)
+        diff._ThresholdBinary (Gray 0.0, Gray 255.)
+        diff.Convert<Gray, byte> ()
 
-    let nucleusMarker = marker imgFilteredParasite filteredGreenWithoutNucleus (1. / config.Parameters.infectionSensitivity)
+    // Nucleus.
+    let nucleusMarker = marker img imgWithoutNucleus (1. / config.Parameters.infectionSensitivity)
 
-    let filteredGreenWithoutCytoplasm = imgFilteredParasite.CopyBlank()
+    // Cytoplasm.
+    let imgWithoutParasite = img.CopyBlank ()
     let kernelSize =
-        let size = roundInt (config.RBCRadius.Pixel / 5.f)
+        let size = roundInt config.RBCRadius.CytoplasmSize
         if size % 2 = 0 then size + 1 else size
     use kernel =
-        if kernelSize <= 3
-        then
-            CvInvoke.GetStructuringElement(CvEnum.ElementShape.Rectangle, Size(3, 3), Point(-1, -1))
+        if kernelSize <= 3 then
+            CvInvoke.GetStructuringElement (CvEnum.ElementShape.Rectangle, Size (3, 3), Point (-1, -1))
         else
-            CvInvoke.GetStructuringElement(CvEnum.ElementShape.Ellipse, Size(kernelSize, kernelSize), Point(-1, -1))
+            CvInvoke.GetStructuringElement (CvEnum.ElementShape.Ellipse, Size (kernelSize, kernelSize), Point (-1, -1))
 
-    CvInvoke.MorphologyEx(imgFilteredParasite, filteredGreenWithoutCytoplasm, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
-    let cytoplasmMarker = marker imgFilteredParasite filteredGreenWithoutCytoplasm (1. / config.Parameters.cytoplasmSensitivity)
+    CvInvoke.MorphologyEx (img, imgWithoutParasite, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
+    let parasiteMarker = marker img imgWithoutParasite (1. / config.Parameters.cytoplasmSensitivity)
 
-    { darkStain = darkStain
-      nucleus = nucleusMarker
-      cytoplasm = cytoplasmMarker },
-    filteredGreenWithoutCytoplasm,
-    filteredGreenWithoutNucleus
+    {
+        darkStain = darkStain
+        nucleus = nucleusMarker
+        parasite = parasiteMarker
+    },
+    imgWithoutParasite,
+    imgWithoutNucleus