X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FParasitesMarker.fs;h=b89caa68c02760b2dc4af0af0be28b48d4d12a1a;hp=22ea041be57de154cc494a7385e650013bdb2121;hb=2d712781def419c9acc98368f7102b19b064f16d;hpb=4bfa3cbdc6145e6944f02e24829ab2ef3a851ac1

diff --git a/Parasitemia/ParasitemiaCore/ParasitesMarker.fs b/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
index 22ea041..b89caa6 100644
--- a/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
+++ b/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
@@ -6,84 +6,61 @@ open System.Linq
 open Emgu.CV
 open Emgu.CV.Structure
 
-open Logger
-
 open Utils
+open Histogram
+open Otsu
+open Morpho
+open ImgTools
 
-type Result = {
-    darkStain: Image<Gray, byte>
-    infection: Image<Gray, byte>
-    stain: Image<Gray, byte> }
-
-// Create three binary markers :
-// * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
-// * 'Stain' corresponds to the stain around the parasites.
-// * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
-let findMa (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
-    // We use the filtered image to find the dark stain.
-    let kmediansResults = Log.LogWithTime("Finding fg/bg (k-medians)", Severity.USER, (fun () -> KMedians.kmedians filteredGreen))
-    let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResults
-    let darkStain = d_fg.Cmp(median_bg * float config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
-    darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))
-    darkStain._And(fg)
-
-    let fgFloat = (fg / 255.0).Convert<Gray, float32>()
-    use greenWithoutBg = ImgTools.gaussianFilter green 1.0
-    greenWithoutBg.SetValue(Gray(0.0), fg.Not())
-
-    let findSmears (sigma: float) (level: float) : Image<Gray, byte> =
-        use greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
-        use fgSmoothed = ImgTools.gaussianFilter fgFloat sigma
-        let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level), CvEnum.CmpType.LessThan)
-        smears._And(fg)
-        smears
-
-    let tmp = filteredGreen.Convert<Gray, byte>()
+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.
+    }
 
-    { darkStain = darkStain;
-      stain = findSmears 10. 0.9
-      infection = findSmears 2.2 0.87 },
-    tmp,
-    tmp
+let find (img : Image<Gray, float32>) (config : Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
 
-// Create three binary markers :
-// * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
-// * 'Stain' corresponds to the stain around the parasites.
-// * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
-let find (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> =
-    use filteredGreenWithoutInfection = filteredGreen.Copy()
-    ImgTools.areaCloseF filteredGreenWithoutInfection (int config.RBCRadius.InfectionArea)
-
-    let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
-    ImgTools.areaCloseF filteredGreenWithoutStain (int config.RBCRadius.StainArea)
+    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 filteredGreenWithoutInfection 300
-            ImgTools.otsu hist
-        filteredGreenWithoutInfection.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel + (float 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 infectionMarker = marker filteredGreen filteredGreenWithoutInfection (1. / config.Parameters.infectionSensitivity)
-    let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain (1. / config.Parameters.stainSensitivity)
-
-    // TODO: comprendre pourquoi des valeurs sont negatives!?!?
-    (*
-    let blackTopHat = filteredGreen.CopyBlank()
-    CvInvoke.Subtract(filteredGreenWithoutInfection, filteredGreen, blackTopHat)
-    ImgTools.saveImg (ImgTools.normalizeAndConvert blackTopHat) "BottomHat.png"
-    *)
-
-    { darkStain = darkStain
-      infection = infectionMarker
-      stain = stainMarker },
-    filteredGreenWithoutStain
+            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> ()
+
+    // Nucleus.
+    let nucleusMarker = marker img imgWithoutNucleus (1. / config.Parameters.infectionSensitivity)
+
+    // Cytoplasm.
+    let imgWithoutParasite = img.CopyBlank ()
+    let kernelSize =
+        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))
+        else
+            CvInvoke.GetStructuringElement (CvEnum.ElementShape.Ellipse, Size (kernelSize, kernelSize), Point (-1, -1))
+
+    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
+        parasite = parasiteMarker
+    },
+    imgWithoutParasite,
+    imgWithoutNucleus