Change the parasite detection method.

[master-thesis.git] / Parasitemia / Parasitemia / ParasitesMarker2.fs

diff --git a/Parasitemia/Parasitemia/ParasitesMarker2.fs b/Parasitemia/Parasitemia/ParasitesMarker2.fs
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+++ b/Parasitemia/Parasitemia/ParasitesMarker2.fs
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+module ParasitesMarker2
+
+open System.Drawing
+
+open Emgu.CV
+open Emgu.CV.Structure
+
+type Result = {
+    darkStain: Image<Gray, byte>
+    stain: Image<Gray, byte>
+    infection: 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 find (filteredGreen: Image<Gray, byte>) (filteredGreenFloat: Image<Gray, float32>) (kmediansResult: KMedians.Result) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
+
+    // We use the filtered image to find the dark stain.
+    let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResult
+    let darkStain = d_fg.Cmp(median_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
+    darkStain._And(filteredGreenFloat.Cmp(median_fg, CvEnum.CmpType.LessThan))
+
+    let marker (area: int) (threshold: float) : Image<Gray, byte> * Image<Gray, byte> =
+        let closed = filteredGreen.Copy()
+        ImgTools.areaClose closed area
+        let diff = closed - filteredGreen
+
+        let min = ref [| 0. |]
+        let minLocation = ref <| [| Point() |]
+        let max = ref [| 0. |]
+        let maxLocation = ref <| [| Point() |]
+        diff.MinMax(min, max, minLocation, maxLocation)
+
+        diff._ThresholdBinary((!max).[0] * threshold |> Gray, Gray(255.))
+        diff, closed
+
+    let parasitesMarker, filteredGreenWithoutParasites  = marker (int config.ParasiteArea) config.Parameters.infectionLevel
+    let stainMarker, filteredGreenWithoutStain = marker (int config.StainArea) config.Parameters.stainLevel
+
+    { darkStain = darkStain
+      stain = parasitesMarker
+      infection = stainMarker },
+    filteredGreenWithoutParasites,
+    filteredGreenWithoutStain
+
+
+
+
+