Add a logger assembly and split the main assembly in two : the UI and the parasitemia...

[master-thesis.git] / Parasitemia / ParasitemiaCore / ParasitesMarker.fs

diff --git a/Parasitemia/ParasitemiaCore/ParasitesMarker.fs b/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
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+++ b/Parasitemia/ParasitemiaCore/ParasitesMarker.fs
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+module ParasitemiaCore.ParasitesMarker
+
+open System.Drawing
+open System.Linq
+
+open Emgu.CV
+open Emgu.CV.Structure
+
+open Logger
+
+open Utils
+
+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>()
+
+    { darkStain = darkStain;
+      stain = findSmears 10. 0.9
+      infection = findSmears 2.2 0.87 },
+    tmp,
+    tmp
+
+// 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 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
+
+