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

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

diff --git a/Parasitemia/Parasitemia/ParasitesMarker.fs b/Parasitemia/Parasitemia/ParasitesMarker.fs
deleted file mode 100644 (file)
index 671755c..0000000
--- a/Parasitemia/Parasitemia/ParasitesMarker.fs
+++ /dev/null
@@ -1,86 +0,0 @@
-module ParasitesMarker
-
-open System.Drawing
-open System.Linq
-
-open Emgu.CV
-open Emgu.CV.Structure
-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 = logTime "Finding fg/bg (k-medians)" (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
-
-