module ParasitemiaCore.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 = 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 (img: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =

    let imgFilteredInfection = ImgTools.gaussianFilter img config.LPFStandardDeviationParasite
    let filteredGreenWithoutInfection = imgFilteredInfection.Copy()
    ImgTools.areaCloseF filteredGreenWithoutInfection (roundInt config.RBCRadius.NucleusArea)

    (*
    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 imgFilteredInfection filteredGreenWithoutInfection (1. / config.Parameters.infectionSensitivity)

    let imgFilteredStain = ImgTools.gaussianFilter img config.LPFStandardDeviationStain
    let areaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
    //ImgTools.areaOpenF imgFilteredStain areaOpening

    let filteredGreenWithoutStain = imgFilteredStain.CopyBlank()
    let kernelSize =
        let size = roundInt (config.RBCRadius.Pixel / 5.f)
        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(imgFilteredStain, filteredGreenWithoutStain, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
    let stainMarker = marker (*filteredGreenWithoutInfection*) imgFilteredStain filteredGreenWithoutStain (1. / config.Parameters.cytoplasmSensitivity)

    //
    (*let blackTopHat = filteredGreenWithoutStain.CopyBlank()
    CvInvoke.Subtract(filteredGreenWithoutStain, imgFilteredStain, blackTopHat)
    ImgTools.saveImg blackTopHat "blackTopHat.png"*)

    { darkStain = darkStain
      infection = infectionMarker
      stain = stainMarker },
    filteredGreenWithoutStain,
    filteredGreenWithoutInfection