module ParasitesMarker

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 (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (kmediansResult: KMedians.Result) (config: Config.Config) : Result =

    let green = ImgTools.gaussianFilter green 1.0

    // 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.darkStainLevel, CvEnum.CmpType.GreaterThan)
    darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))
    darkStain._And(fg)

    let fgFloat = (fg / 255.0).Convert<Gray, float32>()
    let greenWithoutBg = green.Copy()
    greenWithoutBg.SetValue(Gray(0.0), fg.Not())

    let findSmears (sigma: float) (level: float) : Image<Gray, byte> =
        let greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
        let fgSmoothed = ImgTools.gaussianFilter fgFloat sigma

        let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level), CvEnum.CmpType.LessThan)
        smears._And(fg)
        smears

    { darkStain = darkStain;
      stain = findSmears config.stainSigma config.stainLevel
      infection = findSmears config.infectionSigma config.infectionLevel }