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> }

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

    // 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 } = KMedians.kmedians filteredGreen 1.0
    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 }