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 1.0)
    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 * 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> * Image<Gray, float32> =

    let filteredGreenWithoutInfection = filteredGreen.Copy()
    ImgTools.areaCloseF filteredGreenWithoutInfection (int config.InfectionArea)

    let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
    ImgTools.areaCloseF filteredGreenWithoutStain (int config.StainArea)

    // We use the filtered image to find the dark stain.

    // With K-Means.
    let kmeansResults = logTime "Finding fg/bg (k-means)" (fun () -> KMeans.kmeans (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0)
    let { KMeans.mean_bg = value_bg; KMeans.mean_fg = value_fg; KMeans.d_fg = d_fg } = kmeansResults

    // With K-Medians.
    (* let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0) // FIXME: avoid converting this again in MainAnalysis
    let { KMedians.median_bg = value_bg; KMedians.median_fg = value_fg; KMedians.d_fg = d_fg } = kmediansResults *)

    let darkStain = d_fg.Cmp(value_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
    darkStain._And(filteredGreenWithoutInfection.Cmp(value_fg, CvEnum.CmpType.LessThan))

    let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
        let diff = closed - (img * level)
        diff._ThresholdBinary(Gray(0.0), Gray(255.))
        diff.Convert<Gray, byte>()

    let infectionMarker = marker filteredGreen filteredGreenWithoutInfection config.Parameters.infectionLevel
    let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel

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