module ParasitesMarker2

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 find (filteredGreen: Image<Gray, byte>) (filteredGreenFloat: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =

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

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

    // We use the filtered image to find the dark stain.
    let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0) // FIXME: avoid converting again this in MainAnalysis
    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(filteredGreenWithoutInfection.Cmp(median_fg, CvEnum.CmpType.LessThan))

    let marker (img: Image<Gray, byte>) (closed: Image<Gray, byte>) (level: float) : Image<Gray, byte> =
        let diff = closed - img

        let min = ref [| 0. |]
        let minLocation = ref <| [| Point() |]
        let max = ref [| 0. |]
        let maxLocation = ref <| [| Point() |]
        diff.MinMax(min, max, minLocation, maxLocation)
        let max = (!max).[0]

        let threshold = 0.2 * max
        let diff' = diff - threshold

        let m = MathNet.Numerics.Statistics.StreamingStatistics.Mean(seq {
                for m in ImgTools.findMaxima diff' do
                    let p = m.First()
                    yield diff'.Data.[p.Y, p.X, 0] |> float }) + threshold

        let valueThreshold = m * level

        diff._ThresholdBinary(Gray(valueThreshold), Gray(255.))
        diff

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

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