module ParasitemiaCore.ParasitesMarker

open System.Drawing
open System.Linq

open Emgu.CV
open Emgu.CV.Structure

open Utils
open Histogram
open Otsu
open Morpho
open ImgTools

type Result = {
    darkStain: Image<Gray, byte> // Colored pixel, it's independent of the size of the areas. It corresponds to white cells, schizontes, gametocytes, throphozoites.
    nucleus: Image<Gray, byte> // Parasite nucleus. It may contain some debris. It shouldn't contain thrombocytes or larger elements.
    parasite: Image<Gray, byte> } // The whole parasites.

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

    let imgWithoutNucleus = img.Copy()
    areaCloseF imgWithoutNucleus (roundInt config.RBCRadius.NucleusArea)

    let darkStain =
        // We use the filtered image to find the dark stain.
        let _, mean_fg, mean_bg =
            let hist = histogramImg imgWithoutNucleus 300
            otsu hist
        imgWithoutNucleus.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 nucleusMarker = marker img imgWithoutNucleus (1. / config.Parameters.infectionSensitivity)

    let imgWithoutParasite = img.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(img, imgWithoutParasite, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
    let parasiteMarker = marker img imgWithoutParasite (1. / config.Parameters.cytoplasmSensitivity)

    { darkStain = darkStain
      nucleus = nucleusMarker
      parasite = parasiteMarker },
    imgWithoutParasite,
    imgWithoutNucleus