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_fg - config.Parameters.darkStainLevel * float (mean_bg - 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> ()

    // Nucleus.
    let nucleusMarker = marker img imgWithoutNucleus (1. / config.Parameters.infectionSensitivity)

    // Cytoplasm.
    let imgWithoutParasite = img.CopyBlank ()
    let kernelSize =
        let size = roundInt config.RBCRadius.CytoplasmSize
        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