module ImageAnalysis

open System
open System.Drawing

open Emgu.CV
open Emgu.CV.Structure

open Utils
open ImgTools
open Config
open Types


let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =

    use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)

    use green = scaledImg.Item(1)

    let greenFloat = green.Convert<Gray, float32>()

    let filteredGreen = gaussianFilter greenFloat config.Parameters.preFilterSigma

    (*let maximaImg = filteredGreen.Copy()
    let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
    for m in maxima do
        ImgTools.drawPoints maximaImg m 255uy

    let greenOpen1 = filteredGreen.Copy()
    logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)

    let initialAreaOpen = 2000
    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpen)

    config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float

    let secondAreaOpen = int <| config.RBCArea / 3.
    if secondAreaOpen > initialAreaOpen
    then
        logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)

    let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
    //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config

    let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain

    logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)

    let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
        let matchingEllipses = Ellipse.find edges xGradient yGradient config
        matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )

    let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)

    // Output pictures if debug flag is set.
    match config.Debug with
    | DebugOn output ->
        let dirPath = System.IO.Path.Combine(output, name)
        System.IO.Directory.CreateDirectory dirPath |> ignore

        let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)

        //saveImg canny (buildFileName " - canny.png")

        saveMat (edges * 255.0) (buildFileName " - edges.png")

        saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
        saveImg parasites.stain (buildFileName " - parasites - stain.png")
        saveImg parasites.infection (buildFileName " - parasites - infection.png")

        let imgAllEllipses = img.Copy()
        drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
        saveImg imgAllEllipses (buildFileName " - ellipses - all.png")

        let imgEllipses = img.Copy()
        drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
        saveImg imgEllipses (buildFileName " - ellipses.png")

        let imgCells = img.Copy()
        drawCells imgCells false cells
        saveImg imgCells (buildFileName " - cells.png")

        let imgCells' = img.Copy()
        drawCells imgCells' true cells
        saveImg imgCells' (buildFileName " - cells - full.png")

        let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
        for m in ImgTools.findMaxima filteredGreenMaxima do
            ImgTools.drawPoints filteredGreenMaxima m 255.f
        saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")

        saveImg filteredGreen (buildFileName " - filtered.png")
        saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
        saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")

        saveImg green (buildFileName " - green.png")

        use blue  = scaledImg.Item(0)
        saveImg blue (buildFileName " - blue.png")

        use red = scaledImg.Item(2)
        saveImg red (buildFileName " - red.png")
    | _ -> ()

    cells