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 =
    let 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 (float config.Parameters.preFilterSigma)

    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)

    config.RBCRadius <- logTime "Granulometry" (fun() -> Granulometry.findRadius (filteredGreen.Convert<Gray, byte>()) (10, 100) 0.3 |> float32)

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

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

    let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
    logTime "Removing small connected components from thinning" (fun () -> removeArea edges (config.RBCRadius ** 2.f / 50.f |> int))

    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)

        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