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 imgFloat = img.Convert<Bgr, float32>()
    use scaledImg = if config.scale = 1.0 then imgFloat else imgFloat.Resize(config.scale, CvEnum.Inter.Area)

    use green = scaledImg.Item(1)

    use filteredGreen = (gaussianFilter green config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter green config.doGSigma2)

    use sobelKernel =
        new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
                                        [ 2.0f; 0.0f; -2.0f ]
                                        [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))

    use xEdges = filteredGreen.Convolution(sobelKernel).Convert<Gray, float>()
    use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()

    let xEdgesData = xEdges.Data
    let yEdgesData = yEdges.Data
    for r in 0..xEdges.Rows-1 do
        xEdgesData.[r, 0, 0] <- 0.0
        xEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
        yEdgesData.[r, 0, 0] <- 0.0
        yEdgesData.[r, xEdges.Cols-1, 0] <- 0.0

    for c in 0..xEdges.Cols-1 do
        xEdgesData.[0, c, 0] <- 0.0
        xEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
        yEdgesData.[0, c, 0] <- 0.0
        yEdgesData.[xEdges.Rows-1, c, 0] <- 0.0

    use magnitudes = new Matrix<float>(xEdges.Size)
    CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).

    let min = ref 0.0
    let minLocation = ref <| Point()
    let max = ref 0.0
    let maxLocation = ref <| Point()
    magnitudes.MinMax(min, max, minLocation, maxLocation)

    use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
    use edges = new Matrix<byte>(xEdges.Size)
    CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore

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

    let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)

    let parasites = ParasitesMarker.find green filteredGreen kmediansResults config

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

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

    // Output pictures if debug flag is set.
    match config.debug with
    | DebugOn output ->
        let buildFileName postfix = System.IO.Path.Combine(output, 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)) 0.1
        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")

        saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.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")
    | _ -> ()

    cells