module ImgTools

open System
open System.Drawing
open System.Collections.Generic
open System.Linq

open Emgu.CV
open Emgu.CV.Structure

open Utils
open Heap

// Normalize image values between 0uy and 255uy.
let normalizeAndConvert (img: Image<Gray, float32>) : Image<Gray, byte> =
    let min = ref [| 0.0 |]
    let minLocation = ref <| [| Point() |]
    let max = ref [| 0.0 |]
    let maxLocation = ref <| [| Point() |]
    img.MinMax(min, max, minLocation, maxLocation)
    ((img - (!min).[0]) / ((!max).[0] - (!min).[0]) * 255.0).Convert<Gray, byte>()


let gaussianFilter (img : Image<'TColor, 'TDepth>) (standardDeviation : float) : Image<'TColor, 'TDepth> =
    let size = 2 * int (ceil (4.0 * standardDeviation)) + 1
    img.SmoothGaussian(size, size, standardDeviation, standardDeviation)


type Points = HashSet<Point>

let drawPoints (img: Image<Gray, byte>) (points: Points) (intensity: byte) =
    for p in points do
        img.Data.[p.Y, p.X, 0] <- intensity


type ExtremumType =
    | Maxima = 1
    | Minima = 2

let findExtremum (img: Image<Gray, byte>) (extremumType: ExtremumType) : IEnumerable<Points> =
    let w = img.Width
    let h = img.Height
    let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]

    let imgData = img.Data
    let suppress: bool[,] = Array2D.zeroCreate h w

    let result = List<List<Point>>()

    let flood (start: Point) : List<List<Point>> =
        let sameLevelToCheck = Stack<Point>()
        let betterLevelToCheck = Stack<Point>()
        betterLevelToCheck.Push(start)

        let result' = List<List<Point>>()

        while betterLevelToCheck.Count > 0 do
            let p = betterLevelToCheck.Pop()
            if not suppress.[p.Y, p.X]
            then
                suppress.[p.Y, p.X] <- true
                sameLevelToCheck.Push(p)
                let current = List<Point>()

                let mutable betterExists = false

                while sameLevelToCheck.Count > 0 do
                    let p' = sameLevelToCheck.Pop()
                    let currentLevel = imgData.[p'.Y, p'.X, 0]
                    current.Add(p') |> ignore
                    for i, j in se do
                        let ni = i + p'.Y
                        let nj = j + p'.X
                        if ni >= 0 && ni < h && nj >= 0 && nj < w
                        then
                            let level = imgData.[ni, nj, 0]
                            let notSuppressed = not suppress.[ni, nj]

                            if level = currentLevel && notSuppressed
                            then
                                suppress.[ni, nj] <- true
                                sameLevelToCheck.Push(Point(nj, ni))
                            elif if extremumType = ExtremumType.Maxima then level > currentLevel else level < currentLevel
                            then
                                betterExists <- true
                                if notSuppressed
                                then
                                    betterLevelToCheck.Push(Point(nj, ni))

                if not betterExists
                then
                    result'.Add(current)
        result'

    for i in 0 .. h - 1 do
        for j in 0 .. w - 1 do
            let maxima = flood (Point(j, i))
            if maxima.Count > 0
            then
                result.AddRange(maxima)

    result.Select(fun l -> Points(l))


let findMaxima (img: Image<Gray, byte>) : IEnumerable<Points> =
    findExtremum img ExtremumType.Maxima

let findMinima (img: Image<Gray, byte>) : IEnumerable<Points> =
    findExtremum img ExtremumType.Minima


type PriorityQueue () =
    let size = 256
    let q: Points[] = Array.init size (fun i -> Points())
    let mutable highest = -1 // Value of the first elements of 'q'.
    let mutable lowest = size

    member this.NextMax () : byte * Point =
        if this.IsEmpty
        then
            invalidOp "Queue is empty"
        else
            let l = q.[highest]
            let next = l.First()
            l.Remove(next) |> ignore
            let value = byte highest

            if l.Count = 0
            then
                highest <- highest - 1
                while highest > lowest && q.[highest].Count = 0 do
                    highest <- highest - 1
                if highest = lowest
                then
                    highest <- -1
                    lowest <- size

            value, next

    member this.NextMin () : byte * Point =
        if this.IsEmpty
        then
            invalidOp "Queue is empty"
        else
            let l = q.[lowest + 1]
            let next = l.First()
            l.Remove(next) |> ignore
            let value = byte (lowest + 1)

            if l.Count = 0
            then
                lowest <- lowest + 1
                while lowest < highest && q.[lowest + 1].Count = 0 do
                    lowest <- lowest + 1
                if highest = lowest
                then
                    highest <- -1
                    lowest <- size

            value, next

    member this.Max =
        highest |> byte

    member this.Min =
        lowest + 1 |> byte

    member this.Add (value: byte) (p: Point) =
        let vi = int value

        if vi > highest
        then
            highest <- vi
        if vi <= lowest
        then
            lowest <- vi - 1

        q.[vi].Add(p) |> ignore

    member this.Remove (value: byte) (p: Point) =
        let vi = int value
        if q.[vi].Remove(p) && q.[vi].Count = 0
        then
            if vi = highest
            then
                highest <- highest - 1
                while highest > lowest && q.[highest].Count = 0 do
                    highest <- highest - 1
            elif vi - 1 = lowest
            then
                lowest <- lowest + 1
                while lowest < highest && q.[lowest + 1].Count = 0 do
                    lowest <- lowest + 1

            if highest = lowest // The queue is now empty.
            then
                highest <- -1
                lowest <- size

    member this.IsEmpty =
        highest = -1

    member this.Clear () =
        while highest > lowest  do
            q.[highest].Clear()
            highest <- highest - 1
        highest <- -1
        lowest <- size


type private AreaState =
    | Removed = 1
    | Unprocessed = 2
    | Validated = 3

type private AreaOperation =
    | Opening = 1
    | Closing = 2

[<AllowNullLiteral>]
type private Area (elements: Points) =
    member this.Elements = elements
    member val Intensity = None with get, set
    member val State = AreaState.Unprocessed with get, set

let private areaOperation (img: Image<Gray, byte>) (area: int) (op: AreaOperation) =
    let w = img.Width
    let h = img.Height
    let imgData = img.Data
    let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]

    let areas = List<Area>((if op = AreaOperation.Opening then findMaxima img else findMinima img) |> Seq.map Area)

    let pixels: Area[,] = Array2D.create h w null
    for m in areas do
        for e in m.Elements do
            pixels.[e.Y, e.X] <- m

    let queue = PriorityQueue()

    let addEdgeToQueue (elements: Points) =
        for p in elements do
            for i, j in se do
                let ni = i + p.Y
                let nj = j + p.X
                let p' = Point(nj, ni)
                if ni >= 0 && ni < h && nj >= 0 && nj < w && not (elements.Contains(p'))
                then
                    queue.Add (imgData.[ni, nj, 0]) p'

    // Reverse order is quicker.
    for i in areas.Count - 1 .. -1 .. 0 do
        let m = areas.[i]
        if m.Elements.Count <= area && m.State <> AreaState.Removed
        then
            queue.Clear()
            addEdgeToQueue m.Elements

            let mutable intensity = if op = AreaOperation.Opening then queue.Max else queue.Min
            let nextElements = Points()

            let mutable stop = false
            while not stop do
                let intensity', p = if op = AreaOperation.Opening then queue.NextMax () else queue.NextMin ()
                let mutable merged = false

                if intensity' = intensity // The intensity doesn't change.
                then
                    if m.Elements.Count + nextElements.Count + 1 > area
                    then
                        m.State <- AreaState.Validated
                        m.Intensity <- Some intensity
                        stop <- true
                    else
                        nextElements.Add(p) |> ignore

                elif if op = AreaOperation.Opening then intensity' < intensity else intensity' > intensity
                then
                    m.Elements.UnionWith(nextElements)
                    for e in nextElements do
                        pixels.[e.Y, e.X] <- m

                    if m.Elements.Count = area
                    then
                        m.State <- AreaState.Validated
                        m.Intensity <- Some (intensity')
                        stop <- true
                    else
                        intensity <- intensity'
                        nextElements.Clear()
                        nextElements.Add(p) |> ignore

                else
                    let m' = pixels.[p.Y, p.X]
                    if m' <> null
                    then
                        if m'.Elements.Count + m.Elements.Count <= area
                        then
                            m'.State <- AreaState.Removed
                            for e in m'.Elements do
                                pixels.[e.Y, e.X] <- m
                                queue.Remove imgData.[e.Y, e.X, 0] e
                            addEdgeToQueue m'.Elements
                            m.Elements.UnionWith(m'.Elements)
                            let intensityMax = if op = AreaOperation.Opening then queue.Max else queue.Min
                            if intensityMax <> intensity
                            then
                                intensity <- intensityMax
                                nextElements.Clear()
                            merged <- true

                    if not merged
                    then
                        m.State <- AreaState.Validated
                        m.Intensity <- Some (intensity)
                        stop <- true

                if not stop && not merged
                then
                    for i, j in se do
                        let ni = i + p.Y
                        let nj = j + p.X
                        let p' = Point(nj, ni)
                        if ni < 0 || ni >= h || nj < 0 || nj >= w
                        then
                            m.State <- AreaState.Validated
                            m.Intensity <- Some (intensity)
                            stop <- true
                        elif not (m.Elements.Contains(p')) && not (nextElements.Contains(p'))
                        then
                            queue.Add (imgData.[ni, nj, 0]) p'

                if queue.IsEmpty
                then
                    if m.Elements.Count + nextElements.Count <= area
                    then
                        m.State <- AreaState.Validated
                        m.Intensity <- Some intensity'
                        m.Elements.UnionWith(nextElements)
                    stop <- true

    for m in areas do
        if m.State = AreaState.Validated
        then
            match m.Intensity with
            | Some i ->
                for p in m.Elements do
                    imgData.[p.Y, p.X, 0] <- i
            | _ -> ()
    ()


let areaOpen (img: Image<Gray, byte>) (area: int) =
    areaOperation img area AreaOperation.Opening

let areaClose (img: Image<Gray, byte>) (area: int) =
    areaOperation img area AreaOperation.Closing

let areaOpen2 (img: Image<Gray, byte>) (area: int) =
    let w = img.Width
    let h = img.Height
    let imgData = img.Data
    let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]

    let histogram = Array.zeroCreate 256
    for i in 0 .. h - 1 do
        for j in 0 .. w - 1 do
            let v = imgData.[i, j, 0] |> int
            histogram.[v] <- histogram.[v] + 1

    let flooded : bool[,] = Array2D.zeroCreate h w

    let pointsChecked = HashSet<Point>()
    let pointsToCheck = Stack<Point>()

    for level in 255 .. -1 .. 0 do
        let mutable n = histogram.[level]
        if n > 0
        then
            for i in 0 .. h - 1 do
                for j in 0 .. w - 1 do
                    if not flooded.[i, j] && imgData.[i, j, 0] = byte level
                    then
                        let mutable maxNeighborValue = 0uy
                        pointsChecked.Clear()
                        pointsToCheck.Clear()
                        pointsToCheck.Push(Point(j, i))

                        while pointsToCheck.Count > 0 do
                            let next = pointsToCheck.Pop()
                            pointsChecked.Add(next) |> ignore
                            flooded.[next.Y, next.X] <- true

                            for nx, ny in se do
                                let p = Point(next.X + nx, next.Y + ny)
                                if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h
                                then
                                    let v = imgData.[p.Y, p.X, 0]
                                    if v = byte level
                                    then
                                        if not (pointsChecked.Contains(p))
                                        then
                                            pointsToCheck.Push(p)
                                    elif v > maxNeighborValue
                                    then
                                        maxNeighborValue <- v

                        if int maxNeighborValue < level && pointsChecked.Count <= area
                        then
                            for p in pointsChecked do
                                imgData.[p.Y, p.X, 0] <- maxNeighborValue


// Zhang and Suen algorithm.
// Modify 'mat' in place.
let thin (mat: Matrix<byte>) =
    let w = mat.Width
    let h = mat.Height
    let mutable data1 = mat.Data
    let mutable data2 = Array2D.copy data1

    let mutable pixelChanged = true
    let mutable oddIteration = true

    while pixelChanged do
        pixelChanged <- false
        for i in 0..h-1 do
            for j in 0..w-1 do
                if data1.[i, j] = 1uy
                then
                    let p2 = if i = 0 then 0uy else data1.[i-1, j]
                    let p3 = if i = 0 || j = w-1 then 0uy else data1.[i-1, j+1]
                    let p4 = if j = w-1 then 0uy else data1.[i, j+1]
                    let p5 = if i = h-1 || j = w-1 then 0uy else data1.[i+1, j+1]
                    let p6 = if i = h-1 then 0uy else data1.[i+1, j]
                    let p7 = if i = h-1 || j = 0 then 0uy else data1.[i+1, j-1]
                    let p8 = if j = 0 then 0uy else data1.[i, j-1]
                    let p9 = if i = 0 || j = 0 then 0uy else data1.[i-1, j-1]

                    let sumNeighbors = p2 + p3 + p4 + p5 + p6 + p7 + p8 + p9
                    if sumNeighbors >= 2uy && sumNeighbors <= 6uy &&
                        (if p2 = 0uy && p3 = 1uy then 1 else 0) +
                        (if p3 = 0uy && p4 = 1uy then 1 else 0) +
                        (if p4 = 0uy && p5 = 1uy then 1 else 0) +
                        (if p5 = 0uy && p6 = 1uy then 1 else 0) +
                        (if p6 = 0uy && p7 = 1uy then 1 else 0) +
                        (if p7 = 0uy && p8 = 1uy then 1 else 0) +
                        (if p8 = 0uy && p9 = 1uy then 1 else 0) +
                        (if p9 = 0uy && p2 = 1uy then 1 else 0) = 1 &&
                        if oddIteration
                        then p2 * p4 * p6 = 0uy && p4 * p6 * p8 = 0uy
                        else p2 * p4 * p8 = 0uy && p2 * p6 * p8 = 0uy
                    then
                        data2.[i, j] <- 0uy
                        pixelChanged <- true
                else
                    data2.[i, j] <- 0uy

        oddIteration <- not oddIteration
        let tmp = data1
        data1 <- data2
        data2 <- tmp


// FIXME: replace by a queue or stack.
let pop (l: List<'a>) : 'a =
    let n = l.[l.Count - 1]
    l.RemoveAt(l.Count - 1)
    n

// Remove all 8-connected pixels with an area equal or greater than 'areaSize'.
// Modify 'mat' in place.
let removeArea (mat: Matrix<byte>) (areaSize: int) =
    let neighbors = [|
        (-1,  0) // p2
        (-1,  1) // p3
        ( 0,  1) // p4
        ( 1,  1) // p5
        ( 1,  0) // p6
        ( 1, -1) // p7
        ( 0, -1) // p8
        (-1, -1) |] // p9

    let mat' = new Matrix<byte>(mat.Size)
    let w = mat'.Width
    let h = mat'.Height
    mat.CopyTo(mat')

    let data = mat.Data
    let data' = mat'.Data

    for i in 0..h-1 do
        for j in 0..w-1 do
            if data'.[i, j] = 1uy
            then
                let neighborhood = List<(int*int)>()
                let neighborsToCheck = List<(int*int)>()
                neighborsToCheck.Add((i, j))
                data'.[i, j] <- 0uy

                while neighborsToCheck.Count > 0 do
                    let (ci, cj) = pop neighborsToCheck
                    neighborhood.Add((ci, cj))
                    for (ni, nj) in neighbors do
                        let pi = ci + ni
                        let pj = cj + nj
                        if pi >= 0 && pi < h && pj >= 0 && pj < w && data'.[pi, pj] = 1uy
                        then
                            neighborsToCheck.Add((pi, pj))
                            data'.[pi, pj] <- 0uy
                if neighborhood.Count <= areaSize
                then
                    for (ni, nj) in neighborhood do
                        data.[ni, nj] <- 0uy

let connectedComponents (img: Image<Gray, byte>) (startPoints: List<Point>) : List<Point> =
    let w = img.Width
    let h = img.Height

    let pointChecked = Points()
    let pointToCheck = List<Point>(startPoints);

    let data = img.Data

    while pointToCheck.Count > 0 do
        let next = pop pointToCheck
        pointChecked.Add(next) |> ignore
        for ny in -1 .. 1 do
            for nx in -1 .. 1 do
                if ny <> 0 && nx <> 0
                then
                    let p = Point(next.X + nx, next.Y + ny)
                    if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h && data.[p.Y, p.X, 0] > 0uy && not (pointChecked.Contains p)
                    then
                        pointToCheck.Add(p)

    List<Point>(pointChecked)


let saveImg (img: Image<'TColor, 'TDepth>) (filepath: string) =
    img.Save(filepath)


let saveMat (mat: Matrix<'TDepth>) (filepath: string) =
    use img = new Image<Gray, 'TDeph>(mat.Size)
    mat.CopyTo(img)
    saveImg img filepath

let drawLine (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: int) (y0: int) (x1: int) (y1: int) (thickness: int) =
    img.Draw(LineSegment2D(Point(x0, y0), Point(x1, y1)), color, thickness);

let drawLineF (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: float) (y0: float) (x1: float) (y1: float) (thickness: int) =
    img.Draw(LineSegment2DF(PointF(float32 x0, float32 y0), PointF(float32 x1, float32 y1)), color, thickness, CvEnum.LineType.AntiAlias);

let drawEllipse (img: Image<'TColor, 'TDepth>) (e: Types.Ellipse) (color: 'TColor) (alpha: float) =

    if alpha >= 1.0
    then
        img.Draw(Ellipse(PointF(float32 e.Cx, float32 e.Cy), SizeF(2. * e.B |> float32, 2. * e.A |> float32), float32 <| e.Alpha / Math.PI * 180.), color, 1, CvEnum.LineType.AntiAlias)
    else
        let windowPosX = e.Cx - e.A - 5.0
        let gapX = windowPosX - (float (int windowPosX))

        let windowPosY = e.Cy - e.A - 5.0
        let gapY = windowPosY - (float (int windowPosY))

        let roi = Rectangle(int windowPosX, int windowPosY, 2. * (e.A + 5.0) |> int, 2.* (e.A + 5.0) |> int)

        img.ROI <- roi
        if roi = img.ROI // We do not display ellipses touching the edges (FIXME)
        then
            use i = new Image<'TColor, 'TDepth>(img.ROI.Size)
            i.Draw(Ellipse(PointF(float32 <| (e.A + 5. + gapX) , float32 <| (e.A + 5. + gapY)), SizeF(2. * e.B |> float32, 2. * e.A |> float32), float32 <| e.Alpha / Math.PI * 180.), color, 1, CvEnum.LineType.AntiAlias)
            CvInvoke.AddWeighted(img, 1.0, i, alpha, 0.0, img)
        img.ROI <- Rectangle.Empty


let drawEllipses (img: Image<'TColor, 'TDepth>) (ellipses: Types.Ellipse list) (color: 'TColor) (alpha: float) =
    List.iter (fun e -> drawEllipse img e color alpha) ellipses


let rngCell =  System.Random()
let drawCell (img: Image<Bgr, byte>) (drawCellContent: bool) (c: Types.Cell) =
    if drawCellContent
    then
        let colorB = rngCell.Next(20, 70)
        let colorG = rngCell.Next(20, 70)
        let colorR = rngCell.Next(20, 70)

        for y in 0 .. c.elements.Height - 1 do
            for x in 0 .. c.elements.Width - 1 do
                if c.elements.[y, x] > 0uy
                then
                    let dx, dy = c.center.X - c.elements.Width / 2, c.center.Y - c.elements.Height / 2
                    let b = img.Data.[y + dy, x + dx, 0] |> int
                    let g = img.Data.[y + dy, x + dx, 1] |> int
                    let r = img.Data.[y + dy, x + dx, 2] |> int
                    img.Data.[y + dy, x + dx, 0] <- if b + colorB > 255 then 255uy else byte (b + colorB)
                    img.Data.[y + dy, x + dx, 1] <- if g + colorG > 255 then 255uy else byte (g + colorG)
                    img.Data.[y + dy, x + dx, 2] <- if r + colorR > 255 then 255uy else byte (r + colorR)

    let crossColor, crossColor2 =
        match c.cellClass with
        | Types.HealthyRBC -> Bgr(255., 0., 0.), Bgr(255., 255., 255.)
        | Types.InfectedRBC -> Bgr(0., 0., 255.), Bgr(120., 120., 255.)
        | Types.Peculiar -> Bgr(0., 0., 0.), Bgr(80., 80., 80.)

    drawLine img crossColor2 (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 2
    drawLine img crossColor2 c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 2

    drawLine img crossColor (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 1
    drawLine img crossColor c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 1


let drawCells (img: Image<Bgr, byte>) (drawCellContent: bool) (cells: Types.Cell list) =
    List.iter (fun c -> drawCell img drawCellContent c) cells