module ParasitemiaCore.Morpho

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

open Emgu.CV
open Emgu.CV.Structure

open Types

/// <summary>
/// Remove M-adjacent pixels. It may be used after thinning.
/// </summary>
let suppressMAdjacency (img: Matrix<byte>) =
    let w = img.Width
    let h = img.Height
    for i in 1 .. h - 2 do
        for j in 1 .. w - 2 do
            if img.[i, j] > 0uy && img.Data.[i + 1, j] > 0uy && (img.Data.[i, j - 1] > 0uy && img.Data.[i - 1, j + 1] = 0uy || img.Data.[i, j + 1] > 0uy && img.Data.[i - 1, j - 1] = 0uy)
            then
                img.[i, j] <- 0uy
    for i in 1 .. h - 2 do
        for j in 1 .. w - 2 do
            if img.[i, j] > 0uy && img.Data.[i - 1, j] > 0uy && (img.Data.[i, j - 1] > 0uy && img.Data.[i + 1, j + 1] = 0uy || img.Data.[i, j + 1] > 0uy && img.Data.[i + 1, j - 1] = 0uy)
            then
                img.[i, j] <- 0uy

type ExtremumType =
    | Maxima = 1
    | Minima = 2

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

let findMinima (img: Image<Gray, 'TDepth>) : 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
                    match pixels.[p.Y, p.X] with
                    | null -> ()
                    | m' ->
                        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
            | _ -> ()
    ()

/// <summary>
/// Area opening on byte image.
/// </summary>
let areaOpen (img: Image<Gray, byte>) (area: int) =
    areaOperation img area AreaOperation.Opening

/// <summary>
/// Area closing on byte image.
/// </summary>
let areaClose (img: Image<Gray, byte>) (area: int) =
    areaOperation img area AreaOperation.Closing

// A simpler algorithm than 'areaOpen' on byte image but slower.
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

[<AllowNullLiteral>]
type Island (cmp: IComparer<float32>) =
    member val Shore = Heap.Heap<float32, Point>(cmp) with get
    member val Level = 0.f with get, set
    member val Surface = 0 with get, set
    member this.IsInfinite = this.Surface = Int32.MaxValue

let private areaOperationF (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: ('a -> float32 -> unit) option) (op: AreaOperation) =
    let w = img.Width
    let h = img.Height
    let earth = img.Data
    let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]

    let comparer = if op = AreaOperation.Opening
                   then { new IComparer<float32> with member this.Compare(v1, v2) = v1.CompareTo(v2) }
                   else { new IComparer<float32> with member this.Compare(v1, v2) = v2.CompareTo(v1) }

    let ownership: Island[,] = Array2D.create h w null

    // Initialize islands with their shore.
    let islands = List<Island>()
    let extremum = img |> if op = AreaOperation.Opening then findMaxima else findMinima
    for e in extremum do
        let island =
            let p = e.First()
            Island(comparer, Level = earth.[p.Y, p.X, 0], Surface = e.Count)
        islands.Add(island)
        let shorePoints = Points()
        for p in e do
            ownership.[p.Y, p.X] <- island
            for i, j in se do
                let ni = i + p.Y
                let nj = j + p.X
                let neighbor = Point(nj, ni)
                if ni >= 0 && ni < h && nj >= 0 && nj < w && Object.ReferenceEquals(ownership.[ni, nj], null) && not (shorePoints.Contains(neighbor))
                then
                    shorePoints.Add(neighbor) |> ignore
                    island.Shore.Add earth.[ni, nj, 0] neighbor

    for area, obj in areas do
        for island in islands do
            let mutable stop = island.Shore.IsEmpty

            // 'true' if 'p' is owned or adjacent to 'island'.
            let inline ownedOrAdjacent (p: Point) : bool =
                ownership.[p.Y, p.X] = island ||
                (p.Y > 0 && ownership.[p.Y - 1, p.X] = island) ||
                (p.Y < h - 1 && ownership.[p.Y + 1, p.X] = island) ||
                (p.X > 0 && ownership.[p.Y, p.X - 1] = island) ||
                (p.X < w - 1 && ownership.[p.Y, p.X + 1] = island)

            while not stop && island.Surface < area do
                let level, next = island.Shore.Max
                let other = ownership.[next.Y, next.X]
                if other = island // During merging, some points on the shore may be owned by the island itself -> ignored.
                then
                    island.Shore.RemoveNext ()
                else
                    if not <| Object.ReferenceEquals(other, null)
                    then // We touching another island.
                        if island.IsInfinite || other.IsInfinite || island.Surface + other.Surface >= area || comparer.Compare(island.Level, other.Level) < 0
                        then
                            stop <- true
                        else // We can merge 'other' into 'surface'.
                            island.Surface <- island.Surface + other.Surface
                            island.Level <- other.Level
                            // island.Level <- if comparer.Compare(island.Level, other.Level) > 0 then other.Level else island.Level
                            for l, p in other.Shore do
                                let mutable currentY = p.Y + 1
                                while currentY < h && ownership.[currentY, p.X] = other do
                                    ownership.[currentY, p.X] <- island
                                    currentY <- currentY + 1
                                island.Shore.Add l p
                            other.Shore.Clear()

                    elif comparer.Compare(level, island.Level) > 0
                    then
                        stop <- true
                    else
                        island.Shore.RemoveNext ()
                        for i, j in se do
                            let ni = i + next.Y
                            let nj = j + next.X
                            if ni < 0 || ni >= h || nj < 0 || nj >= w
                            then
                                island.Surface <- Int32.MaxValue
                                stop <- true
                            else
                                let neighbor = Point(nj, ni)
                                if not <| ownedOrAdjacent neighbor
                                then
                                    island.Shore.Add earth.[ni, nj, 0] neighbor
                        if not stop
                        then
                            ownership.[next.Y, next.X] <- island
                            island.Level <- level
                            island.Surface <- island.Surface + 1

        let mutable diff = 0.f

        for i in 0 .. h - 1 do
            for j in 0 .. w - 1 do
                match ownership.[i, j] with
                | null -> ()
                | island ->
                    let l = island.Level
                    diff <- diff + l - earth.[i, j, 0]
                    earth.[i, j, 0] <- l

        match f with
        | Some f' -> f' obj diff
        | _ -> ()
    ()

/// <summary>
/// Area opening on float image.
/// </summary>
let areaOpenF (img: Image<Gray, float32>) (area: int) =
    areaOperationF img [ area, () ] None AreaOperation.Opening

/// <summary>
/// Area closing on float image.
/// </summary>
let areaCloseF (img: Image<Gray, float32>) (area: int) =
    areaOperationF img [ area, () ] None AreaOperation.Closing

/// <summary>
/// Area closing on float image with different areas. Given areas must be sorted increasingly.
/// For each area the function 'f' is called with the associated area value of type 'a and the volume difference
/// Between the previous and the current closing.
/// </summary>
let areaOpenFWithFun (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: 'a -> float32 -> unit) =
    areaOperationF img areas (Some f) AreaOperation.Opening

/// <summary>
/// Same as 'areaOpenFWithFun' for closing operation.
/// </summary>
let areaCloseFWithFun (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: 'a -> float32 -> unit) =
    areaOperationF img areas (Some f) AreaOperation.Closing

/// <summary>
/// Zhang and Suen thinning algorithm.
/// Modify 'mat' in place.
/// </summary>
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

/// <summary>
/// Remove all 8-connected pixels with an area equal or greater than 'areaSize'.
/// Modify 'mat' in place.
/// </summary>
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

    use 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<Point>()
                let neighborsToCheck = Stack<Point>()
                neighborsToCheck.Push(Point(j, i))
                data'.[i, j] <- 0uy

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

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

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

    let data = img.Data

    while pointToCheck.Count > 0 do
        let next = pointToCheck.Pop()
        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.Push(p)

    pointChecked