--- /dev/null
+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
projects / master-thesis.git / blobdiff