module ParasitemiaCore.Morpho open System open System.Drawing open System.Collections.Generic open System.Linq open Emgu.CV open Emgu.CV.Structure open Types /// /// Remove M-adjacent pixels. It may be used after thinning. /// let suppressMAdjacency (img: Matrix) = 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) (extremumType: ExtremumType) : IEnumerable = 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>() let flood (start: Point) : List> = let sameLevelToCheck = Stack() let betterLevelToCheck = Stack() betterLevelToCheck.Push(start) let result' = List>() 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() 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) : IEnumerable = findExtremum img ExtremumType.Maxima let findMinima (img: Image) : IEnumerable = 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 [] 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) (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((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 | _ -> () () /// /// Area opening on byte image. /// let areaOpen (img: Image) (area: int) = areaOperation img area AreaOperation.Opening /// /// Area closing on byte image. /// let areaClose (img: Image) (area: int) = areaOperation img area AreaOperation.Closing // A simpler algorithm than 'areaOpen' on byte image but slower. let areaOpen2 (img: Image) (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() let pointsToCheck = Stack() 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 [] type Island (cmp: IComparer) = member val Shore = Heap.Heap(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) (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 with member this.Compare(v1, v2) = v1.CompareTo(v2) } else { new IComparer 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() 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 | _ -> () () /// /// Area opening on float image. /// let areaOpenF (img: Image) (area: int) = areaOperationF img [ area, () ] None AreaOperation.Opening /// /// Area closing on float image. /// let areaCloseF (img: Image) (area: int) = areaOperationF img [ area, () ] None AreaOperation.Closing /// /// 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. /// let areaOpenFWithFun (img: Image) (areas: (int * 'a) list) (f: 'a -> float32 -> unit) = areaOperationF img areas (Some f) AreaOperation.Opening /// /// Same as 'areaOpenFWithFun' for closing operation. /// let areaCloseFWithFun (img: Image) (areas: (int * 'a) list) (f: 'a -> float32 -> unit) = areaOperationF img areas (Some f) AreaOperation.Closing /// /// Zhang and Suen thinning algorithm. /// Modify 'mat' in place. /// let thin (mat: Matrix) = 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 /// /// Remove all 8-connected pixels with an area equal or greater than 'areaSize'. /// Modify 'mat' in place. /// let removeArea (mat: Matrix) (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(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() let neighborsToCheck = Stack() 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) (startPoints: List) : Points = let w = img.Width let h = img.Height let pointChecked = Points() let pointToCheck = Stack(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