X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FImgTools.fs;h=f567e682decb86c97b81aefeb8c7a44eeab1f347;hb=bef2e9f0bf1bba21d4c988fdf654c2dc303ec34a;hp=e9cbbe9ee0f59f7a4f54c557ff345ca2f20be6df;hpb=b070295cf67b2025164a34b6594e84f0d771cdc9;p=master-thesis.git diff --git a/Parasitemia/Parasitemia/ImgTools.fs b/Parasitemia/Parasitemia/ImgTools.fs index e9cbbe9..f567e68 100644 --- a/Parasitemia/Parasitemia/ImgTools.fs +++ b/Parasitemia/Parasitemia/ImgTools.fs @@ -21,18 +21,146 @@ let normalizeAndConvert (img: Image) : Image = ((img - (!min).[0]) / ((!max).[0] - (!min).[0]) * 255.0).Convert() +let saveImg (img: Image<'TColor, 'TDepth>) (filepath: string) = + img.Save(filepath) + + +let saveMat (mat: Matrix<'TDepth>) (filepath: string) = + use img = new Image(mat.Size) + mat.CopyTo(img) + saveImg img filepath + + +let suppressMConnections (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 + +let findEdges (img: Image) : Matrix * Image * Image = + let w = img.Width + let h = img.Height + + use sobelKernel = + new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ] + [ 2.0f; 0.0f; -2.0f ] + [ 1.0f; 0.0f; -1.0f ]], Point(1, 1)) + + let xGradient = img.Convolution(sobelKernel).Convert() + let yGradient = img.Convolution(sobelKernel.Transpose()).Convert() + + let xGradientData = xGradient.Data + let yGradientData = yGradient.Data + for r in 0 .. h - 1 do + xGradientData.[r, 0, 0] <- 0.0 + xGradientData.[r, w - 1, 0] <- 0.0 + yGradientData.[r, 0, 0] <- 0.0 + yGradientData.[r, w - 1, 0] <- 0.0 + + for c in 0 .. w - 1 do + xGradientData.[0, c, 0] <- 0.0 + xGradientData.[h - 1, c, 0] <- 0.0 + yGradientData.[0, c, 0] <- 0.0 + yGradientData.[h - 1, c, 0] <- 0.0 + + use magnitudes = new Matrix(xGradient.Size) + CvInvoke.CartToPolar(xGradient, yGradient, magnitudes, new Mat()) // Compute the magnitudes (without angles). + + let thresholdHigh, thresholdLow = + let sensibility = 0.1 + use magnitudesByte = magnitudes.Convert() + let threshold = CvInvoke.Threshold(magnitudesByte, magnitudesByte, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) + threshold + (sensibility * threshold), threshold - (sensibility * threshold) + + // Non-maximum suppression. + use nms = new Matrix(xGradient.Size) + nms.SetValue(1.0) + + for i in 0 .. h - 1 do + nms.Data.[i, 0] <- 0uy + nms.Data.[i, w - 1] <- 0uy + + for j in 0 .. w - 1 do + nms.Data.[0, j] <- 0uy + nms.Data.[h - 1, j] <- 0uy + + for i in 1 .. h - 2 do + for j in 1 .. w - 2 do + let vx = xGradient.Data.[i, j, 0] + let vy = yGradient.Data.[i, j, 0] + let angle = + let a = atan2 vy vx + if a < 0.0 then 2. * Math.PI + a else a + + let mNeigbors (sign: int) : float = + if angle < Math.PI / 8. || angle >= 15.0 * Math.PI / 8. then magnitudes.Data.[i, j + sign] + elif angle < 3.0 * Math.PI / 8. then magnitudes.Data.[i + sign, j + sign] + elif angle < 5.0 * Math.PI / 8. then magnitudes.Data.[i + sign, j] + elif angle < 7.0 * Math.PI / 8. then magnitudes.Data.[i + sign, j - sign] + elif angle < 9.0 * Math.PI / 8. then magnitudes.Data.[i, j - sign] + elif angle < 11.0 * Math.PI / 8. then magnitudes.Data.[i - sign, j - sign] + elif angle < 13.0 * Math.PI / 8. then magnitudes.Data.[i - sign, j] + else magnitudes.Data.[i - sign, j + sign] + + let m = magnitudes.Data.[i, j] + if m < mNeigbors 1 || m < mNeigbors -1 || m < thresholdLow then + nms.Data.[i, j] <- 0uy + + // suppressMConnections nms // It's not usefull for the rest of the process (ellipse detection). + + let edges = new Matrix(xGradient.Size) + + // Histeresis thresholding. + let toVisit = Stack() + for i in 0 .. h - 1 do + for j in 0 .. w - 1 do + if nms.Data.[i, j] = 1uy && magnitudes.Data.[i, j] >= thresholdHigh then + nms.Data.[i, j] <- 0uy + toVisit.Push(Point(j, i)) + while toVisit.Count > 0 do + let p = toVisit.Pop() + edges.Data.[p.Y, p.X] <- 1uy + for i' in -1 .. 1 do + for j' in -1 .. 1 do + if i' <> 0 || j' <> 0 then + let ni = p.Y + i' + let nj = p.X + j' + if ni >= 0 && ni < h && nj >= 0 && nj < w && nms.Data.[ni, nj] = 1uy then + nms.Data.[ni, nj] <- 0uy + toVisit.Push(Point(nj, ni)) + + + edges, xGradient, yGradient + + 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) -let findMaxima (img: Image) : IEnumerable> = - use suppress = new Image(img.Size) +type Points = HashSet + +let drawPoints (img: Image) (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) (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 suppressData = suppress.Data + let suppress: bool[,] = Array2D.zeroCreate h w let result = List>() @@ -45,9 +173,9 @@ let findMaxima (img: Image) : IEnumerable> = while betterLevelToCheck.Count > 0 do let p = betterLevelToCheck.Pop() - if suppressData.[p.Y, p.X, 0] = 0uy + if not suppress.[p.Y, p.X] then - suppressData.[p.Y, p.X, 0] <- 1uy + suppress.[p.Y, p.X] <- true sameLevelToCheck.Push(p) let current = List() @@ -57,27 +185,24 @@ let findMaxima (img: Image) : IEnumerable> = let p' = sameLevelToCheck.Pop() let currentLevel = imgData.[p'.Y, p'.X, 0] current.Add(p') |> ignore - for i in -1 .. 1 do - for j in -1 .. 1 do - if i <> 0 || j <> 0 + 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 - let ni = i + p'.Y - let nj = j + p'.X - if ni >= 0 && ni < h && nj >= 0 && nj < w + betterExists <- true + if notSuppressed then - let level = imgData.[ni, nj, 0] - let notSuppressed = suppressData.[ni, nj, 0] = 0uy - - if level = currentLevel && notSuppressed - then - suppressData.[ni, nj, 0] <- 1uy - sameLevelToCheck.Push(Point(nj, ni)) - elif level > currentLevel - then - betterExists <- true - if notSuppressed - then - betterLevelToCheck.Push(Point(nj, ni)) + betterLevelToCheck.Push(Point(nj, ni)) if not betterExists then @@ -88,198 +213,322 @@ let findMaxima (img: Image) : IEnumerable> = for j in 0 .. w - 1 do let maxima = flood (Point(j, i)) if maxima.Count > 0 - then result.AddRange(maxima) + then + result.AddRange(maxima) - result.Select(fun l -> HashSet(l)) + 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 q = List>() // TODO: Check performance with an HasSet + 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.Next () : byte * Point = + member this.NextMax () : byte * Point = if this.IsEmpty then invalidOp "Queue is empty" else - let l = q.[0] + let l = q.[highest] let next = l.First() l.Remove(next) |> ignore let value = byte highest + if l.Count = 0 then - q.RemoveAt(0) highest <- highest - 1 - while q.Count > 0 && q.[0] = null do - q.RemoveAt(0) + 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.UnionWith (other: PriorityQueue) = - while not other.IsEmpty do - let p, v = other.Next - this.Add p v*) + member this.Min = + lowest + 1 |> byte member this.Add (value: byte) (p: Point) = let vi = int value - if this.IsEmpty + if vi > highest then - highest <- int value - q.Insert(0, null) - elif vi > highest - then - for i in highest .. vi - 1 do - q.Insert(0, null) highest <- vi - elif highest - vi >= q.Count + if vi <= lowest then - for i in 0 .. highest - vi - q.Count do - q.Add(null) + lowest <- vi - 1 + + q.[vi].Add(p) |> ignore - let pos = highest - vi - if q.[pos] = null + member this.Remove (value: byte) (p: Point) = + let vi = int value + if q.[vi].Remove(p) && q.[vi].Count = 0 then - q.[pos] <- HashSet([p]) - else - q.[pos].Add(p) |> ignore + 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 = - q.Count = 0 + highest = -1 member this.Clear () = - while highest >= 0 do - q.[highest] <- null + while highest > lowest do + q.[highest].Clear() highest <- highest - 1 + highest <- -1 + lowest <- size +type private AreaState = + | Removed = 1 + | Unprocessed = 2 + | Validated = 3 -type MaximaState = Uncertain | Validated | TooBig -type Maxima = { - elements : HashSet - mutable intensity: byte option - mutable state: MaximaState } +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 areaOpen (img: Image) (area: int) = +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 maxima = findMaxima img |> Seq.map (fun m -> { elements = m; intensity = None; state = Uncertain }) |> List.ofSeq - let toValidated = Stack(maxima) + let queue = PriorityQueue() - while toValidated.Count > 0 do - let m = toValidated.Pop() - if m.elements.Count <= area + 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 - let queue = - let q = PriorityQueue() - let firstElements = HashSet() - for p in m.elements do - for i in -1 .. 1 do - for j in -1 .. 1 do - if i <> 0 || j <> 0 - then - 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 (m.elements.Contains(p')) && not (firstElements.Contains(p')) - then - firstElements.Add(p') |> ignore - q.Add (img.Data.[ni, nj, 0]) p' - q + queue.Clear() + addEdgeToQueue m.Elements - let mutable intensity = queue.Max - let nextElements = HashSet() + 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 = queue.Next () + 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 + if m.Elements.Count + nextElements.Count + 1 > area then - m.state <- Validated - m.intensity <- Some intensity + m.State <- AreaState.Validated + m.Intensity <- Some intensity stop <- true else nextElements.Add(p) |> ignore - elif intensity' < intensity + + elif if op = AreaOperation.Opening then intensity' < intensity else intensity' > intensity then - m.elements.UnionWith(nextElements) - if m.elements.Count = area + m.Elements.UnionWith(nextElements) + for e in nextElements do + pixels.[e.Y, e.X] <- m + + if m.Elements.Count = area then - m.state <- Validated - m.intensity <- Some (intensity') + m.State <- AreaState.Validated + m.Intensity <- Some (intensity') stop <- true else intensity <- intensity' nextElements.Clear() nextElements.Add(p) |> ignore - else // i' > i - seq { - for m' in maxima do - if m' <> m && m'.elements.Contains(p) then - if m'.elements.Count + m.elements.Count <= area - then - m'.state <- Uncertain - m'.elements.UnionWith(m.elements) - if not <| toValidated.Contains m' // FIXME: Maybe use state instead of scanning the whole list. - then - toValidated.Push(m') - stop <- true - yield false - } |> Seq.forall id |> ignore - if not stop + 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 <- Validated - m.intensity <- Some (intensity) + m.State <- AreaState.Validated + m.Intensity <- Some (intensity) stop <- true - if not stop + if not stop && not merged then - for i in -1 .. 1 do - for j in -1 .. 1 do - if i <> 0 || j <> 0 - then - 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 <- Validated - m.intensity <- Some (intensity) - stop <- true - elif not (m.elements.Contains(p')) && not (nextElements.Contains(p')) - then - queue.Add (img.Data.[ni, nj, 0]) p' + 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 + if m.Elements.Count + nextElements.Count <= area then - m.state <- Validated - m.intensity <- Some intensity' - m.elements.UnionWith(nextElements) + m.State <- AreaState.Validated + m.Intensity <- Some intensity' + m.Elements.UnionWith(nextElements) stop <- true - for m in maxima do - if m.state = Validated + for m in areas do + if m.State = AreaState.Validated then - match m.intensity with + match m.Intensity with | Some i -> - for p in m.elements do - img.Data.[p.Y, p.X, 0] <- i + for p in m.Elements do + imgData.[p.Y, p.X, 0] <- i | _ -> () () +let areaOpen (img: Image) (area: int) = + areaOperation img area AreaOperation.Opening + +let areaClose (img: Image) (area: int) = + areaOperation img area AreaOperation.Closing + +// A simpler algorithm than 'areaOpen' 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 + + // Zhang and Suen algorithm. // Modify 'mat' in place. let thin (mat: Matrix) = @@ -386,7 +635,7 @@ let connectedComponents (img: Image) (startPoints: List) : Li let w = img.Width let h = img.Height - let pointChecked = HashSet() + let pointChecked = Points() let pointToCheck = List(startPoints); let data = img.Data @@ -406,21 +655,14 @@ let connectedComponents (img: Image) (startPoints: List) : Li List(pointChecked) -let saveImg (img: Image<'TColor, 'TDepth>) (filepath: string) = - img.Save(filepath) - - -let saveMat (mat: Matrix<'TDepth>) (filepath: string) = - use img = new Image(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