Parasitemia/ParasitemiaCore/ImgTools.fs

   1 module ParasitemiaCore.ImgTools
   2
   3 open System
   4 open System.Drawing
   5 open System.Collections.Generic
   6 open System.Linq
   7
   8 open Emgu.CV
   9 open Emgu.CV.Structure
  10
  11 open Heap
  12 open Const
  13 open Types
  14 open Utils
  15
  16 let normalize (img: Image<Gray, float32>) (upperLimit: float) : Image<Gray, float32> =
  17     let min = ref [| 0.0 |]
  18     let minLocation = ref <| [| Point() |]
  19     let max = ref [| 0.0 |]
  20     let maxLocation = ref <| [| Point() |]
  21     img.MinMax(min, max, minLocation, maxLocation)
  22     let normalized = (img - (!min).[0]) / ((!max).[0] - (!min).[0])
  23     if upperLimit = 1.0
  24     then normalized
  25     else upperLimit * normalized
  26
  27 let mergeChannels (img: Image<Bgr, float32>) (rgbWeights: float * float * float) : Image<Gray, float32> =
  28     match rgbWeights with
  29     | 1., 0., 0. -> img.[2]
  30     | 0., 1., 0. -> img.[1]
  31     | 0., 0., 1. -> img.[0]
  32     | redFactor, greenFactor, blueFactor ->
  33         let result = new Image<Gray, float32>(img.Size)
  34         CvInvoke.AddWeighted(result, 1., img.[2], redFactor, 0., result)
  35         CvInvoke.AddWeighted(result, 1., img.[1], greenFactor, 0., result)
  36         CvInvoke.AddWeighted(result, 1., img.[0], blueFactor, 0., result)
  37         result
  38
  39 let mergeChannelsWithProjection (img: Image<Bgr, float32>) (v1r: float32, v1g: float32, v1b: float32) (v2r: float32, v2g: float32, v2b: float32) (upperLimit: float)  : Image<Gray, float32> =
  40     let vr, vg, vb = v2r - v1r, v2g - v1g, v2b - v1b
  41     let vMagnitude = sqrt (vr ** 2.f + vg ** 2.f + vb ** 2.f)
  42     let project (r: float32) (g: float32) (b: float32) = ((r - v1r) * vr + (g - v1g) * vg + (b - v1b) * vb) / vMagnitude
  43     let result = new Image<Gray, float32>(img.Size)
  44     // TODO: Essayer en bindant Data pour gagner du temps
  45     for i in 0 .. img.Height - 1 do
  46         for j in 0 .. img.Width - 1 do
  47             result.Data.[i, j, 0] <- project img.Data.[i, j, 2] img.Data.[i, j, 1] img.Data.[i, j, 0]
  48     normalize result upperLimit
  49
  50 // Normalize image values between 0uy and 255uy.
  51 let normalizeAndConvert (img: Image<Gray, 'TDepth>) : Image<Gray, byte> =
  52     (normalize (img.Convert<Gray, float32>()) 255.).Convert<Gray, byte>()
  53
  54 let saveImg (img: Image<'TColor, 'TDepth>) (filepath: string) =
  55     img.Save(filepath)
  56
  57 let saveMat (mat: Matrix<'TDepth>) (filepath: string) =
  58     use img = new Image<Gray, 'TDeph>(mat.Size)
  59     mat.CopyTo(img)
  60     saveImg img filepath
  61
  62 type Histogram = { data: int[]; total: int; sum: int; min: float32; max: float32 }
  63
  64 let histogramImg (img: Image<Gray, float32>) (nbSamples: int) : Histogram =
  65     let imgData = img.Data
  66
  67     let min, max =
  68         let min = ref [| 0.0 |]
  69         let minLocation = ref <| [| Point() |]
  70         let max = ref [| 0.0 |]
  71         let maxLocation = ref <| [| Point() |]
  72         img.MinMax(min, max, minLocation, maxLocation)
  73         float32 (!min).[0], float32 (!max).[0]
  74
  75     let inline bin (x: float32) : int =
  76         let p = int ((x - min) / (max - min) * float32 nbSamples)
  77         if p >= nbSamples then nbSamples - 1 else p
  78
  79     let data = Array.zeroCreate nbSamples
  80
  81     for i in 0 .. img.Height - 1 do
  82         for j in 0 .. img.Width - 1 do
  83             let p = bin imgData.[i, j, 0]
  84             data.[p] <- data.[p] + 1
  85
  86     { data = data; total = img.Height * img.Width; sum = Array.sum data; min = min; max = max }
  87
  88 let histogramMat (mat: Matrix<float32>) (nbSamples: int) : Histogram =
  89     let matData = mat.Data
  90
  91     let min, max =
  92         let min = ref 0.0
  93         let minLocation = ref <| Point()
  94         let max = ref 0.0
  95         let maxLocation = ref <| Point()
  96         mat.MinMax(min, max, minLocation, maxLocation)
  97         float32 !min, float32 !max
  98
  99     let inline bin (x: float32) : int =
 100         let p = int ((x - min) / (max - min) * float32 nbSamples)
 101         if p >= nbSamples then nbSamples - 1 else p
 102
 103     let data = Array.zeroCreate nbSamples
 104
 105     for i in 0 .. mat.Height - 1 do
 106         for j in 0 .. mat.Width - 1 do
 107             let p = bin matData.[i, j]
 108             data.[p] <- data.[p] + 1
 109
 110     { data = data; total = mat.Height * mat.Width; sum = Array.sum data; min = min; max = max }
 111
 112 let histogram (values: float32 seq) (nbSamples: int) : Histogram =
 113     let mutable min = Single.MaxValue
 114     let mutable max = Single.MinValue
 115     let mutable n = 0
 116
 117     for v in values do
 118         n <- n + 1
 119         if v < min then min <- v
 120         if v > max then max <- v
 121
 122     let inline bin (x: float32) : int =
 123         let p = int ((x - min) / (max - min) * float32 nbSamples)
 124         if p >= nbSamples then nbSamples - 1 else p
 125
 126     let data = Array.zeroCreate nbSamples
 127
 128     for v in values do
 129         let p = bin v
 130         data.[p] <- data.[p] + 1
 131
 132     { data = data; total = n; sum = Array.sum data; min = min; max = max }
 133
 134 let otsu (hist: Histogram) : float32 * float32 * float32 =
 135     let mutable sumB = 0
 136     let mutable wB = 0
 137     let mutable maximum = 0.0
 138     let mutable level = 0
 139     let sum = hist.data |> Array.mapi (fun i v -> i * v |> float) |> Array.sum
 140
 141     for i in 0 .. hist.data.Length - 1 do
 142         wB <- wB + hist.data.[i]
 143         if wB <> 0
 144         then
 145             let wF = hist.total - wB
 146             if wF <> 0
 147             then
 148                 sumB <- sumB + i * hist.data.[i]
 149                 let mB = (float sumB) / (float wB)
 150                 let mF = (sum - float sumB) / (float wF)
 151                 let between = (float wB) * (float wF) * (mB - mF) ** 2.;
 152                 if between >= maximum
 153                 then
 154                     level <- i
 155                     maximum <- between
 156
 157     let mean1 =
 158         let mutable sum = 0
 159         let mutable nb = 0
 160         for i in 0 .. level - 1 do
 161             sum <- sum + i * hist.data.[i]
 162             nb <- nb + hist.data.[i]
 163         (sum + level * hist.data.[level] / 2) / (nb + hist.data.[level] / 2)
 164
 165     let mean2 =
 166         let mutable sum = 0
 167         let mutable nb = 0
 168         for i in level + 1 .. hist.data.Length - 1 do
 169             sum <- sum + i * hist.data.[i]
 170             nb <- nb + hist.data.[i]
 171         (sum + level * hist.data.[level] / 2) / (nb + hist.data.[level] / 2)
 172
 173     let toFloat l =
 174         float32 l / float32 hist.data.Length * (hist.max - hist.min) + hist.min
 175
 176     toFloat level, toFloat mean1, toFloat mean2
 177
 178 /// <summary>
 179 /// Remove M-adjacent pixels. It may be used after thinning.
 180 /// </summary>
 181 let suppressMAdjacency (img: Matrix<byte>) =
 182     let w = img.Width
 183     let h = img.Height
 184     for i in 1 .. h - 2 do
 185         for j in 1 .. w - 2 do
 186             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)
 187             then
 188                 img.[i, j] <- 0uy
 189     for i in 1 .. h - 2 do
 190         for j in 1 .. w - 2 do
 191             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)
 192             then
 193                 img.[i, j] <- 0uy
 194
 195 /// <summary>
 196 /// Find edges of an image by using the Canny approach.
 197 /// The thresholds are automatically defined with otsu on gradient magnitudes.
 198 /// </summary>
 199 /// <param name="img"></param>
 200 let findEdges (img: Image<Gray, float32>) : Matrix<byte> * Matrix<float32> * Matrix<float32> =
 201     let w = img.Width
 202     let h = img.Height
 203
 204     use sobelKernel =
 205         new Matrix<float32>(array2D [[ 1.0f; 0.0f; -1.0f ]
 206                                      [ 2.0f; 0.0f; -2.0f ]
 207                                      [ 1.0f; 0.0f; -1.0f ]])
 208
 209     let xGradient = new Matrix<float32>(img.Size)
 210     let yGradient = new Matrix<float32>(img.Size)
 211     CvInvoke.Filter2D(img, xGradient, sobelKernel, Point(1, 1))
 212     CvInvoke.Filter2D(img, yGradient, sobelKernel.Transpose(), Point(1, 1))
 213
 214     use magnitudes = new Matrix<float32>(xGradient.Size)
 215     use angles = new Matrix<float32>(xGradient.Size)
 216     CvInvoke.CartToPolar(xGradient, yGradient, magnitudes, angles) // Compute the magnitudes and angles.
 217
 218     let thresholdHigh, thresholdLow =
 219         let sensibilityHigh = 0.1f
 220         let sensibilityLow = 0.0f
 221         let threshold, _, _ = otsu (histogramMat magnitudes 300)
 222         threshold + (sensibilityHigh * threshold), threshold - (sensibilityLow * threshold)
 223
 224     // Non-maximum suppression.
 225     use nms = new Matrix<byte>(xGradient.Size)
 226
 227     let nmsData = nms.Data
 228     let anglesData = angles.Data
 229     let magnitudesData = magnitudes.Data
 230     let xGradientData = xGradient.Data
 231     let yGradientData = yGradient.Data
 232
 233     for i in 0 .. h - 1 do
 234         nmsData.[i, 0] <- 0uy
 235         nmsData.[i, w - 1] <- 0uy
 236
 237     for j in 0 .. w - 1 do
 238         nmsData.[0, j] <- 0uy
 239         nmsData.[h - 1, j] <- 0uy
 240
 241     for i in 1 .. h - 2 do
 242         for j in 1 .. w - 2 do
 243             let vx = xGradientData.[i, j]
 244             let vy = yGradientData.[i, j]
 245             if vx <> 0.f || vy <> 0.f
 246             then
 247                 let angle = anglesData.[i, j]
 248
 249                 let vx', vy' = abs vx, abs vy
 250                 let ratio2 = if vx' > vy' then vy' / vx' else vx' / vy'
 251                 let ratio1 = 1.f - ratio2
 252
 253                 let mNeigbors (sign: int) : float32 =
 254                     if angle < PI / 4.f
 255                     then ratio1 * magnitudesData.[i, j + sign] + ratio2 * magnitudesData.[i + sign, j + sign]
 256                     elif angle < PI / 2.f
 257                     then ratio2 * magnitudesData.[i + sign, j + sign] + ratio1 * magnitudesData.[i + sign, j]
 258                     elif angle < 3.f * PI / 4.f
 259                     then ratio1 * magnitudesData.[i + sign, j] + ratio2 * magnitudesData.[i + sign, j - sign]
 260                     elif angle < PI
 261                     then ratio2 * magnitudesData.[i + sign, j - sign] + ratio1 * magnitudesData.[i, j - sign]
 262                     elif angle < 5.f * PI / 4.f
 263                     then ratio1 * magnitudesData.[i, j - sign] + ratio2 * magnitudesData.[i - sign, j - sign]
 264                     elif angle < 3.f * PI / 2.f
 265                     then ratio2 * magnitudesData.[i - sign, j - sign] + ratio1 * magnitudesData.[i - sign, j]
 266                     elif angle < 7.f * PI / 4.f
 267                     then ratio1 * magnitudesData.[i - sign, j] + ratio2 * magnitudesData.[i - sign, j + sign]
 268                     else ratio2 * magnitudesData.[i - sign, j + sign] + ratio1 * magnitudesData.[i, j + sign]
 269
 270                 let m = magnitudesData.[i, j]
 271                 if m >= thresholdLow && m > mNeigbors 1 && m > mNeigbors -1
 272                 then
 273                     nmsData.[i, j] <- 1uy
 274
 275     // suppressMConnections nms // It's not helpful for the rest of the process (ellipse detection).
 276
 277     let edges = new Matrix<byte>(xGradient.Size)
 278     let edgesData = edges.Data
 279
 280     // Hysteresis thresholding.
 281     let toVisit = Stack<Point>()
 282     for i in 0 .. h - 1 do
 283         for j in 0 .. w - 1 do
 284             if nmsData.[i, j] = 1uy && magnitudesData.[i, j] >= thresholdHigh
 285             then
 286                 nmsData.[i, j] <- 0uy
 287                 toVisit.Push(Point(j, i))
 288                 while toVisit.Count > 0 do
 289                     let p = toVisit.Pop()
 290                     edgesData.[p.Y, p.X] <- 1uy
 291                     for i' in -1 .. 1  do
 292                         for j' in -1 .. 1 do
 293                             if i' <> 0 || j' <> 0
 294                             then
 295                                 let ni = p.Y + i'
 296                                 let nj = p.X + j'
 297                                 if ni >= 0 && ni < h && nj >= 0 && nj < w && nmsData.[ni, nj] = 1uy
 298                                 then
 299                                     nmsData.[ni, nj] <- 0uy
 300                                     toVisit.Push(Point(nj, ni))
 301
 302     edges, xGradient, yGradient
 303
 304 let gaussianFilter (img : Image<'TColor, 'TDepth>) (standardDeviation : float) : Image<'TColor, 'TDepth> =
 305     let size = 2 * int (ceil (4.0 * standardDeviation)) + 1
 306     img.SmoothGaussian(size, size, standardDeviation, standardDeviation)
 307
 308 let drawPoints (img: Image<Gray, 'TDepth>) (points: Points) (intensity: 'TDepth) =
 309     for p in points do
 310         img.Data.[p.Y, p.X, 0] <- intensity
 311
 312 type ExtremumType =
 313     | Maxima = 1
 314     | Minima = 2
 315
 316 let findExtremum (img: Image<Gray, 'TDepth>) (extremumType: ExtremumType) : IEnumerable<Points> =
 317     let w = img.Width
 318     let h = img.Height
 319     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 320
 321     let imgData = img.Data
 322     let suppress: bool[,] = Array2D.zeroCreate h w
 323
 324     let result = List<List<Point>>()
 325
 326     let flood (start: Point) : List<List<Point>> =
 327         let sameLevelToCheck = Stack<Point>()
 328         let betterLevelToCheck = Stack<Point>()
 329         betterLevelToCheck.Push(start)
 330
 331         let result' = List<List<Point>>()
 332
 333         while betterLevelToCheck.Count > 0 do
 334             let p = betterLevelToCheck.Pop()
 335             if not suppress.[p.Y, p.X]
 336             then
 337                 suppress.[p.Y, p.X] <- true
 338                 sameLevelToCheck.Push(p)
 339                 let current = List<Point>()
 340
 341                 let mutable betterExists = false
 342
 343                 while sameLevelToCheck.Count > 0 do
 344                     let p' = sameLevelToCheck.Pop()
 345                     let currentLevel = imgData.[p'.Y, p'.X, 0]
 346                     current.Add(p') |> ignore
 347                     for i, j in se do
 348                         let ni = i + p'.Y
 349                         let nj = j + p'.X
 350                         if ni >= 0 && ni < h && nj >= 0 && nj < w
 351                         then
 352                             let level = imgData.[ni, nj, 0]
 353                             let notSuppressed = not suppress.[ni, nj]
 354
 355                             if level = currentLevel && notSuppressed
 356                             then
 357                                 suppress.[ni, nj] <- true
 358                                 sameLevelToCheck.Push(Point(nj, ni))
 359                             elif if extremumType = ExtremumType.Maxima then level > currentLevel else level < currentLevel
 360                             then
 361                                 betterExists <- true
 362                                 if notSuppressed
 363                                 then
 364                                     betterLevelToCheck.Push(Point(nj, ni))
 365
 366                 if not betterExists
 367                 then
 368                     result'.Add(current)
 369         result'
 370
 371     for i in 0 .. h - 1 do
 372         for j in 0 .. w - 1 do
 373             let maxima = flood (Point(j, i))
 374             if maxima.Count > 0
 375             then
 376                 result.AddRange(maxima)
 377
 378     result.Select(fun l -> Points(l))
 379
 380 let findMaxima (img: Image<Gray, 'TDepth>) : IEnumerable<Points> =
 381     findExtremum img ExtremumType.Maxima
 382
 383 let findMinima (img: Image<Gray, 'TDepth>) : IEnumerable<Points> =
 384     findExtremum img ExtremumType.Minima
 385
 386 type PriorityQueue () =
 387     let size = 256
 388     let q: Points[] = Array.init size (fun i -> Points())
 389     let mutable highest = -1 // Value of the first elements of 'q'.
 390     let mutable lowest = size
 391
 392     member this.NextMax () : byte * Point =
 393         if this.IsEmpty
 394         then
 395             invalidOp "Queue is empty"
 396         else
 397             let l = q.[highest]
 398             let next = l.First()
 399             l.Remove(next) |> ignore
 400             let value = byte highest
 401
 402             if l.Count = 0
 403             then
 404                 highest <- highest - 1
 405                 while highest > lowest && q.[highest].Count = 0 do
 406                     highest <- highest - 1
 407                 if highest = lowest
 408                 then
 409                     highest <- -1
 410                     lowest <- size
 411
 412             value, next
 413
 414     member this.NextMin () : byte * Point =
 415         if this.IsEmpty
 416         then
 417             invalidOp "Queue is empty"
 418         else
 419             let l = q.[lowest + 1]
 420             let next = l.First()
 421             l.Remove(next) |> ignore
 422             let value = byte (lowest + 1)
 423
 424             if l.Count = 0
 425             then
 426                 lowest <- lowest + 1
 427                 while lowest < highest && q.[lowest + 1].Count = 0 do
 428                     lowest <- lowest + 1
 429                 if highest = lowest
 430                 then
 431                     highest <- -1
 432                     lowest <- size
 433
 434             value, next
 435
 436     member this.Max =
 437         highest |> byte
 438
 439     member this.Min =
 440         lowest + 1 |> byte
 441
 442     member this.Add (value: byte) (p: Point) =
 443         let vi = int value
 444
 445         if vi > highest
 446         then
 447             highest <- vi
 448         if vi <= lowest
 449         then
 450             lowest <- vi - 1
 451
 452         q.[vi].Add(p) |> ignore
 453
 454     member this.Remove (value: byte) (p: Point) =
 455         let vi = int value
 456         if q.[vi].Remove(p) && q.[vi].Count = 0
 457         then
 458             if vi = highest
 459             then
 460                 highest <- highest - 1
 461                 while highest > lowest && q.[highest].Count = 0 do
 462                     highest <- highest - 1
 463             elif vi - 1 = lowest
 464             then
 465                 lowest <- lowest + 1
 466                 while lowest < highest && q.[lowest + 1].Count = 0 do
 467                     lowest <- lowest + 1
 468
 469             if highest = lowest // The queue is now empty.
 470             then
 471                 highest <- -1
 472                 lowest <- size
 473
 474     member this.IsEmpty =
 475         highest = -1
 476
 477     member this.Clear () =
 478         while highest > lowest  do
 479             q.[highest].Clear()
 480             highest <- highest - 1
 481         highest <- -1
 482         lowest <- size
 483
 484 type private AreaState =
 485     | Removed = 1
 486     | Unprocessed = 2
 487     | Validated = 3
 488
 489 type private AreaOperation =
 490     | Opening = 1
 491     | Closing = 2
 492
 493 [<AllowNullLiteral>]
 494 type private Area (elements: Points) =
 495     member this.Elements = elements
 496     member val Intensity = None with get, set
 497     member val State = AreaState.Unprocessed with get, set
 498
 499 let private areaOperation (img: Image<Gray, byte>) (area: int) (op: AreaOperation) =
 500     let w = img.Width
 501     let h = img.Height
 502     let imgData = img.Data
 503     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 504
 505     let areas = List<Area>((if op = AreaOperation.Opening then findMaxima img else findMinima img) |> Seq.map Area)
 506
 507     let pixels: Area[,] = Array2D.create h w null
 508     for m in areas do
 509         for e in m.Elements do
 510             pixels.[e.Y, e.X] <- m
 511
 512     let queue = PriorityQueue()
 513
 514     let addEdgeToQueue (elements: Points) =
 515         for p in elements do
 516             for i, j in se do
 517                 let ni = i + p.Y
 518                 let nj = j + p.X
 519                 let p' = Point(nj, ni)
 520                 if ni >= 0 && ni < h && nj >= 0 && nj < w && not (elements.Contains(p'))
 521                 then
 522                     queue.Add (imgData.[ni, nj, 0]) p'
 523
 524     // Reverse order is quicker.
 525     for i in areas.Count - 1 .. -1 .. 0 do
 526         let m = areas.[i]
 527         if m.Elements.Count <= area && m.State <> AreaState.Removed
 528         then
 529             queue.Clear()
 530             addEdgeToQueue m.Elements
 531
 532             let mutable intensity = if op = AreaOperation.Opening then queue.Max else queue.Min
 533             let nextElements = Points()
 534
 535             let mutable stop = false
 536             while not stop do
 537                 let intensity', p = if op = AreaOperation.Opening then queue.NextMax () else queue.NextMin ()
 538                 let mutable merged = false
 539
 540                 if intensity' = intensity // The intensity doesn't change.
 541                 then
 542                     if m.Elements.Count + nextElements.Count + 1 > area
 543                     then
 544                         m.State <- AreaState.Validated
 545                         m.Intensity <- Some intensity
 546                         stop <- true
 547                     else
 548                         nextElements.Add(p) |> ignore
 549
 550                 elif if op = AreaOperation.Opening then intensity' < intensity else intensity' > intensity
 551                 then
 552                     m.Elements.UnionWith(nextElements)
 553                     for e in nextElements do
 554                         pixels.[e.Y, e.X] <- m
 555
 556                     if m.Elements.Count = area
 557                     then
 558                         m.State <- AreaState.Validated
 559                         m.Intensity <- Some (intensity')
 560                         stop <- true
 561                     else
 562                         intensity <- intensity'
 563                         nextElements.Clear()
 564                         nextElements.Add(p) |> ignore
 565
 566                 else
 567                     match pixels.[p.Y, p.X] with
 568                     | null -> ()
 569                     | m' ->
 570                         if m'.Elements.Count + m.Elements.Count <= area
 571                         then
 572                             m'.State <- AreaState.Removed
 573                             for e in m'.Elements do
 574                                 pixels.[e.Y, e.X] <- m
 575                                 queue.Remove imgData.[e.Y, e.X, 0] e
 576                             addEdgeToQueue m'.Elements
 577                             m.Elements.UnionWith(m'.Elements)
 578                             let intensityMax = if op = AreaOperation.Opening then queue.Max else queue.Min
 579                             if intensityMax <> intensity
 580                             then
 581                                 intensity <- intensityMax
 582                                 nextElements.Clear()
 583                             merged <- true
 584
 585                     if not merged
 586                     then
 587                         m.State <- AreaState.Validated
 588                         m.Intensity <- Some (intensity)
 589                         stop <- true
 590
 591                 if not stop && not merged
 592                 then
 593                     for i, j in se do
 594                         let ni = i + p.Y
 595                         let nj = j + p.X
 596                         let p' = Point(nj, ni)
 597                         if ni < 0 || ni >= h || nj < 0 || nj >= w
 598                         then
 599                             m.State <- AreaState.Validated
 600                             m.Intensity <- Some (intensity)
 601                             stop <- true
 602                         elif not (m.Elements.Contains(p')) && not (nextElements.Contains(p'))
 603                         then
 604                             queue.Add (imgData.[ni, nj, 0]) p'
 605
 606                 if queue.IsEmpty
 607                 then
 608                     if m.Elements.Count + nextElements.Count <= area
 609                     then
 610                         m.State <- AreaState.Validated
 611                         m.Intensity <- Some intensity'
 612                         m.Elements.UnionWith(nextElements)
 613                     stop <- true
 614
 615     for m in areas do
 616         if m.State = AreaState.Validated
 617         then
 618             match m.Intensity with
 619             | Some i ->
 620                 for p in m.Elements do
 621                     imgData.[p.Y, p.X, 0] <- i
 622             | _ -> ()
 623     ()
 624
 625 /// <summary>
 626 /// Area opening on byte image.
 627 /// </summary>
 628 let areaOpen (img: Image<Gray, byte>) (area: int) =
 629     areaOperation img area AreaOperation.Opening
 630
 631 /// <summary>
 632 /// Area closing on byte image.
 633 /// </summary>
 634 let areaClose (img: Image<Gray, byte>) (area: int) =
 635     areaOperation img area AreaOperation.Closing
 636
 637 // A simpler algorithm than 'areaOpen' on byte image but slower.
 638 let areaOpen2 (img: Image<Gray, byte>) (area: int) =
 639     let w = img.Width
 640     let h = img.Height
 641     let imgData = img.Data
 642     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 643
 644     let histogram = Array.zeroCreate 256
 645     for i in 0 .. h - 1 do
 646         for j in 0 .. w - 1 do
 647             let v = imgData.[i, j, 0] |> int
 648             histogram.[v] <- histogram.[v] + 1
 649
 650     let flooded : bool[,] = Array2D.zeroCreate h w
 651
 652     let pointsChecked = HashSet<Point>()
 653     let pointsToCheck = Stack<Point>()
 654
 655     for level in 255 .. -1 .. 0 do
 656         let mutable n = histogram.[level]
 657         if n > 0
 658         then
 659             for i in 0 .. h - 1 do
 660                 for j in 0 .. w - 1 do
 661                     if not flooded.[i, j] && imgData.[i, j, 0] = byte level
 662                     then
 663                         let mutable maxNeighborValue = 0uy
 664                         pointsChecked.Clear()
 665                         pointsToCheck.Clear()
 666                         pointsToCheck.Push(Point(j, i))
 667
 668                         while pointsToCheck.Count > 0 do
 669                             let next = pointsToCheck.Pop()
 670                             pointsChecked.Add(next) |> ignore
 671                             flooded.[next.Y, next.X] <- true
 672
 673                             for nx, ny in se do
 674                                 let p = Point(next.X + nx, next.Y + ny)
 675                                 if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h
 676                                 then
 677                                     let v = imgData.[p.Y, p.X, 0]
 678                                     if v = byte level
 679                                     then
 680                                         if not (pointsChecked.Contains(p))
 681                                         then
 682                                             pointsToCheck.Push(p)
 683                                     elif v > maxNeighborValue
 684                                     then
 685                                         maxNeighborValue <- v
 686
 687                         if int maxNeighborValue < level && pointsChecked.Count <= area
 688                         then
 689                             for p in pointsChecked do
 690                                 imgData.[p.Y, p.X, 0] <- maxNeighborValue
 691
 692 [<AllowNullLiteral>]
 693 type Island (cmp: IComparer<float32>) =
 694     member val Shore = Heap.Heap<float32, Point>(cmp) with get
 695     member val Level = 0.f with get, set
 696     member val Surface = 0 with get, set
 697     member this.IsInfinite = this.Surface = Int32.MaxValue
 698
 699 let private areaOperationF (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: ('a -> float32 -> unit) option) (op: AreaOperation) =
 700     let w = img.Width
 701     let h = img.Height
 702     let earth = img.Data
 703     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 704
 705     let comparer = if op = AreaOperation.Opening
 706                    then { new IComparer<float32> with member this.Compare(v1, v2) = v1.CompareTo(v2) }
 707                    else { new IComparer<float32> with member this.Compare(v1, v2) = v2.CompareTo(v1) }
 708
 709     let ownership: Island[,] = Array2D.create h w null
 710
 711     // Initialize islands with their shore.
 712     let islands = List<Island>()
 713     let extremum = img |> if op = AreaOperation.Opening then findMaxima else findMinima
 714     for e in extremum do
 715         let island =
 716             let p = e.First()
 717             Island(comparer, Level = earth.[p.Y, p.X, 0], Surface = e.Count)
 718         islands.Add(island)
 719         let shorePoints = Points()
 720         for p in e do
 721             ownership.[p.Y, p.X] <- island
 722             for i, j in se do
 723                 let ni = i + p.Y
 724                 let nj = j + p.X
 725                 let neighbor = Point(nj, ni)
 726                 if ni >= 0 && ni < h && nj >= 0 && nj < w && Object.ReferenceEquals(ownership.[ni, nj], null) && not (shorePoints.Contains(neighbor))
 727                 then
 728                     shorePoints.Add(neighbor) |> ignore
 729                     island.Shore.Add earth.[ni, nj, 0] neighbor
 730
 731     for area, obj in areas do
 732         for island in islands do
 733             let mutable stop = island.Shore.IsEmpty
 734
 735             // 'true' if 'p' is owned or adjacent to 'island'.
 736             let inline ownedOrAdjacent (p: Point) : bool =
 737                 ownership.[p.Y, p.X] = island ||
 738                 (p.Y > 0 && ownership.[p.Y - 1, p.X] = island) ||
 739                 (p.Y < h - 1 && ownership.[p.Y + 1, p.X] = island) ||
 740                 (p.X > 0 && ownership.[p.Y, p.X - 1] = island) ||
 741                 (p.X < w - 1 && ownership.[p.Y, p.X + 1] = island)
 742
 743             while not stop && island.Surface < area do
 744                 let level, next = island.Shore.Max
 745                 let other = ownership.[next.Y, next.X]
 746                 if other = island // During merging, some points on the shore may be owned by the island itself -> ignored.
 747                 then
 748                     island.Shore.RemoveNext ()
 749                 else
 750                     if not <| Object.ReferenceEquals(other, null)
 751                     then // We touching another island.
 752                         if island.IsInfinite || other.IsInfinite || island.Surface + other.Surface >= area || comparer.Compare(island.Level, other.Level) < 0
 753                         then
 754                             stop <- true
 755                         else // We can merge 'other' into 'surface'.
 756                             island.Surface <- island.Surface + other.Surface
 757                             island.Level <- other.Level
 758                             // island.Level <- if comparer.Compare(island.Level, other.Level) > 0 then other.Level else island.Level
 759                             for l, p in other.Shore do
 760                                 let mutable currentY = p.Y + 1
 761                                 while currentY < h && ownership.[currentY, p.X] = other do
 762                                     ownership.[currentY, p.X] <- island
 763                                     currentY <- currentY + 1
 764                                 island.Shore.Add l p
 765                             other.Shore.Clear()
 766
 767                     elif comparer.Compare(level, island.Level) > 0
 768                     then
 769                         stop <- true
 770                     else
 771                         island.Shore.RemoveNext ()
 772                         for i, j in se do
 773                             let ni = i + next.Y
 774                             let nj = j + next.X
 775                             if ni < 0 || ni >= h || nj < 0 || nj >= w
 776                             then
 777                                 island.Surface <- Int32.MaxValue
 778                                 stop <- true
 779                             else
 780                                 let neighbor = Point(nj, ni)
 781                                 if not <| ownedOrAdjacent neighbor
 782                                 then
 783                                     island.Shore.Add earth.[ni, nj, 0] neighbor
 784                         if not stop
 785                         then
 786                             ownership.[next.Y, next.X] <- island
 787                             island.Level <- level
 788                             island.Surface <- island.Surface + 1
 789
 790         let mutable diff = 0.f
 791
 792         for i in 0 .. h - 1 do
 793             for j in 0 .. w - 1 do
 794                 match ownership.[i, j] with
 795                 | null -> ()
 796                 | island ->
 797                     let l = island.Level
 798                     diff <- diff + l - earth.[i, j, 0]
 799                     earth.[i, j, 0] <- l
 800
 801         match f with
 802         | Some f' -> f' obj diff
 803         | _ -> ()
 804     ()
 805
 806 /// <summary>
 807 /// Area opening on float image.
 808 /// </summary>
 809 let areaOpenF (img: Image<Gray, float32>) (area: int) =
 810     areaOperationF img [ area, () ] None AreaOperation.Opening
 811
 812 /// <summary>
 813 /// Area closing on float image.
 814 /// </summary>
 815 let areaCloseF (img: Image<Gray, float32>) (area: int) =
 816     areaOperationF img [ area, () ] None AreaOperation.Closing
 817
 818 /// <summary>
 819 /// Area closing on float image with different areas. Given areas must be sorted increasingly.
 820 /// For each area the function 'f' is called with the associated area value of type 'a and the volume difference
 821 /// Between the previous and the current closing.
 822 /// </summary>
 823 let areaOpenFWithFun (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: 'a -> float32 -> unit) =
 824     areaOperationF img areas (Some f) AreaOperation.Opening
 825
 826 /// <summary>
 827 /// Same as 'areaOpenFWithFun' for closing operation.
 828 /// </summary>
 829 let areaCloseFWithFun (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: 'a -> float32 -> unit) =
 830     areaOperationF img areas (Some f) AreaOperation.Closing
 831
 832 /// <summary>
 833 /// Zhang and Suen thinning algorithm.
 834 /// Modify 'mat' in place.
 835 /// </summary>
 836 let thin (mat: Matrix<byte>) =
 837     let w = mat.Width
 838     let h = mat.Height
 839     let mutable data1 = mat.Data
 840     let mutable data2 = Array2D.copy data1
 841
 842     let mutable pixelChanged = true
 843     let mutable oddIteration = true
 844
 845     while pixelChanged do
 846         pixelChanged <- false
 847         for i in 0..h-1 do
 848             for j in 0..w-1 do
 849                 if data1.[i, j] = 1uy
 850                 then
 851                     let p2 = if i = 0 then 0uy else data1.[i-1, j]
 852                     let p3 = if i = 0 || j = w-1 then 0uy else data1.[i-1, j+1]
 853                     let p4 = if j = w-1 then 0uy else data1.[i, j+1]
 854                     let p5 = if i = h-1 || j = w-1 then 0uy else data1.[i+1, j+1]
 855                     let p6 = if i = h-1 then 0uy else data1.[i+1, j]
 856                     let p7 = if i = h-1 || j = 0 then 0uy else data1.[i+1, j-1]
 857                     let p8 = if j = 0 then 0uy else data1.[i, j-1]
 858                     let p9 = if i = 0 || j = 0 then 0uy else data1.[i-1, j-1]
 859
 860                     let sumNeighbors = p2 + p3 + p4 + p5 + p6 + p7 + p8 + p9
 861                     if sumNeighbors >= 2uy && sumNeighbors <= 6uy &&
 862                         (if p2 = 0uy && p3 = 1uy then 1 else 0) +
 863                         (if p3 = 0uy && p4 = 1uy then 1 else 0) +
 864                         (if p4 = 0uy && p5 = 1uy then 1 else 0) +
 865                         (if p5 = 0uy && p6 = 1uy then 1 else 0) +
 866                         (if p6 = 0uy && p7 = 1uy then 1 else 0) +
 867                         (if p7 = 0uy && p8 = 1uy then 1 else 0) +
 868                         (if p8 = 0uy && p9 = 1uy then 1 else 0) +
 869                         (if p9 = 0uy && p2 = 1uy then 1 else 0) = 1 &&
 870                         if oddIteration
 871                         then p2 * p4 * p6 = 0uy && p4 * p6 * p8 = 0uy
 872                         else p2 * p4 * p8 = 0uy && p2 * p6 * p8 = 0uy
 873                     then
 874                         data2.[i, j] <- 0uy
 875                         pixelChanged <- true
 876                 else
 877                     data2.[i, j] <- 0uy
 878
 879         oddIteration <- not oddIteration
 880         let tmp = data1
 881         data1 <- data2
 882         data2 <- tmp
 883
 884 /// <summary>
 885 /// Remove all 8-connected pixels with an area equal or greater than 'areaSize'.
 886 /// Modify 'mat' in place.
 887 /// </summary>
 888 let removeArea (mat: Matrix<byte>) (areaSize: int) =
 889     let neighbors = [|
 890         (-1,  0) // p2
 891         (-1,  1) // p3
 892         ( 0,  1) // p4
 893         ( 1,  1) // p5
 894         ( 1,  0) // p6
 895         ( 1, -1) // p7
 896         ( 0, -1) // p8
 897         (-1, -1) |] // p9
 898
 899     use mat' = new Matrix<byte>(mat.Size)
 900     let w = mat'.Width
 901     let h = mat'.Height
 902     mat.CopyTo(mat')
 903
 904     let data = mat.Data
 905     let data' = mat'.Data
 906
 907     for i in 0..h-1 do
 908         for j in 0..w-1 do
 909             if data'.[i, j] = 1uy
 910             then
 911                 let neighborhood = List<Point>()
 912                 let neighborsToCheck = Stack<Point>()
 913                 neighborsToCheck.Push(Point(j, i))
 914                 data'.[i, j] <- 0uy
 915
 916                 while neighborsToCheck.Count > 0 do
 917                     let n = neighborsToCheck.Pop()
 918                     neighborhood.Add(n)
 919                     for (ni, nj) in neighbors do
 920                         let pi = n.Y + ni
 921                         let pj = n.X + nj
 922                         if pi >= 0 && pi < h && pj >= 0 && pj < w && data'.[pi, pj] = 1uy
 923                         then
 924                             neighborsToCheck.Push(Point(pj, pi))
 925                             data'.[pi, pj] <- 0uy
 926                 if neighborhood.Count <= areaSize
 927                 then
 928                     for n in neighborhood do
 929                         data.[n.Y, n.X] <- 0uy
 930
 931 let connectedComponents (img: Image<Gray, byte>) (startPoints: List<Point>) : Points =
 932     let w = img.Width
 933     let h = img.Height
 934
 935     let pointChecked = Points()
 936     let pointToCheck = Stack<Point>(startPoints);
 937
 938     let data = img.Data
 939
 940     while pointToCheck.Count > 0 do
 941         let next = pointToCheck.Pop()
 942         pointChecked.Add(next) |> ignore
 943         for ny in -1 .. 1 do
 944             for nx in -1 .. 1 do
 945                 if ny <> 0 && nx <> 0
 946                 then
 947                     let p = Point(next.X + nx, next.Y + ny)
 948                     if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h && data.[p.Y, p.X, 0] > 0uy && not (pointChecked.Contains p)
 949                     then
 950                         pointToCheck.Push(p)
 951
 952     pointChecked
 953
 954 let drawLine (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: int) (y0: int) (x1: int) (y1: int) (thickness: int) =
 955     img.Draw(LineSegment2D(Point(x0, y0), Point(x1, y1)), color, thickness);
 956
 957 let drawLineF (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: float) (y0: float) (x1: float) (y1: float) (thickness: int) =
 958     img.Draw(LineSegment2DF(PointF(float32 x0, float32 y0), PointF(float32 x1, float32 y1)), color, thickness, CvEnum.LineType.AntiAlias);
 959
 960 let drawEllipse (img: Image<'TColor, 'TDepth>) (e: Ellipse) (color: 'TColor) (alpha: float) =
 961     if alpha >= 1.0
 962     then
 963         img.Draw(Emgu.CV.Structure.Ellipse(PointF(e.Cx, e.Cy), SizeF(2.f * e.B, 2.f * e.A), e.Alpha / PI * 180.f), color, 1, CvEnum.LineType.AntiAlias)
 964     else
 965         let windowPosX = e.Cx - e.A - 5.f
 966         let gapX = windowPosX - (float32 (int windowPosX))
 967
 968         let windowPosY = e.Cy - e.A - 5.f
 969         let gapY = windowPosY - (float32 (int windowPosY))
 970
 971         let roi = Rectangle(int windowPosX, int windowPosY, 2.f * (e.A + 5.f) |> int, 2.f * (e.A + 5.f) |> int)
 972
 973         img.ROI <- roi
 974         if roi = img.ROI // We do not display ellipses touching the edges (FIXME)
 975         then
 976             use i = new Image<'TColor, 'TDepth>(img.ROI.Size)
 977             i.Draw(Emgu.CV.Structure.Ellipse(PointF(e.A + 5.f + gapX, e.A + 5.f + gapY), SizeF(2.f * e.B, 2.f * e.A), e.Alpha / PI * 180.f), color, 1, CvEnum.LineType.AntiAlias)
 978             CvInvoke.AddWeighted(img, 1.0, i, alpha, 0.0, img)
 979         img.ROI <- Rectangle.Empty
 980
 981 let drawEllipses (img: Image<'TColor, 'TDepth>) (ellipses: Ellipse list) (color: 'TColor) (alpha: float) =
 982     List.iter (fun e -> drawEllipse img e color alpha) ellipses
 983
 984 let rngCell =  System.Random()
 985 let drawCell (img: Image<Bgr, byte>) (drawCellContent: bool) (c: Cell) =
 986     if drawCellContent
 987     then
 988         let colorB = rngCell.Next(20, 70)
 989         let colorG = rngCell.Next(20, 70)
 990         let colorR = rngCell.Next(20, 70)
 991
 992         for y in 0 .. c.elements.Height - 1 do
 993             for x in 0 .. c.elements.Width - 1 do
 994                 if c.elements.[y, x] > 0uy
 995                 then
 996                     let dx, dy = c.center.X - c.elements.Width / 2, c.center.Y - c.elements.Height / 2
 997                     let b = img.Data.[y + dy, x + dx, 0] |> int
 998                     let g = img.Data.[y + dy, x + dx, 1] |> int
 999                     let r = img.Data.[y + dy, x + dx, 2] |> int
1000                     img.Data.[y + dy, x + dx, 0] <- if b + colorB > 255 then 255uy else byte (b + colorB)
1001                     img.Data.[y + dy, x + dx, 1] <- if g + colorG > 255 then 255uy else byte (g + colorG)
1002                     img.Data.[y + dy, x + dx, 2] <- if r + colorR > 255 then 255uy else byte (r + colorR)
1003
1004     let crossColor, crossColor2 =
1005         match c.cellClass with
1006         | HealthyRBC -> Bgr(255., 0., 0.), Bgr(255., 255., 255.)
1007         | InfectedRBC -> Bgr(0., 0., 255.), Bgr(120., 120., 255.)
1008         | Peculiar -> Bgr(0., 0., 0.), Bgr(80., 80., 80.)
1009
1010     drawLine img crossColor2 (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 2
1011     drawLine img crossColor2 c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 2
1012
1013     drawLine img crossColor (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 1
1014     drawLine img crossColor c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 1
1015
1016
1017 let drawCells (img: Image<Bgr, byte>) (drawCellContent: bool) (cells: Cell list) =
1018     List.iter (fun c -> drawCell img drawCellContent c) cells