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 Utils
  14
  15 // Normalize image values between 0uy and 255uy.
  16 let normalizeAndConvert (img: Image<Gray, 'TDepth>) : Image<Gray, byte> =
  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     ((img.Convert<Gray, float32>() - (!min).[0]) / ((!max).[0] - (!min).[0]) * 255.0).Convert<Gray, byte>()
  23
  24 let saveImg (img: Image<'TColor, 'TDepth>) (filepath: string) =
  25     img.Save(filepath)
  26
  27 let saveMat (mat: Matrix<'TDepth>) (filepath: string) =
  28     use img = new Image<Gray, 'TDeph>(mat.Size)
  29     mat.CopyTo(img)
  30     saveImg img filepath
  31
  32 type Histogram = { data: int[]; total: int; sum: int; min: float32; max: float32 }
  33
  34 let histogramImg (img: Image<Gray, float32>) (nbSamples: int) : Histogram =
  35     let imgData = img.Data
  36
  37     let min, max =
  38         let min = ref [| 0.0 |]
  39         let minLocation = ref <| [| Point() |]
  40         let max = ref [| 0.0 |]
  41         let maxLocation = ref <| [| Point() |]
  42         img.MinMax(min, max, minLocation, maxLocation)
  43         float32 (!min).[0], float32 (!max).[0]
  44
  45     let bin (x: float32) : int =
  46         let p = int ((x - min) / (max - min) * float32 nbSamples)
  47         if p >= nbSamples then nbSamples - 1 else p
  48
  49     let data = Array.zeroCreate nbSamples
  50
  51     for i in 0 .. img.Height - 1 do
  52         for j in 0 .. img.Width - 1 do
  53             let p = bin imgData.[i, j, 0]
  54             data.[p] <- data.[p] + 1
  55
  56     { data = data; total = img.Height * img.Width; sum = Array.sum data; min = min; max = max }
  57
  58 let histogramMat (mat: Matrix<float32>) (nbSamples: int) : Histogram =
  59     let matData = mat.Data
  60
  61     let min, max =
  62         let min = ref 0.0
  63         let minLocation = ref <| Point()
  64         let max = ref 0.0
  65         let maxLocation = ref <| Point()
  66         mat.MinMax(min, max, minLocation, maxLocation)
  67         float32 !min, float32 !max
  68
  69     let bin (x: float32) : int =
  70         let p = int ((x - min) / (max - min) * float32 nbSamples)
  71         if p >= nbSamples then nbSamples - 1 else p
  72
  73     let data = Array.zeroCreate nbSamples
  74
  75     for i in 0 .. mat.Height - 1 do
  76         for j in 0 .. mat.Width - 1 do
  77             let p = bin matData.[i, j]
  78             data.[p] <- data.[p] + 1
  79
  80     { data = data; total = mat.Height * mat.Width; sum = Array.sum data; min = min; max = max }
  81
  82 let histogram (values: float32 seq) (nbSamples: int) : Histogram =
  83     let mutable min = Single.MaxValue
  84     let mutable max = Single.MinValue
  85     let mutable n = 0
  86
  87     for v in values do
  88         n <- n + 1
  89         if v < min then min <- v
  90         if v > max then max <- v
  91
  92     let bin (x: float32) : int =
  93         let p = int ((x - min) / (max - min) * float32 nbSamples)
  94         if p >= nbSamples then nbSamples - 1 else p
  95
  96     let data = Array.zeroCreate nbSamples
  97
  98     for v in values do
  99         let p = bin v
 100         data.[p] <- data.[p] + 1
 101
 102     { data = data; total = n; sum = Array.sum data; min = min; max = max }
 103
 104 let otsu (hist: Histogram) : float32 * float32 * float32 =
 105     let mutable sumB = 0
 106     let mutable wB = 0
 107     let mutable maximum = 0.0
 108     let mutable level = 0
 109     let sum = hist.data |> Array.mapi (fun i v -> i * v) |> Array.sum |> float
 110
 111     for i in 0 .. hist.data.Length - 1 do
 112         wB <- wB + hist.data.[i]
 113         if wB <> 0
 114         then
 115             let wF = hist.total - wB
 116             if wF <> 0
 117             then
 118                 sumB <- sumB + i * hist.data.[i]
 119                 let mB = (float sumB) / (float wB)
 120                 let mF = (sum - float sumB) / (float wF)
 121                 let between = (float wB) * (float wF) * (mB - mF) ** 2.;
 122                 if between >= maximum
 123                 then
 124                     level <- i
 125                     maximum <- between
 126
 127     let mean1 =
 128         let mutable sum = 0
 129         let mutable nb = 0
 130         for i in 0 .. level - 1 do
 131             sum <- sum + i * hist.data.[i]
 132             nb <- nb + hist.data.[i]
 133         (sum + level * hist.data.[level] / 2) / (nb + hist.data.[level] / 2)
 134
 135     let mean2 =
 136         let mutable sum = 0
 137         let mutable nb = 0
 138         for i in level + 1 .. hist.data.Length - 1 do
 139             sum <- sum + i * hist.data.[i]
 140             nb <- nb + hist.data.[i]
 141         (sum + level * hist.data.[level] / 2) / (nb + hist.data.[level] / 2)
 142
 143     let toFloat l =
 144         float32 l / float32 hist.data.Length * (hist.max - hist.min) + hist.min
 145
 146     toFloat level, toFloat mean1, toFloat mean2
 147
 148 let suppressMConnections (img: Matrix<byte>) =
 149     let w = img.Width
 150     let h = img.Height
 151     for i in 1 .. h - 2 do
 152         for j in 1 .. w - 2 do
 153             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)
 154             then
 155                 img.[i, j] <- 0uy
 156     for i in 1 .. h - 2 do
 157         for j in 1 .. w - 2 do
 158             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)
 159             then
 160                 img.[i, j] <- 0uy
 161
 162 let findEdges (img: Image<Gray, float32>) : Matrix<byte> * Image<Gray, float32> * Image<Gray, float32> =
 163     let w = img.Width
 164     let h = img.Height
 165
 166     use sobelKernel =
 167         new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
 168                                         [ 2.0f; 0.0f; -2.0f ]
 169                                         [ 1.0f; 0.0f; -1.0f ]], Point(1, 1))
 170
 171     let xGradient = img.Convolution(sobelKernel)
 172     let yGradient = img.Convolution(sobelKernel.Transpose())
 173
 174     let xGradientData = xGradient.Data
 175     let yGradientData = yGradient.Data
 176     for r in 0 .. h - 1 do
 177         xGradientData.[r, 0, 0] <- 0.f
 178         xGradientData.[r, w - 1, 0] <- 0.f
 179         yGradientData.[r, 0, 0] <- 0.f
 180         yGradientData.[r, w - 1, 0] <- 0.f
 181
 182     for c in 0 .. w - 1 do
 183         xGradientData.[0, c, 0] <- 0.f
 184         xGradientData.[h - 1, c, 0] <- 0.f
 185         yGradientData.[0, c, 0] <- 0.f
 186         yGradientData.[h - 1, c, 0] <- 0.f
 187
 188     use magnitudes = new Matrix<float32>(xGradient.Size)
 189     use angles = new Matrix<float32>(xGradient.Size)
 190     CvInvoke.CartToPolar(xGradient, yGradient, magnitudes, angles) // Compute the magnitudes (without angles).
 191
 192     let thresholdHigh, thresholdLow =
 193         let sensibilityHigh = 0.1f
 194         let sensibilityLow = 0.0f
 195         use magnitudesByte = magnitudes.Convert<byte>()
 196         let threshold, _, _ = otsu (histogramMat magnitudes 300)
 197         threshold + (sensibilityHigh * threshold), threshold - (sensibilityLow * threshold)
 198
 199     // Non-maximum suppression.
 200     use nms = new Matrix<byte>(xGradient.Size)
 201
 202     let nmsData = nms.Data
 203     let anglesData = angles.Data
 204     let magnitudesData = magnitudes.Data
 205     let xGradientData = xGradient.Data
 206     let yGradientData = yGradient.Data
 207
 208     let PI = float32 Math.PI
 209
 210     for i in 0 .. h - 1 do
 211         nmsData.[i, 0] <- 0uy
 212         nmsData.[i, w - 1] <- 0uy
 213
 214     for j in 0 .. w - 1 do
 215         nmsData.[0, j] <- 0uy
 216         nmsData.[h - 1, j] <- 0uy
 217
 218     for i in 1 .. h - 2 do
 219         for j in 1 .. w - 2 do
 220             let vx = xGradientData.[i, j, 0]
 221             let vy = yGradientData.[i, j, 0]
 222             if vx <> 0.f || vy <> 0.f
 223             then
 224                 let angle = anglesData.[i, j]
 225
 226                 let vx', vy' = abs vx, abs vy
 227                 let ratio2 = if vx' > vy' then vy' / vx' else vx' / vy'
 228                 let ratio1 = 1.f - ratio2
 229
 230                 let mNeigbors (sign: int) : float32 =
 231                     if angle < PI / 4.f
 232                     then ratio1 * magnitudesData.[i, j + sign] + ratio2 * magnitudesData.[i + sign, j + sign]
 233                     elif angle < PI / 2.f
 234                     then ratio2 * magnitudesData.[i + sign, j + sign] + ratio1 * magnitudesData.[i + sign, j]
 235                     elif angle < 3.f * PI / 4.f
 236                     then ratio1 * magnitudesData.[i + sign, j] + ratio2 * magnitudesData.[i + sign, j - sign]
 237                     elif angle < PI
 238                     then ratio2 * magnitudesData.[i + sign, j - sign] + ratio1 * magnitudesData.[i, j - sign]
 239                     elif angle < 5.f * PI / 4.f
 240                     then ratio1 * magnitudesData.[i, j - sign] + ratio2 * magnitudesData.[i - sign, j - sign]
 241                     elif angle < 3.f * PI / 2.f
 242                     then ratio2 * magnitudesData.[i - sign, j - sign] + ratio1 * magnitudesData.[i - sign, j]
 243                     elif angle < 7.f * PI / 4.f
 244                     then ratio1 * magnitudesData.[i - sign, j] + ratio2 * magnitudesData.[i - sign, j + sign]
 245                     else ratio2 * magnitudesData.[i - sign, j + sign] + ratio1 * magnitudesData.[i, j + sign]
 246
 247                 let m = magnitudesData.[i, j]
 248                 if m >= thresholdLow && m > mNeigbors 1 && m > mNeigbors -1
 249                 then
 250                     nmsData.[i, j] <- 1uy
 251
 252     // suppressMConnections nms // It's not helpful for the rest of the process (ellipse detection).
 253
 254     let edges = new Matrix<byte>(xGradient.Size)
 255     let edgesData = edges.Data
 256
 257     // Hysteresis thresholding.
 258     let toVisit = Stack<Point>()
 259     for i in 0 .. h - 1 do
 260         for j in 0 .. w - 1 do
 261             if nmsData.[i, j] = 1uy && magnitudesData.[i, j] >= thresholdHigh
 262             then
 263                 nmsData.[i, j] <- 0uy
 264                 toVisit.Push(Point(j, i))
 265                 while toVisit.Count > 0 do
 266                     let p = toVisit.Pop()
 267                     edgesData.[p.Y, p.X] <- 1uy
 268                     for i' in -1 .. 1  do
 269                         for j' in -1 .. 1 do
 270                             if i' <> 0 || j' <> 0
 271                             then
 272                                 let ni = p.Y + i'
 273                                 let nj = p.X + j'
 274                                 if ni >= 0 && ni < h && nj >= 0 && nj < w && nmsData.[ni, nj] = 1uy
 275                                 then
 276                                     nmsData.[ni, nj] <- 0uy
 277                                     toVisit.Push(Point(nj, ni))
 278
 279     edges, xGradient, yGradient
 280
 281 let gaussianFilter (img : Image<'TColor, 'TDepth>) (standardDeviation : float) : Image<'TColor, 'TDepth> =
 282     let size = 2 * int (ceil (4.0 * standardDeviation)) + 1
 283     img.SmoothGaussian(size, size, standardDeviation, standardDeviation)
 284
 285 type Points = HashSet<Point>
 286
 287 let drawPoints (img: Image<Gray, 'TDepth>) (points: Points) (intensity: 'TDepth) =
 288     for p in points do
 289         img.Data.[p.Y, p.X, 0] <- intensity
 290
 291 type ExtremumType =
 292     | Maxima = 1
 293     | Minima = 2
 294
 295 let findExtremum (img: Image<Gray, 'TDepth>) (extremumType: ExtremumType) : IEnumerable<Points> =
 296     let w = img.Width
 297     let h = img.Height
 298     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 299
 300     let imgData = img.Data
 301     let suppress: bool[,] = Array2D.zeroCreate h w
 302
 303     let result = List<List<Point>>()
 304
 305     let flood (start: Point) : List<List<Point>> =
 306         let sameLevelToCheck = Stack<Point>()
 307         let betterLevelToCheck = Stack<Point>()
 308         betterLevelToCheck.Push(start)
 309
 310         let result' = List<List<Point>>()
 311
 312         while betterLevelToCheck.Count > 0 do
 313             let p = betterLevelToCheck.Pop()
 314             if not suppress.[p.Y, p.X]
 315             then
 316                 suppress.[p.Y, p.X] <- true
 317                 sameLevelToCheck.Push(p)
 318                 let current = List<Point>()
 319
 320                 let mutable betterExists = false
 321
 322                 while sameLevelToCheck.Count > 0 do
 323                     let p' = sameLevelToCheck.Pop()
 324                     let currentLevel = imgData.[p'.Y, p'.X, 0]
 325                     current.Add(p') |> ignore
 326                     for i, j in se do
 327                         let ni = i + p'.Y
 328                         let nj = j + p'.X
 329                         if ni >= 0 && ni < h && nj >= 0 && nj < w
 330                         then
 331                             let level = imgData.[ni, nj, 0]
 332                             let notSuppressed = not suppress.[ni, nj]
 333
 334                             if level = currentLevel && notSuppressed
 335                             then
 336                                 suppress.[ni, nj] <- true
 337                                 sameLevelToCheck.Push(Point(nj, ni))
 338                             elif if extremumType = ExtremumType.Maxima then level > currentLevel else level < currentLevel
 339                             then
 340                                 betterExists <- true
 341                                 if notSuppressed
 342                                 then
 343                                     betterLevelToCheck.Push(Point(nj, ni))
 344
 345                 if not betterExists
 346                 then
 347                     result'.Add(current)
 348         result'
 349
 350     for i in 0 .. h - 1 do
 351         for j in 0 .. w - 1 do
 352             let maxima = flood (Point(j, i))
 353             if maxima.Count > 0
 354             then
 355                 result.AddRange(maxima)
 356
 357     result.Select(fun l -> Points(l))
 358
 359 let findMaxima (img: Image<Gray, 'TDepth>) : IEnumerable<Points> =
 360     findExtremum img ExtremumType.Maxima
 361
 362 let findMinima (img: Image<Gray, 'TDepth>) : IEnumerable<Points> =
 363     findExtremum img ExtremumType.Minima
 364
 365 type PriorityQueue () =
 366     let size = 256
 367     let q: Points[] = Array.init size (fun i -> Points())
 368     let mutable highest = -1 // Value of the first elements of 'q'.
 369     let mutable lowest = size
 370
 371     member this.NextMax () : byte * Point =
 372         if this.IsEmpty
 373         then
 374             invalidOp "Queue is empty"
 375         else
 376             let l = q.[highest]
 377             let next = l.First()
 378             l.Remove(next) |> ignore
 379             let value = byte highest
 380
 381             if l.Count = 0
 382             then
 383                 highest <- highest - 1
 384                 while highest > lowest && q.[highest].Count = 0 do
 385                     highest <- highest - 1
 386                 if highest = lowest
 387                 then
 388                     highest <- -1
 389                     lowest <- size
 390
 391             value, next
 392
 393     member this.NextMin () : byte * Point =
 394         if this.IsEmpty
 395         then
 396             invalidOp "Queue is empty"
 397         else
 398             let l = q.[lowest + 1]
 399             let next = l.First()
 400             l.Remove(next) |> ignore
 401             let value = byte (lowest + 1)
 402
 403             if l.Count = 0
 404             then
 405                 lowest <- lowest + 1
 406                 while lowest < highest && q.[lowest + 1].Count = 0 do
 407                     lowest <- lowest + 1
 408                 if highest = lowest
 409                 then
 410                     highest <- -1
 411                     lowest <- size
 412
 413             value, next
 414
 415     member this.Max =
 416         highest |> byte
 417
 418     member this.Min =
 419         lowest + 1 |> byte
 420
 421     member this.Add (value: byte) (p: Point) =
 422         let vi = int value
 423
 424         if vi > highest
 425         then
 426             highest <- vi
 427         if vi <= lowest
 428         then
 429             lowest <- vi - 1
 430
 431         q.[vi].Add(p) |> ignore
 432
 433     member this.Remove (value: byte) (p: Point) =
 434         let vi = int value
 435         if q.[vi].Remove(p) && q.[vi].Count = 0
 436         then
 437             if vi = highest
 438             then
 439                 highest <- highest - 1
 440                 while highest > lowest && q.[highest].Count = 0 do
 441                     highest <- highest - 1
 442             elif vi - 1 = lowest
 443             then
 444                 lowest <- lowest + 1
 445                 while lowest < highest && q.[lowest + 1].Count = 0 do
 446                     lowest <- lowest + 1
 447
 448             if highest = lowest // The queue is now empty.
 449             then
 450                 highest <- -1
 451                 lowest <- size
 452
 453     member this.IsEmpty =
 454         highest = -1
 455
 456     member this.Clear () =
 457         while highest > lowest  do
 458             q.[highest].Clear()
 459             highest <- highest - 1
 460         highest <- -1
 461         lowest <- size
 462
 463 type private AreaState =
 464     | Removed = 1
 465     | Unprocessed = 2
 466     | Validated = 3
 467
 468 type private AreaOperation =
 469     | Opening = 1
 470     | Closing = 2
 471
 472 [<AllowNullLiteral>]
 473 type private Area (elements: Points) =
 474     member this.Elements = elements
 475     member val Intensity = None with get, set
 476     member val State = AreaState.Unprocessed with get, set
 477
 478 let private areaOperation (img: Image<Gray, byte>) (area: int) (op: AreaOperation) =
 479     let w = img.Width
 480     let h = img.Height
 481     let imgData = img.Data
 482     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 483
 484     let areas = List<Area>((if op = AreaOperation.Opening then findMaxima img else findMinima img) |> Seq.map Area)
 485
 486     let pixels: Area[,] = Array2D.create h w null
 487     for m in areas do
 488         for e in m.Elements do
 489             pixels.[e.Y, e.X] <- m
 490
 491     let queue = PriorityQueue()
 492
 493     let addEdgeToQueue (elements: Points) =
 494         for p in elements do
 495             for i, j in se do
 496                 let ni = i + p.Y
 497                 let nj = j + p.X
 498                 let p' = Point(nj, ni)
 499                 if ni >= 0 && ni < h && nj >= 0 && nj < w && not (elements.Contains(p'))
 500                 then
 501                     queue.Add (imgData.[ni, nj, 0]) p'
 502
 503     // Reverse order is quicker.
 504     for i in areas.Count - 1 .. -1 .. 0 do
 505         let m = areas.[i]
 506         if m.Elements.Count <= area && m.State <> AreaState.Removed
 507         then
 508             queue.Clear()
 509             addEdgeToQueue m.Elements
 510
 511             let mutable intensity = if op = AreaOperation.Opening then queue.Max else queue.Min
 512             let nextElements = Points()
 513
 514             let mutable stop = false
 515             while not stop do
 516                 let intensity', p = if op = AreaOperation.Opening then queue.NextMax () else queue.NextMin ()
 517                 let mutable merged = false
 518
 519                 if intensity' = intensity // The intensity doesn't change.
 520                 then
 521                     if m.Elements.Count + nextElements.Count + 1 > area
 522                     then
 523                         m.State <- AreaState.Validated
 524                         m.Intensity <- Some intensity
 525                         stop <- true
 526                     else
 527                         nextElements.Add(p) |> ignore
 528
 529                 elif if op = AreaOperation.Opening then intensity' < intensity else intensity' > intensity
 530                 then
 531                     m.Elements.UnionWith(nextElements)
 532                     for e in nextElements do
 533                         pixels.[e.Y, e.X] <- m
 534
 535                     if m.Elements.Count = area
 536                     then
 537                         m.State <- AreaState.Validated
 538                         m.Intensity <- Some (intensity')
 539                         stop <- true
 540                     else
 541                         intensity <- intensity'
 542                         nextElements.Clear()
 543                         nextElements.Add(p) |> ignore
 544
 545                 else
 546                     match pixels.[p.Y, p.X] with
 547                     | null -> ()
 548                     | m' ->
 549                         if m'.Elements.Count + m.Elements.Count <= area
 550                         then
 551                             m'.State <- AreaState.Removed
 552                             for e in m'.Elements do
 553                                 pixels.[e.Y, e.X] <- m
 554                                 queue.Remove imgData.[e.Y, e.X, 0] e
 555                             addEdgeToQueue m'.Elements
 556                             m.Elements.UnionWith(m'.Elements)
 557                             let intensityMax = if op = AreaOperation.Opening then queue.Max else queue.Min
 558                             if intensityMax <> intensity
 559                             then
 560                                 intensity <- intensityMax
 561                                 nextElements.Clear()
 562                             merged <- true
 563
 564                     if not merged
 565                     then
 566                         m.State <- AreaState.Validated
 567                         m.Intensity <- Some (intensity)
 568                         stop <- true
 569
 570                 if not stop && not merged
 571                 then
 572                     for i, j in se do
 573                         let ni = i + p.Y
 574                         let nj = j + p.X
 575                         let p' = Point(nj, ni)
 576                         if ni < 0 || ni >= h || nj < 0 || nj >= w
 577                         then
 578                             m.State <- AreaState.Validated
 579                             m.Intensity <- Some (intensity)
 580                             stop <- true
 581                         elif not (m.Elements.Contains(p')) && not (nextElements.Contains(p'))
 582                         then
 583                             queue.Add (imgData.[ni, nj, 0]) p'
 584
 585                 if queue.IsEmpty
 586                 then
 587                     if m.Elements.Count + nextElements.Count <= area
 588                     then
 589                         m.State <- AreaState.Validated
 590                         m.Intensity <- Some intensity'
 591                         m.Elements.UnionWith(nextElements)
 592                     stop <- true
 593
 594     for m in areas do
 595         if m.State = AreaState.Validated
 596         then
 597             match m.Intensity with
 598             | Some i ->
 599                 for p in m.Elements do
 600                     imgData.[p.Y, p.X, 0] <- i
 601             | _ -> ()
 602     ()
 603
 604 let areaOpen (img: Image<Gray, byte>) (area: int) =
 605     areaOperation img area AreaOperation.Opening
 606
 607 let areaClose (img: Image<Gray, byte>) (area: int) =
 608     areaOperation img area AreaOperation.Closing
 609
 610 [<AllowNullLiteral>]
 611 type Island (cmp: IComparer<float32>) =
 612     member val Shore = Heap.Heap<float32, Point>(cmp) with get
 613     member val Level = 0.f with get, set
 614     member val Surface = 0 with get, set
 615     member this.IsInfinite = this.Surface = Int32.MaxValue
 616
 617 let private areaOperationF (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: ('a -> float32 -> unit) option) (op: AreaOperation) =
 618     let w = img.Width
 619     let h = img.Height
 620     let earth = img.Data
 621     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 622
 623     let comparer = if op = AreaOperation.Opening
 624                    then { new IComparer<float32> with member this.Compare(v1, v2) = v1.CompareTo(v2) }
 625                    else { new IComparer<float32> with member this.Compare(v1, v2) = v2.CompareTo(v1) }
 626
 627     let ownership: Island[,] = Array2D.create h w null
 628
 629     // Initialize islands with their shore.
 630     let islands = List<Island>()
 631     let extremum = img |> if op = AreaOperation.Opening then findMaxima else findMinima
 632     for e in extremum do
 633         let island =
 634             let p = e.First()
 635             Island(comparer, Level = earth.[p.Y, p.X, 0], Surface = e.Count)
 636         islands.Add(island)
 637         let shorePoints = Points()
 638         for p in e do
 639             ownership.[p.Y, p.X] <- island
 640             for i, j in se do
 641                 let ni = i + p.Y
 642                 let nj = j + p.X
 643                 let neighbor = Point(nj, ni)
 644                 if ni >= 0 && ni < h && nj >= 0 && nj < w && Object.ReferenceEquals(ownership.[ni, nj], null) && not (shorePoints.Contains(neighbor))
 645                 then
 646                     shorePoints.Add(neighbor) |> ignore
 647                     island.Shore.Add earth.[ni, nj, 0] neighbor
 648
 649     for area, obj in areas do
 650         for island in islands do
 651             let mutable stop = island.Shore.IsEmpty
 652
 653             // 'true' if 'p' is owned or adjacent to 'island'.
 654             let inline ownedOrAdjacent (p: Point) : bool =
 655                 ownership.[p.Y, p.X] = island ||
 656                 (p.Y > 0 && ownership.[p.Y - 1, p.X] = island) ||
 657                 (p.Y < h - 1 && ownership.[p.Y + 1, p.X] = island) ||
 658                 (p.X > 0 && ownership.[p.Y, p.X - 1] = island) ||
 659                 (p.X < w - 1 && ownership.[p.Y, p.X + 1] = island)
 660
 661             while not stop && island.Surface < area do
 662                 let level, next = island.Shore.Max
 663                 let other = ownership.[next.Y, next.X]
 664                 if other = island // During merging, some points on the shore may be owned by the island itself -> ignored.
 665                 then
 666                     island.Shore.RemoveNext ()
 667                 else
 668                     if not <| Object.ReferenceEquals(other, null)
 669                     then // We touching another island.
 670                         if island.IsInfinite || other.IsInfinite || island.Surface + other.Surface >= area
 671                         then
 672                             stop <- true
 673                         else // We can merge 'other' into 'surface'.
 674                             island.Surface <- island.Surface + other.Surface
 675                             island.Level <- if comparer.Compare(island.Level, other.Level) > 0 then island.Level else other.Level
 676                             for l, p in other.Shore do
 677                                 let mutable currentY = p.Y + 1
 678                                 while currentY < h && ownership.[currentY, p.X] = other do
 679                                     ownership.[currentY, p.X] <- island
 680                                     currentY <- currentY + 1
 681                                 island.Shore.Add l p
 682                             other.Shore.Clear()
 683
 684                     elif comparer.Compare(level, island.Level) > 0
 685                     then
 686                         stop <- true
 687                     else
 688                         island.Shore.RemoveNext ()
 689                         for i, j in se do
 690                             let ni = i + next.Y
 691                             let nj = j + next.X
 692                             if ni < 0 || ni >= h || nj < 0 || nj >= w
 693                             then
 694                                 island.Surface <- Int32.MaxValue
 695                                 stop <- true
 696                             else
 697                                 let neighbor = Point(nj, ni)
 698                                 if not <| ownedOrAdjacent neighbor
 699                                 then
 700                                     island.Shore.Add earth.[ni, nj, 0] neighbor
 701                         if not stop
 702                         then
 703                             ownership.[next.Y, next.X] <- island
 704                             island.Level <- level
 705                             island.Surface <- island.Surface + 1
 706
 707         let mutable diff = 0.f
 708
 709         for i in 0 .. h - 1 do
 710             for j in 0 .. w - 1 do
 711                 match ownership.[i, j] with
 712                 | null -> ()
 713                 | island ->
 714                     let l = island.Level
 715                     diff <- diff + l - earth.[i, j, 0]
 716                     earth.[i, j, 0] <- l
 717
 718         match f with
 719         | Some f' -> f' obj diff
 720         | _ -> ()
 721     ()
 722
 723 let areaOpenF (img: Image<Gray, float32>) (area: int) =
 724     areaOperationF img [ area, () ] None AreaOperation.Opening
 725
 726 let areaCloseF (img: Image<Gray, float32>) (area: int) =
 727     areaOperationF img [ area, () ] None AreaOperation.Closing
 728
 729 let areaOpenFWithFun (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: 'a -> float32 -> unit) =
 730     areaOperationF img areas (Some f) AreaOperation.Opening
 731
 732 let areaCloseFWithFun (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: 'a -> float32 -> unit) =
 733     areaOperationF img areas (Some f) AreaOperation.Closing
 734
 735 // A simpler algorithm than 'areaOpen' but slower.
 736 let areaOpen2 (img: Image<Gray, byte>) (area: int) =
 737     let w = img.Width
 738     let h = img.Height
 739     let imgData = img.Data
 740     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 741
 742     let histogram = Array.zeroCreate 256
 743     for i in 0 .. h - 1 do
 744         for j in 0 .. w - 1 do
 745             let v = imgData.[i, j, 0] |> int
 746             histogram.[v] <- histogram.[v] + 1
 747
 748     let flooded : bool[,] = Array2D.zeroCreate h w
 749
 750     let pointsChecked = HashSet<Point>()
 751     let pointsToCheck = Stack<Point>()
 752
 753     for level in 255 .. -1 .. 0 do
 754         let mutable n = histogram.[level]
 755         if n > 0
 756         then
 757             for i in 0 .. h - 1 do
 758                 for j in 0 .. w - 1 do
 759                     if not flooded.[i, j] && imgData.[i, j, 0] = byte level
 760                     then
 761                         let mutable maxNeighborValue = 0uy
 762                         pointsChecked.Clear()
 763                         pointsToCheck.Clear()
 764                         pointsToCheck.Push(Point(j, i))
 765
 766                         while pointsToCheck.Count > 0 do
 767                             let next = pointsToCheck.Pop()
 768                             pointsChecked.Add(next) |> ignore
 769                             flooded.[next.Y, next.X] <- true
 770
 771                             for nx, ny in se do
 772                                 let p = Point(next.X + nx, next.Y + ny)
 773                                 if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h
 774                                 then
 775                                     let v = imgData.[p.Y, p.X, 0]
 776                                     if v = byte level
 777                                     then
 778                                         if not (pointsChecked.Contains(p))
 779                                         then
 780                                             pointsToCheck.Push(p)
 781                                     elif v > maxNeighborValue
 782                                     then
 783                                         maxNeighborValue <- v
 784
 785                         if int maxNeighborValue < level && pointsChecked.Count <= area
 786                         then
 787                             for p in pointsChecked do
 788                                 imgData.[p.Y, p.X, 0] <- maxNeighborValue
 789
 790 // Zhang and Suen algorithm.
 791 // Modify 'mat' in place.
 792 let thin (mat: Matrix<byte>) =
 793     let w = mat.Width
 794     let h = mat.Height
 795     let mutable data1 = mat.Data
 796     let mutable data2 = Array2D.copy data1
 797
 798     let mutable pixelChanged = true
 799     let mutable oddIteration = true
 800
 801     while pixelChanged do
 802         pixelChanged <- false
 803         for i in 0..h-1 do
 804             for j in 0..w-1 do
 805                 if data1.[i, j] = 1uy
 806                 then
 807                     let p2 = if i = 0 then 0uy else data1.[i-1, j]
 808                     let p3 = if i = 0 || j = w-1 then 0uy else data1.[i-1, j+1]
 809                     let p4 = if j = w-1 then 0uy else data1.[i, j+1]
 810                     let p5 = if i = h-1 || j = w-1 then 0uy else data1.[i+1, j+1]
 811                     let p6 = if i = h-1 then 0uy else data1.[i+1, j]
 812                     let p7 = if i = h-1 || j = 0 then 0uy else data1.[i+1, j-1]
 813                     let p8 = if j = 0 then 0uy else data1.[i, j-1]
 814                     let p9 = if i = 0 || j = 0 then 0uy else data1.[i-1, j-1]
 815
 816                     let sumNeighbors = p2 + p3 + p4 + p5 + p6 + p7 + p8 + p9
 817                     if sumNeighbors >= 2uy && sumNeighbors <= 6uy &&
 818                         (if p2 = 0uy && p3 = 1uy then 1 else 0) +
 819                         (if p3 = 0uy && p4 = 1uy then 1 else 0) +
 820                         (if p4 = 0uy && p5 = 1uy then 1 else 0) +
 821                         (if p5 = 0uy && p6 = 1uy then 1 else 0) +
 822                         (if p6 = 0uy && p7 = 1uy then 1 else 0) +
 823                         (if p7 = 0uy && p8 = 1uy then 1 else 0) +
 824                         (if p8 = 0uy && p9 = 1uy then 1 else 0) +
 825                         (if p9 = 0uy && p2 = 1uy then 1 else 0) = 1 &&
 826                         if oddIteration
 827                         then p2 * p4 * p6 = 0uy && p4 * p6 * p8 = 0uy
 828                         else p2 * p4 * p8 = 0uy && p2 * p6 * p8 = 0uy
 829                     then
 830                         data2.[i, j] <- 0uy
 831                         pixelChanged <- true
 832                 else
 833                     data2.[i, j] <- 0uy
 834
 835         oddIteration <- not oddIteration
 836         let tmp = data1
 837         data1 <- data2
 838         data2 <- tmp
 839
 840 // Remove all 8-connected pixels with an area equal or greater than 'areaSize'.
 841 // Modify 'mat' in place.
 842 let removeArea (mat: Matrix<byte>) (areaSize: int) =
 843     let neighbors = [|
 844         (-1,  0) // p2
 845         (-1,  1) // p3
 846         ( 0,  1) // p4
 847         ( 1,  1) // p5
 848         ( 1,  0) // p6
 849         ( 1, -1) // p7
 850         ( 0, -1) // p8
 851         (-1, -1) |] // p9
 852
 853     use mat' = new Matrix<byte>(mat.Size)
 854     let w = mat'.Width
 855     let h = mat'.Height
 856     mat.CopyTo(mat')
 857
 858     let data = mat.Data
 859     let data' = mat'.Data
 860
 861     for i in 0..h-1 do
 862         for j in 0..w-1 do
 863             if data'.[i, j] = 1uy
 864             then
 865                 let neighborhood = List<Point>()
 866                 let neighborsToCheck = Stack<Point>()
 867                 neighborsToCheck.Push(Point(j, i))
 868                 data'.[i, j] <- 0uy
 869
 870                 while neighborsToCheck.Count > 0 do
 871                     let n = neighborsToCheck.Pop()
 872                     neighborhood.Add(n)
 873                     for (ni, nj) in neighbors do
 874                         let pi = n.Y + ni
 875                         let pj = n.X + nj
 876                         if pi >= 0 && pi < h && pj >= 0 && pj < w && data'.[pi, pj] = 1uy
 877                         then
 878                             neighborsToCheck.Push(Point(pj, pi))
 879                             data'.[pi, pj] <- 0uy
 880                 if neighborhood.Count <= areaSize
 881                 then
 882                     for n in neighborhood do
 883                         data.[n.Y, n.X] <- 0uy
 884
 885 let connectedComponents (img: Image<Gray, byte>) (startPoints: List<Point>) : List<Point> =
 886     let w = img.Width
 887     let h = img.Height
 888
 889     let pointChecked = Points()
 890     let pointToCheck = Stack<Point>(startPoints);
 891
 892     let data = img.Data
 893
 894     while pointToCheck.Count > 0 do
 895         let next = pointToCheck.Pop()
 896         pointChecked.Add(next) |> ignore
 897         for ny in -1 .. 1 do
 898             for nx in -1 .. 1 do
 899                 if ny <> 0 && nx <> 0
 900                 then
 901                     let p = Point(next.X + nx, next.Y + ny)
 902                     if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h && data.[p.Y, p.X, 0] > 0uy && not (pointChecked.Contains p)
 903                     then
 904                         pointToCheck.Push(p)
 905
 906     List<Point>(pointChecked)
 907
 908 let drawLine (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: int) (y0: int) (x1: int) (y1: int) (thickness: int) =
 909     img.Draw(LineSegment2D(Point(x0, y0), Point(x1, y1)), color, thickness);
 910
 911 let drawLineF (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: float) (y0: float) (x1: float) (y1: float) (thickness: int) =
 912     img.Draw(LineSegment2DF(PointF(float32 x0, float32 y0), PointF(float32 x1, float32 y1)), color, thickness, CvEnum.LineType.AntiAlias);
 913
 914 let drawEllipse (img: Image<'TColor, 'TDepth>) (e: Types.Ellipse) (color: 'TColor) (alpha: float) =
 915     if alpha >= 1.0
 916     then
 917         img.Draw(Ellipse(PointF(float32 e.Cx, float32 e.Cy), SizeF(2.f * e.B, 2.f * e.A), e.Alpha / PI * 180.f), color, 1, CvEnum.LineType.AntiAlias)
 918     else
 919         let windowPosX = e.Cx - e.A - 5.f
 920         let gapX = windowPosX - (float32 (int windowPosX))
 921
 922         let windowPosY = e.Cy - e.A - 5.f
 923         let gapY = windowPosY - (float32 (int windowPosY))
 924
 925         let roi = Rectangle(int windowPosX, int windowPosY, 2.f * (e.A + 5.f) |> int, 2.f * (e.A + 5.f) |> int)
 926
 927         img.ROI <- roi
 928         if roi = img.ROI // We do not display ellipses touching the edges (FIXME)
 929         then
 930             use i = new Image<'TColor, 'TDepth>(img.ROI.Size)
 931             i.Draw(Ellipse(PointF(float32 <| (e.A + 5.f + gapX) , float32 <| (e.A + 5.f + gapY)), SizeF(2.f * e.B, 2.f * e.A), e.Alpha / PI * 180.f), color, 1, CvEnum.LineType.AntiAlias)
 932             CvInvoke.AddWeighted(img, 1.0, i, alpha, 0.0, img)
 933         img.ROI <- Rectangle.Empty
 934
 935 let drawEllipses (img: Image<'TColor, 'TDepth>) (ellipses: Types.Ellipse list) (color: 'TColor) (alpha: float) =
 936     List.iter (fun e -> drawEllipse img e color alpha) ellipses
 937
 938 let rngCell =  System.Random()
 939 let drawCell (img: Image<Bgr, byte>) (drawCellContent: bool) (c: Types.Cell) =
 940     if drawCellContent
 941     then
 942         let colorB = rngCell.Next(20, 70)
 943         let colorG = rngCell.Next(20, 70)
 944         let colorR = rngCell.Next(20, 70)
 945
 946         for y in 0 .. c.elements.Height - 1 do
 947             for x in 0 .. c.elements.Width - 1 do
 948                 if c.elements.[y, x] > 0uy
 949                 then
 950                     let dx, dy = c.center.X - c.elements.Width / 2, c.center.Y - c.elements.Height / 2
 951                     let b = img.Data.[y + dy, x + dx, 0] |> int
 952                     let g = img.Data.[y + dy, x + dx, 1] |> int
 953                     let r = img.Data.[y + dy, x + dx, 2] |> int
 954                     img.Data.[y + dy, x + dx, 0] <- if b + colorB > 255 then 255uy else byte (b + colorB)
 955                     img.Data.[y + dy, x + dx, 1] <- if g + colorG > 255 then 255uy else byte (g + colorG)
 956                     img.Data.[y + dy, x + dx, 2] <- if r + colorR > 255 then 255uy else byte (r + colorR)
 957
 958     let crossColor, crossColor2 =
 959         match c.cellClass with
 960         | Types.HealthyRBC -> Bgr(255., 0., 0.), Bgr(255., 255., 255.)
 961         | Types.InfectedRBC -> Bgr(0., 0., 255.), Bgr(120., 120., 255.)
 962         | Types.Peculiar -> Bgr(0., 0., 0.), Bgr(80., 80., 80.)
 963
 964     drawLine img crossColor2 (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 2
 965     drawLine img crossColor2 c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 2
 966
 967     drawLine img crossColor (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 1
 968     drawLine img crossColor c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 1
 969
 970
 971 let drawCells (img: Image<Bgr, byte>) (drawCellContent: bool) (cells: Types.Cell list) =
 972     List.iter (fun c -> drawCell img drawCellContent c) cells