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 // Normalize image values between 0uy and 255uy.
  17 let normalizeAndConvert (img: Image<Gray, 'TDepth>) : Image<Gray, byte> =
  18     let min = ref [| 0.0 |]
  19     let minLocation = ref <| [| Point() |]
  20     let max = ref [| 0.0 |]
  21     let maxLocation = ref <| [| Point() |]
  22     img.MinMax(min, max, minLocation, maxLocation)
  23     ((img.Convert<Gray, float32>() - (!min).[0]) / ((!max).[0] - (!min).[0]) * 255.0).Convert<Gray, byte>()
  24
  25 let saveImg (img: Image<'TColor, 'TDepth>) (filepath: string) =
  26     img.Save(filepath)
  27
  28 let saveMat (mat: Matrix<'TDepth>) (filepath: string) =
  29     use img = new Image<Gray, 'TDeph>(mat.Size)
  30     mat.CopyTo(img)
  31     saveImg img filepath
  32
  33 type Histogram = { data: int[]; total: int; sum: int; min: float32; max: float32 }
  34
  35 let histogramImg (img: Image<Gray, float32>) (nbSamples: int) : Histogram =
  36     let imgData = img.Data
  37
  38     let min, max =
  39         let min = ref [| 0.0 |]
  40         let minLocation = ref <| [| Point() |]
  41         let max = ref [| 0.0 |]
  42         let maxLocation = ref <| [| Point() |]
  43         img.MinMax(min, max, minLocation, maxLocation)
  44         float32 (!min).[0], float32 (!max).[0]
  45
  46     let inline bin (x: float32) : int =
  47         let p = int ((x - min) / (max - min) * float32 nbSamples)
  48         if p >= nbSamples then nbSamples - 1 else p
  49
  50     let data = Array.zeroCreate nbSamples
  51
  52     for i in 0 .. img.Height - 1 do
  53         for j in 0 .. img.Width - 1 do
  54             let p = bin imgData.[i, j, 0]
  55             data.[p] <- data.[p] + 1
  56
  57     { data = data; total = img.Height * img.Width; sum = Array.sum data; min = min; max = max }
  58
  59 let histogramMat (mat: Matrix<float32>) (nbSamples: int) : Histogram =
  60     let matData = mat.Data
  61
  62     let min, max =
  63         let min = ref 0.0
  64         let minLocation = ref <| Point()
  65         let max = ref 0.0
  66         let maxLocation = ref <| Point()
  67         mat.MinMax(min, max, minLocation, maxLocation)
  68         float32 !min, float32 !max
  69
  70     let inline bin (x: float32) : int =
  71         let p = int ((x - min) / (max - min) * float32 nbSamples)
  72         if p >= nbSamples then nbSamples - 1 else p
  73
  74     let data = Array.zeroCreate nbSamples
  75
  76     for i in 0 .. mat.Height - 1 do
  77         for j in 0 .. mat.Width - 1 do
  78             let p = bin matData.[i, j]
  79             data.[p] <- data.[p] + 1
  80
  81     { data = data; total = mat.Height * mat.Width; sum = Array.sum data; min = min; max = max }
  82
  83 let histogram (values: float32 seq) (nbSamples: int) : Histogram =
  84     let mutable min = Single.MaxValue
  85     let mutable max = Single.MinValue
  86     let mutable n = 0
  87
  88     for v in values do
  89         n <- n + 1
  90         if v < min then min <- v
  91         if v > max then max <- v
  92
  93     let inline bin (x: float32) : int =
  94         let p = int ((x - min) / (max - min) * float32 nbSamples)
  95         if p >= nbSamples then nbSamples - 1 else p
  96
  97     let data = Array.zeroCreate nbSamples
  98
  99     for v in values do
 100         let p = bin v
 101         data.[p] <- data.[p] + 1
 102
 103     { data = data; total = n; sum = Array.sum data; min = min; max = max }
 104
 105 let otsu (hist: Histogram) : float32 * float32 * float32 =
 106     let mutable sumB = 0
 107     let mutable wB = 0
 108     let mutable maximum = 0.0
 109     let mutable level = 0
 110     let sum = hist.data |> Array.mapi (fun i v -> i * v) |> Array.sum |> float
 111
 112     for i in 0 .. hist.data.Length - 1 do
 113         wB <- wB + hist.data.[i]
 114         if wB <> 0
 115         then
 116             let wF = hist.total - wB
 117             if wF <> 0
 118             then
 119                 sumB <- sumB + i * hist.data.[i]
 120                 let mB = (float sumB) / (float wB)
 121                 let mF = (sum - float sumB) / (float wF)
 122                 let between = (float wB) * (float wF) * (mB - mF) ** 2.;
 123                 if between >= maximum
 124                 then
 125                     level <- i
 126                     maximum <- between
 127
 128     let mean1 =
 129         let mutable sum = 0
 130         let mutable nb = 0
 131         for i in 0 .. level - 1 do
 132             sum <- sum + i * hist.data.[i]
 133             nb <- nb + hist.data.[i]
 134         (sum + level * hist.data.[level] / 2) / (nb + hist.data.[level] / 2)
 135
 136     let mean2 =
 137         let mutable sum = 0
 138         let mutable nb = 0
 139         for i in level + 1 .. hist.data.Length - 1 do
 140             sum <- sum + i * hist.data.[i]
 141             nb <- nb + hist.data.[i]
 142         (sum + level * hist.data.[level] / 2) / (nb + hist.data.[level] / 2)
 143
 144     let toFloat l =
 145         float32 l / float32 hist.data.Length * (hist.max - hist.min) + hist.min
 146
 147     toFloat level, toFloat mean1, toFloat mean2
 148
 149 /// <summary>
 150 /// Remove M-adjacent pixels. It may be used after thinning.
 151 /// </summary>
 152 let suppressMAdjacency (img: Matrix<byte>) =
 153     let w = img.Width
 154     let h = img.Height
 155     for i in 1 .. h - 2 do
 156         for j in 1 .. w - 2 do
 157             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)
 158             then
 159                 img.[i, j] <- 0uy
 160     for i in 1 .. h - 2 do
 161         for j in 1 .. w - 2 do
 162             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)
 163             then
 164                 img.[i, j] <- 0uy
 165
 166 /// <summary>
 167 /// Find edges of an image by using the Canny approach.
 168 /// The thresholds are automatically defined with otsu on gradient magnitudes.
 169 /// </summary>
 170 /// <param name="img"></param>
 171 let findEdges (img: Image<Gray, float32>) : Matrix<byte> * Matrix<float32> * Matrix<float32> =
 172     let w = img.Width
 173     let h = img.Height
 174
 175     use sobelKernel =
 176         new Matrix<float32>(array2D [[ 1.0f; 0.0f; -1.0f ]
 177                                      [ 2.0f; 0.0f; -2.0f ]
 178                                      [ 1.0f; 0.0f; -1.0f ]])
 179
 180     let xGradient = new Matrix<float32>(img.Size)
 181     let yGradient = new Matrix<float32>(img.Size)
 182     CvInvoke.Filter2D(img, xGradient, sobelKernel, Point(1, 1))
 183     CvInvoke.Filter2D(img, yGradient, sobelKernel.Transpose(), Point(1, 1))
 184
 185     use magnitudes = new Matrix<float32>(xGradient.Size)
 186     use angles = new Matrix<float32>(xGradient.Size)
 187     CvInvoke.CartToPolar(xGradient, yGradient, magnitudes, angles) // Compute the magnitudes and angles.
 188
 189     let thresholdHigh, thresholdLow =
 190         let sensibilityHigh = 0.1f
 191         let sensibilityLow = 0.0f
 192         let threshold, _, _ = otsu (histogramMat magnitudes 300)
 193         threshold + (sensibilityHigh * threshold), threshold - (sensibilityLow * threshold)
 194
 195     // Non-maximum suppression.
 196     use nms = new Matrix<byte>(xGradient.Size)
 197
 198     let nmsData = nms.Data
 199     let anglesData = angles.Data
 200     let magnitudesData = magnitudes.Data
 201     let xGradientData = xGradient.Data
 202     let yGradientData = yGradient.Data
 203
 204     for i in 0 .. h - 1 do
 205         nmsData.[i, 0] <- 0uy
 206         nmsData.[i, w - 1] <- 0uy
 207
 208     for j in 0 .. w - 1 do
 209         nmsData.[0, j] <- 0uy
 210         nmsData.[h - 1, j] <- 0uy
 211
 212     for i in 1 .. h - 2 do
 213         for j in 1 .. w - 2 do
 214             let vx = xGradientData.[i, j]
 215             let vy = yGradientData.[i, j]
 216             if vx <> 0.f || vy <> 0.f
 217             then
 218                 let angle = anglesData.[i, j]
 219
 220                 let vx', vy' = abs vx, abs vy
 221                 let ratio2 = if vx' > vy' then vy' / vx' else vx' / vy'
 222                 let ratio1 = 1.f - ratio2
 223
 224                 let mNeigbors (sign: int) : float32 =
 225                     if angle < PI / 4.f
 226                     then ratio1 * magnitudesData.[i, j + sign] + ratio2 * magnitudesData.[i + sign, j + sign]
 227                     elif angle < PI / 2.f
 228                     then ratio2 * magnitudesData.[i + sign, j + sign] + ratio1 * magnitudesData.[i + sign, j]
 229                     elif angle < 3.f * PI / 4.f
 230                     then ratio1 * magnitudesData.[i + sign, j] + ratio2 * magnitudesData.[i + sign, j - sign]
 231                     elif angle < PI
 232                     then ratio2 * magnitudesData.[i + sign, j - sign] + ratio1 * magnitudesData.[i, j - sign]
 233                     elif angle < 5.f * PI / 4.f
 234                     then ratio1 * magnitudesData.[i, j - sign] + ratio2 * magnitudesData.[i - sign, j - sign]
 235                     elif angle < 3.f * PI / 2.f
 236                     then ratio2 * magnitudesData.[i - sign, j - sign] + ratio1 * magnitudesData.[i - sign, j]
 237                     elif angle < 7.f * PI / 4.f
 238                     then ratio1 * magnitudesData.[i - sign, j] + ratio2 * magnitudesData.[i - sign, j + sign]
 239                     else ratio2 * magnitudesData.[i - sign, j + sign] + ratio1 * magnitudesData.[i, j + sign]
 240
 241                 let m = magnitudesData.[i, j]
 242                 if m >= thresholdLow && m > mNeigbors 1 && m > mNeigbors -1
 243                 then
 244                     nmsData.[i, j] <- 1uy
 245
 246     // suppressMConnections nms // It's not helpful for the rest of the process (ellipse detection).
 247
 248     let edges = new Matrix<byte>(xGradient.Size)
 249     let edgesData = edges.Data
 250
 251     // Hysteresis thresholding.
 252     let toVisit = Stack<Point>()
 253     for i in 0 .. h - 1 do
 254         for j in 0 .. w - 1 do
 255             if nmsData.[i, j] = 1uy && magnitudesData.[i, j] >= thresholdHigh
 256             then
 257                 nmsData.[i, j] <- 0uy
 258                 toVisit.Push(Point(j, i))
 259                 while toVisit.Count > 0 do
 260                     let p = toVisit.Pop()
 261                     edgesData.[p.Y, p.X] <- 1uy
 262                     for i' in -1 .. 1  do
 263                         for j' in -1 .. 1 do
 264                             if i' <> 0 || j' <> 0
 265                             then
 266                                 let ni = p.Y + i'
 267                                 let nj = p.X + j'
 268                                 if ni >= 0 && ni < h && nj >= 0 && nj < w && nmsData.[ni, nj] = 1uy
 269                                 then
 270                                     nmsData.[ni, nj] <- 0uy
 271                                     toVisit.Push(Point(nj, ni))
 272
 273     edges, xGradient, yGradient
 274
 275 let gaussianFilter (img : Image<'TColor, 'TDepth>) (standardDeviation : float) : Image<'TColor, 'TDepth> =
 276     let size = 2 * int (ceil (4.0 * standardDeviation)) + 1
 277     img.SmoothGaussian(size, size, standardDeviation, standardDeviation)
 278
 279 let drawPoints (img: Image<Gray, 'TDepth>) (points: Points) (intensity: 'TDepth) =
 280     for p in points do
 281         img.Data.[p.Y, p.X, 0] <- intensity
 282
 283 type ExtremumType =
 284     | Maxima = 1
 285     | Minima = 2
 286
 287 let findExtremum (img: Image<Gray, 'TDepth>) (extremumType: ExtremumType) : IEnumerable<Points> =
 288     let w = img.Width
 289     let h = img.Height
 290     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 291
 292     let imgData = img.Data
 293     let suppress: bool[,] = Array2D.zeroCreate h w
 294
 295     let result = List<List<Point>>()
 296
 297     let flood (start: Point) : List<List<Point>> =
 298         let sameLevelToCheck = Stack<Point>()
 299         let betterLevelToCheck = Stack<Point>()
 300         betterLevelToCheck.Push(start)
 301
 302         let result' = List<List<Point>>()
 303
 304         while betterLevelToCheck.Count > 0 do
 305             let p = betterLevelToCheck.Pop()
 306             if not suppress.[p.Y, p.X]
 307             then
 308                 suppress.[p.Y, p.X] <- true
 309                 sameLevelToCheck.Push(p)
 310                 let current = List<Point>()
 311
 312                 let mutable betterExists = false
 313
 314                 while sameLevelToCheck.Count > 0 do
 315                     let p' = sameLevelToCheck.Pop()
 316                     let currentLevel = imgData.[p'.Y, p'.X, 0]
 317                     current.Add(p') |> ignore
 318                     for i, j in se do
 319                         let ni = i + p'.Y
 320                         let nj = j + p'.X
 321                         if ni >= 0 && ni < h && nj >= 0 && nj < w
 322                         then
 323                             let level = imgData.[ni, nj, 0]
 324                             let notSuppressed = not suppress.[ni, nj]
 325
 326                             if level = currentLevel && notSuppressed
 327                             then
 328                                 suppress.[ni, nj] <- true
 329                                 sameLevelToCheck.Push(Point(nj, ni))
 330                             elif if extremumType = ExtremumType.Maxima then level > currentLevel else level < currentLevel
 331                             then
 332                                 betterExists <- true
 333                                 if notSuppressed
 334                                 then
 335                                     betterLevelToCheck.Push(Point(nj, ni))
 336
 337                 if not betterExists
 338                 then
 339                     result'.Add(current)
 340         result'
 341
 342     for i in 0 .. h - 1 do
 343         for j in 0 .. w - 1 do
 344             let maxima = flood (Point(j, i))
 345             if maxima.Count > 0
 346             then
 347                 result.AddRange(maxima)
 348
 349     result.Select(fun l -> Points(l))
 350
 351 let findMaxima (img: Image<Gray, 'TDepth>) : IEnumerable<Points> =
 352     findExtremum img ExtremumType.Maxima
 353
 354 let findMinima (img: Image<Gray, 'TDepth>) : IEnumerable<Points> =
 355     findExtremum img ExtremumType.Minima
 356
 357 type PriorityQueue () =
 358     let size = 256
 359     let q: Points[] = Array.init size (fun i -> Points())
 360     let mutable highest = -1 // Value of the first elements of 'q'.
 361     let mutable lowest = size
 362
 363     member this.NextMax () : byte * Point =
 364         if this.IsEmpty
 365         then
 366             invalidOp "Queue is empty"
 367         else
 368             let l = q.[highest]
 369             let next = l.First()
 370             l.Remove(next) |> ignore
 371             let value = byte highest
 372
 373             if l.Count = 0
 374             then
 375                 highest <- highest - 1
 376                 while highest > lowest && q.[highest].Count = 0 do
 377                     highest <- highest - 1
 378                 if highest = lowest
 379                 then
 380                     highest <- -1
 381                     lowest <- size
 382
 383             value, next
 384
 385     member this.NextMin () : byte * Point =
 386         if this.IsEmpty
 387         then
 388             invalidOp "Queue is empty"
 389         else
 390             let l = q.[lowest + 1]
 391             let next = l.First()
 392             l.Remove(next) |> ignore
 393             let value = byte (lowest + 1)
 394
 395             if l.Count = 0
 396             then
 397                 lowest <- lowest + 1
 398                 while lowest < highest && q.[lowest + 1].Count = 0 do
 399                     lowest <- lowest + 1
 400                 if highest = lowest
 401                 then
 402                     highest <- -1
 403                     lowest <- size
 404
 405             value, next
 406
 407     member this.Max =
 408         highest |> byte
 409
 410     member this.Min =
 411         lowest + 1 |> byte
 412
 413     member this.Add (value: byte) (p: Point) =
 414         let vi = int value
 415
 416         if vi > highest
 417         then
 418             highest <- vi
 419         if vi <= lowest
 420         then
 421             lowest <- vi - 1
 422
 423         q.[vi].Add(p) |> ignore
 424
 425     member this.Remove (value: byte) (p: Point) =
 426         let vi = int value
 427         if q.[vi].Remove(p) && q.[vi].Count = 0
 428         then
 429             if vi = highest
 430             then
 431                 highest <- highest - 1
 432                 while highest > lowest && q.[highest].Count = 0 do
 433                     highest <- highest - 1
 434             elif vi - 1 = lowest
 435             then
 436                 lowest <- lowest + 1
 437                 while lowest < highest && q.[lowest + 1].Count = 0 do
 438                     lowest <- lowest + 1
 439
 440             if highest = lowest // The queue is now empty.
 441             then
 442                 highest <- -1
 443                 lowest <- size
 444
 445     member this.IsEmpty =
 446         highest = -1
 447
 448     member this.Clear () =
 449         while highest > lowest  do
 450             q.[highest].Clear()
 451             highest <- highest - 1
 452         highest <- -1
 453         lowest <- size
 454
 455 type private AreaState =
 456     | Removed = 1
 457     | Unprocessed = 2
 458     | Validated = 3
 459
 460 type private AreaOperation =
 461     | Opening = 1
 462     | Closing = 2
 463
 464 [<AllowNullLiteral>]
 465 type private Area (elements: Points) =
 466     member this.Elements = elements
 467     member val Intensity = None with get, set
 468     member val State = AreaState.Unprocessed with get, set
 469
 470 let private areaOperation (img: Image<Gray, byte>) (area: int) (op: AreaOperation) =
 471     let w = img.Width
 472     let h = img.Height
 473     let imgData = img.Data
 474     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 475
 476     let areas = List<Area>((if op = AreaOperation.Opening then findMaxima img else findMinima img) |> Seq.map Area)
 477
 478     let pixels: Area[,] = Array2D.create h w null
 479     for m in areas do
 480         for e in m.Elements do
 481             pixels.[e.Y, e.X] <- m
 482
 483     let queue = PriorityQueue()
 484
 485     let addEdgeToQueue (elements: Points) =
 486         for p in elements do
 487             for i, j in se do
 488                 let ni = i + p.Y
 489                 let nj = j + p.X
 490                 let p' = Point(nj, ni)
 491                 if ni >= 0 && ni < h && nj >= 0 && nj < w && not (elements.Contains(p'))
 492                 then
 493                     queue.Add (imgData.[ni, nj, 0]) p'
 494
 495     // Reverse order is quicker.
 496     for i in areas.Count - 1 .. -1 .. 0 do
 497         let m = areas.[i]
 498         if m.Elements.Count <= area && m.State <> AreaState.Removed
 499         then
 500             queue.Clear()
 501             addEdgeToQueue m.Elements
 502
 503             let mutable intensity = if op = AreaOperation.Opening then queue.Max else queue.Min
 504             let nextElements = Points()
 505
 506             let mutable stop = false
 507             while not stop do
 508                 let intensity', p = if op = AreaOperation.Opening then queue.NextMax () else queue.NextMin ()
 509                 let mutable merged = false
 510
 511                 if intensity' = intensity // The intensity doesn't change.
 512                 then
 513                     if m.Elements.Count + nextElements.Count + 1 > area
 514                     then
 515                         m.State <- AreaState.Validated
 516                         m.Intensity <- Some intensity
 517                         stop <- true
 518                     else
 519                         nextElements.Add(p) |> ignore
 520
 521                 elif if op = AreaOperation.Opening then intensity' < intensity else intensity' > intensity
 522                 then
 523                     m.Elements.UnionWith(nextElements)
 524                     for e in nextElements do
 525                         pixels.[e.Y, e.X] <- m
 526
 527                     if m.Elements.Count = area
 528                     then
 529                         m.State <- AreaState.Validated
 530                         m.Intensity <- Some (intensity')
 531                         stop <- true
 532                     else
 533                         intensity <- intensity'
 534                         nextElements.Clear()
 535                         nextElements.Add(p) |> ignore
 536
 537                 else
 538                     match pixels.[p.Y, p.X] with
 539                     | null -> ()
 540                     | m' ->
 541                         if m'.Elements.Count + m.Elements.Count <= area
 542                         then
 543                             m'.State <- AreaState.Removed
 544                             for e in m'.Elements do
 545                                 pixels.[e.Y, e.X] <- m
 546                                 queue.Remove imgData.[e.Y, e.X, 0] e
 547                             addEdgeToQueue m'.Elements
 548                             m.Elements.UnionWith(m'.Elements)
 549                             let intensityMax = if op = AreaOperation.Opening then queue.Max else queue.Min
 550                             if intensityMax <> intensity
 551                             then
 552                                 intensity <- intensityMax
 553                                 nextElements.Clear()
 554                             merged <- true
 555
 556                     if not merged
 557                     then
 558                         m.State <- AreaState.Validated
 559                         m.Intensity <- Some (intensity)
 560                         stop <- true
 561
 562                 if not stop && not merged
 563                 then
 564                     for i, j in se do
 565                         let ni = i + p.Y
 566                         let nj = j + p.X
 567                         let p' = Point(nj, ni)
 568                         if ni < 0 || ni >= h || nj < 0 || nj >= w
 569                         then
 570                             m.State <- AreaState.Validated
 571                             m.Intensity <- Some (intensity)
 572                             stop <- true
 573                         elif not (m.Elements.Contains(p')) && not (nextElements.Contains(p'))
 574                         then
 575                             queue.Add (imgData.[ni, nj, 0]) p'
 576
 577                 if queue.IsEmpty
 578                 then
 579                     if m.Elements.Count + nextElements.Count <= area
 580                     then
 581                         m.State <- AreaState.Validated
 582                         m.Intensity <- Some intensity'
 583                         m.Elements.UnionWith(nextElements)
 584                     stop <- true
 585
 586     for m in areas do
 587         if m.State = AreaState.Validated
 588         then
 589             match m.Intensity with
 590             | Some i ->
 591                 for p in m.Elements do
 592                     imgData.[p.Y, p.X, 0] <- i
 593             | _ -> ()
 594     ()
 595
 596 /// <summary>
 597 /// Area opening on byte image.
 598 /// </summary>
 599 let areaOpen (img: Image<Gray, byte>) (area: int) =
 600     areaOperation img area AreaOperation.Opening
 601
 602 /// <summary>
 603 /// Area closing on byte image.
 604 /// </summary>
 605 let areaClose (img: Image<Gray, byte>) (area: int) =
 606     areaOperation img area AreaOperation.Closing
 607
 608 // A simpler algorithm than 'areaOpen' on byte image but slower.
 609 let areaOpen2 (img: Image<Gray, byte>) (area: int) =
 610     let w = img.Width
 611     let h = img.Height
 612     let imgData = img.Data
 613     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 614
 615     let histogram = Array.zeroCreate 256
 616     for i in 0 .. h - 1 do
 617         for j in 0 .. w - 1 do
 618             let v = imgData.[i, j, 0] |> int
 619             histogram.[v] <- histogram.[v] + 1
 620
 621     let flooded : bool[,] = Array2D.zeroCreate h w
 622
 623     let pointsChecked = HashSet<Point>()
 624     let pointsToCheck = Stack<Point>()
 625
 626     for level in 255 .. -1 .. 0 do
 627         let mutable n = histogram.[level]
 628         if n > 0
 629         then
 630             for i in 0 .. h - 1 do
 631                 for j in 0 .. w - 1 do
 632                     if not flooded.[i, j] && imgData.[i, j, 0] = byte level
 633                     then
 634                         let mutable maxNeighborValue = 0uy
 635                         pointsChecked.Clear()
 636                         pointsToCheck.Clear()
 637                         pointsToCheck.Push(Point(j, i))
 638
 639                         while pointsToCheck.Count > 0 do
 640                             let next = pointsToCheck.Pop()
 641                             pointsChecked.Add(next) |> ignore
 642                             flooded.[next.Y, next.X] <- true
 643
 644                             for nx, ny in se do
 645                                 let p = Point(next.X + nx, next.Y + ny)
 646                                 if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h
 647                                 then
 648                                     let v = imgData.[p.Y, p.X, 0]
 649                                     if v = byte level
 650                                     then
 651                                         if not (pointsChecked.Contains(p))
 652                                         then
 653                                             pointsToCheck.Push(p)
 654                                     elif v > maxNeighborValue
 655                                     then
 656                                         maxNeighborValue <- v
 657
 658                         if int maxNeighborValue < level && pointsChecked.Count <= area
 659                         then
 660                             for p in pointsChecked do
 661                                 imgData.[p.Y, p.X, 0] <- maxNeighborValue
 662
 663 [<AllowNullLiteral>]
 664 type Island (cmp: IComparer<float32>) =
 665     member val Shore = Heap.Heap<float32, Point>(cmp) with get
 666     member val Level = 0.f with get, set
 667     member val Surface = 0 with get, set
 668     member this.IsInfinite = this.Surface = Int32.MaxValue
 669
 670 let private areaOperationF (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: ('a -> float32 -> unit) option) (op: AreaOperation) =
 671     let w = img.Width
 672     let h = img.Height
 673     let earth = img.Data
 674     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 675
 676     let comparer = if op = AreaOperation.Opening
 677                    then { new IComparer<float32> with member this.Compare(v1, v2) = v1.CompareTo(v2) }
 678                    else { new IComparer<float32> with member this.Compare(v1, v2) = v2.CompareTo(v1) }
 679
 680     let ownership: Island[,] = Array2D.create h w null
 681
 682     // Initialize islands with their shore.
 683     let islands = List<Island>()
 684     let extremum = img |> if op = AreaOperation.Opening then findMaxima else findMinima
 685     for e in extremum do
 686         let island =
 687             let p = e.First()
 688             Island(comparer, Level = earth.[p.Y, p.X, 0], Surface = e.Count)
 689         islands.Add(island)
 690         let shorePoints = Points()
 691         for p in e do
 692             ownership.[p.Y, p.X] <- island
 693             for i, j in se do
 694                 let ni = i + p.Y
 695                 let nj = j + p.X
 696                 let neighbor = Point(nj, ni)
 697                 if ni >= 0 && ni < h && nj >= 0 && nj < w && Object.ReferenceEquals(ownership.[ni, nj], null) && not (shorePoints.Contains(neighbor))
 698                 then
 699                     shorePoints.Add(neighbor) |> ignore
 700                     island.Shore.Add earth.[ni, nj, 0] neighbor
 701
 702     for area, obj in areas do
 703         for island in islands do
 704             let mutable stop = island.Shore.IsEmpty
 705
 706             // 'true' if 'p' is owned or adjacent to 'island'.
 707             let inline ownedOrAdjacent (p: Point) : bool =
 708                 ownership.[p.Y, p.X] = island ||
 709                 (p.Y > 0 && ownership.[p.Y - 1, p.X] = island) ||
 710                 (p.Y < h - 1 && ownership.[p.Y + 1, p.X] = island) ||
 711                 (p.X > 0 && ownership.[p.Y, p.X - 1] = island) ||
 712                 (p.X < w - 1 && ownership.[p.Y, p.X + 1] = island)
 713
 714             while not stop && island.Surface < area do
 715                 let level, next = island.Shore.Max
 716                 let other = ownership.[next.Y, next.X]
 717                 if other = island // During merging, some points on the shore may be owned by the island itself -> ignored.
 718                 then
 719                     island.Shore.RemoveNext ()
 720                 else
 721                     if not <| Object.ReferenceEquals(other, null)
 722                     then // We touching another island.
 723                         if island.IsInfinite || other.IsInfinite || island.Surface + other.Surface >= area || comparer.Compare(island.Level, other.Level) < 0
 724                         then
 725                             stop <- true
 726                         else // We can merge 'other' into 'surface'.
 727                             island.Surface <- island.Surface + other.Surface
 728                             island.Level <- other.Level
 729                             // island.Level <- if comparer.Compare(island.Level, other.Level) > 0 then other.Level else island.Level
 730                             for l, p in other.Shore do
 731                                 let mutable currentY = p.Y + 1
 732                                 while currentY < h && ownership.[currentY, p.X] = other do
 733                                     ownership.[currentY, p.X] <- island
 734                                     currentY <- currentY + 1
 735                                 island.Shore.Add l p
 736                             other.Shore.Clear()
 737
 738                     elif comparer.Compare(level, island.Level) > 0
 739                     then
 740                         stop <- true
 741                     else
 742                         island.Shore.RemoveNext ()
 743                         for i, j in se do
 744                             let ni = i + next.Y
 745                             let nj = j + next.X
 746                             if ni < 0 || ni >= h || nj < 0 || nj >= w
 747                             then
 748                                 island.Surface <- Int32.MaxValue
 749                                 stop <- true
 750                             else
 751                                 let neighbor = Point(nj, ni)
 752                                 if not <| ownedOrAdjacent neighbor
 753                                 then
 754                                     island.Shore.Add earth.[ni, nj, 0] neighbor
 755                         if not stop
 756                         then
 757                             ownership.[next.Y, next.X] <- island
 758                             island.Level <- level
 759                             island.Surface <- island.Surface + 1
 760
 761         let mutable diff = 0.f
 762
 763         for i in 0 .. h - 1 do
 764             for j in 0 .. w - 1 do
 765                 match ownership.[i, j] with
 766                 | null -> ()
 767                 | island ->
 768                     let l = island.Level
 769                     diff <- diff + l - earth.[i, j, 0]
 770                     earth.[i, j, 0] <- l
 771
 772         match f with
 773         | Some f' -> f' obj diff
 774         | _ -> ()
 775     ()
 776
 777 /// <summary>
 778 /// Area opening on float image.
 779 /// </summary>
 780 let areaOpenF (img: Image<Gray, float32>) (area: int) =
 781     areaOperationF img [ area, () ] None AreaOperation.Opening
 782
 783 /// <summary>
 784 /// Area closing on float image.
 785 /// </summary>
 786 let areaCloseF (img: Image<Gray, float32>) (area: int) =
 787     areaOperationF img [ area, () ] None AreaOperation.Closing
 788
 789 /// <summary>
 790 /// Area closing on float image with different areas. Given areas must be sorted increasingly.
 791 /// For each area the function 'f' is called with the associated area value of type 'a and the volume difference
 792 /// Between the previous and the current closing.
 793 /// </summary>
 794 let areaOpenFWithFun (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: 'a -> float32 -> unit) =
 795     areaOperationF img areas (Some f) AreaOperation.Opening
 796
 797 /// <summary>
 798 /// Same as 'areaOpenFWithFun' for closing operation.
 799 /// </summary>
 800 let areaCloseFWithFun (img: Image<Gray, float32>) (areas: (int * 'a) list) (f: 'a -> float32 -> unit) =
 801     areaOperationF img areas (Some f) AreaOperation.Closing
 802
 803 /// <summary>
 804 /// Zhang and Suen thinning algorithm.
 805 /// Modify 'mat' in place.
 806 /// </summary>
 807 let thin (mat: Matrix<byte>) =
 808     let w = mat.Width
 809     let h = mat.Height
 810     let mutable data1 = mat.Data
 811     let mutable data2 = Array2D.copy data1
 812
 813     let mutable pixelChanged = true
 814     let mutable oddIteration = true
 815
 816     while pixelChanged do
 817         pixelChanged <- false
 818         for i in 0..h-1 do
 819             for j in 0..w-1 do
 820                 if data1.[i, j] = 1uy
 821                 then
 822                     let p2 = if i = 0 then 0uy else data1.[i-1, j]
 823                     let p3 = if i = 0 || j = w-1 then 0uy else data1.[i-1, j+1]
 824                     let p4 = if j = w-1 then 0uy else data1.[i, j+1]
 825                     let p5 = if i = h-1 || j = w-1 then 0uy else data1.[i+1, j+1]
 826                     let p6 = if i = h-1 then 0uy else data1.[i+1, j]
 827                     let p7 = if i = h-1 || j = 0 then 0uy else data1.[i+1, j-1]
 828                     let p8 = if j = 0 then 0uy else data1.[i, j-1]
 829                     let p9 = if i = 0 || j = 0 then 0uy else data1.[i-1, j-1]
 830
 831                     let sumNeighbors = p2 + p3 + p4 + p5 + p6 + p7 + p8 + p9
 832                     if sumNeighbors >= 2uy && sumNeighbors <= 6uy &&
 833                         (if p2 = 0uy && p3 = 1uy then 1 else 0) +
 834                         (if p3 = 0uy && p4 = 1uy then 1 else 0) +
 835                         (if p4 = 0uy && p5 = 1uy then 1 else 0) +
 836                         (if p5 = 0uy && p6 = 1uy then 1 else 0) +
 837                         (if p6 = 0uy && p7 = 1uy then 1 else 0) +
 838                         (if p7 = 0uy && p8 = 1uy then 1 else 0) +
 839                         (if p8 = 0uy && p9 = 1uy then 1 else 0) +
 840                         (if p9 = 0uy && p2 = 1uy then 1 else 0) = 1 &&
 841                         if oddIteration
 842                         then p2 * p4 * p6 = 0uy && p4 * p6 * p8 = 0uy
 843                         else p2 * p4 * p8 = 0uy && p2 * p6 * p8 = 0uy
 844                     then
 845                         data2.[i, j] <- 0uy
 846                         pixelChanged <- true
 847                 else
 848                     data2.[i, j] <- 0uy
 849
 850         oddIteration <- not oddIteration
 851         let tmp = data1
 852         data1 <- data2
 853         data2 <- tmp
 854
 855 /// <summary>
 856 /// Remove all 8-connected pixels with an area equal or greater than 'areaSize'.
 857 /// Modify 'mat' in place.
 858 /// </summary>
 859 let removeArea (mat: Matrix<byte>) (areaSize: int) =
 860     let neighbors = [|
 861         (-1,  0) // p2
 862         (-1,  1) // p3
 863         ( 0,  1) // p4
 864         ( 1,  1) // p5
 865         ( 1,  0) // p6
 866         ( 1, -1) // p7
 867         ( 0, -1) // p8
 868         (-1, -1) |] // p9
 869
 870     use mat' = new Matrix<byte>(mat.Size)
 871     let w = mat'.Width
 872     let h = mat'.Height
 873     mat.CopyTo(mat')
 874
 875     let data = mat.Data
 876     let data' = mat'.Data
 877
 878     for i in 0..h-1 do
 879         for j in 0..w-1 do
 880             if data'.[i, j] = 1uy
 881             then
 882                 let neighborhood = List<Point>()
 883                 let neighborsToCheck = Stack<Point>()
 884                 neighborsToCheck.Push(Point(j, i))
 885                 data'.[i, j] <- 0uy
 886
 887                 while neighborsToCheck.Count > 0 do
 888                     let n = neighborsToCheck.Pop()
 889                     neighborhood.Add(n)
 890                     for (ni, nj) in neighbors do
 891                         let pi = n.Y + ni
 892                         let pj = n.X + nj
 893                         if pi >= 0 && pi < h && pj >= 0 && pj < w && data'.[pi, pj] = 1uy
 894                         then
 895                             neighborsToCheck.Push(Point(pj, pi))
 896                             data'.[pi, pj] <- 0uy
 897                 if neighborhood.Count <= areaSize
 898                 then
 899                     for n in neighborhood do
 900                         data.[n.Y, n.X] <- 0uy
 901
 902 let connectedComponents (img: Image<Gray, byte>) (startPoints: List<Point>) : Points =
 903     let w = img.Width
 904     let h = img.Height
 905
 906     let pointChecked = Points()
 907     let pointToCheck = Stack<Point>(startPoints);
 908
 909     let data = img.Data
 910
 911     while pointToCheck.Count > 0 do
 912         let next = pointToCheck.Pop()
 913         pointChecked.Add(next) |> ignore
 914         for ny in -1 .. 1 do
 915             for nx in -1 .. 1 do
 916                 if ny <> 0 && nx <> 0
 917                 then
 918                     let p = Point(next.X + nx, next.Y + ny)
 919                     if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h && data.[p.Y, p.X, 0] > 0uy && not (pointChecked.Contains p)
 920                     then
 921                         pointToCheck.Push(p)
 922
 923     pointChecked
 924
 925 let drawLine (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: int) (y0: int) (x1: int) (y1: int) (thickness: int) =
 926     img.Draw(LineSegment2D(Point(x0, y0), Point(x1, y1)), color, thickness);
 927
 928 let drawLineF (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: float) (y0: float) (x1: float) (y1: float) (thickness: int) =
 929     img.Draw(LineSegment2DF(PointF(float32 x0, float32 y0), PointF(float32 x1, float32 y1)), color, thickness, CvEnum.LineType.AntiAlias);
 930
 931 let drawEllipse (img: Image<'TColor, 'TDepth>) (e: Ellipse) (color: 'TColor) (alpha: float) =
 932     if alpha >= 1.0
 933     then
 934         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)
 935     else
 936         let windowPosX = e.Cx - e.A - 5.f
 937         let gapX = windowPosX - (float32 (int windowPosX))
 938
 939         let windowPosY = e.Cy - e.A - 5.f
 940         let gapY = windowPosY - (float32 (int windowPosY))
 941
 942         let roi = Rectangle(int windowPosX, int windowPosY, 2.f * (e.A + 5.f) |> int, 2.f * (e.A + 5.f) |> int)
 943
 944         img.ROI <- roi
 945         if roi = img.ROI // We do not display ellipses touching the edges (FIXME)
 946         then
 947             use i = new Image<'TColor, 'TDepth>(img.ROI.Size)
 948             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)
 949             CvInvoke.AddWeighted(img, 1.0, i, alpha, 0.0, img)
 950         img.ROI <- Rectangle.Empty
 951
 952 let drawEllipses (img: Image<'TColor, 'TDepth>) (ellipses: Ellipse list) (color: 'TColor) (alpha: float) =
 953     List.iter (fun e -> drawEllipse img e color alpha) ellipses
 954
 955 let rngCell =  System.Random()
 956 let drawCell (img: Image<Bgr, byte>) (drawCellContent: bool) (c: Cell) =
 957     if drawCellContent
 958     then
 959         let colorB = rngCell.Next(20, 70)
 960         let colorG = rngCell.Next(20, 70)
 961         let colorR = rngCell.Next(20, 70)
 962
 963         for y in 0 .. c.elements.Height - 1 do
 964             for x in 0 .. c.elements.Width - 1 do
 965                 if c.elements.[y, x] > 0uy
 966                 then
 967                     let dx, dy = c.center.X - c.elements.Width / 2, c.center.Y - c.elements.Height / 2
 968                     let b = img.Data.[y + dy, x + dx, 0] |> int
 969                     let g = img.Data.[y + dy, x + dx, 1] |> int
 970                     let r = img.Data.[y + dy, x + dx, 2] |> int
 971                     img.Data.[y + dy, x + dx, 0] <- if b + colorB > 255 then 255uy else byte (b + colorB)
 972                     img.Data.[y + dy, x + dx, 1] <- if g + colorG > 255 then 255uy else byte (g + colorG)
 973                     img.Data.[y + dy, x + dx, 2] <- if r + colorR > 255 then 255uy else byte (r + colorR)
 974
 975     let crossColor, crossColor2 =
 976         match c.cellClass with
 977         | HealthyRBC -> Bgr(255., 0., 0.), Bgr(255., 255., 255.)
 978         | InfectedRBC -> Bgr(0., 0., 255.), Bgr(120., 120., 255.)
 979         | Peculiar -> Bgr(0., 0., 0.), Bgr(80., 80., 80.)
 980
 981     drawLine img crossColor2 (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 2
 982     drawLine img crossColor2 c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 2
 983
 984     drawLine img crossColor (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 1
 985     drawLine img crossColor c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 1
 986
 987
 988 let drawCells (img: Image<Bgr, byte>) (drawCellContent: bool) (cells: Cell list) =
 989     List.iter (fun c -> drawCell img drawCellContent c) cells