Parasitemia/Parasitemia/ImgTools.fs

   1 module 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 Utils
  12 open Heap
  13
  14 // Normalize image values between 0uy and 255uy.
  15 let normalizeAndConvert (img: Image<Gray, float32>) : Image<Gray, byte> =
  16     let min = ref [| 0.0 |]
  17     let minLocation = ref <| [| Point() |]
  18     let max = ref [| 0.0 |]
  19     let maxLocation = ref <| [| Point() |]
  20     img.MinMax(min, max, minLocation, maxLocation)
  21     ((img - (!min).[0]) / ((!max).[0] - (!min).[0]) * 255.0).Convert<Gray, byte>()
  22
  23
  24 let saveImg (img: Image<'TColor, 'TDepth>) (filepath: string) =
  25     img.Save(filepath)
  26
  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
  34 let suppressMConnections (img: Matrix<byte>) =
  35     let w = img.Width
  36     let h = img.Height
  37     for i in 1 .. h - 2 do
  38         for j in 1 .. w - 2 do
  39             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)
  40             then
  41                 img.[i, j] <- 0uy
  42     for i in 1 .. h - 2 do
  43         for j in 1 .. w - 2 do
  44             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)
  45             then
  46                 img.[i, j] <- 0uy
  47
  48
  49 let findEdges (img: Image<Gray, float32>) : Matrix<byte> * Image<Gray, float> * Image<Gray, float> =
  50     let w = img.Width
  51     let h = img.Height
  52
  53     use sobelKernel =
  54         new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
  55                                         [ 2.0f; 0.0f; -2.0f ]
  56                                         [ 1.0f; 0.0f; -1.0f ]], Point(1, 1))
  57
  58     let xGradient = img.Convolution(sobelKernel).Convert<Gray, float>()
  59     let yGradient = img.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
  60
  61     let xGradientData = xGradient.Data
  62     let yGradientData = yGradient.Data
  63     for r in 0 .. h - 1 do
  64         xGradientData.[r, 0, 0] <- 0.0
  65         xGradientData.[r, w - 1, 0] <- 0.0
  66         yGradientData.[r, 0, 0] <- 0.0
  67         yGradientData.[r, w - 1, 0] <- 0.0
  68
  69     for c in 0 .. w - 1 do
  70         xGradientData.[0, c, 0] <- 0.0
  71         xGradientData.[h - 1, c, 0] <- 0.0
  72         yGradientData.[0, c, 0] <- 0.0
  73         yGradientData.[h - 1, c, 0] <- 0.0
  74
  75     use magnitudes = new Matrix<float>(xGradient.Size)
  76     use angles = new Matrix<float>(xGradient.Size)
  77     CvInvoke.CartToPolar(xGradient, yGradient, magnitudes, angles) // Compute the magnitudes (without angles).
  78
  79     let thresholdHigh, thresholdLow =
  80         let sensibilityHigh = 0.1
  81         let sensibilityLow = 0.1
  82         use magnitudesByte = magnitudes.Convert<byte>()
  83         let threshold = CvInvoke.Threshold(magnitudesByte, magnitudesByte, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary)
  84         threshold + (sensibilityHigh * threshold), threshold - (sensibilityLow * threshold)
  85
  86     // Non-maximum suppression.
  87     use nms = new Matrix<byte>(xGradient.Size)
  88
  89     for i in 0 .. h - 1 do
  90         nms.Data.[i, 0] <- 0uy
  91         nms.Data.[i, w - 1] <- 0uy
  92
  93     for j in 0 .. w - 1 do
  94         nms.Data.[0, j] <- 0uy
  95         nms.Data.[h - 1, j] <- 0uy
  96
  97     for i in 1 .. h - 2 do
  98         for j in 1 .. w - 2 do
  99             let vx = xGradient.Data.[i, j, 0]
 100             let vy = yGradient.Data.[i, j, 0]
 101             if vx <> 0. || vy <> 0.
 102             then
 103                 let angle = angles.[i, j]
 104
 105                 let vx', vy' = abs vx, abs vy
 106                 let ratio2 = if vx' > vy' then vy' / vx' else vx' / vy'
 107                 let ratio1 = 1. - ratio2
 108
 109                 let mNeigbors (sign: int) : float =
 110                     if angle < Math.PI / 4.
 111                     then ratio1 * magnitudes.Data.[i, j + sign] + ratio2 * magnitudes.Data.[i + sign, j + sign]
 112                     elif angle < Math.PI / 2.
 113                     then ratio2 * magnitudes.Data.[i + sign, j + sign] + ratio1 * magnitudes.Data.[i + sign, j]
 114                     elif angle < 3.0 * Math.PI / 4.
 115                     then ratio1 * magnitudes.Data.[i + sign, j] + ratio2 * magnitudes.Data.[i + sign, j - sign]
 116                     elif angle < Math.PI
 117                     then ratio2 * magnitudes.Data.[i + sign, j - sign] + ratio1 * magnitudes.Data.[i, j - sign]
 118                     elif angle < 5. * Math.PI / 4.
 119                     then ratio1 * magnitudes.Data.[i, j - sign] + ratio2 * magnitudes.Data.[i - sign, j - sign]
 120                     elif angle < 3. * Math.PI / 2.
 121                     then ratio2 * magnitudes.Data.[i - sign, j - sign] + ratio1 * magnitudes.Data.[i - sign, j]
 122                     elif angle < 7. * Math.PI / 4.
 123                     then ratio1 * magnitudes.Data.[i - sign, j] + ratio2 * magnitudes.Data.[i - sign, j + sign]
 124                     else ratio2 * magnitudes.Data.[i - sign, j + sign] + ratio1 * magnitudes.Data.[i, j + sign]
 125
 126                 let m = magnitudes.Data.[i, j]
 127                 if m >= thresholdLow && m > mNeigbors 1 && m > mNeigbors -1
 128                 then
 129                     nms.Data.[i, j] <- 1uy
 130
 131     // suppressMConnections nms // It's not helpful for the rest of the process (ellipse detection).
 132
 133     let edges = new Matrix<byte>(xGradient.Size)
 134
 135     // Histeresis thresholding.
 136     let toVisit = Stack<Point>()
 137     for i in 0 .. h - 1 do
 138         for j in 0 .. w - 1 do
 139             if nms.Data.[i, j] = 1uy && magnitudes.Data.[i, j] >= thresholdHigh
 140             then
 141                 nms.Data.[i, j] <- 0uy
 142                 toVisit.Push(Point(j, i))
 143                 while toVisit.Count > 0 do
 144                     let p = toVisit.Pop()
 145                     edges.Data.[p.Y, p.X] <- 1uy
 146                     for i' in -1 .. 1  do
 147                         for j' in -1 .. 1 do
 148                             if i' <> 0 || j' <> 0
 149                             then
 150                                 let ni = p.Y + i'
 151                                 let nj = p.X + j'
 152                                 if ni >= 0 && ni < h && nj >= 0 && nj < w && nms.Data.[ni, nj] = 1uy
 153                                 then
 154                                     nms.Data.[ni, nj] <- 0uy
 155                                     toVisit.Push(Point(nj, ni))
 156
 157     edges, xGradient, yGradient
 158
 159
 160 let gaussianFilter (img : Image<'TColor, 'TDepth>) (standardDeviation : float) : Image<'TColor, 'TDepth> =
 161     let size = 2 * int (ceil (4.0 * standardDeviation)) + 1
 162     img.SmoothGaussian(size, size, standardDeviation, standardDeviation)
 163
 164
 165 type Points = HashSet<Point>
 166
 167 let drawPoints (img: Image<Gray, 'TDepth>) (points: Points) (intensity: 'TDepth) =
 168     for p in points do
 169         img.Data.[p.Y, p.X, 0] <- intensity
 170
 171 type ExtremumType =
 172     | Maxima = 1
 173     | Minima = 2
 174
 175 let findExtremum (img: Image<Gray, 'TDepth>) (extremumType: ExtremumType) : IEnumerable<Points> =
 176     let w = img.Width
 177     let h = img.Height
 178     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 179
 180     let imgData = img.Data
 181     let suppress: bool[,] = Array2D.zeroCreate h w
 182
 183     let result = List<List<Point>>()
 184
 185     let flood (start: Point) : List<List<Point>> =
 186         let sameLevelToCheck = Stack<Point>()
 187         let betterLevelToCheck = Stack<Point>()
 188         betterLevelToCheck.Push(start)
 189
 190         let result' = List<List<Point>>()
 191
 192         while betterLevelToCheck.Count > 0 do
 193             let p = betterLevelToCheck.Pop()
 194             if not suppress.[p.Y, p.X]
 195             then
 196                 suppress.[p.Y, p.X] <- true
 197                 sameLevelToCheck.Push(p)
 198                 let current = List<Point>()
 199
 200                 let mutable betterExists = false
 201
 202                 while sameLevelToCheck.Count > 0 do
 203                     let p' = sameLevelToCheck.Pop()
 204                     let currentLevel = imgData.[p'.Y, p'.X, 0]
 205                     current.Add(p') |> ignore
 206                     for i, j in se do
 207                         let ni = i + p'.Y
 208                         let nj = j + p'.X
 209                         if ni >= 0 && ni < h && nj >= 0 && nj < w
 210                         then
 211                             let level = imgData.[ni, nj, 0]
 212                             let notSuppressed = not suppress.[ni, nj]
 213
 214                             if level = currentLevel && notSuppressed
 215                             then
 216                                 suppress.[ni, nj] <- true
 217                                 sameLevelToCheck.Push(Point(nj, ni))
 218                             elif if extremumType = ExtremumType.Maxima then level > currentLevel else level < currentLevel
 219                             then
 220                                 betterExists <- true
 221                                 if notSuppressed
 222                                 then
 223                                     betterLevelToCheck.Push(Point(nj, ni))
 224
 225                 if not betterExists
 226                 then
 227                     result'.Add(current)
 228         result'
 229
 230     for i in 0 .. h - 1 do
 231         for j in 0 .. w - 1 do
 232             let maxima = flood (Point(j, i))
 233             if maxima.Count > 0
 234             then
 235                 result.AddRange(maxima)
 236
 237     result.Select(fun l -> Points(l))
 238
 239
 240 let findMaxima (img: Image<Gray, 'TDepth>) : IEnumerable<Points> =
 241     findExtremum img ExtremumType.Maxima
 242
 243
 244 let findMinima (img: Image<Gray, 'TDepth>) : IEnumerable<Points> =
 245     findExtremum img ExtremumType.Minima
 246
 247
 248 type PriorityQueue () =
 249     let size = 256
 250     let q: Points[] = Array.init size (fun i -> Points())
 251     let mutable highest = -1 // Value of the first elements of 'q'.
 252     let mutable lowest = size
 253
 254     member this.NextMax () : byte * Point =
 255         if this.IsEmpty
 256         then
 257             invalidOp "Queue is empty"
 258         else
 259             let l = q.[highest]
 260             let next = l.First()
 261             l.Remove(next) |> ignore
 262             let value = byte highest
 263
 264             if l.Count = 0
 265             then
 266                 highest <- highest - 1
 267                 while highest > lowest && q.[highest].Count = 0 do
 268                     highest <- highest - 1
 269                 if highest = lowest
 270                 then
 271                     highest <- -1
 272                     lowest <- size
 273
 274             value, next
 275
 276     member this.NextMin () : byte * Point =
 277         if this.IsEmpty
 278         then
 279             invalidOp "Queue is empty"
 280         else
 281             let l = q.[lowest + 1]
 282             let next = l.First()
 283             l.Remove(next) |> ignore
 284             let value = byte (lowest + 1)
 285
 286             if l.Count = 0
 287             then
 288                 lowest <- lowest + 1
 289                 while lowest < highest && q.[lowest + 1].Count = 0 do
 290                     lowest <- lowest + 1
 291                 if highest = lowest
 292                 then
 293                     highest <- -1
 294                     lowest <- size
 295
 296             value, next
 297
 298     member this.Max =
 299         highest |> byte
 300
 301     member this.Min =
 302         lowest + 1 |> byte
 303
 304     member this.Add (value: byte) (p: Point) =
 305         let vi = int value
 306
 307         if vi > highest
 308         then
 309             highest <- vi
 310         if vi <= lowest
 311         then
 312             lowest <- vi - 1
 313
 314         q.[vi].Add(p) |> ignore
 315
 316     member this.Remove (value: byte) (p: Point) =
 317         let vi = int value
 318         if q.[vi].Remove(p) && q.[vi].Count = 0
 319         then
 320             if vi = highest
 321             then
 322                 highest <- highest - 1
 323                 while highest > lowest && q.[highest].Count = 0 do
 324                     highest <- highest - 1
 325             elif vi - 1 = lowest
 326             then
 327                 lowest <- lowest + 1
 328                 while lowest < highest && q.[lowest + 1].Count = 0 do
 329                     lowest <- lowest + 1
 330
 331             if highest = lowest // The queue is now empty.
 332             then
 333                 highest <- -1
 334                 lowest <- size
 335
 336     member this.IsEmpty =
 337         highest = -1
 338
 339     member this.Clear () =
 340         while highest > lowest  do
 341             q.[highest].Clear()
 342             highest <- highest - 1
 343         highest <- -1
 344         lowest <- size
 345
 346
 347 type private AreaState =
 348     | Removed = 1
 349     | Unprocessed = 2
 350     | Validated = 3
 351
 352 type private AreaOperation =
 353     | Opening = 1
 354     | Closing = 2
 355
 356 [<AllowNullLiteral>]
 357 type private Area (elements: Points) =
 358     member this.Elements = elements
 359     member val Intensity = None with get, set
 360     member val State = AreaState.Unprocessed with get, set
 361
 362 let private areaOperation (img: Image<Gray, byte>) (area: int) (op: AreaOperation) =
 363     let w = img.Width
 364     let h = img.Height
 365     let imgData = img.Data
 366     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 367
 368     let areas = List<Area>((if op = AreaOperation.Opening then findMaxima img else findMinima img) |> Seq.map Area)
 369
 370     let pixels: Area[,] = Array2D.create h w null
 371     for m in areas do
 372         for e in m.Elements do
 373             pixels.[e.Y, e.X] <- m
 374
 375     let queue = PriorityQueue()
 376
 377     let addEdgeToQueue (elements: Points) =
 378         for p in elements do
 379             for i, j in se do
 380                 let ni = i + p.Y
 381                 let nj = j + p.X
 382                 let p' = Point(nj, ni)
 383                 if ni >= 0 && ni < h && nj >= 0 && nj < w && not (elements.Contains(p'))
 384                 then
 385                     queue.Add (imgData.[ni, nj, 0]) p'
 386
 387     // Reverse order is quicker.
 388     for i in areas.Count - 1 .. -1 .. 0 do
 389         let m = areas.[i]
 390         if m.Elements.Count <= area && m.State <> AreaState.Removed
 391         then
 392             queue.Clear()
 393             addEdgeToQueue m.Elements
 394
 395             let mutable intensity = if op = AreaOperation.Opening then queue.Max else queue.Min
 396             let nextElements = Points()
 397
 398             let mutable stop = false
 399             while not stop do
 400                 let intensity', p = if op = AreaOperation.Opening then queue.NextMax () else queue.NextMin ()
 401                 let mutable merged = false
 402
 403                 if intensity' = intensity // The intensity doesn't change.
 404                 then
 405                     if m.Elements.Count + nextElements.Count + 1 > area
 406                     then
 407                         m.State <- AreaState.Validated
 408                         m.Intensity <- Some intensity
 409                         stop <- true
 410                     else
 411                         nextElements.Add(p) |> ignore
 412
 413                 elif if op = AreaOperation.Opening then intensity' < intensity else intensity' > intensity
 414                 then
 415                     m.Elements.UnionWith(nextElements)
 416                     for e in nextElements do
 417                         pixels.[e.Y, e.X] <- m
 418
 419                     if m.Elements.Count = area
 420                     then
 421                         m.State <- AreaState.Validated
 422                         m.Intensity <- Some (intensity')
 423                         stop <- true
 424                     else
 425                         intensity <- intensity'
 426                         nextElements.Clear()
 427                         nextElements.Add(p) |> ignore
 428
 429                 else
 430                     let m' = pixels.[p.Y, p.X]
 431                     if m' <> null
 432                     then
 433                         if m'.Elements.Count + m.Elements.Count <= area
 434                         then
 435                             m'.State <- AreaState.Removed
 436                             for e in m'.Elements do
 437                                 pixels.[e.Y, e.X] <- m
 438                                 queue.Remove imgData.[e.Y, e.X, 0] e
 439                             addEdgeToQueue m'.Elements
 440                             m.Elements.UnionWith(m'.Elements)
 441                             let intensityMax = if op = AreaOperation.Opening then queue.Max else queue.Min
 442                             if intensityMax <> intensity
 443                             then
 444                                 intensity <- intensityMax
 445                                 nextElements.Clear()
 446                             merged <- true
 447
 448                     if not merged
 449                     then
 450                         m.State <- AreaState.Validated
 451                         m.Intensity <- Some (intensity)
 452                         stop <- true
 453
 454                 if not stop && not merged
 455                 then
 456                     for i, j in se do
 457                         let ni = i + p.Y
 458                         let nj = j + p.X
 459                         let p' = Point(nj, ni)
 460                         if ni < 0 || ni >= h || nj < 0 || nj >= w
 461                         then
 462                             m.State <- AreaState.Validated
 463                             m.Intensity <- Some (intensity)
 464                             stop <- true
 465                         elif not (m.Elements.Contains(p')) && not (nextElements.Contains(p'))
 466                         then
 467                             queue.Add (imgData.[ni, nj, 0]) p'
 468
 469                 if queue.IsEmpty
 470                 then
 471                     if m.Elements.Count + nextElements.Count <= area
 472                     then
 473                         m.State <- AreaState.Validated
 474                         m.Intensity <- Some intensity'
 475                         m.Elements.UnionWith(nextElements)
 476                     stop <- true
 477
 478     for m in areas do
 479         if m.State = AreaState.Validated
 480         then
 481             match m.Intensity with
 482             | Some i ->
 483                 for p in m.Elements do
 484                     imgData.[p.Y, p.X, 0] <- i
 485             | _ -> ()
 486     ()
 487
 488
 489 let areaOpen (img: Image<Gray, byte>) (area: int) =
 490     areaOperation img area AreaOperation.Opening
 491
 492 let areaClose (img: Image<Gray, byte>) (area: int) =
 493     areaOperation img area AreaOperation.Closing
 494
 495 [<AllowNullLiteral>]
 496 type Island (cmp: IComparer<float32>) =
 497     member val Shore = Heap.Heap<float32, Point>(cmp) with get
 498     member val Level = 0.f with get, set
 499     member val Surface = 0 with get, set
 500
 501
 502 let private areaOperationF (img: Image<Gray, float32>) (area: int) (op: AreaOperation) =
 503     let w = img.Width
 504     let h = img.Height
 505     let earth = img.Data
 506     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 507
 508     let comparer = if op = AreaOperation.Opening
 509                    then { new IComparer<float32> with member this.Compare(v1, v2) = v1.CompareTo(v2) }
 510                    else { new IComparer<float32> with member this.Compare(v1, v2) = v2.CompareTo(v1) }
 511
 512     let ownership: Island[,] = Array2D.create h w null
 513
 514     // Initialize islands with their shore.
 515     let islands = List<Island>()
 516     let extremum = img |> if op = AreaOperation.Opening then findMaxima else findMinima
 517     for e in extremum do
 518         let island =
 519             let p = e.First()
 520             Island(comparer, Level = earth.[p.Y, p.X, 0], Surface = e.Count)
 521         islands.Add(island)
 522         let shorePoints = Points()
 523         for p in e do
 524             ownership.[p.Y, p.X] <- island
 525             for i, j in se do
 526                 let ni = i + p.Y
 527                 let nj = j + p.X
 528                 let neighbor = Point(nj, ni)
 529                 if ni >= 0 && ni < h && nj >= 0 && nj < w && ownership.[ni, nj] = null && not (shorePoints.Contains(neighbor))
 530                 then
 531                     shorePoints.Add(neighbor) |> ignore
 532                     island.Shore.Add earth.[ni, nj, 0] neighbor
 533
 534     for island in islands do
 535         let mutable stop = island.Shore.IsEmpty
 536
 537         // 'true' if 'p' is owned or adjacent to 'island'.
 538         let ownedOrAdjacent (p: Point) : bool =
 539             ownership.[p.Y, p.X] = island ||
 540             (p.Y > 0 && ownership.[p.Y - 1, p.X] = island) ||
 541             (p.Y < h - 1 && ownership.[p.Y + 1, p.X] = island) ||
 542             (p.X > 0 && ownership.[p.Y, p.X - 1] = island) ||
 543             (p.X < w - 1 && ownership.[p.Y, p.X + 1] = island)
 544
 545         while not stop && island.Surface < area do
 546             let level, next = island.Shore.Max
 547             let other = ownership.[next.Y, next.X]
 548             if other = island // During merging, some points on the shore may be owned by the island itself -> ignored.
 549             then
 550                 island.Shore.RemoveNext ()
 551             else
 552                 if other <> null
 553                 then // We touching another island.
 554                     if island.Surface + other.Surface >= area
 555                     then
 556                         stop <- true
 557                     else // We can merge 'other' into 'surface'.
 558                         island.Surface <- island.Surface + other.Surface
 559                         island.Level <- if comparer.Compare(island.Level, other.Level) > 0 then island.Level else other.Level
 560                         for l, p in other.Shore do
 561                             let mutable currentY = p.Y + 1
 562                             while currentY < h && ownership.[currentY, p.X] = other do
 563                                 ownership.[currentY, p.X] <- island
 564                                 currentY <- currentY + 1
 565                             island.Shore.Add l p
 566                         other.Shore.Clear()
 567
 568                 elif comparer.Compare(level, island.Level) > 0
 569                 then
 570                     stop <- true
 571                 else
 572                     island.Shore.RemoveNext ()
 573                     for i, j in se do
 574                         let ni = i + next.Y
 575                         let nj = j + next.X
 576                         if ni < 0 || ni >= h || nj < 0 || nj >= w
 577                         then
 578                             island.Surface <- Int32.MaxValue
 579                             stop <- true
 580                         else
 581                             let neighbor = Point(nj, ni)
 582                             if not <| ownedOrAdjacent neighbor
 583                             then
 584                                 island.Shore.Add earth.[ni, nj, 0] neighbor
 585                     if not stop
 586                     then
 587                         ownership.[next.Y, next.X] <- island
 588                         island.Level <- level
 589                         island.Surface <- island.Surface + 1
 590
 591     for i in 0 .. h - 1 do
 592         for j in 0 .. w - 1 do
 593             let island = ownership.[i, j]
 594             if island <> null
 595             then
 596                 earth.[i, j, 0] <- island.Level
 597     ()
 598
 599
 600 let areaOpenF (img: Image<Gray, float32>) (area: int) =
 601     areaOperationF img area AreaOperation.Opening
 602
 603 let areaCloseF (img: Image<Gray, float32>) (area: int) =
 604     areaOperationF img area AreaOperation.Closing
 605
 606 // A simpler algorithm than 'areaOpen' but slower.
 607 let areaOpen2 (img: Image<Gray, byte>) (area: int) =
 608     let w = img.Width
 609     let h = img.Height
 610     let imgData = img.Data
 611     let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
 612
 613     let histogram = Array.zeroCreate 256
 614     for i in 0 .. h - 1 do
 615         for j in 0 .. w - 1 do
 616             let v = imgData.[i, j, 0] |> int
 617             histogram.[v] <- histogram.[v] + 1
 618
 619     let flooded : bool[,] = Array2D.zeroCreate h w
 620
 621     let pointsChecked = HashSet<Point>()
 622     let pointsToCheck = Stack<Point>()
 623
 624     for level in 255 .. -1 .. 0 do
 625         let mutable n = histogram.[level]
 626         if n > 0
 627         then
 628             for i in 0 .. h - 1 do
 629                 for j in 0 .. w - 1 do
 630                     if not flooded.[i, j] && imgData.[i, j, 0] = byte level
 631                     then
 632                         let mutable maxNeighborValue = 0uy
 633                         pointsChecked.Clear()
 634                         pointsToCheck.Clear()
 635                         pointsToCheck.Push(Point(j, i))
 636
 637                         while pointsToCheck.Count > 0 do
 638                             let next = pointsToCheck.Pop()
 639                             pointsChecked.Add(next) |> ignore
 640                             flooded.[next.Y, next.X] <- true
 641
 642                             for nx, ny in se do
 643                                 let p = Point(next.X + nx, next.Y + ny)
 644                                 if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h
 645                                 then
 646                                     let v = imgData.[p.Y, p.X, 0]
 647                                     if v = byte level
 648                                     then
 649                                         if not (pointsChecked.Contains(p))
 650                                         then
 651                                             pointsToCheck.Push(p)
 652                                     elif v > maxNeighborValue
 653                                     then
 654                                         maxNeighborValue <- v
 655
 656                         if int maxNeighborValue < level && pointsChecked.Count <= area
 657                         then
 658                             for p in pointsChecked do
 659                                 imgData.[p.Y, p.X, 0] <- maxNeighborValue
 660
 661
 662 // Zhang and Suen algorithm.
 663 // Modify 'mat' in place.
 664 let thin (mat: Matrix<byte>) =
 665     let w = mat.Width
 666     let h = mat.Height
 667     let mutable data1 = mat.Data
 668     let mutable data2 = Array2D.copy data1
 669
 670     let mutable pixelChanged = true
 671     let mutable oddIteration = true
 672
 673     while pixelChanged do
 674         pixelChanged <- false
 675         for i in 0..h-1 do
 676             for j in 0..w-1 do
 677                 if data1.[i, j] = 1uy
 678                 then
 679                     let p2 = if i = 0 then 0uy else data1.[i-1, j]
 680                     let p3 = if i = 0 || j = w-1 then 0uy else data1.[i-1, j+1]
 681                     let p4 = if j = w-1 then 0uy else data1.[i, j+1]
 682                     let p5 = if i = h-1 || j = w-1 then 0uy else data1.[i+1, j+1]
 683                     let p6 = if i = h-1 then 0uy else data1.[i+1, j]
 684                     let p7 = if i = h-1 || j = 0 then 0uy else data1.[i+1, j-1]
 685                     let p8 = if j = 0 then 0uy else data1.[i, j-1]
 686                     let p9 = if i = 0 || j = 0 then 0uy else data1.[i-1, j-1]
 687
 688                     let sumNeighbors = p2 + p3 + p4 + p5 + p6 + p7 + p8 + p9
 689                     if sumNeighbors >= 2uy && sumNeighbors <= 6uy &&
 690                         (if p2 = 0uy && p3 = 1uy then 1 else 0) +
 691                         (if p3 = 0uy && p4 = 1uy then 1 else 0) +
 692                         (if p4 = 0uy && p5 = 1uy then 1 else 0) +
 693                         (if p5 = 0uy && p6 = 1uy then 1 else 0) +
 694                         (if p6 = 0uy && p7 = 1uy then 1 else 0) +
 695                         (if p7 = 0uy && p8 = 1uy then 1 else 0) +
 696                         (if p8 = 0uy && p9 = 1uy then 1 else 0) +
 697                         (if p9 = 0uy && p2 = 1uy then 1 else 0) = 1 &&
 698                         if oddIteration
 699                         then p2 * p4 * p6 = 0uy && p4 * p6 * p8 = 0uy
 700                         else p2 * p4 * p8 = 0uy && p2 * p6 * p8 = 0uy
 701                     then
 702                         data2.[i, j] <- 0uy
 703                         pixelChanged <- true
 704                 else
 705                     data2.[i, j] <- 0uy
 706
 707         oddIteration <- not oddIteration
 708         let tmp = data1
 709         data1 <- data2
 710         data2 <- tmp
 711
 712
 713 // Remove all 8-connected pixels with an area equal or greater than 'areaSize'.
 714 // Modify 'mat' in place.
 715 let removeArea (mat: Matrix<byte>) (areaSize: int) =
 716     let neighbors = [|
 717         (-1,  0) // p2
 718         (-1,  1) // p3
 719         ( 0,  1) // p4
 720         ( 1,  1) // p5
 721         ( 1,  0) // p6
 722         ( 1, -1) // p7
 723         ( 0, -1) // p8
 724         (-1, -1) |] // p9
 725
 726     let mat' = new Matrix<byte>(mat.Size)
 727     let w = mat'.Width
 728     let h = mat'.Height
 729     mat.CopyTo(mat')
 730
 731     let data = mat.Data
 732     let data' = mat'.Data
 733
 734     for i in 0..h-1 do
 735         for j in 0..w-1 do
 736             if data'.[i, j] = 1uy
 737             then
 738                 let neighborhood = List<Point>()
 739                 let neighborsToCheck = Stack<Point>()
 740                 neighborsToCheck.Push(Point(j, i))
 741                 data'.[i, j] <- 0uy
 742
 743                 while neighborsToCheck.Count > 0 do
 744                     let n = neighborsToCheck.Pop()
 745                     neighborhood.Add(n)
 746                     for (ni, nj) in neighbors do
 747                         let pi = n.Y + ni
 748                         let pj = n.X + nj
 749                         if pi >= 0 && pi < h && pj >= 0 && pj < w && data'.[pi, pj] = 1uy
 750                         then
 751                             neighborsToCheck.Push(Point(pj, pi))
 752                             data'.[pi, pj] <- 0uy
 753                 if neighborhood.Count <= areaSize
 754                 then
 755                     for n in neighborhood do
 756                         data.[n.Y, n.X] <- 0uy
 757
 758 let connectedComponents (img: Image<Gray, byte>) (startPoints: List<Point>) : List<Point> =
 759     let w = img.Width
 760     let h = img.Height
 761
 762     let pointChecked = Points()
 763     let pointToCheck = Stack<Point>(startPoints);
 764
 765     let data = img.Data
 766
 767     while pointToCheck.Count > 0 do
 768         let next = pointToCheck.Pop()
 769         pointChecked.Add(next) |> ignore
 770         for ny in -1 .. 1 do
 771             for nx in -1 .. 1 do
 772                 if ny <> 0 && nx <> 0
 773                 then
 774                     let p = Point(next.X + nx, next.Y + ny)
 775                     if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h && data.[p.Y, p.X, 0] > 0uy && not (pointChecked.Contains p)
 776                     then
 777                         pointToCheck.Push(p)
 778
 779     List<Point>(pointChecked)
 780
 781
 782 let drawLine (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: int) (y0: int) (x1: int) (y1: int) (thickness: int) =
 783     img.Draw(LineSegment2D(Point(x0, y0), Point(x1, y1)), color, thickness);
 784
 785
 786 let drawLineF (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: float) (y0: float) (x1: float) (y1: float) (thickness: int) =
 787     img.Draw(LineSegment2DF(PointF(float32 x0, float32 y0), PointF(float32 x1, float32 y1)), color, thickness, CvEnum.LineType.AntiAlias);
 788
 789
 790 let drawEllipse (img: Image<'TColor, 'TDepth>) (e: Types.Ellipse) (color: 'TColor) (alpha: float) =
 791
 792     if alpha >= 1.0
 793     then
 794         img.Draw(Ellipse(PointF(float32 e.Cx, float32 e.Cy), SizeF(2. * e.B |> float32, 2. * e.A |> float32), float32 <| e.Alpha / Math.PI * 180.), color, 1, CvEnum.LineType.AntiAlias)
 795     else
 796         let windowPosX = e.Cx - e.A - 5.0
 797         let gapX = windowPosX - (float (int windowPosX))
 798
 799         let windowPosY = e.Cy - e.A - 5.0
 800         let gapY = windowPosY - (float (int windowPosY))
 801
 802         let roi = Rectangle(int windowPosX, int windowPosY, 2. * (e.A + 5.0) |> int, 2.* (e.A + 5.0) |> int)
 803
 804         img.ROI <- roi
 805         if roi = img.ROI // We do not display ellipses touching the edges (FIXME)
 806         then
 807             use i = new Image<'TColor, 'TDepth>(img.ROI.Size)
 808             i.Draw(Ellipse(PointF(float32 <| (e.A + 5. + gapX) , float32 <| (e.A + 5. + gapY)), SizeF(2. * e.B |> float32, 2. * e.A |> float32), float32 <| e.Alpha / Math.PI * 180.), color, 1, CvEnum.LineType.AntiAlias)
 809             CvInvoke.AddWeighted(img, 1.0, i, alpha, 0.0, img)
 810         img.ROI <- Rectangle.Empty
 811
 812
 813 let drawEllipses (img: Image<'TColor, 'TDepth>) (ellipses: Types.Ellipse list) (color: 'TColor) (alpha: float) =
 814     List.iter (fun e -> drawEllipse img e color alpha) ellipses
 815
 816
 817 let rngCell =  System.Random()
 818 let drawCell (img: Image<Bgr, byte>) (drawCellContent: bool) (c: Types.Cell) =
 819     if drawCellContent
 820     then
 821         let colorB = rngCell.Next(20, 70)
 822         let colorG = rngCell.Next(20, 70)
 823         let colorR = rngCell.Next(20, 70)
 824
 825         for y in 0 .. c.elements.Height - 1 do
 826             for x in 0 .. c.elements.Width - 1 do
 827                 if c.elements.[y, x] > 0uy
 828                 then
 829                     let dx, dy = c.center.X - c.elements.Width / 2, c.center.Y - c.elements.Height / 2
 830                     let b = img.Data.[y + dy, x + dx, 0] |> int
 831                     let g = img.Data.[y + dy, x + dx, 1] |> int
 832                     let r = img.Data.[y + dy, x + dx, 2] |> int
 833                     img.Data.[y + dy, x + dx, 0] <- if b + colorB > 255 then 255uy else byte (b + colorB)
 834                     img.Data.[y + dy, x + dx, 1] <- if g + colorG > 255 then 255uy else byte (g + colorG)
 835                     img.Data.[y + dy, x + dx, 2] <- if r + colorR > 255 then 255uy else byte (r + colorR)
 836
 837     let crossColor, crossColor2 =
 838         match c.cellClass with
 839         | Types.HealthyRBC -> Bgr(255., 0., 0.), Bgr(255., 255., 255.)
 840         | Types.InfectedRBC -> Bgr(0., 0., 255.), Bgr(120., 120., 255.)
 841         | Types.Peculiar -> Bgr(0., 0., 0.), Bgr(80., 80., 80.)
 842
 843     drawLine img crossColor2 (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 2
 844     drawLine img crossColor2 c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 2
 845
 846     drawLine img crossColor (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 1
 847     drawLine img crossColor c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 1
 848
 849
 850 let drawCells (img: Image<Bgr, byte>) (drawCellContent: bool) (cells: Types.Cell list) =
 851     List.iter (fun c -> drawCell img drawCellContent c) cells