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