Change the parasite detection method.
[master-thesis.git] / 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 gaussianFilter (img : Image<'TColor, 'TDepth>) (standardDeviation : float) : Image<'TColor, 'TDepth> =
25 let size = 2 * int (ceil (4.0 * standardDeviation)) + 1
26 img.SmoothGaussian(size, size, standardDeviation, standardDeviation)
27
28
29 type Points = HashSet<Point>
30
31 let drawPoints (img: Image<Gray, byte>) (points: Points) (intensity: byte) =
32 for p in points do
33 img.Data.[p.Y, p.X, 0] <- intensity
34
35
36 type ExtremumType =
37 | Maxima = 1
38 | Minima = 2
39
40 let findExtremum (img: Image<Gray, byte>) (extremumType: ExtremumType) : IEnumerable<Points> =
41 let w = img.Width
42 let h = img.Height
43 let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
44
45 let imgData = img.Data
46 let suppress: bool[,] = Array2D.zeroCreate h w
47
48 let result = List<List<Point>>()
49
50 let flood (start: Point) : List<List<Point>> =
51 let sameLevelToCheck = Stack<Point>()
52 let betterLevelToCheck = Stack<Point>()
53 betterLevelToCheck.Push(start)
54
55 let result' = List<List<Point>>()
56
57 while betterLevelToCheck.Count > 0 do
58 let p = betterLevelToCheck.Pop()
59 if not suppress.[p.Y, p.X]
60 then
61 suppress.[p.Y, p.X] <- true
62 sameLevelToCheck.Push(p)
63 let current = List<Point>()
64
65 let mutable betterExists = false
66
67 while sameLevelToCheck.Count > 0 do
68 let p' = sameLevelToCheck.Pop()
69 let currentLevel = imgData.[p'.Y, p'.X, 0]
70 current.Add(p') |> ignore
71 for i, j in se do
72 let ni = i + p'.Y
73 let nj = j + p'.X
74 if ni >= 0 && ni < h && nj >= 0 && nj < w
75 then
76 let level = imgData.[ni, nj, 0]
77 let notSuppressed = not suppress.[ni, nj]
78
79 if level = currentLevel && notSuppressed
80 then
81 suppress.[ni, nj] <- true
82 sameLevelToCheck.Push(Point(nj, ni))
83 elif if extremumType = ExtremumType.Maxima then level > currentLevel else level < currentLevel
84 then
85 betterExists <- true
86 if notSuppressed
87 then
88 betterLevelToCheck.Push(Point(nj, ni))
89
90 if not betterExists
91 then
92 result'.Add(current)
93 result'
94
95 for i in 0 .. h - 1 do
96 for j in 0 .. w - 1 do
97 let maxima = flood (Point(j, i))
98 if maxima.Count > 0
99 then
100 result.AddRange(maxima)
101
102 result.Select(fun l -> Points(l))
103
104
105 let findMaxima (img: Image<Gray, byte>) : IEnumerable<Points> =
106 findExtremum img ExtremumType.Maxima
107
108 let findMinima (img: Image<Gray, byte>) : IEnumerable<Points> =
109 findExtremum img ExtremumType.Minima
110
111
112 type PriorityQueue () =
113 let size = 256
114 let q: Points[] = Array.init size (fun i -> Points())
115 let mutable highest = -1 // Value of the first elements of 'q'.
116 let mutable lowest = size
117
118 member this.NextMax () : byte * Point =
119 if this.IsEmpty
120 then
121 invalidOp "Queue is empty"
122 else
123 let l = q.[highest]
124 let next = l.First()
125 l.Remove(next) |> ignore
126 let value = byte highest
127
128 if l.Count = 0
129 then
130 highest <- highest - 1
131 while highest > lowest && q.[highest].Count = 0 do
132 highest <- highest - 1
133 if highest = lowest
134 then
135 highest <- -1
136 lowest <- size
137
138 value, next
139
140 member this.NextMin () : byte * Point =
141 if this.IsEmpty
142 then
143 invalidOp "Queue is empty"
144 else
145 let l = q.[lowest + 1]
146 let next = l.First()
147 l.Remove(next) |> ignore
148 let value = byte (lowest + 1)
149
150 if l.Count = 0
151 then
152 lowest <- lowest + 1
153 while lowest < highest && q.[lowest + 1].Count = 0 do
154 lowest <- lowest + 1
155 if highest = lowest
156 then
157 highest <- -1
158 lowest <- size
159
160 value, next
161
162 member this.Max =
163 highest |> byte
164
165 member this.Min =
166 lowest + 1 |> byte
167
168 member this.Add (value: byte) (p: Point) =
169 let vi = int value
170
171 if vi > highest
172 then
173 highest <- vi
174 if vi <= lowest
175 then
176 lowest <- vi - 1
177
178 q.[vi].Add(p) |> ignore
179
180 member this.Remove (value: byte) (p: Point) =
181 let vi = int value
182 if q.[vi].Remove(p) && q.[vi].Count = 0
183 then
184 if vi = highest
185 then
186 highest <- highest - 1
187 while highest > lowest && q.[highest].Count = 0 do
188 highest <- highest - 1
189 elif vi - 1 = lowest
190 then
191 lowest <- lowest + 1
192 while lowest < highest && q.[lowest + 1].Count = 0 do
193 lowest <- lowest + 1
194
195 if highest = lowest // The queue is now empty.
196 then
197 highest <- -1
198 lowest <- size
199
200 member this.IsEmpty =
201 highest = -1
202
203 member this.Clear () =
204 while highest > lowest do
205 q.[highest].Clear()
206 highest <- highest - 1
207 highest <- -1
208 lowest <- size
209
210
211 type private AreaState =
212 | Removed = 1
213 | Unprocessed = 2
214 | Validated = 3
215
216 type private AreaOperation =
217 | Opening = 1
218 | Closing = 2
219
220 [<AllowNullLiteral>]
221 type private Area (elements: Points) =
222 member this.Elements = elements
223 member val Intensity = None with get, set
224 member val State = AreaState.Unprocessed with get, set
225
226 let private areaOperation (img: Image<Gray, byte>) (area: int) (op: AreaOperation) =
227 let w = img.Width
228 let h = img.Height
229 let imgData = img.Data
230 let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
231
232 let areas = List<Area>((if op = AreaOperation.Opening then findMaxima img else findMinima img) |> Seq.map Area)
233
234 let pixels: Area[,] = Array2D.create h w null
235 for m in areas do
236 for e in m.Elements do
237 pixels.[e.Y, e.X] <- m
238
239 let queue = PriorityQueue()
240
241 let addEdgeToQueue (elements: Points) =
242 for p in elements do
243 for i, j in se do
244 let ni = i + p.Y
245 let nj = j + p.X
246 let p' = Point(nj, ni)
247 if ni >= 0 && ni < h && nj >= 0 && nj < w && not (elements.Contains(p'))
248 then
249 queue.Add (imgData.[ni, nj, 0]) p'
250
251 // Reverse order is quicker.
252 for i in areas.Count - 1 .. -1 .. 0 do
253 let m = areas.[i]
254 if m.Elements.Count <= area && m.State <> AreaState.Removed
255 then
256 queue.Clear()
257 addEdgeToQueue m.Elements
258
259 let mutable intensity = if op = AreaOperation.Opening then queue.Max else queue.Min
260 let nextElements = Points()
261
262 let mutable stop = false
263 while not stop do
264 let intensity', p = if op = AreaOperation.Opening then queue.NextMax () else queue.NextMin ()
265 let mutable merged = false
266
267 if intensity' = intensity // The intensity doesn't change.
268 then
269 if m.Elements.Count + nextElements.Count + 1 > area
270 then
271 m.State <- AreaState.Validated
272 m.Intensity <- Some intensity
273 stop <- true
274 else
275 nextElements.Add(p) |> ignore
276
277 elif if op = AreaOperation.Opening then intensity' < intensity else intensity' > intensity
278 then
279 m.Elements.UnionWith(nextElements)
280 for e in nextElements do
281 pixels.[e.Y, e.X] <- m
282
283 if m.Elements.Count = area
284 then
285 m.State <- AreaState.Validated
286 m.Intensity <- Some (intensity')
287 stop <- true
288 else
289 intensity <- intensity'
290 nextElements.Clear()
291 nextElements.Add(p) |> ignore
292
293 else
294 let m' = pixels.[p.Y, p.X]
295 if m' <> null
296 then
297 if m'.Elements.Count + m.Elements.Count <= area
298 then
299 m'.State <- AreaState.Removed
300 for e in m'.Elements do
301 pixels.[e.Y, e.X] <- m
302 queue.Remove imgData.[e.Y, e.X, 0] e
303 addEdgeToQueue m'.Elements
304 m.Elements.UnionWith(m'.Elements)
305 let intensityMax = if op = AreaOperation.Opening then queue.Max else queue.Min
306 if intensityMax <> intensity
307 then
308 intensity <- intensityMax
309 nextElements.Clear()
310 merged <- true
311
312 if not merged
313 then
314 m.State <- AreaState.Validated
315 m.Intensity <- Some (intensity)
316 stop <- true
317
318 if not stop && not merged
319 then
320 for i, j in se do
321 let ni = i + p.Y
322 let nj = j + p.X
323 let p' = Point(nj, ni)
324 if ni < 0 || ni >= h || nj < 0 || nj >= w
325 then
326 m.State <- AreaState.Validated
327 m.Intensity <- Some (intensity)
328 stop <- true
329 elif not (m.Elements.Contains(p')) && not (nextElements.Contains(p'))
330 then
331 queue.Add (imgData.[ni, nj, 0]) p'
332
333 if queue.IsEmpty
334 then
335 if m.Elements.Count + nextElements.Count <= area
336 then
337 m.State <- AreaState.Validated
338 m.Intensity <- Some intensity'
339 m.Elements.UnionWith(nextElements)
340 stop <- true
341
342 for m in areas do
343 if m.State = AreaState.Validated
344 then
345 match m.Intensity with
346 | Some i ->
347 for p in m.Elements do
348 imgData.[p.Y, p.X, 0] <- i
349 | _ -> ()
350 ()
351
352
353 let areaOpen (img: Image<Gray, byte>) (area: int) =
354 areaOperation img area AreaOperation.Opening
355
356 let areaClose (img: Image<Gray, byte>) (area: int) =
357 areaOperation img area AreaOperation.Closing
358
359 let areaOpen2 (img: Image<Gray, byte>) (area: int) =
360 let w = img.Width
361 let h = img.Height
362 let imgData = img.Data
363 let se = [| -1, 0; 0, -1; 1, 0; 0, 1 |]
364
365 let histogram = Array.zeroCreate 256
366 for i in 0 .. h - 1 do
367 for j in 0 .. w - 1 do
368 let v = imgData.[i, j, 0] |> int
369 histogram.[v] <- histogram.[v] + 1
370
371 let flooded : bool[,] = Array2D.zeroCreate h w
372
373 let pointsChecked = HashSet<Point>()
374 let pointsToCheck = Stack<Point>()
375
376 for level in 255 .. -1 .. 0 do
377 let mutable n = histogram.[level]
378 if n > 0
379 then
380 for i in 0 .. h - 1 do
381 for j in 0 .. w - 1 do
382 if not flooded.[i, j] && imgData.[i, j, 0] = byte level
383 then
384 let mutable maxNeighborValue = 0uy
385 pointsChecked.Clear()
386 pointsToCheck.Clear()
387 pointsToCheck.Push(Point(j, i))
388
389 while pointsToCheck.Count > 0 do
390 let next = pointsToCheck.Pop()
391 pointsChecked.Add(next) |> ignore
392 flooded.[next.Y, next.X] <- true
393
394 for nx, ny in se do
395 let p = Point(next.X + nx, next.Y + ny)
396 if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h
397 then
398 let v = imgData.[p.Y, p.X, 0]
399 if v = byte level
400 then
401 if not (pointsChecked.Contains(p))
402 then
403 pointsToCheck.Push(p)
404 elif v > maxNeighborValue
405 then
406 maxNeighborValue <- v
407
408 if int maxNeighborValue < level && pointsChecked.Count <= area
409 then
410 for p in pointsChecked do
411 imgData.[p.Y, p.X, 0] <- maxNeighborValue
412
413
414 // Zhang and Suen algorithm.
415 // Modify 'mat' in place.
416 let thin (mat: Matrix<byte>) =
417 let w = mat.Width
418 let h = mat.Height
419 let mutable data1 = mat.Data
420 let mutable data2 = Array2D.copy data1
421
422 let mutable pixelChanged = true
423 let mutable oddIteration = true
424
425 while pixelChanged do
426 pixelChanged <- false
427 for i in 0..h-1 do
428 for j in 0..w-1 do
429 if data1.[i, j] = 1uy
430 then
431 let p2 = if i = 0 then 0uy else data1.[i-1, j]
432 let p3 = if i = 0 || j = w-1 then 0uy else data1.[i-1, j+1]
433 let p4 = if j = w-1 then 0uy else data1.[i, j+1]
434 let p5 = if i = h-1 || j = w-1 then 0uy else data1.[i+1, j+1]
435 let p6 = if i = h-1 then 0uy else data1.[i+1, j]
436 let p7 = if i = h-1 || j = 0 then 0uy else data1.[i+1, j-1]
437 let p8 = if j = 0 then 0uy else data1.[i, j-1]
438 let p9 = if i = 0 || j = 0 then 0uy else data1.[i-1, j-1]
439
440 let sumNeighbors = p2 + p3 + p4 + p5 + p6 + p7 + p8 + p9
441 if sumNeighbors >= 2uy && sumNeighbors <= 6uy &&
442 (if p2 = 0uy && p3 = 1uy then 1 else 0) +
443 (if p3 = 0uy && p4 = 1uy then 1 else 0) +
444 (if p4 = 0uy && p5 = 1uy then 1 else 0) +
445 (if p5 = 0uy && p6 = 1uy then 1 else 0) +
446 (if p6 = 0uy && p7 = 1uy then 1 else 0) +
447 (if p7 = 0uy && p8 = 1uy then 1 else 0) +
448 (if p8 = 0uy && p9 = 1uy then 1 else 0) +
449 (if p9 = 0uy && p2 = 1uy then 1 else 0) = 1 &&
450 if oddIteration
451 then p2 * p4 * p6 = 0uy && p4 * p6 * p8 = 0uy
452 else p2 * p4 * p8 = 0uy && p2 * p6 * p8 = 0uy
453 then
454 data2.[i, j] <- 0uy
455 pixelChanged <- true
456 else
457 data2.[i, j] <- 0uy
458
459 oddIteration <- not oddIteration
460 let tmp = data1
461 data1 <- data2
462 data2 <- tmp
463
464
465 // FIXME: replace by a queue or stack.
466 let pop (l: List<'a>) : 'a =
467 let n = l.[l.Count - 1]
468 l.RemoveAt(l.Count - 1)
469 n
470
471 // Remove all 8-connected pixels with an area equal or greater than 'areaSize'.
472 // Modify 'mat' in place.
473 let removeArea (mat: Matrix<byte>) (areaSize: int) =
474 let neighbors = [|
475 (-1, 0) // p2
476 (-1, 1) // p3
477 ( 0, 1) // p4
478 ( 1, 1) // p5
479 ( 1, 0) // p6
480 ( 1, -1) // p7
481 ( 0, -1) // p8
482 (-1, -1) |] // p9
483
484 let mat' = new Matrix<byte>(mat.Size)
485 let w = mat'.Width
486 let h = mat'.Height
487 mat.CopyTo(mat')
488
489 let data = mat.Data
490 let data' = mat'.Data
491
492 for i in 0..h-1 do
493 for j in 0..w-1 do
494 if data'.[i, j] = 1uy
495 then
496 let neighborhood = List<(int*int)>()
497 let neighborsToCheck = List<(int*int)>()
498 neighborsToCheck.Add((i, j))
499 data'.[i, j] <- 0uy
500
501 while neighborsToCheck.Count > 0 do
502 let (ci, cj) = pop neighborsToCheck
503 neighborhood.Add((ci, cj))
504 for (ni, nj) in neighbors do
505 let pi = ci + ni
506 let pj = cj + nj
507 if pi >= 0 && pi < h && pj >= 0 && pj < w && data'.[pi, pj] = 1uy
508 then
509 neighborsToCheck.Add((pi, pj))
510 data'.[pi, pj] <- 0uy
511 if neighborhood.Count <= areaSize
512 then
513 for (ni, nj) in neighborhood do
514 data.[ni, nj] <- 0uy
515
516 let connectedComponents (img: Image<Gray, byte>) (startPoints: List<Point>) : List<Point> =
517 let w = img.Width
518 let h = img.Height
519
520 let pointChecked = Points()
521 let pointToCheck = List<Point>(startPoints);
522
523 let data = img.Data
524
525 while pointToCheck.Count > 0 do
526 let next = pop pointToCheck
527 pointChecked.Add(next) |> ignore
528 for ny in -1 .. 1 do
529 for nx in -1 .. 1 do
530 if ny <> 0 && nx <> 0
531 then
532 let p = Point(next.X + nx, next.Y + ny)
533 if p.X >= 0 && p.X < w && p.Y >= 0 && p.Y < h && data.[p.Y, p.X, 0] > 0uy && not (pointChecked.Contains p)
534 then
535 pointToCheck.Add(p)
536
537 List<Point>(pointChecked)
538
539
540 let saveImg (img: Image<'TColor, 'TDepth>) (filepath: string) =
541 img.Save(filepath)
542
543
544 let saveMat (mat: Matrix<'TDepth>) (filepath: string) =
545 use img = new Image<Gray, 'TDeph>(mat.Size)
546 mat.CopyTo(img)
547 saveImg img filepath
548
549 let drawLine (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: int) (y0: int) (x1: int) (y1: int) (thickness: int) =
550 img.Draw(LineSegment2D(Point(x0, y0), Point(x1, y1)), color, thickness);
551
552 let drawLineF (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: float) (y0: float) (x1: float) (y1: float) (thickness: int) =
553 img.Draw(LineSegment2DF(PointF(float32 x0, float32 y0), PointF(float32 x1, float32 y1)), color, thickness, CvEnum.LineType.AntiAlias);
554
555 let drawEllipse (img: Image<'TColor, 'TDepth>) (e: Types.Ellipse) (color: 'TColor) (alpha: float) =
556
557 if alpha >= 1.0
558 then
559 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)
560 else
561 let windowPosX = e.Cx - e.A - 5.0
562 let gapX = windowPosX - (float (int windowPosX))
563
564 let windowPosY = e.Cy - e.A - 5.0
565 let gapY = windowPosY - (float (int windowPosY))
566
567 let roi = Rectangle(int windowPosX, int windowPosY, 2. * (e.A + 5.0) |> int, 2.* (e.A + 5.0) |> int)
568
569 img.ROI <- roi
570 if roi = img.ROI // We do not display ellipses touching the edges (FIXME)
571 then
572 use i = new Image<'TColor, 'TDepth>(img.ROI.Size)
573 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)
574 CvInvoke.AddWeighted(img, 1.0, i, alpha, 0.0, img)
575 img.ROI <- Rectangle.Empty
576
577
578 let drawEllipses (img: Image<'TColor, 'TDepth>) (ellipses: Types.Ellipse list) (color: 'TColor) (alpha: float) =
579 List.iter (fun e -> drawEllipse img e color alpha) ellipses
580
581
582 let rngCell = System.Random()
583 let drawCell (img: Image<Bgr, byte>) (drawCellContent: bool) (c: Types.Cell) =
584 if drawCellContent
585 then
586 let colorB = rngCell.Next(20, 70)
587 let colorG = rngCell.Next(20, 70)
588 let colorR = rngCell.Next(20, 70)
589
590 for y in 0 .. c.elements.Height - 1 do
591 for x in 0 .. c.elements.Width - 1 do
592 if c.elements.[y, x] > 0uy
593 then
594 let dx, dy = c.center.X - c.elements.Width / 2, c.center.Y - c.elements.Height / 2
595 let b = img.Data.[y + dy, x + dx, 0] |> int
596 let g = img.Data.[y + dy, x + dx, 1] |> int
597 let r = img.Data.[y + dy, x + dx, 2] |> int
598 img.Data.[y + dy, x + dx, 0] <- if b + colorB > 255 then 255uy else byte (b + colorB)
599 img.Data.[y + dy, x + dx, 1] <- if g + colorG > 255 then 255uy else byte (g + colorG)
600 img.Data.[y + dy, x + dx, 2] <- if r + colorR > 255 then 255uy else byte (r + colorR)
601
602 let crossColor, crossColor2 =
603 match c.cellClass with
604 | Types.HealthyRBC -> Bgr(255., 0., 0.), Bgr(255., 255., 255.)
605 | Types.InfectedRBC -> Bgr(0., 0., 255.), Bgr(120., 120., 255.)
606 | Types.Peculiar -> Bgr(0., 0., 0.), Bgr(80., 80., 80.)
607
608 drawLine img crossColor2 (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 2
609 drawLine img crossColor2 c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 2
610
611 drawLine img crossColor (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 1
612 drawLine img crossColor c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 1
613
614
615 let drawCells (img: Image<Bgr, byte>) (drawCellContent: bool) (cells: Types.Cell list) =
616 List.iter (fun c -> drawCell img drawCellContent c) cells