Parasitemia/ParasitemiaCore/Classifier.fs

   1 module ParasitemiaCore.Classifier
   2
   3 open System
   4 open System.Collections.Generic
   5 open System.Drawing
   6
   7 open Emgu.CV
   8 open Emgu.CV.Structure
   9
  10 open Types
  11 open Utils
  12
  13 type CellState = RBC = 1 | Removed = 2 | Peculiar = 3
  14
  15 type private EllipseFlaggedKd (e: Ellipse) =
  16     inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha)
  17
  18     member val State = CellState.RBC with get, set
  19
  20     interface KdTree.I2DCoords with
  21         member this.X = this.Cx
  22         member this.Y = this.Cy
  23
  24 let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (width: int) (height: int) (config: Config.Config) : Cell list =
  25     if ellipses.IsEmpty
  26     then
  27         []
  28     else
  29         // This is the minimum window size to check if other ellipses touch 'e'.
  30         let searchRegion (e: Ellipse) = { KdTree.minX = e.Cx - (e.A + config.RBCRadius.Max)
  31                                           KdTree.maxX = e.Cx + (e.A + config.RBCRadius.Max)
  32                                           KdTree.minY = e.Cy - (e.A + config.RBCRadius.Max)
  33                                           KdTree.maxY = e.Cy + (e.A + config.RBCRadius.Max) }
  34
  35         // The minimum window to contain a given ellipse.
  36         let ellipseWindow (e: Ellipse) =
  37             let cx, cy = roundInt e.Cx, roundInt e.Cy
  38             let a = int (e.A + 0.5f)
  39             cx - a, cy - a, cx + a, cy + a
  40
  41         // Return 'true' if the point 'p' is owned by e.
  42         // The lines represents all intersections with other ellipses.
  43         let pixelOwnedByE (p: PointF) (e: EllipseFlaggedKd) (neighbors: (EllipseFlaggedKd * PointF * PointF) list) =
  44             e.Contains p.X p.Y &&
  45             seq {
  46                 let c = PointF(e.Cx, e.Cy)
  47
  48                 for e', d1 in neighbors
  49                               |> List.choose (fun (otherE, p1, p2) ->
  50                                                 if otherE.State = CellState.Removed
  51                                                 then None
  52                                                 else Some (otherE, Utils.lineFromTwoPoints p1 p2)) do
  53                     if e'.State = e.State // Peculiar vs peculiar or RBC vs RBC.
  54                     then
  55                         let d2 = lineFromTwoPoints c p
  56                         let c' = PointF(e'.Cx, e'.Cy)
  57                         let v = pointFromTwoLines d1 (lineFromTwoPoints c c')
  58                         let case1 = sign (v.X - c.X) <> sign (v.X - c'.X) || Utils.squaredDistanceTwoPoints v c > Utils.squaredDistanceTwoPoints v c'
  59                         if not (Single.IsInfinity d2.A)
  60                         then
  61                             let p' = Utils.pointFromTwoLines d1 d2
  62                             let delta, delta' =
  63                                 let dx1, dx2 = (c.X - p.X), (c.X - p'.X)
  64                                 // To avoid rounding issue.
  65                                 if abs dx1 < 0.01f || abs dx2 < 0.01f then c.Y - p.Y, c.Y - p'.Y else dx1, dx2
  66
  67                             // Yield 'false' when the point is owned by another ellipse.
  68                             if case1
  69                             then
  70                                 yield sign delta <> sign delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p
  71                             else
  72                                 yield sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p
  73                         else
  74                             yield case1
  75
  76                     elif e.State = CellState.Peculiar // A peculiar always win against a RBC.
  77                     then
  78                         yield true
  79                     else
  80                         yield not <| e'.Contains p.X p.Y
  81
  82             } |> Seq.forall id
  83
  84         let ellipses = ellipses |> List.map EllipseFlaggedKd
  85
  86         // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections.
  87         let tree = KdTree.Tree.BuildTree ellipses
  88         let neighbors (e: EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list =
  89             if e.State <> CellState.Removed
  90             then
  91                 tree.Search (searchRegion e)
  92                     // We only keep the ellipses touching 'e'.
  93                     |> List.choose (fun otherE ->
  94                         if e <> otherE
  95                         then
  96                             match EEOver.EEOverlapArea e otherE with
  97                             | Some (_, px, _) when px.Length > 2 ->
  98                                 otherE.State <- CellState.Removed
  99                                 None
 100                             | Some (area, px, py) when area > 0.f && px.Length = 2 ->
 101                                 Some (otherE, PointF(px.[0], py.[0]), PointF(px.[1], py.[1]))
 102                             | _ ->
 103                                 None
 104                         else
 105                             None)
 106             else
 107                 []
 108
 109         let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e)
 110
 111         // 2) Remove ellipses touching the edges.
 112         let widthF, heightF = float32 width, float32 height
 113         for e in ellipses do
 114             if e.isOutside widthF heightF then e.State <- CellState.Removed
 115
 116         // 3) Remove ellipses with a high standard deviation (high contrast).
 117         // Obsolete. It was useful when the ellipses result quality wasn't good.
 118         (* let imgData = img.Data
 119         let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation(seq {
 120             for y in 0 .. h - 1 do
 121                 for x in 0 .. w - 1 do
 122                     yield float imgData.[y, x, 0] })
 123
 124         for e in ellipses do
 125             if not e.Removed
 126             then
 127                 let shrinkedE = e.Scale 0.9f
 128                 let minX, minY, maxX, maxY = ellipseWindow shrinkedE
 129
 130                 let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
 131                     for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 132                         for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 133                             if shrinkedE.Contains (float32 x) (float32 y)
 134                             then
 135                                 yield float imgData.[y, x, 0] })
 136
 137                 if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
 138                     e.Removed <- true *)
 139
 140         // 4) Remove ellipses with little area.
 141         let minArea = config.RBCRadius.MinArea
 142         for e, neighbors in ellipsesWithNeigbors do
 143             if e.State <> CellState.Removed
 144             then
 145                 let minX, minY, maxX, maxY = ellipseWindow e
 146
 147                 let mutable area = 0
 148                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= height then height - 1 else maxY) do
 149                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= width then width - 1 else maxX) do
 150                         let p = PointF(float32 x, float32 y)
 151                         if pixelOwnedByE p e neighbors
 152                         then
 153                             area <- area + 1
 154
 155                 if area < int minArea
 156                 then
 157                     e.State <- CellState.Removed
 158
 159         // 5) Define non-rbc (peculiar) cells.
 160         let darkStainData = parasites.darkStain.Data
 161         ellipsesWithNeigbors
 162         |> List.choose (fun (e, neighbors) ->
 163             if e.State = CellState.Removed
 164             then
 165                 None
 166             else
 167                 let mutable darkStainPixels = 0
 168                 let mutable nbElement = 0
 169                 let minX, minY, maxX, maxY = ellipseWindow e
 170                 for y in minY .. maxY do
 171                     for x in minX .. maxX do
 172                         let p = PointF(float32 x, float32 y)
 173                         if pixelOwnedByE p e neighbors
 174                         then
 175                             nbElement <- nbElement + 1
 176                             if darkStainData.[y, x, 0] > 0uy
 177                             then
 178                                 darkStainPixels <- darkStainPixels + 1
 179
 180                 if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) then Some e else None)
 181
 182         // We do not change the state during the process to avoid to have peculiar neighbors which change the behavior of 'pixelOwnedByE'.
 183         |> List.iter (fun e -> e.State <- CellState.Peculiar)
 184
 185         // 5) Define pixels associated to each ellipse and create the cells.
 186         let diameterParasiteSquared = (2.f * config.RBCRadius.ParasiteRadius) ** 2.f |> roundInt
 187         let minimumParasiteArea = config.RBCRadius.MinimumParasiteArea |> roundInt
 188
 189         let nucleusData = parasites.nucleus.Copy().Data // Will be modified thus the copy.
 190         let parasiteData = parasites.parasite.Data
 191         let darkStainData = parasites.darkStain.Data
 192
 193         ellipsesWithNeigbors
 194         |> List.choose (fun (e, neighbors) ->
 195             if e.State = CellState.Removed
 196             then
 197                 None
 198             else
 199                 let minX, minY, maxX, maxY = ellipseWindow e
 200
 201                 let nucleusPixels = List<Point>()
 202                 let parasitePixels = List<Point>()
 203
 204                 let mutable nbElement = 0
 205
 206                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
 207                 for y in minY .. maxY do
 208                     for x in minX .. maxX do
 209                         let p = PointF(float32 x, float32 y)
 210                         if pixelOwnedByE p e neighbors
 211                         then
 212                             elements.[y - minY, x - minX] <- 1uy
 213                             nbElement <- nbElement + 1
 214
 215                             if nucleusData.[y, x, 0] > 0uy
 216                             then
 217                                 nucleusPixels.Add(Point(x, y))
 218
 219                             if parasiteData.[y, x, 0] > 0uy
 220                             then
 221                                 parasitePixels.Add(Point(x, y))
 222
 223                 let parasiteArea =
 224                     if nucleusPixels.Count > 0
 225                     then
 226                         seq {
 227                             for parasitePixel in parasitePixels do
 228                                 if nucleusPixels.Exists(fun p -> pown (p.X - parasitePixel.X) 2 + pown (p.Y - parasitePixel.Y) 2 <= diameterParasiteSquared)
 229                                 then yield 1 } |> Seq.sum
 230                     else
 231                         0
 232
 233                 let cellClass =
 234                     if e.State = CellState.Peculiar
 235                     then
 236                         Peculiar
 237
 238                     elif nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea
 239                     then
 240                         let infectionToRemove = Morpho.connectedComponents parasites.parasite nucleusPixels
 241                         for p in infectionToRemove do
 242                             nucleusData.[p.Y, p.X, 0] <- 0uy
 243                         InfectedRBC
 244
 245                     else
 246                         HealthyRBC
 247
 248                 Some { cellClass = cellClass
 249                        center = Point(roundInt e.Cx, roundInt e.Cy)
 250                        nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0
 251                        parasiteArea = parasiteArea
 252                        elements = elements })