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 private EllipseFlaggedKd (e: Ellipse) =
  14     inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha)
  15
  16     member val Removed = false with get, set
  17
  18     interface KdTree.I2DCoords with
  19         member this.X = this.Cx
  20         member this.Y = this.Cy
  21
  22 let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: Image<Gray, float32>) (config: Config.Config) : Cell list =
  23     if ellipses.IsEmpty
  24     then
  25         []
  26     else
  27         let infection = parasites.infection.Copy() // To avoid to modify the parameter.
  28
  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         let w = img.Width
  42         let w_f = float32 w
  43         let h = img.Height
  44         let h_f = float32 h
  45
  46         // Return 'true' if the point 'p' is owned by e.
  47         // The lines represents all intersections with other ellipses.
  48         let pixelOwnedByE (p: PointF) (e: Ellipse) (others: (Ellipse * Line) list) =
  49             e.Contains p.X p.Y &&
  50             seq {
  51                 let c = PointF(e.Cx, e.Cy)
  52
  53                 for e', d1 in others do
  54                     let d2 = lineFromTwoPoints c p
  55                     let c' = PointF(e'.Cx, e'.Cy)
  56                     let v = pointFromTwoLines d1 (lineFromTwoPoints c c')
  57                     let case1 = sign (v.X - c.X) <> sign (v.X - c'.X) || Utils.squaredDistanceTwoPoints v c > Utils.squaredDistanceTwoPoints v c'
  58                     if not (Single.IsInfinity d2.A)
  59                     then
  60                         let p' = Utils.pointFromTwoLines d1 d2
  61                         let delta, delta' =
  62                             let dx1, dx2 = (c.X - p.X), (c.X - p'.X)
  63                             // To avoid rounding issue.
  64                             if abs dx1 < 0.01f || abs dx2 < 0.01f then c.Y - p.Y, c.Y - p'.Y else dx1, dx2
  65
  66                         // Yield 'false' when the point is owned by another ellipse.
  67                         if case1
  68                         then
  69                             yield sign delta <> sign delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p
  70                         else
  71                             yield sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p
  72                     else
  73                         yield case1
  74             } |> Seq.forall id
  75
  76         let ellipses = ellipses |> List.map EllipseFlaggedKd
  77
  78         // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections.
  79         let tree = KdTree.Tree.BuildTree ellipses
  80         let neighbors (e: EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list =
  81             if not e.Removed
  82             then
  83                 tree.Search (searchRegion e)
  84                     // We only keep the ellipses touching 'e'.
  85                     |> List.choose (fun otherE ->
  86                         if e <> otherE
  87                         then
  88                             match EEOver.EEOverlapArea e otherE with
  89                             | Some (_, px, _) when px.Length > 2 ->
  90                                 otherE.Removed <- true
  91                                 None
  92                             | Some (area, px, py) when area > 0.f && px.Length = 2 ->
  93                                 Some (otherE, PointF(px.[0], py.[0]), PointF(px.[1], py.[1]))
  94                             | _ ->
  95                                 None
  96                         else
  97                             None )
  98             else
  99                 []
 100
 101         // We reverse the list to get the lower score ellipses first.
 102         let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) |> List.rev
 103
 104         // 2) Remove ellipses touching the edges.
 105         for e in ellipses do
 106             if e.isOutside w_f h_f then e.Removed <- true
 107
 108         // 3) Remove ellipses with a high standard deviation (high contrast).
 109         let imgData = img.Data
 110         let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation(seq {
 111             for y in 0 .. h - 1 do
 112                 for x in 0 .. w - 1 do
 113                     yield float imgData.[y, x, 0] })
 114
 115         for e in ellipses do
 116             if not e.Removed
 117             then
 118                 let shrinkedE = e.Scale 0.9f
 119                 let minX, minY, maxX, maxY = ellipseWindow shrinkedE
 120
 121                 let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
 122                     for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 123                         for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 124                             if shrinkedE.Contains (float32 x) (float32 y)
 125                             then
 126                                 yield float imgData.[y, x, 0] })
 127
 128                 if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
 129                     e.Removed <- true
 130
 131         // 4) Remove ellipses with little area.
 132         let minArea = config.RBCRadius.MinArea
 133         for e, neighbors in ellipsesWithNeigbors do
 134             if not e.Removed
 135             then
 136                 let minX, minY, maxX, maxY = ellipseWindow e
 137
 138                 let mutable area = 0
 139                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 140                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 141                         let p = PointF(float32 x, float32 y)
 142                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 143                         then
 144                             area <- area + 1
 145
 146                 if area < int minArea
 147                 then
 148                     e.Removed <- true
 149
 150         // 5) Define pixels associated to each ellipse and create the cells.
 151         let radiusParasiteRatio = 0.4f
 152         let radiusParasite = config.RBCRadius.Pixel * 0.5f
 153         let perimeterParasiteSquared = (2.f * radiusParasite) ** 2.f |> roundInt
 154         let parasiteOccupation = 0.08f // 8 %
 155         let minimumParasiteArea = Const.PI * radiusParasite ** 2.f * parasiteOccupation |> roundInt
 156         //let minimumStainArea = roundInt <| config.RBCRadius.Area * 0.02f // 1.5 %
 157         ellipsesWithNeigbors
 158         |> List.choose (fun (e, neighbors) ->
 159             if e.Removed
 160             then
 161                 None
 162             else
 163                 let minX, minY, maxX, maxY = ellipseWindow e
 164
 165                 let infectedPixels = List<Point>()
 166                 let stainPixels = List<Point>()
 167
 168                 //let mutable stainPixels = 0
 169                 let mutable darkStainPixels = 0
 170                 let mutable nbElement = 0
 171
 172                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
 173                 for y in minY .. maxY do
 174                     for x in minX .. maxX do
 175                         let p = PointF(float32 x, float32 y)
 176                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 177                         then
 178                             elements.[y-minY, x-minX] <- 1uy
 179                             nbElement <- nbElement + 1
 180
 181                             let infected = infection.Data.[y, x, 0] > 0uy
 182                             let stain = parasites.stain.Data.[y, x, 0] > 0uy
 183                             let darkStain = parasites.darkStain.Data.[y, x, 0] > 0uy
 184
 185                             if infected
 186                             then
 187                                 infectedPixels.Add(Point(x, y))
 188
 189                             if stain
 190                             then
 191                                 stainPixels.Add(Point(x, y))
 192
 193                             if darkStain
 194                             then
 195                                 darkStainPixels <- darkStainPixels + 1
 196
 197                 let mutable stainArea = 0
 198                 if infectedPixels.Count > 0
 199                 then
 200                     for stainPixel in stainPixels do
 201                         if infectedPixels.Exists(fun p -> pown (p.X - stainPixel.X) 2 + pown (p.Y - stainPixel.Y) 2 <= perimeterParasiteSquared)
 202                         then
 203                             stainArea <- stainArea + 1
 204
 205
 206                 let cellClass =
 207                     if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement)
 208                        //|| float stainPixels > config.Parameters.maxStainRatio * (float nbElement)
 209                     then
 210                         Peculiar
 211
 212                     elif infectedPixels.Count > 0 && stainArea >= minimumParasiteArea
 213                     then
 214                         let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
 215                         for p in infectionToRemove do
 216                             infection.Data.[p.Y, p.X, 0] <- 0uy
 217                         InfectedRBC
 218
 219                     else
 220                         HealthyRBC
 221
 222                 Some { cellClass = cellClass
 223                        center = Point(roundInt e.Cx, roundInt e.Cy)
 224                        infectedArea = if cellClass = InfectedRBC then infectedPixels.Count else 0
 225                        stainArea = stainArea
 226                        elements = elements })