Parasitemia/Parasitemia/Classifier.fs

   1 module 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
  14 type private EllipseFlaggedKd (e: Ellipse) =
  15     inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha)
  16
  17     member val Removed = false with get, set
  18
  19     interface KdTree.I2DCoords with
  20         member this.X = this.Cx
  21         member this.Y = this.Cy
  22
  23
  24 let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: Image<Gray, float32>) (config: Config.Config) : Cell list =
  25     if ellipses.IsEmpty
  26     then
  27         []
  28     else
  29         let infection = parasites.infection.Copy() // To avoid to modify the parameter.
  30
  31         // This is the minimum window size to check if other ellipses touch 'e'.
  32         let searchRegion (e: Ellipse) = { KdTree.minX = e.Cx - (e.A + config.RBCMaxRadius)
  33                                           KdTree.maxX = e.Cx + (e.A + config.RBCMaxRadius)
  34                                           KdTree.minY = e.Cy - (e.A + config.RBCMaxRadius)
  35                                           KdTree.maxY = e.Cy + (e.A + config.RBCMaxRadius) }
  36
  37         // The minimum window to contain a given ellipse.
  38         let ellipseWindow (e: Ellipse) =
  39             let cx, cy = roundInt e.Cx, roundInt e.Cy
  40             let a = int (e.A + 0.5f)
  41             cx - a, cy - a, cx + a, cy + a
  42
  43         let w = img.Width
  44         let w_f = float32 w
  45         let h = img.Height
  46         let h_f = float32 h
  47
  48         // Return 'true' if the point 'p' is owned by e.
  49         // The lines represents all intersections with other ellipses.
  50         let pixelOwnedByE (p: PointD) (e: Ellipse) (others: (Ellipse * Line) list) =
  51             e.Contains p.X p.Y &&
  52             seq {
  53                 let c = PointD(e.Cx, e.Cy)
  54                 for e', d1 in others do
  55                     let d2 = Utils.lineFromTwoPoints c p
  56                     let c' = PointD(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 d2.Valid
  60                     then
  61                         let p' = Utils.pointFromTwoLines d1 d2
  62                         // Yield 'false' when the point is owned by another ellipse.
  63                         if case1
  64                         then
  65                             yield sign (c.X - p.X) <> sign (c.X - p'.X) || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p
  66                         else
  67                             yield sign (c.X - p.X) = sign (c.X - p'.X) && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p
  68                     else
  69                         yield case1
  70             } |> Seq.forall id
  71
  72         let ellipses = ellipses |> List.map EllipseFlaggedKd
  73
  74         // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections.
  75         let tree = KdTree.Tree.BuildTree ellipses
  76         let neighbors (e: EllipseFlaggedKd) : (EllipseFlaggedKd * PointD * PointD) list =
  77             if not e.Removed
  78             then
  79                 tree.Search (searchRegion e)
  80                     // We only keep the ellipses touching 'e'.
  81                     |> List.choose (fun otherE ->
  82                         if e <> otherE
  83                         then
  84                             match EEOver.EEOverlapArea e otherE with
  85                             | Some (_, px, _) when px.Length > 2 ->
  86                                 otherE.Removed <- true
  87                                 None
  88                             | Some (area, px, py) when area > 0.f && px.Length = 2 ->
  89                                 Some (otherE, PointD(px.[0], py.[0]), PointD(px.[1], py.[1]))
  90                             | _ ->
  91                                 None
  92                         else
  93                             None )
  94             else
  95                 []
  96
  97         // We reverse the list to get the lower score ellipses first.
  98         let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) |> List.rev
  99
 100
 101         // 2) Remove ellipses touching the edges.
 102         for e in ellipses do
 103             if e.isOutside w_f h_f then e.Removed <- true
 104
 105         // 3) Remove ellipses with a high standard deviation (high contrast).
 106         let imgData = img.Data
 107         let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation(seq {
 108             for y in 0 .. h - 1 do
 109                 for x in 0 .. w - 1 do
 110                     yield float imgData.[y, x, 0] })
 111
 112         for e in ellipses do
 113             if not e.Removed
 114             then
 115                 let shrinkedE = e.Scale 0.9f
 116                 let minX, minY, maxX, maxY = ellipseWindow shrinkedE
 117
 118                 let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
 119                     for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 120                         for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 121                             if shrinkedE.Contains (float32 x) (float32 y)
 122                             then
 123                                 yield float imgData.[y, x, 0] })
 124
 125                 if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
 126                     e.Removed <- true
 127
 128 (*
 129         let imgData = img.Data
 130                 let stdDeviations = [
 131                     for e in ellipses do
 132                         if not e.Removed
 133                         then
 134                             let shrinkedE = e.Scale 0.9f
 135                             let minX, minY, maxX, maxY = ellipseWindow shrinkedE
 136
 137                             let stdDeviation = float32 <| MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
 138                                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 139                                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 140                                         if shrinkedE.Contains (float32 x) (float32 y)
 141                                         then
 142                                             yield float imgData.[y, x, 0] })
 143
 144                             e.StdDeviation <- stdDeviation
 145                             yield stdDeviation ]
 146
 147                 // We use Otsu and eliminate some cells only if the curve may be bimodal.
 148                 // See https://en.wikipedia.org/wiki/Multimodal_distribution#Bimodality_coefficient
 149                 let skewness, kurtosis = MathNet.Numerics.Statistics.Statistics.PopulationSkewnessKurtosis (stdDeviations |> List.map float)
 150                 let n = float stdDeviations.Length
 151                 let bimodalityCoefficient = (skewness ** 2. + 1.) / (kurtosis + 3. * (n - 1.) ** 2. / ((n - 2.) * (n - 3.)))
 152
 153                 if bimodalityCoefficient > 5. / 9.
 154                 then
 155                     let hist = ImgTools.histogram stdDeviations 200
 156                     let thresh, _, _ = ImgTools.otsu hist
 157                     for e in ellipses do
 158                         if not e.Removed && e.StdDeviation > thresh
 159                         then e.Removed <- true
 160 *)
 161
 162         // 4) Remove ellipses with little area.
 163         let minArea = config.RBCMinArea
 164         for e, neighbors in ellipsesWithNeigbors do
 165             if not e.Removed
 166             then
 167                 let minX, minY, maxX, maxY = ellipseWindow e
 168
 169                 let mutable area = 0
 170                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 171                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 172                         let p = PointD(float32 x, float32 y)
 173                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 174                         then
 175                             area <- area + 1
 176
 177                 if area < int minArea
 178                 then
 179                     e.Removed <- true
 180
 181         // 5) Define pixels associated to each ellipse and create the cells.
 182         ellipsesWithNeigbors
 183         |> List.choose (fun (e, neighbors) ->
 184             if e.Removed
 185             then
 186                 None
 187             else
 188                 let minX, minY, maxX, maxY = ellipseWindow e
 189
 190                 let infectedPixels = List<Point>()
 191                 let mutable stainPixels = 0
 192                 let mutable darkStainPixels = 0
 193                 let mutable nbElement = 0
 194
 195                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
 196                 for y in minY .. maxY do
 197                     for x in minX .. maxX do
 198                         let p = PointD(float32 x, float32 y)
 199                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 200                         then
 201                             elements.[y-minY, x-minX] <- 1uy
 202                             nbElement <- nbElement + 1
 203
 204                             if infection.Data.[y, x, 0] > 0uy
 205                             then
 206                                 infectedPixels.Add(Point(x, y))
 207
 208                             if parasites.stain.Data.[y, x, 0] > 0uy
 209                             then
 210                                 stainPixels <- stainPixels + 1
 211
 212                             if parasites.darkStain.Data.[y, x, 0] > 0uy
 213                             then
 214                                 darkStainPixels <- darkStainPixels + 1
 215
 216                 let cellClass =
 217                     if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) ||
 218                        float stainPixels > config.Parameters.maxStainRatio * (float nbElement)
 219                     then
 220                         Peculiar
 221                     elif infectedPixels.Count >= 1
 222                     then
 223                         let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
 224                         for p in infectionToRemove do
 225                             infection.Data.[p.Y, p.X, 0] <- 0uy
 226                         InfectedRBC
 227                     else
 228                         HealthyRBC
 229
 230                 Some { cellClass = cellClass
 231                        center = Point(roundInt e.Cx, roundInt e.Cy)
 232                        stainArea = stainPixels
 233                        elements = elements })