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
  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.RBCRadius.Max)
  33                                           KdTree.maxX = e.Cx + (e.A + config.RBCRadius.Max)
  34                                           KdTree.minY = e.Cy - (e.A + config.RBCRadius.Max)
  35                                           KdTree.maxY = e.Cy + (e.A + config.RBCRadius.Max) }
  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: PointF) (e: Ellipse) (others: (Ellipse * Line) list) =
  51             e.Contains p.X p.Y &&
  52             seq {
  53                 let c = PointF(e.Cx, e.Cy)
  54
  55                 for e', d1 in others do
  56                     let d2 = lineFromTwoPoints c p
  57                     let c' = PointF(e'.Cx, e'.Cy)
  58                     let v = pointFromTwoLines d1 (lineFromTwoPoints c c')
  59                     let case1 = sign (v.X - c.X) <> sign (v.X - c'.X) || Utils.squaredDistanceTwoPoints v c > Utils.squaredDistanceTwoPoints v c'
  60                     if d2.Valid
  61                     then
  62                         let p' = Utils.pointFromTwoLines d1 d2
  63                         let delta, delta' =
  64                             let d = c.X - p.X
  65                             // To avoid rounding.
  66                             if abs d < 0.001f then c.Y - p.Y, c.Y - p'.Y else d, c.X - p'.X
  67
  68                         // Yield 'false' when the point is owned by another ellipse.
  69                         if case1
  70                         then
  71                             yield sign delta <> sign delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p
  72                         else
  73                             yield sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p
  74                     else
  75                         yield case1
  76             } |> Seq.forall id
  77
  78         let ellipses = ellipses |> List.map EllipseFlaggedKd
  79
  80         // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections.
  81         let tree = KdTree.Tree.BuildTree ellipses
  82         let neighbors (e: EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list =
  83             if not e.Removed
  84             then
  85                 tree.Search (searchRegion e)
  86                     // We only keep the ellipses touching 'e'.
  87                     |> List.choose (fun otherE ->
  88                         if e <> otherE
  89                         then
  90                             match EEOver.EEOverlapArea e otherE with
  91                             | Some (_, px, _) when px.Length > 2 ->
  92                                 otherE.Removed <- true
  93                                 None
  94                             | Some (area, px, py) when area > 0.f && px.Length = 2 ->
  95                                 Some (otherE, PointF(px.[0], py.[0]), PointF(px.[1], py.[1]))
  96                             | _ ->
  97                                 None
  98                         else
  99                             None )
 100             else
 101                 []
 102
 103         // We reverse the list to get the lower score ellipses first.
 104         let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) |> List.rev
 105
 106         // 2) Remove ellipses touching the edges.
 107         for e in ellipses do
 108             if e.isOutside w_f h_f then e.Removed <- true
 109
 110         // 3) Remove ellipses with a high standard deviation (high contrast).
 111         let imgData = img.Data
 112         let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation(seq {
 113             for y in 0 .. h - 1 do
 114                 for x in 0 .. w - 1 do
 115                     yield float imgData.[y, x, 0] })
 116
 117         for e in ellipses do
 118             if not e.Removed
 119             then
 120                 let shrinkedE = e.Scale 0.9f
 121                 let minX, minY, maxX, maxY = ellipseWindow shrinkedE
 122
 123                 let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
 124                     for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 125                         for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 126                             if shrinkedE.Contains (float32 x) (float32 y)
 127                             then
 128                                 yield float imgData.[y, x, 0] })
 129
 130                 if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
 131                     e.Removed <- true
 132
 133
 134         // 4) Remove ellipses with little area.
 135         let minArea = config.RBCRadius.MinArea
 136         for e, neighbors in ellipsesWithNeigbors do
 137             if not e.Removed
 138             then
 139                 let minX, minY, maxX, maxY = ellipseWindow e
 140
 141                 let mutable area = 0
 142                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 143                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 144                         let p = PointF(float32 x, float32 y)
 145                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 146                         then
 147                             area <- area + 1
 148
 149                 if area < int minArea
 150                 then
 151                     e.Removed <- true
 152
 153         // 5) Define pixels associated to each ellipse and create the cells.
 154         ellipsesWithNeigbors
 155         |> List.choose (fun (e, neighbors) ->
 156             if e.Removed
 157             then
 158                 None
 159             else
 160                 let minX, minY, maxX, maxY = ellipseWindow e
 161
 162                 let infectedPixels = List<Point>()
 163                 let mutable stainPixels = 0
 164                 let mutable darkStainPixels = 0
 165                 let mutable nbElement = 0
 166
 167                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
 168                 for y in minY .. maxY do
 169                     for x in minX .. maxX do
 170                         let p = PointF(float32 x, float32 y)
 171                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 172                         then
 173                             elements.[y-minY, x-minX] <- 1uy
 174                             nbElement <- nbElement + 1
 175
 176                             if infection.Data.[y, x, 0] > 0uy
 177                             then
 178                                 infectedPixels.Add(Point(x, y))
 179
 180                             if parasites.stain.Data.[y, x, 0] > 0uy
 181                             then
 182                                 stainPixels <- stainPixels + 1
 183
 184                             if parasites.darkStain.Data.[y, x, 0] > 0uy
 185                             then
 186                                 darkStainPixels <- darkStainPixels + 1
 187
 188                 let cellClass =
 189                     if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) ||
 190                        float stainPixels > config.Parameters.maxStainRatio * (float nbElement)
 191                     then
 192                         Peculiar
 193                     elif infectedPixels.Count >= 1
 194                     then
 195                         let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
 196                         for p in infectionToRemove do
 197                             infection.Data.[p.Y, p.X, 0] <- 0uy
 198                         InfectedRBC
 199                     else
 200                         HealthyRBC
 201
 202                 Some { cellClass = cellClass
 203                        center = Point(roundInt e.Cx, roundInt e.Cy)
 204                        infectedArea = infectedPixels.Count
 205                        stainArea = stainPixels
 206                        elements = elements })