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: 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         // 2) Remove ellipses touching the edges.
 101         for e in ellipses do
 102             if e.isOutside w_f h_f then e.Removed <- true
 103
 104         // 3) Remove ellipses with a high standard deviation (high contrast).
 105         let imgData = img.Data
 106         let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation(seq {
 107             for y in 0 .. h - 1 do
 108                 for x in 0 .. w - 1 do
 109                     yield float imgData.[y, x, 0] })
 110
 111         for e in ellipses do
 112             if not e.Removed
 113             then
 114                 let shrinkedE = e.Scale 0.9f
 115                 let minX, minY, maxX, maxY = ellipseWindow shrinkedE
 116
 117                 let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
 118                     for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 119                         for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 120                             if shrinkedE.Contains (float32 x) (float32 y)
 121                             then
 122                                 yield float imgData.[y, x, 0] })
 123
 124                 if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
 125                     e.Removed <- true
 126
 127
 128         // 4) Remove ellipses with little area.
 129         let minArea = config.RBCRadius.MinArea
 130         for e, neighbors in ellipsesWithNeigbors do
 131             if not e.Removed
 132             then
 133                 let minX, minY, maxX, maxY = ellipseWindow e
 134
 135                 let mutable area = 0
 136                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 137                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 138                         let p = PointD(float32 x, float32 y)
 139                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 140                         then
 141                             area <- area + 1
 142
 143                 if area < int minArea
 144                 then
 145                     e.Removed <- true
 146
 147         // 5) Define pixels associated to each ellipse and create the cells.
 148         ellipsesWithNeigbors
 149         |> List.choose (fun (e, neighbors) ->
 150             if e.Removed
 151             then
 152                 None
 153             else
 154                 let minX, minY, maxX, maxY = ellipseWindow e
 155
 156                 let infectedPixels = List<Point>()
 157                 let mutable stainPixels = 0
 158                 let mutable darkStainPixels = 0
 159                 let mutable nbElement = 0
 160
 161                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
 162                 for y in minY .. maxY do
 163                     for x in minX .. maxX do
 164                         let p = PointD(float32 x, float32 y)
 165                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 166                         then
 167                             elements.[y-minY, x-minX] <- 1uy
 168                             nbElement <- nbElement + 1
 169
 170                             if infection.Data.[y, x, 0] > 0uy
 171                             then
 172                                 infectedPixels.Add(Point(x, y))
 173
 174                             if parasites.stain.Data.[y, x, 0] > 0uy
 175                             then
 176                                 stainPixels <- stainPixels + 1
 177
 178                             if parasites.darkStain.Data.[y, x, 0] > 0uy
 179                             then
 180                                 darkStainPixels <- darkStainPixels + 1
 181
 182                 let cellClass =
 183                     if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) ||
 184                        float stainPixels > config.Parameters.maxStainRatio * (float nbElement)
 185                     then
 186                         Peculiar
 187                     elif infectedPixels.Count >= 1
 188                     then
 189                         let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
 190                         for p in infectionToRemove do
 191                             infection.Data.[p.Y, p.X, 0] <- 0uy
 192                         InfectedRBC
 193                     else
 194                         HealthyRBC
 195
 196                 Some { cellClass = cellClass
 197                        center = Point(roundInt e.Cx, roundInt e.Cy)
 198                        infectedArea = infectedPixels.Count
 199                        stainArea = stainPixels
 200                        elements = elements })