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 + 0.5)
  41             cx - a, cy - a, cx + a, cy + a
  42
  43         let w = img.Width
  44         let w_f = float w
  45         let h = img.Height
  46         let h_f = float 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                         match EEOver.EEOverlapArea e otherE with
  83                         | Some (_, px, _) when px.Length > 2 ->
  84                             otherE.Removed <- true
  85                             None
  86                         | Some (area, px, py) when area > 0.0 && px.Length = 2 ->
  87                             Some (otherE, PointD(px.[0], py.[0]), PointD(px.[1], py.[1]))
  88                         | _ ->
  89                             None )
  90             else
  91                 []
  92
  93         // We reverse the list to get the lower score ellipses first.
  94         let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) |> List.rev
  95
  96         // 2) Remove ellipses with a high standard deviation (high contrast).
  97
  98         // CvInvoke.Normalize(img, img, 0.0, 255.0, CvEnum.NormType.MinMax) // Not needed.
  99
 100         let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation(seq {
 101             for y in 0 .. h - 1 do
 102                 for x in 0 .. w - 1 do
 103                     yield float img.Data.[y, x, 0] })
 104
 105         for e in ellipses do
 106             let minX, minY, maxX, maxY = ellipseWindow e
 107
 108             let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
 109                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 110                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 111                         if e.Contains (float x) (float y)
 112                         then
 113                             yield float img.Data.[y, x, 0] })
 114
 115             if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
 116                 e.Removed <- true
 117
 118         // 3) Remove ellipses touching the edges.
 119         for e in ellipses do
 120             if e.isOutside w_f h_f then e.Removed <- true
 121
 122         // 4) Remove ellipses with little area.
 123         let minArea = config.RBCMinArea
 124         for e, neighbors in ellipsesWithNeigbors do
 125             if not e.Removed
 126             then
 127                 let minX, minY, maxX, maxY = ellipseWindow e
 128
 129                 let mutable area = 0
 130                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 131                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 132                         let p = PointD(float x, float y)
 133                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 134                         then
 135                             area <- area + 1
 136
 137                 if area < int minArea
 138                 then
 139                     e.Removed <- true
 140
 141         // 5) Define pixels associated to each ellipse and create the cells.
 142         ellipsesWithNeigbors
 143         |> List.choose (fun (e, neighbors) ->
 144             if e.Removed
 145             then
 146                 None
 147             else
 148                 let minX, minY, maxX, maxY = ellipseWindow e
 149
 150                 let infectedPixels = List<Point>()
 151                 let mutable stainPixels = 0
 152                 let mutable darkStainPixels = 0
 153                 let mutable nbElement = 0
 154
 155                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
 156                 for y in minY .. maxY do
 157                     for x in minX .. maxX do
 158                         let p = PointD(float x, float y)
 159                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 160                         then
 161                             elements.[y-minY, x-minX] <- 1uy
 162                             nbElement <- nbElement + 1
 163
 164                             if infection.Data.[y, x, 0] > 0uy
 165                             then
 166                                 infectedPixels.Add(Point(x, y))
 167
 168                             if parasites.stain.Data.[y, x, 0] > 0uy
 169                             then
 170                                 stainPixels <- stainPixels + 1
 171
 172                             if parasites.darkStain.Data.[y, x, 0] > 0uy
 173                             then
 174                                 darkStainPixels <- darkStainPixels + 1
 175
 176                 let cellClass =
 177                     if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) ||
 178                        float stainPixels > config.Parameters.maxStainRatio * (float nbElement) (* ||
 179                         sqrt (((float sumCoords_x) / (float nbElement) - e.Cx) ** 2.0 + ((float sumCoords_y) / (float nbElement) - e.Cy) ** 2.0) > e.A * config.maxOffcenter *)
 180                     then
 181                         Peculiar
 182                     elif infectedPixels.Count >= 1
 183                     then
 184                         let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
 185                         for p in infectionToRemove do
 186                             infection.Data.[p.Y, p.X, 0] <- 0uy
 187                         InfectedRBC
 188                     else
 189                         HealthyRBC
 190
 191                 Some { cellClass = cellClass
 192                        center = Point(roundInt e.Cx, roundInt e.Cy)
 193                        elements = elements })