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, byte>) (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) * config.Parameters.scale
  33                                           KdTree.maxX = e.Cx + (e.A + config.RBCMaxRadius) * config.Parameters.scale
  34                                           KdTree.minY = e.Cy - (e.A + config.RBCMaxRadius) * config.Parameters.scale
  35                                           KdTree.maxY = e.Cy + (e.A + config.RBCMaxRadius) * config.Parameters.scale }
  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) (lines: Line list) =
  51             e.Contains p.X p.Y &&
  52             seq {
  53                 let c = PointD(e.Cx, e.Cy)
  54                 for d1 in lines do
  55                     let d2 = Utils.lineFromTwoPoints c p
  56                     if d2.Valid
  57                     then
  58                         let p' = Utils.pointFromTwoLines d1 d2
  59                         yield sign (c.X - p.X) <> sign (c.X - p'.X) || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p // 'false' -> the point is owned by another ellipse.
  60                     else
  61                         yield true
  62             } |> Seq.forall id
  63
  64         let ellipses = ellipses |> List.map EllipseFlaggedKd
  65
  66         // 1) Associate touching ellipses with each ellipses.
  67         let tree = KdTree.Tree.BuildTree ellipses
  68         let neighbors (e: Ellipse) : (EllipseFlaggedKd * PointD * PointD) list =
  69             tree.Search (searchRegion e)
  70                 // We only keep the ellipses touching 'e'.
  71                 |> List.choose (fun otherE ->
  72                     match EEOver.EEOverlapArea e otherE with
  73                     | Some (area, px, py) when area > 0.0 && px.Length >= 2 && py.Length >= 2 ->
  74                         Some (otherE, PointD(px.[0], py.[0]), PointD(px.[1], py.[1]))
  75                     | _ ->
  76                         None )
  77
  78         // We reverse the list to get the lower score ellipses first.
  79         let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) |> List.rev
  80
  81         // 2) Remove ellipses with a high standard deviation (high contrast).
  82         let globalStdDiviation = MathNet.Numerics.Statistics.StreamingStatistics.StandardDeviation(seq {
  83             for y in 0 .. h - 1 do
  84                 for x in 0 .. w - 1 do
  85                     yield img.Data.[y, x, 0] |> float })
  86
  87         for e in ellipses do
  88             let minX, minY, maxX, maxY = ellipseWindow e
  89
  90             let stdDiviation = MathNet.Numerics.Statistics.StreamingStatistics.StandardDeviation(seq {
  91                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
  92                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
  93                         if e.Contains (float x) (float y)
  94                         then
  95                             yield img.Data.[y, x, 0] |> float })
  96
  97             if stdDiviation > globalStdDiviation * config.Parameters.standardDeviationMaxRatio
  98             then
  99                 e.Removed <- true
 100
 101         // 3) 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         // 4) Remove ellipses with little area.
 106         let minArea = config.RBCMinArea
 107         for e, neighbors in ellipsesWithNeigbors do
 108             if not e.Removed
 109             then
 110                 let minX, minY, maxX, maxY = ellipseWindow e
 111
 112                 let mutable area = 0
 113                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 114                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 115                         let p = PointD(float x, float y)
 116                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (Utils.lineFromTwoPoints p1 p2)))
 117                         then
 118                             area <- area + 1
 119
 120                 if area < int minArea
 121                 then
 122                     e.Removed <- true
 123
 124         // 5) Define pixels associated to each ellipse and create the cells.
 125         ellipsesWithNeigbors
 126         |> List.choose (fun (e, neighbors) ->
 127             if e.Removed
 128             then
 129                 None
 130             else
 131                 let minX, minY, maxX, maxY = ellipseWindow e
 132
 133                 let infectedPixels = List<Point>()
 134                 let mutable stainPixels = 0
 135                 let mutable darkStainPixels = 0
 136                 let mutable nbElement = 0
 137
 138                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
 139                 for y in minY .. maxY do
 140                     for x in minX .. maxX do
 141                         let p = PointD(float x, float y)
 142                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (Utils.lineFromTwoPoints p1 p2)))
 143                         then
 144                             elements.[y-minY, x-minX] <- 1uy
 145                             nbElement <- nbElement + 1
 146
 147                             if infection.Data.[y, x, 0] > 0uy
 148                             then
 149                                 infectedPixels.Add(Point(x, y))
 150
 151                             if parasites.stain.Data.[y, x, 0] > 0uy
 152                             then
 153                                 stainPixels <- stainPixels + 1
 154
 155                             if parasites.darkStain.Data.[y, x, 0] > 0uy
 156                             then
 157                                 darkStainPixels <- darkStainPixels + 1
 158
 159                 let cellClass =
 160                     if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) ||
 161                        float stainPixels > config.Parameters.maxStainRatio * (float nbElement) (* ||
 162                         sqrt (((float sumCoords_x) / (float nbElement) - e.Cx) ** 2.0 + ((float sumCoords_y) / (float nbElement) - e.Cy) ** 2.0) > e.A * config.maxOffcenter *)
 163                     then
 164                         Peculiar
 165                     elif infectedPixels.Count >= 1
 166                     then
 167                         let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
 168                         for p in infectionToRemove do
 169                             infection.Data.[p.Y, p.X, 0] <- 0uy
 170                         InfectedRBC
 171                     else
 172                         HealthyRBC
 173
 174                 Some { cellClass = cellClass
 175                        center = Point(roundInt e.Cx, roundInt e.Cy)
 176                        elements = elements })