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) (fg: 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.maxRBCSize) * config.scale
  33                                           KdTree.maxX = e.Cx + (e.A + config.maxRBCSize) * config.scale
  34                                           KdTree.minY = e.Cy - (e.A + config.maxRBCSize) * config.scale
  35                                           KdTree.maxY = e.Cy + (e.A + config.maxRBCSize) * config.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 = float fg.Width
  44         let h = float fg.Height
  45
  46         let ellipses = ellipses |> List.map EllipseFlaggedKd
  47
  48         // 1) Associate touching ellipses with each ellipses.
  49         let tree = KdTree.Tree.BuildTree ellipses
  50         let neighbors (e: Ellipse) : (EllipseFlaggedKd * PointD * PointD) list =
  51             tree.Search (searchRegion e)
  52                 // We only keep the ellipses touching 'e'.
  53                 |> List.choose (fun otherE ->
  54                     match EEOver.EEOverlapArea e otherE with
  55                     | Some (area, px, py) when area > 0.0 && px.Length >= 2 && py.Length >= 2 ->
  56                         Some (otherE, PointD(px.[0], py.[0]), PointD(px.[1], py.[1]))
  57                     | _ ->
  58                         None )
  59
  60         let ellipsesWithNeigbors = ellipses |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e))
  61
  62         // 2) Remove ellipses with a lower percentage of foreground. (taken from the lower score to the highest).
  63         for e, neighbors in List.rev ellipsesWithNeigbors do
  64             let minX, minY, maxX, maxY = ellipseWindow e
  65
  66             let mutable totalElement = 0
  67             let mutable fgElement = 0
  68             for y in (if minY < 0 then 0 else minY) .. (if maxY >= fg.Height then fg.Height - 1 else maxY) do
  69                 for x in (if minX < 0 then 0 else minX) .. (if maxX >= fg.Width then fg.Width - 1 else maxX) do
  70                     let yf, xf = float y, float x
  71                     if e.Contains xf yf && neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf)
  72                         then
  73                             totalElement <- totalElement + 1
  74                             if fg.Data.[y, x, 0] > 0uy
  75                             then
  76                                 fgElement <- fgElement + 1
  77
  78             if (float fgElement) / (float totalElement) < config.percentageOfFgValidCell
  79             then
  80                 e.Removed <- true
  81
  82         // 3) Remove ellipses touching the edges.
  83         for e in ellipses do
  84             if e.isOutside w h then e.Removed <- true
  85
  86         // 4) Remove ellipses with little area.
  87         for e, neighbors in ellipsesWithNeigbors do
  88             if not e.Removed
  89             then
  90                 let minX, minY, maxX, maxY = ellipseWindow e
  91
  92                 let mutable area = 0
  93                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= fg.Height then fg.Height - 1 else maxY) do
  94                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= fg.Width then fg.Width - 1 else maxX) do
  95                         let yf, xf = float y, float x
  96                         if fg.Data.[y, x, 0] > 0uy &&
  97                            e.Contains xf yf &&
  98                            neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf)
  99                             then
 100                                 area <- area + 1
 101
 102                 if area < config.minimumCellArea
 103                 then
 104                     e.Removed <- true
 105
 106         // 5) Define pixels associated to each ellipse and create the cells.
 107
 108         // Return 'true' if the point 'p' is owned by e.
 109         // The lines represents all intersections with other ellipses.
 110         let pixelOwnedByE (p: PointD) (e: Ellipse) (lines: Line list) =
 111             e.Contains p.X p.Y &&
 112             seq {
 113                 let c = PointD(e.Cx, e.Cy)
 114                 for d1 in lines do
 115                     let d2 = Utils.lineFromTwoPoints c p
 116                     let p' = Utils.pointFromTwoLines d1 d2
 117                     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.
 118             } |> Seq.forall id
 119
 120         ellipsesWithNeigbors
 121         |> List.choose (fun (e, neighbors) ->
 122             if e.Removed
 123             then
 124                 None
 125             else
 126                 let minX, minY, maxX, maxY = ellipseWindow e
 127
 128                 let infectedPixels = List<Point>()
 129                 let mutable stainPixels = 0
 130                 let mutable darkStainPixels = 0
 131                 let mutable nbElement = 0
 132
 133                 let mutable stain_x = 0.0
 134                 let mutable stain_x2 = 0.0
 135                 let mutable stain_y = 0.0
 136                 let mutable stain_y2 = 0.0
 137
 138                 let mutable sumCoords_y = 0
 139                 let mutable sumCoords_x = 0
 140
 141                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
 142                 for y in minY .. maxY do
 143                     for x in minX .. maxX do
 144                         let p = PointD(float x, float y)
 145                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (Utils.lineFromTwoPoints p1 p2))) &&
 146                            fg.Data.[y, x, 0] > 0uy
 147                         then
 148                             elements.[y-minY, x-minX] <- 1uy
 149                             nbElement <- nbElement + 1
 150                             sumCoords_y <- sumCoords_y + y
 151                             sumCoords_x <- sumCoords_x + x
 152
 153                             if infection.Data.[y, x, 0] > 0uy
 154                             then
 155                                 infectedPixels.Add(Point(x, y))
 156
 157                             if parasites.stain.Data.[y, x, 0] > 0uy
 158                             then
 159                                 stainPixels <- stainPixels + 1
 160                                 stain_x <- stain_x + (float x)
 161                                 stain_x2 <- stain_x2 + (float x) ** 2.0
 162                                 stain_y <- stain_y + (float y)
 163                                 stain_y2 <- stain_y2 + (float y) ** 2.0
 164
 165                             if parasites.darkStain.Data.[y, x, 0] > 0uy
 166                             then
 167                                 darkStainPixels <- darkStainPixels + 1
 168
 169                 let cellClass =
 170                     if float darkStainPixels > config.MaxDarkStainRatio * (float nbElement) (* ||
 171                         sqrt (((float sumCoords_x) / (float nbElement) - e.Cx) ** 2.0 + ((float sumCoords_y) / (float nbElement) - e.Cy) ** 2.0) > e.A * config.maxOffcenter *)
 172                     then
 173                         Peculiar
 174                     elif infectedPixels.Count > config.infectionPixelsRequired
 175                     then
 176                         let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
 177                         for p in infectionToRemove do
 178                             infection.Data.[p.Y, p.X, 0] <- 0uy
 179                         InfectedRBC
 180                     else
 181                         HealthyRBC
 182
 183                 Some { cellClass = cellClass
 184                        center = Point(roundInt e.Cx, roundInt e.Cy)
 185                        elements = elements })