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 type private EllipseFlaggedKd (e: Ellipse) =
  14     inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha)
  15
  16     member val Removed = false with get, set
  17
  18     interface KdTree.I2DCoords with
  19         member this.X = this.Cx
  20         member this.Y = this.Cy
  21
  22 let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: Image<Gray, float32>) (config: Config.Config) : Cell list =
  23     if ellipses.IsEmpty
  24     then
  25         []
  26     else
  27         // This is the minimum window size to check if other ellipses touch 'e'.
  28         let searchRegion (e: Ellipse) = { KdTree.minX = e.Cx - (e.A + config.RBCRadius.Max)
  29                                           KdTree.maxX = e.Cx + (e.A + config.RBCRadius.Max)
  30                                           KdTree.minY = e.Cy - (e.A + config.RBCRadius.Max)
  31                                           KdTree.maxY = e.Cy + (e.A + config.RBCRadius.Max) }
  32
  33         // The minimum window to contain a given ellipse.
  34         let ellipseWindow (e: Ellipse) =
  35             let cx, cy = roundInt e.Cx, roundInt e.Cy
  36             let a = int (e.A + 0.5f)
  37             cx - a, cy - a, cx + a, cy + a
  38
  39         let w = img.Width
  40         let w_f = float32 w
  41         let h = img.Height
  42         let h_f = float32 h
  43
  44         // Return 'true' if the point 'p' is owned by e.
  45         // The lines represents all intersections with other ellipses.
  46         let pixelOwnedByE (p: PointF) (e: Ellipse) (others: (Ellipse * Line) list) =
  47             e.Contains p.X p.Y &&
  48             seq {
  49                 let c = PointF(e.Cx, e.Cy)
  50
  51                 for e', d1 in others do
  52                     let d2 = lineFromTwoPoints c p
  53                     let c' = PointF(e'.Cx, e'.Cy)
  54                     let v = pointFromTwoLines d1 (lineFromTwoPoints c c')
  55                     let case1 = sign (v.X - c.X) <> sign (v.X - c'.X) || Utils.squaredDistanceTwoPoints v c > Utils.squaredDistanceTwoPoints v c'
  56                     if not (Single.IsInfinity d2.A)
  57                     then
  58                         let p' = Utils.pointFromTwoLines d1 d2
  59                         let delta, delta' =
  60                             let dx1, dx2 = (c.X - p.X), (c.X - p'.X)
  61                             // To avoid rounding issue.
  62                             if abs dx1 < 0.01f || abs dx2 < 0.01f then c.Y - p.Y, c.Y - p'.Y else dx1, dx2
  63
  64                         // Yield 'false' when the point is owned by another ellipse.
  65                         if case1
  66                         then
  67                             yield sign delta <> sign delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p
  68                         else
  69                             yield sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p
  70                     else
  71                         yield case1
  72             } |> Seq.forall id
  73
  74         let ellipses = ellipses |> List.map EllipseFlaggedKd
  75
  76         // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections.
  77         let tree = KdTree.Tree.BuildTree ellipses
  78         let neighbors (e: EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list =
  79             if not e.Removed
  80             then
  81                 tree.Search (searchRegion e)
  82                     // We only keep the ellipses touching 'e'.
  83                     |> List.choose (fun otherE ->
  84                         if e <> otherE
  85                         then
  86                             match EEOver.EEOverlapArea e otherE with
  87                             | Some (_, px, _) when px.Length > 2 ->
  88                                 otherE.Removed <- true
  89                                 None
  90                             | Some (area, px, py) when area > 0.f && px.Length = 2 ->
  91                                 Some (otherE, PointF(px.[0], py.[0]), PointF(px.[1], py.[1]))
  92                             | _ ->
  93                                 None
  94                         else
  95                             None )
  96             else
  97                 []
  98
  99         // We reverse the list to get the lower score ellipses first.
 100         let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) |> List.rev
 101
 102         // 2) Remove ellipses touching the edges.
 103         for e in ellipses do
 104             if e.isOutside w_f h_f then e.Removed <- true
 105
 106         // 3) Remove ellipses with a high standard deviation (high contrast).
 107         let imgData = img.Data
 108         let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation(seq {
 109             for y in 0 .. h - 1 do
 110                 for x in 0 .. w - 1 do
 111                     yield float imgData.[y, x, 0] })
 112
 113         for e in ellipses do
 114             if not e.Removed
 115             then
 116                 let shrinkedE = e.Scale 0.9f
 117                 let minX, minY, maxX, maxY = ellipseWindow shrinkedE
 118
 119                 let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
 120                     for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 121                         for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 122                             if shrinkedE.Contains (float32 x) (float32 y)
 123                             then
 124                                 yield float imgData.[y, x, 0] })
 125
 126                 if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
 127                     e.Removed <- true
 128
 129         // 4) Remove ellipses with little area.
 130         let minArea = config.RBCRadius.MinArea
 131         for e, neighbors in ellipsesWithNeigbors do
 132             if not e.Removed
 133             then
 134                 let minX, minY, maxX, maxY = ellipseWindow e
 135
 136                 let mutable area = 0
 137                 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 138                     for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 139                         let p = PointF(float32 x, float32 y)
 140                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 141                         then
 142                             area <- area + 1
 143
 144                 if area < int minArea
 145                 then
 146                     e.Removed <- true
 147
 148         // 5) Define pixels associated to each ellipse and create the cells.
 149         let perimeterParasiteSquared = (2.f * config.RBCRadius.ParasiteRadius) ** 2.f |> roundInt
 150         let minimumParasiteArea = config.RBCRadius.MinimumParasiteArea |> roundInt
 151
 152         let nucleusData = parasites.nucleus.Copy().Data // Will be modified thus the copy.
 153         let parasiteData = parasites.parasite.Data
 154         let darkStainData = parasites.darkStain.Data
 155
 156         ellipsesWithNeigbors
 157         |> List.choose (fun (e, neighbors) ->
 158             if e.Removed
 159             then
 160                 None
 161             else
 162                 let minX, minY, maxX, maxY = ellipseWindow e
 163
 164                 let nucleusPixels = List<Point>()
 165                 let parasitePixels = List<Point>()
 166
 167                 let mutable darkStainPixels = 0
 168                 let mutable nbElement = 0
 169
 170                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
 171                 for y in minY .. maxY do
 172                     for x in minX .. maxX do
 173                         let p = PointF(float32 x, float32 y)
 174                         if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
 175                         then
 176                             elements.[y - minY, x - minX] <- 1uy
 177                             nbElement <- nbElement + 1
 178
 179                             if nucleusData.[y, x, 0] > 0uy
 180                             then
 181                                 nucleusPixels.Add(Point(x, y))
 182
 183                             if parasiteData.[y, x, 0] > 0uy
 184                             then
 185                                 parasitePixels.Add(Point(x, y))
 186
 187                             if darkStainData.[y, x, 0] > 0uy
 188                             then
 189                                 darkStainPixels <- darkStainPixels + 1
 190
 191                 let mutable parasiteArea = 0
 192                 if nucleusPixels.Count > 0
 193                 then
 194                     for parasitePixel in parasitePixels do
 195                         if nucleusPixels.Exists(fun p -> pown (p.X - parasitePixel.X) 2 + pown (p.Y - parasitePixel.Y) 2 <= perimeterParasiteSquared)
 196                         then
 197                             parasiteArea <- parasiteArea + 1
 198
 199                 let cellClass =
 200                     if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement)
 201                     then
 202                         Peculiar
 203
 204                     elif nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea
 205                     then
 206                         let infectionToRemove = Morpho.connectedComponents parasites.parasite nucleusPixels
 207                         for p in infectionToRemove do
 208                             nucleusData.[p.Y, p.X, 0] <- 0uy
 209                         InfectedRBC
 210
 211                     else
 212                         HealthyRBC
 213
 214                 Some { cellClass = cellClass
 215                        center = Point(roundInt e.Cx, roundInt e.Cy)
 216                        nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0
 217                        parasiteArea = parasiteArea
 218                        elements = elements })