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