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 CellState = RBC = 1 | Removed = 2 | Peculiar = 3
  14
  15 type private EllipseFlaggedKd (e : Ellipse) =
  16     inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha)
  17
  18     member val State = CellState.RBC with get, set
  19
  20     interface KdTree.I2DCoords with
  21         member this.X = this.Cx
  22         member this.Y = this.Cy
  23
  24 let findCells (ellipses : Ellipse list) (parasites : ParasitesMarker.Result) (width : int) (height : int) (config : Config.Config) : Cell list =
  25     if ellipses.IsEmpty then
  26         []
  27     else
  28         // This is the minimum window size to check if other ellipses touch 'e'.
  29         let searchRegion (e : Ellipse) =
  30             {
  31                 KdTree.minX = e.Cx - (e.A + config.RBCRadius.Max)
  32                 KdTree.maxX = e.Cx + (e.A + config.RBCRadius.Max)
  33                 KdTree.minY = e.Cy - (e.A + config.RBCRadius.Max)
  34                 KdTree.maxY = e.Cy + (e.A + config.RBCRadius.Max)
  35             }
  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 + 0.5f)
  41             cx - a, cy - a, cx + a, cy + a
  42
  43         // Return 'true' if the point 'p' is owned by e.
  44         // The lines represents all intersections with other ellipses.
  45         let pixelOwnedByE (p : PointF) (e : EllipseFlaggedKd) (neighbors : (EllipseFlaggedKd * PointF * PointF) list) =
  46             e.Contains p.X p.Y &&
  47             seq {
  48                 let c = PointF (e.Cx, e.Cy)
  49
  50                 for e', d1 in
  51                     (neighbors
  52                     |> List.choose (
  53                         fun (otherE, p1, p2) ->
  54                             if otherE.State = CellState.Removed then
  55                                 None
  56                             else
  57                                 Some (otherE, Utils.lineFromTwoPoints p1 p2)
  58                     )) do
  59                     if e'.State = e.State then // Peculiar vs peculiar or RBC vs RBC.
  60                         let d2 = lineFromTwoPoints c p
  61                         let c' = PointF (e'.Cx, e'.Cy)
  62                         let v = pointFromTwoLines d1 (lineFromTwoPoints c c')
  63                         let case1 = sign (v.X - c.X) <> sign (v.X - c'.X) || Utils.squaredDistanceTwoPoints v c > Utils.squaredDistanceTwoPoints v c'
  64                         if not (Single.IsInfinity d2.A) then
  65                             let p' = Utils.pointFromTwoLines d1 d2
  66                             let delta, delta' =
  67                                 let dx1, dx2 = (c.X - p.X), (c.X - p'.X)
  68                                 // To avoid rounding issue.
  69                                 if abs dx1 < 0.01f || abs dx2 < 0.01f then c.Y - p.Y, c.Y - p'.Y else dx1, dx2
  70
  71                             // Yield 'false' when the point is owned by another ellipse.
  72                             if case1 then
  73                                 yield sign delta <> sign delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p
  74                             else
  75                                 yield sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p
  76                         else
  77                             yield case1
  78
  79                     elif e.State = CellState.Peculiar then // A peculiar always win against a RBC.
  80                         yield true
  81                     else
  82                         yield not <| e'.Contains p.X p.Y
  83
  84             } |> Seq.forall id
  85
  86         let ellipses = ellipses |> List.map EllipseFlaggedKd
  87
  88         // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections.
  89         let tree = KdTree.Tree.BuildTree ellipses
  90         let neighbors (e : EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list =
  91             if e.State <> CellState.Removed then
  92                 tree.Search (searchRegion e)
  93                     // We only keep the ellipses touching 'e'.
  94                     |> List.choose (
  95                         fun otherE ->
  96                             if e <> otherE then
  97                                 match EEOver.EEOverlapArea e otherE with
  98                                 | Some (_, px, _) when px.Length > 2 ->
  99                                     otherE.State <- CellState.Removed
 100                                     None
 101                                 | Some (area, px, py) when area > 0.f && px.Length = 2 ->
 102                                     Some (otherE, PointF (px.[0], py.[0]), PointF (px.[1], py.[1]))
 103                                 | _ ->
 104                                     None
 105                             else
 106                                 None
 107                     )
 108             else
 109                 []
 110
 111         let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e)
 112
 113         // 2) Remove ellipses touching the edges.
 114         let widthF, heightF = float32 width, float32 height
 115         for e in ellipses do
 116             if e.IsOutside widthF heightF then e.State <- CellState.Removed
 117
 118         // 3) Remove ellipses with a high standard deviation (high contrast).
 119         // Obsolete. It was useful when the ellipses result quality wasn't good.
 120         (* let imgData = img.Data
 121         let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation (seq {
 122             for y in 0 .. h - 1 do
 123                 for x in 0 .. w - 1 do
 124                     yield float imgData.[y, x, 0] })
 125
 126         for e in ellipses do
 127             if not e.Removed then
 128                 let shrinkedE = e.Scale 0.9f
 129                 let minX, minY, maxX, maxY = ellipseWindow shrinkedE
 130
 131                 let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
 132                     for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 133                         for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 134                             if shrinkedE.Contains (float32 x) (float32 y) then
 135                                 yield float imgData.[y, x, 0] })
 136
 137                 if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
 138                     e.Removed <- true *)
 139
 140         // 4) Remove ellipses with little area.
 141         let minArea = config.RBCRadius.MinArea
 142         for e, neighbors in ellipsesWithNeigbors do
 143             if e.State <> CellState.Removed then
 144                 let minX, minY, maxX, maxY = ellipseWindow e
 145
 146                 let mutable area = 0
 147                 for y = (if minY < 0 then 0 else minY) to (if maxY >= height then height - 1 else maxY) do
 148                     for x = (if minX < 0 then 0 else minX) to (if maxX >= width then width - 1 else maxX) do
 149                         let p = PointF (float32 x, float32 y)
 150                         if pixelOwnedByE p e neighbors then
 151                             area <- area + 1
 152
 153                 if area < int minArea then
 154                     e.State <- CellState.Removed
 155
 156         // 5) Define non-rbc (peculiar) cells.
 157         let darkStainData = parasites.darkStain.Data
 158         ellipsesWithNeigbors
 159         |> List.choose (
 160             fun (e, neighbors) ->
 161                 if e.State = CellState.Removed then
 162                     None
 163                 else
 164                     let mutable darkStainPixels = 0
 165                     let mutable nbElement = 0
 166                     let minX, minY, maxX, maxY = ellipseWindow e
 167                     for y = minY to maxY do
 168                         for x = minX to maxX do
 169                             let p = PointF (float32 x, float32 y)
 170                             if pixelOwnedByE p e neighbors then
 171                                 nbElement <- nbElement + 1
 172                                 if darkStainData.[y, x, 0] > 0uy then
 173                                     darkStainPixels <- darkStainPixels + 1
 174
 175                     if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) then Some e else None
 176         )
 177
 178         // We do not change the state during the process to avoid to have peculiar neighbors which change the behavior of 'pixelOwnedByE'.
 179         |> List.iter (fun e -> e.State <- CellState.Peculiar)
 180
 181         // 5) Define pixels associated to each ellipse and create the cells.
 182         let diameterParasiteSquared = (2.f * config.RBCRadius.ParasiteRadius) ** 2.f |> roundInt
 183         let minimumParasiteArea = config.RBCRadius.MinimumParasiteArea |> roundInt
 184
 185         let nucleusData = parasites.nucleus.Copy().Data // Will be modified thus the copy.
 186         let parasiteData = parasites.parasite.Data
 187         let darkStainData = parasites.darkStain.Data
 188
 189         ellipsesWithNeigbors
 190         |> List.choose (
 191             fun (e, neighbors) ->
 192                 if e.State = CellState.Removed then
 193                     None
 194                 else
 195                     let minX, minY, maxX, maxY = ellipseWindow e
 196
 197                     let nucleusPixels = List<Point> ()
 198                     let parasitePixels = List<Point> ()
 199
 200                     let mutable nbElement = 0
 201
 202                     let elements = new Matrix<byte> (maxY - minY + 1, maxX - minX + 1)
 203                     for y = minY to maxY do
 204                         for x = minX to maxX do
 205                             let p = PointF (float32 x, float32 y)
 206                             if pixelOwnedByE p e neighbors then
 207                                 elements.[y - minY, x - minX] <- 1uy
 208                                 nbElement <- nbElement + 1
 209
 210                                 if nucleusData.[y, x, 0] > 0uy then
 211                                     nucleusPixels.Add (Point (x, y))
 212
 213                                 if parasiteData.[y, x, 0] > 0uy then
 214                                     parasitePixels.Add (Point (x, y))
 215
 216                     let parasiteArea =
 217                         if nucleusPixels.Count > 0 then
 218                             seq {
 219                                 for parasitePixel in parasitePixels do
 220                                     if nucleusPixels.Exists (fun p -> pown (p.X - parasitePixel.X) 2 + pown (p.Y - parasitePixel.Y) 2 <= diameterParasiteSquared) then
 221                                         yield 1
 222                             } |> Seq.sum
 223                         else
 224                             0
 225
 226                     let cellClass =
 227                         if e.State = CellState.Peculiar then
 228                             Peculiar
 229
 230                         elif nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea then
 231                             let infectionToRemove = Morpho.connectedComponents parasites.parasite nucleusPixels
 232                             for p in infectionToRemove do
 233                                 nucleusData.[p.Y, p.X, 0] <- 0uy
 234                             InfectedRBC
 235
 236                         else
 237                             HealthyRBC
 238
 239                     Some
 240                         {
 241                             cellClass = cellClass
 242                             center = Point (roundInt e.Cx, roundInt e.Cy)
 243                             nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0
 244                             parasiteArea = parasiteArea
 245                             elements = elements
 246                         }
 247         )