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
   9 open Types
  10 open Utils
  11
  12 type CellState = RBC = 1 | Removed = 2 | Peculiar = 3
  13
  14 type private EllipseFlaggedKd (e : Ellipse) =
  15     inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha)
  16
  17     member val State = CellState.RBC with get, set
  18
  19     interface KdTree.I2DCoords with
  20         member this.X = this.Cx
  21         member this.Y = this.Cy
  22
  23 let findCells (ellipses : Ellipse list) (parasites : ParasitesMarker.Result) (width : int) (height : int) (config : Config.Config) : Cell list =
  24     if ellipses.IsEmpty then
  25         []
  26     else
  27         // This is the minimum window size to check if other ellipses touch 'e'.
  28         let searchRegion (e : Ellipse) =
  29             {
  30                 KdTree.minX = e.Cx - (e.A + config.RBCRadius.Max)
  31                 KdTree.maxX = e.Cx + (e.A + config.RBCRadius.Max)
  32                 KdTree.minY = e.Cy - (e.A + config.RBCRadius.Max)
  33                 KdTree.maxY = e.Cy + (e.A + config.RBCRadius.Max)
  34             }
  35
  36         // The minimum window to contain a given ellipse.
  37         let ellipseWindow (e : Ellipse) =
  38             let cx, cy = roundInt e.Cx, roundInt e.Cy
  39             let a = int (e.A + 0.5f)
  40             cx - a, cy - a, cx + a, cy + a
  41
  42         // Return 'true' if the point 'p' is owned by e.
  43         // The lines represents all intersections with other ellipses.
  44         let pixelOwnedByE (p : PointF) (e : EllipseFlaggedKd) (neighbors : (EllipseFlaggedKd * PointF * PointF) list) =
  45             e.Contains p.X p.Y &&
  46             seq {
  47                 let c = PointF (e.Cx, e.Cy)
  48
  49                 for e', d1 in
  50                     (neighbors
  51                     |> List.choose (
  52                         fun (otherE, p1, p2) ->
  53                             if otherE.State = CellState.Removed then
  54                                 None
  55                             else
  56                                 Some (otherE, Utils.lineFromTwoPoints p1 p2)
  57                     )) do
  58                     if e'.State = e.State then // Peculiar vs peculiar or RBC vs RBC.
  59                         let d2 = lineFromTwoPoints c p
  60                         let c' = PointF (e'.Cx, e'.Cy)
  61                         let v = pointFromTwoLines d1 (lineFromTwoPoints c c')
  62                         let case1 = sign (v.X - c.X) <> sign (v.X - c'.X) || Utils.squaredDistanceTwoPoints v c > Utils.squaredDistanceTwoPoints v c'
  63                         if not (Single.IsInfinity d2.A) then
  64                             let p' = Utils.pointFromTwoLines d1 d2
  65                             let delta, delta' =
  66                                 let dx1, dx2 = (c.X - p.X), (c.X - p'.X)
  67                                 // To avoid rounding issue.
  68                                 if abs dx1 < 0.01f || abs dx2 < 0.01f then c.Y - p.Y, c.Y - p'.Y else dx1, dx2
  69
  70                             // Yield 'false' when the point is owned by another ellipse.
  71                             if case1 then
  72                                 sign delta <> sign delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p
  73                             else
  74                                 sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p
  75                         else
  76                             case1
  77
  78                     elif e.State = CellState.Peculiar then // A peculiar always win against a RBC.
  79                         true
  80                     else
  81                         not <| e'.Contains p.X p.Y
  82
  83             } |> Seq.forall id
  84
  85         let ellipses = ellipses |> List.map EllipseFlaggedKd
  86
  87         // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections.
  88         let tree = KdTree.Tree.BuildTree ellipses
  89         let neighbors (e : EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list =
  90             if e.State <> CellState.Removed then
  91                 tree.Search (searchRegion e)
  92                     // We only keep the ellipses touching 'e'.
  93                     |> List.choose (
  94                         fun otherE ->
  95                             if e <> otherE then
  96                                 match EEOver.EEOverlapArea e otherE with
  97                                 | Some (_, px, _) when px.Length > 2 ->
  98                                     otherE.State <- CellState.Removed
  99                                     None
 100                                 | Some (area, px, py) when area > 0.f && px.Length = 2 ->
 101                                     Some (otherE, PointF (px.[0], py.[0]), PointF (px.[1], py.[1]))
 102                                 | _ ->
 103                                     None
 104                             else
 105                                 None
 106                     )
 107             else
 108                 []
 109
 110         let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e)
 111
 112         // 2) Remove ellipses touching the edges.
 113         let widthF, heightF = float32 width, float32 height
 114         for e in ellipses do
 115             if e.IsOutside widthF heightF then e.State <- CellState.Removed
 116
 117         // 3) Remove ellipses with a high standard deviation (high contrast).
 118         // Obsolete. It was useful when the ellipses result quality wasn't good.
 119         (* let imgData = img.Data
 120         let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation (seq {
 121             for y in 0 .. h - 1 do
 122                 for x in 0 .. w - 1 do
 123                     float imgData.[y, x, 0] })
 124
 125         for e in ellipses do
 126             if not e.Removed then
 127                 let shrinkedE = e.Scale 0.9f
 128                 let minX, minY, maxX, maxY = ellipseWindow shrinkedE
 129
 130                 let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
 131                     for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
 132                         for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
 133                             if shrinkedE.Contains (float32 x) (float32 y) then
 134                                 float imgData.[y, x, 0] })
 135
 136                 if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
 137                     e.Removed <- true *)
 138
 139         // 4) Remove ellipses with little area.
 140         let minArea = config.RBCRadius.MinArea
 141         for e, neighbors in ellipsesWithNeigbors do
 142             if e.State <> CellState.Removed then
 143                 let minX, minY, maxX, maxY = ellipseWindow e
 144
 145                 let mutable area = 0
 146                 for y = (if minY < 0 then 0 else minY) to (if maxY >= height then height - 1 else maxY) do
 147                     for x = (if minX < 0 then 0 else minX) to (if maxX >= width then width - 1 else maxX) do
 148                         let p = PointF (float32 x, float32 y)
 149                         if pixelOwnedByE p e neighbors then
 150                             area <- area + 1
 151
 152                 if area < int minArea then
 153                     e.State <- CellState.Removed
 154
 155         // 5) Define non-rbc (peculiar) cells.
 156         let darkStainData = parasites.darkStain.Data
 157         ellipsesWithNeigbors
 158         |> List.choose (
 159             fun (e, neighbors) ->
 160                 if e.State = CellState.Removed then
 161                     None
 162                 else
 163                     let mutable darkStainPixels = 0
 164                     let mutable nbElement = 0
 165                     let minX, minY, maxX, maxY = ellipseWindow e
 166                     for y = minY to maxY do
 167                         for x = minX to maxX do
 168                             let p = PointF (float32 x, float32 y)
 169                             if pixelOwnedByE p e neighbors then
 170                                 nbElement <- nbElement + 1
 171                                 if darkStainData.[y, x, 0] > 0uy then
 172                                     darkStainPixels <- darkStainPixels + 1
 173
 174                     if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) then Some e else None
 175         )
 176
 177         // We do not change the state during the process to avoid to have peculiar neighbors which change the behavior of 'pixelOwnedByE'.
 178         |> List.iter (fun e -> e.State <- CellState.Peculiar)
 179
 180         // 5) Define pixels associated to each ellipse and create the cells.
 181         let diameterParasiteSquared = (2.f * config.RBCRadius.ParasiteRadius) ** 2.f |> roundInt
 182         let minimumParasiteArea = config.RBCRadius.MinimumParasiteArea |> roundInt
 183
 184         let nucleusData = parasites.nucleus.Copy().Data // Will be modified thus the copy.
 185         let parasiteData = parasites.parasite.Data
 186         let darkStainData = parasites.darkStain.Data
 187
 188         ellipsesWithNeigbors
 189         |> List.choose (
 190             fun (e, neighbors) ->
 191                 if e.State = CellState.Removed then
 192                     None
 193                 else
 194                     let minX, minY, maxX, maxY = ellipseWindow e
 195
 196                     let nucleusPixels = List<Point> ()
 197                     let parasitePixels = List<Point> ()
 198
 199                     let mutable nbElement = 0
 200
 201                     let elements = new Matrix<byte> (maxY - minY + 1, maxX - minX + 1)
 202                     for y = minY to maxY do
 203                         for x = minX to maxX do
 204                             let p = PointF (float32 x, float32 y)
 205                             if pixelOwnedByE p e neighbors then
 206                                 elements.[y - minY, x - minX] <- 1uy
 207                                 nbElement <- nbElement + 1
 208
 209                                 if nucleusData.[y, x, 0] > 0uy then
 210                                     nucleusPixels.Add (Point (x, y))
 211
 212                                 if parasiteData.[y, x, 0] > 0uy then
 213                                     parasitePixels.Add (Point (x, y))
 214
 215                     let parasiteArea =
 216                         if nucleusPixels.Count > 0 then
 217                             seq {
 218                                 for parasitePixel in parasitePixels do
 219                                     if nucleusPixels.Exists (fun p -> pown (p.X - parasitePixel.X) 2 + pown (p.Y - parasitePixel.Y) 2 <= diameterParasiteSquared) then
 220                                         1
 221                             } |> Seq.sum
 222                         else
 223                             0
 224
 225                     let cellClass =
 226                         if e.State = CellState.Peculiar then
 227                             Peculiar
 228
 229                         elif nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea then
 230                             let infectionToRemove = Morpho.connectedComponents parasites.parasite nucleusPixels
 231                             for p in infectionToRemove do
 232                                 nucleusData.[p.Y, p.X, 0] <- 0uy
 233                             InfectedRBC
 234
 235                         else
 236                             HealthyRBC
 237
 238                     Some
 239                         {
 240                             cellClass = cellClass
 241                             center = Point (roundInt e.Cx, roundInt e.Cy)
 242                             nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0
 243                             parasiteArea = parasiteArea
 244                             elements = elements
 245                         }
 246         )