module ParasitemiaCore.Classifier open System open System.Collections.Generic open System.Drawing open Emgu.CV open Types open Utils type CellState = RBC = 1 | Removed = 2 | Peculiar = 3 type private EllipseFlaggedKd (e : Ellipse) = inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha) member val State = CellState.RBC with get, set interface KdTree.I2DCoords with member this.X = this.Cx member this.Y = this.Cy let findCells (ellipses : Ellipse list) (parasites : ParasitesMarker.Result) (width : int) (height : int) (config : Config.Config) : Cell list = if ellipses.IsEmpty then [] else // This is the minimum window size to check if other ellipses touch 'e'. let searchRegion (e : Ellipse) = { KdTree.minX = e.Cx - (e.A + config.RBCRadius.Max) KdTree.maxX = e.Cx + (e.A + config.RBCRadius.Max) KdTree.minY = e.Cy - (e.A + config.RBCRadius.Max) KdTree.maxY = e.Cy + (e.A + config.RBCRadius.Max) } // The minimum window to contain a given ellipse. let ellipseWindow (e : Ellipse) = let cx, cy = roundInt e.Cx, roundInt e.Cy let a = int (e.A + 0.5f) cx - a, cy - a, cx + a, cy + a // Return 'true' if the point 'p' is owned by e. // The lines represents all intersections with other ellipses. let pixelOwnedByE (p : PointF) (e : EllipseFlaggedKd) (neighbors : (EllipseFlaggedKd * PointF * PointF) list) = e.Contains p.X p.Y && seq { let c = PointF (e.Cx, e.Cy) for e', d1 in (neighbors |> List.choose ( fun (otherE, p1, p2) -> if otherE.State = CellState.Removed then None else Some (otherE, Utils.lineFromTwoPoints p1 p2) )) do if e'.State = e.State then // Peculiar vs peculiar or RBC vs RBC. let d2 = lineFromTwoPoints c p let c' = PointF (e'.Cx, e'.Cy) let v = pointFromTwoLines d1 (lineFromTwoPoints c c') let case1 = sign (v.X - c.X) <> sign (v.X - c'.X) || Utils.squaredDistanceTwoPoints v c > Utils.squaredDistanceTwoPoints v c' if not (Single.IsInfinity d2.A) then let p' = Utils.pointFromTwoLines d1 d2 let delta, delta' = let dx1, dx2 = (c.X - p.X), (c.X - p'.X) // To avoid rounding issue. if abs dx1 < 0.01f || abs dx2 < 0.01f then c.Y - p.Y, c.Y - p'.Y else dx1, dx2 // Yield 'false' when the point is owned by another ellipse. if case1 then sign delta <> sign delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p else sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p else case1 elif e.State = CellState.Peculiar then // A peculiar always win against a RBC. true else not <| e'.Contains p.X p.Y } |> Seq.forall id let ellipses = ellipses |> List.map EllipseFlaggedKd // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections. let tree = KdTree.Tree.BuildTree ellipses let neighbors (e : EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list = if e.State <> CellState.Removed then tree.Search (searchRegion e) // We only keep the ellipses touching 'e'. |> Seq.choose ( fun otherE -> if e <> otherE then match EEOver.EEOverlapArea e otherE with | Some (_, px, _) when px.Length > 2 -> otherE.State <- CellState.Removed None | Some (area, px, py) when area > 0.f && px.Length = 2 -> Some (otherE, PointF (px.[0], py.[0]), PointF (px.[1], py.[1])) | _ -> None else None ) |> List.ofSeq else [] let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) // 2) Remove ellipses touching the edges. let widthF, heightF = float32 width, float32 height for e in ellipses do if e.IsOutside widthF heightF then e.State <- CellState.Removed // 3) Remove ellipses with a high standard deviation (high contrast). // Obsolete. It was useful when the ellipses result quality wasn't good. (* let imgData = img.Data let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation (seq { for y in 0 .. h - 1 do for x in 0 .. w - 1 do float imgData.[y, x, 0] }) for e in ellipses do if not e.Removed then let shrinkedE = e.Scale 0.9f let minX, minY, maxX, maxY = ellipseWindow shrinkedE let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq { for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do if shrinkedE.Contains (float32 x) (float32 y) then float imgData.[y, x, 0] }) if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then e.Removed <- true *) // 4) Remove ellipses with little area. let minArea = config.RBCRadius.MinArea for e, neighbors in ellipsesWithNeigbors do if e.State <> CellState.Removed then let minX, minY, maxX, maxY = ellipseWindow e let mutable area = 0 for y = (if minY < 0 then 0 else minY) to (if maxY >= height then height - 1 else maxY) do for x = (if minX < 0 then 0 else minX) to (if maxX >= width then width - 1 else maxX) do let p = PointF (float32 x, float32 y) if pixelOwnedByE p e neighbors then area <- area + 1 if area < int minArea then e.State <- CellState.Removed // 5) Define non-rbc (peculiar) cells. let darkStainData = parasites.darkStain.Data ellipsesWithNeigbors |> List.choose ( fun (e, neighbors) -> if e.State = CellState.Removed then None else let mutable darkStainPixels = 0 let mutable nbElement = 0 let minX, minY, maxX, maxY = ellipseWindow e for y = minY to maxY do for x = minX to maxX do let p = PointF (float32 x, float32 y) if pixelOwnedByE p e neighbors then nbElement <- nbElement + 1 if darkStainData.[y, x, 0] > 0uy then darkStainPixels <- darkStainPixels + 1 if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) then Some e else None ) // We do not change the state during the process to avoid to have peculiar neighbors which change the behavior of 'pixelOwnedByE'. |> List.iter (fun e -> e.State <- CellState.Peculiar) // 5) Define pixels associated to each ellipse and create the cells. let diameterParasiteSquared = (2.f * config.RBCRadius.ParasiteRadius) ** 2.f |> roundInt let minimumParasiteArea = config.RBCRadius.MinimumParasiteArea |> roundInt let nucleusData = parasites.nucleus.Copy().Data // Will be modified thus the copy. let parasiteData = parasites.parasite.Data let darkStainData = parasites.darkStain.Data ellipsesWithNeigbors |> List.choose ( fun (e, neighbors) -> if e.State = CellState.Removed then None else let minX, minY, maxX, maxY = ellipseWindow e let nucleusPixels = List () let parasitePixels = List () let mutable nbElement = 0 let elements = new Matrix (maxY - minY + 1, maxX - minX + 1) for y = minY to maxY do for x = minX to maxX do let p = PointF (float32 x, float32 y) if pixelOwnedByE p e neighbors then elements.[y - minY, x - minX] <- 1uy nbElement <- nbElement + 1 if nucleusData.[y, x, 0] > 0uy then nucleusPixels.Add (Point (x, y)) if parasiteData.[y, x, 0] > 0uy then parasitePixels.Add (Point (x, y)) let parasiteArea = if nucleusPixels.Count > 0 then seq { for parasitePixel in parasitePixels do if nucleusPixels.Exists (fun p -> pown (p.X - parasitePixel.X) 2 + pown (p.Y - parasitePixel.Y) 2 <= diameterParasiteSquared) then 1 } |> Seq.sum else 0 let cellClass = if e.State = CellState.Peculiar then Peculiar elif nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea then let infectionToRemove = Morpho.connectedComponents parasites.parasite nucleusPixels for p in infectionToRemove do nucleusData.[p.Y, p.X, 0] <- 0uy InfectedRBC else HealthyRBC Some { cellClass = cellClass center = Point (roundInt e.Cx, roundInt e.Cy) nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0 parasiteArea = parasiteArea elements = elements } )