module ParasitemiaCore.Classifier open System open System.Collections.Generic open System.Drawing open Emgu.CV open Emgu.CV.Structure open Types open Utils type private EllipseFlaggedKd (e: Ellipse) = inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha) member val Removed = false 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) (img: Image) (config: Config.Config) : Cell list = if ellipses.IsEmpty then [] else let infection = parasites.nucleus.Copy() // To avoid to modify the parameter. // 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 let w = img.Width let w_f = float32 w let h = img.Height let h_f = float32 h // Return 'true' if the point 'p' is owned by e. // The lines represents all intersections with other ellipses. let pixelOwnedByE (p: PointF) (e: Ellipse) (others: (Ellipse * Line) list) = e.Contains p.X p.Y && seq { let c = PointF(e.Cx, e.Cy) for e', d1 in others do 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 yield sign delta <> sign delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p else yield sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p else yield case1 } |> 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 not e.Removed then tree.Search (searchRegion e) // We only keep the ellipses touching 'e'. |> List.choose (fun otherE -> if e <> otherE then match EEOver.EEOverlapArea e otherE with | Some (_, px, _) when px.Length > 2 -> otherE.Removed <- true 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 ) else [] // We reverse the list to get the lower score ellipses first. let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) |> List.rev // 2) Remove ellipses touching the edges. for e in ellipses do if e.isOutside w_f h_f then e.Removed <- true // 3) Remove ellipses with a high standard deviation (high contrast). 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 yield 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 yield 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 not e.Removed then let minX, minY, maxX, maxY = ellipseWindow e let mutable area = 0 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 let p = PointF(float32 x, float32 y) if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2))) then area <- area + 1 if area < int minArea then e.Removed <- true // 5) Define pixels associated to each ellipse and create the cells. let perimeterParasiteSquared = (2.f * config.RBCRadius.ParasiteRadius) ** 2.f |> roundInt let minimumParasiteArea = config.RBCRadius.MinimumParasiteArea |> roundInt ellipsesWithNeigbors |> List.choose (fun (e, neighbors) -> if e.Removed then None else let minX, minY, maxX, maxY = ellipseWindow e let infectedPixels = List() let cytoplasmPixels = List() //let mutable stainPixels = 0 let mutable darkStainPixels = 0 let mutable nbElement = 0 let elements = new Matrix(maxY - minY + 1, maxX - minX + 1) for y in minY .. maxY do for x in minX .. maxX do let p = PointF(float32 x, float32 y) if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2))) then elements.[y-minY, x-minX] <- 1uy nbElement <- nbElement + 1 let infected = infection.Data.[y, x, 0] > 0uy let stain = parasites.cytoplasm.Data.[y, x, 0] > 0uy let darkStain = parasites.darkStain.Data.[y, x, 0] > 0uy if infected then infectedPixels.Add(Point(x, y)) if stain then cytoplasmPixels.Add(Point(x, y)) if darkStain then darkStainPixels <- darkStainPixels + 1 let mutable cytoplasmArea = 0 if infectedPixels.Count > 0 then for cytoplasmPixel in cytoplasmPixels do if infectedPixels.Exists(fun p -> pown (p.X - cytoplasmPixel.X) 2 + pown (p.Y - cytoplasmPixel.Y) 2 <= perimeterParasiteSquared) then cytoplasmArea <- cytoplasmArea + 1 let cellClass = if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) //|| float stainPixels > config.Parameters.maxStainRatio * (float nbElement) then Peculiar elif infectedPixels.Count > 0 && cytoplasmArea >= minimumParasiteArea then let infectionToRemove = ImgTools.connectedComponents parasites.cytoplasm infectedPixels for p in infectionToRemove do infection.Data.[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 infectedPixels.Count else 0 parasiteArea = cytoplasmArea elements = elements })