module 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) (fg: Image) (config: Config.Config) : Cell list = if ellipses.IsEmpty then [] else let infection = parasites.infection.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.maxRBCSize) * config.scale KdTree.maxX = e.Cx + (e.A + config.maxRBCSize) * config.scale KdTree.minY = e.Cy - (e.A + config.maxRBCSize) * config.scale KdTree.maxY = e.Cy + (e.A + config.maxRBCSize) * config.scale } // 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 + 0.5) cx - a, cy - a, cx + a, cy + a // 1) Remove ellipses touching the edges. let w = float fg.Width let h = float fg.Height let ellipsesInside = ellipses |> List.map (fun e -> EllipseFlaggedKd (e, Removed = e.isOutside w h)) // 2) Associate touching ellipses with each ellipses. let tree = KdTree.Tree.BuildTree ellipsesInside let neighbors (e: Ellipse) : (EllipseFlaggedKd * PointD * PointD) list = tree.Search (searchRegion e) // We only keep the ellipses touching 'e'. |> List.choose (fun otherE -> match EEOver.EEOverlapArea e otherE with | Some (area, px, py) when area > 0.0 && px.Length >= 2 && py.Length >= 2 -> Some (otherE, PointD(px.[0], py.[0]), PointD(px.[1], py.[1])) | _ -> None ) let ellipsesWithNeigbors = ellipsesInside |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e)) // 3) Remove ellipses with a lower percentage of foreground. for e, neighbors in ellipsesWithNeigbors do let minX, minY, maxX, maxY = ellipseWindow e let mutable totalElement = 0 let mutable fgElement = 0 for y in (if minY < 0 then 0 else minY) .. (if maxY >= fg.Height then fg.Height - 1 else maxY) do for x in (if minX < 0 then 0 else minX) .. (if maxX >= fg.Width then fg.Width - 1 else maxX) do let yf, xf = float y, float x if e.Contains xf yf && neighbors |> List.forall (fun (otherE, _, _) -> not <| otherE.Contains xf yf) then totalElement <- totalElement + 1 if fg.Data.[y, x, 0] > 0uy then fgElement <- fgElement + 1 if (float fgElement) / (float totalElement) < config.percentageOfFgValidCell then e.Removed <- true // 4) Remove ellipses with little area. 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 >= fg.Height then fg.Height - 1 else maxY) do for x in (if minX < 0 then 0 else minX) .. (if maxX >= fg.Width then fg.Width - 1 else maxX) do let yf, xf = float y, float x if fg.Data.[y, x, 0] > 0uy && e.Contains xf yf && neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf) then area <- area + 1 if area < config.minimumCellArea then e.Removed <- true // 5) Define pixels associated to each ellipse and create the cells. // Return 'true' if the point 'p' is owned by e. // The lines represents all intersections with other ellipses. let pixelOwnedByE (p: PointD) (e: Ellipse) (lines: Line list) = e.Contains p.X p.Y && seq { let c = PointD(e.Cx, e.Cy) for d1 in lines do let d2 = Utils.lineFromTwoPoints c p let p' = Utils.pointFromTwoLines d1 d2 yield sign (c.X - p.X) <> sign (c.X - p'.X) || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p // 'false' -> the point is owned by another ellipse. } |> Seq.forall id ellipsesWithNeigbors |> List.choose (fun (e, neighbors) -> if e.Removed then None else let minX, minY, maxX, maxY = ellipseWindow e let infectedPixels = List() let mutable stainPixels = 0 let mutable darkStainPixels = 0 let mutable nbElement = 0 let mutable stain_x = 0.0 let mutable stain_x2 = 0.0 let mutable stain_y = 0.0 let mutable stain_y2 = 0.0 let mutable sumCoords_y = 0 let mutable sumCoords_x = 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 = PointD(float x, float y) if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (Utils.lineFromTwoPoints p1 p2))) && fg.Data.[y, x, 0] > 0uy then elements.[y-minY, x-minX] <- 1uy nbElement <- nbElement + 1 sumCoords_y <- sumCoords_y + y sumCoords_x <- sumCoords_x + x if infection.Data.[y, x, 0] > 0uy then infectedPixels.Add(Point(x, y)) if parasites.stain.Data.[y, x, 0] > 0uy then stainPixels <- stainPixels + 1 stain_x <- stain_x + (float x) stain_x2 <- stain_x2 + (float x) ** 2.0 stain_y <- stain_y + (float y) stain_y2 <- stain_y2 + (float y) ** 2.0 if parasites.darkStain.Data.[y, x, 0] > 0uy then darkStainPixels <- darkStainPixels + 1 let cellClass = if float darkStainPixels > config.MaxDarkStainRatio * (float nbElement) (* || sqrt (((float sumCoords_x) / (float nbElement) - e.Cx) ** 2.0 + ((float sumCoords_y) / (float nbElement) - e.Cy) ** 2.0) > e.A * config.maxOffcenter *) then Peculiar elif infectedPixels.Count > config.infectionPixelsRequired then let infectionToRemove = ImgTools.connectedComponents parasites.stain 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) elements = elements })