X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FClassifier.fs;h=0d2137545334091fc551d17610ff5f6f69d49243;hp=24ea4a72f61ef20411d447207d96017f0090118c;hb=53440e757b4a4ab2a81b0f6a5dd1a2002c0133ba;hpb=d9a6e072ecf299db691c05bb559a71265f812ba3 diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs index 24ea4a7..0d21375 100644 --- a/Parasitemia/Parasitemia/Classifier.fs +++ b/Parasitemia/Parasitemia/Classifier.fs @@ -1,31 +1,197 @@ module Classifier open System +open System.Collections.Generic open System.Drawing open Emgu.CV open Emgu.CV.Structure +open Types +open Utils -type CellClass = HealthyRBC | InfectedRBC | Peculiar -type Cell = { - cellClass: CellClass - center: Point - elements: Matrix } +type private EllipseFlaggedKd (e: Ellipse) = + inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha) -type KdEllipse (e: Types.Ellipse) = - inherit Types.Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha) - - interface KdTree.I2DCoords with + member val Removed = false with get, set + + interface KdTree.I2DCoords with member this.X = this.Cx member this.Y = this.Cy - - -let findCells (ellipses: Types.Ellipse list) (parasites: ParasitesMarker.Result) (fg: Image) : Cell list = + + +let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: Image) (config: Config.Config) : Cell list = if ellipses.IsEmpty then [] else - let tree = KdTree.Tree.buildTree (ellipses |> List.map KdEllipse) - [] \ No newline at end of file + 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.RBCMaxRadius) + KdTree.maxX = e.Cx + (e.A + config.RBCMaxRadius) + KdTree.minY = e.Cy - (e.A + config.RBCMaxRadius) + KdTree.maxY = e.Cy + (e.A + config.RBCMaxRadius) } + + // 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 + + let w = img.Width + let w_f = float w + let h = img.Height + let h_f = float h + + // Return 'true' if the point 'p' is owned by e. + // The lines represents all intersections with other ellipses. + let pixelOwnedByE (p: PointD) (e: Ellipse) (others: (Ellipse * Line) list) = + e.Contains p.X p.Y && + seq { + let c = PointD(e.Cx, e.Cy) + for e', d1 in others do + let d2 = Utils.lineFromTwoPoints c p + let c' = PointD(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 d2.Valid + then + let p' = Utils.pointFromTwoLines d1 d2 + // Yield 'false' when the point is owned by another ellipse. + if case1 + then + yield sign (c.X - p.X) <> sign (c.X - p'.X) || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p + else + yield sign (c.X - p.X) = sign (c.X - p'.X) && 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 * PointD * PointD) list = + if not e.Removed + then + tree.Search (searchRegion e) + // We only keep the ellipses touching 'e'. + |> List.choose (fun otherE -> + match EEOver.EEOverlapArea e otherE with + | Some (_, px, _) when px.Length > 2 -> + otherE.Removed <- true + None + | Some (area, px, py) when area > 0.0 && px.Length = 2 -> + Some (otherE, PointD(px.[0], py.[0]), PointD(px.[1], py.[1])) + | _ -> + 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). + + // CvInvoke.Normalize(img, img, 0.0, 255.0, CvEnum.NormType.MinMax) // Not needed. + + let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation(seq { + for y in 0 .. h - 1 do + for x in 0 .. w - 1 do + yield float img.Data.[y, x, 0] }) + + for e in ellipses do + if not e.Removed + then + let shrinkedE = e.Scale 0.9 + 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 (float x) (float y) + then + yield float img.Data.[y, x, 0] }) + + if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then + e.Removed <- true + + // 4) Remove ellipses with little area. + let minArea = config.RBCMinArea + 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 = PointD(float x, float 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. + 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 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 (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2))) + then + elements.[y-minY, x-minX] <- 1uy + nbElement <- nbElement + 1 + + 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 + + if parasites.darkStain.Data.[y, x, 0] > 0uy + then + darkStainPixels <- darkStainPixels + 1 + + let cellClass = + if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) || + float stainPixels > config.Parameters.maxStainRatio * (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 >= 1 + 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 })