X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FClassifier.fs;fp=Parasitemia%2FParasitemia%2FClassifier.fs;h=0000000000000000000000000000000000000000;hp=121a7f53d3bbfaddebee7ba2265602c9950d12e7;hb=4bfa3cbdc6145e6944f02e24829ab2ef3a851ac1;hpb=48ecdfc43001c444eff6ad442986049384674af2 diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs deleted file mode 100644 index 121a7f5..0000000 --- a/Parasitemia/Parasitemia/Classifier.fs +++ /dev/null @@ -1,200 +0,0 @@ -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) (img: 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.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: 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 -> - 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, PointD(px.[0], py.[0]), PointD(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 = PointD(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. - 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(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 - - 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) - 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) - infectedArea = infectedPixels.Count - stainArea = stainPixels - elements = elements })