X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FClassifier.fs;h=615840c19c8d6ee5f6f3b2e7244c4ec55d4f2404;hb=e3842630f4d36c5ea8c8a0c3d4762684e1c510f4;hp=0bea08451e899f3cca981bc39037d043dce37c9c;hpb=4bfa3cbdc6145e6944f02e24829ab2ef3a851ac1;p=master-thesis.git diff --git a/Parasitemia/ParasitemiaCore/Classifier.fs b/Parasitemia/ParasitemiaCore/Classifier.fs index 0bea084..615840c 100644 --- a/Parasitemia/ParasitemiaCore/Classifier.fs +++ b/Parasitemia/ParasitemiaCore/Classifier.fs @@ -10,7 +10,6 @@ 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) @@ -20,14 +19,11 @@ type private EllipseFlaggedKd (e: Ellipse) = 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) @@ -47,24 +43,30 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: // 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) = + let pixelOwnedByE (p: PointF) (e: Ellipse) (others: (Ellipse * Line) list) = e.Contains p.X p.Y && seq { - let c = PointD(e.Cx, e.Cy) + let c = PointF(e.Cx, e.Cy) + for e', d1 in others do - let d2 = Utils.lineFromTwoPoints c p - let c' = PointD(e'.Cx, e'.Cy) + 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 d2.Valid + 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 (c.X - p.X) <> sign (c.X - p'.X) || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p + yield sign delta <> sign delta' || 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 + yield sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p else yield case1 } |> Seq.forall id @@ -73,7 +75,7 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: // 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 = + let neighbors (e: EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list = if not e.Removed then tree.Search (searchRegion e) @@ -86,7 +88,7 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: 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])) + Some (otherE, PointF(px.[0], py.[0]), PointF(px.[1], py.[1])) | _ -> None else @@ -124,7 +126,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: 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 @@ -135,7 +136,7 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: 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) + 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 @@ -145,6 +146,13 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: 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 + + 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.Removed @@ -153,48 +161,59 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: else let minX, minY, maxX, maxY = ellipseWindow e - let infectedPixels = List() - let mutable stainPixels = 0 + let nucleusPixels = List() + let parasitePixels = List() + 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) + 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 + elements.[y - minY, x - minX] <- 1uy nbElement <- nbElement + 1 - if infection.Data.[y, x, 0] > 0uy + if nucleusData.[y, x, 0] > 0uy then - infectedPixels.Add(Point(x, y)) + nucleusPixels.Add(Point(x, y)) - if parasites.stain.Data.[y, x, 0] > 0uy + if parasiteData.[y, x, 0] > 0uy then - stainPixels <- stainPixels + 1 + parasitePixels.Add(Point(x, y)) - if parasites.darkStain.Data.[y, x, 0] > 0uy + if darkStainData.[y, x, 0] > 0uy then darkStainPixels <- darkStainPixels + 1 + let mutable parasiteArea = 0 + if nucleusPixels.Count > 0 + then + for parasitePixel in parasitePixels do + if nucleusPixels.Exists(fun p -> pown (p.X - parasitePixel.X) 2 + pown (p.Y - parasitePixel.Y) 2 <= perimeterParasiteSquared) + then + parasiteArea <- parasiteArea + 1 + + let cellClass = - if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) || - float stainPixels > config.Parameters.maxStainRatio * (float nbElement) + if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) then Peculiar - elif infectedPixels.Count >= 1 + + elif nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea then - let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels + let infectionToRemove = ImgTools.connectedComponents parasites.parasite nucleusPixels for p in infectionToRemove do - infection.Data.[p.Y, p.X, 0] <- 0uy + nucleusData.[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 + nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0 + parasiteArea = parasiteArea elements = elements })