X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FClassifier.fs;h=9b247f43db4599e702ce0b469659d5e881773765;hp=a3bfa9c92aa3f139776f08282296dde26ce5d1eb;hb=2d712781def419c9acc98368f7102b19b064f16d;hpb=db49e167a602ef1df02a8b5f7de334355a4917dd diff --git a/Parasitemia/ParasitemiaCore/Classifier.fs b/Parasitemia/ParasitemiaCore/Classifier.fs index a3bfa9c..9b247f4 100644 --- a/Parasitemia/ParasitemiaCore/Classifier.fs +++ b/Parasitemia/ParasitemiaCore/Classifier.fs @@ -10,217 +10,238 @@ open Emgu.CV.Structure open Types open Utils -type private EllipseFlaggedKd (e: Ellipse) = +type CellState = RBC = 1 | Removed = 2 | Peculiar = 3 + +type private EllipseFlaggedKd (e : Ellipse) = inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha) - member val Removed = false with get, set + member val State = CellState.RBC 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 +let findCells (ellipses : Ellipse list) (parasites : ParasitesMarker.Result) (width : int) (height : int) (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) } + 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 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) = + let pixelOwnedByE (p : PointF) (e : EllipseFlaggedKd) (neighbors : (EllipseFlaggedKd * PointF * PointF) 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 + let c = PointF (e.Cx, e.Cy) + + for e', d1 in + (neighbors + |> List.choose ( + fun (otherE, p1, p2) -> + if otherE.State = CellState.Removed then + None + else + Some (otherE, Utils.lineFromTwoPoints p1 p2) + )) do + if e'.State = e.State then // Peculiar vs peculiar or RBC vs RBC. + 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 sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p + yield case1 + + elif e.State = CellState.Peculiar then // A peculiar always win against a RBC. + yield true else - yield case1 + yield not <| e'.Contains p.X p.Y + } |> 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 + let neighbors (e : EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list = + if e.State <> CellState.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 + |> List.choose ( + fun otherE -> + if e <> otherE then + match EEOver.EEOverlapArea e otherE with + | Some (_, px, _) when px.Length > 2 -> + otherE.State <- CellState.Removed + 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 - | 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 + let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) // 2) Remove ellipses touching the edges. + let widthF, heightF = float32 width, float32 height for e in ellipses do - if e.isOutside w_f h_f then e.Removed <- true + if e.IsOutside widthF heightF then e.State <- CellState.Removed // 3) Remove ellipses with a high standard deviation (high contrast). - let imgData = img.Data - let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation(seq { + // Obsolete. It was useful when the ellipses result quality wasn't good. + (* 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 + 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 + if shrinkedE.Contains (float32 x) (float32 y) then yield float imgData.[y, x, 0] }) if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then - e.Removed <- true + 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 + if e.State <> CellState.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 + for y = (if minY < 0 then 0 else minY) to (if maxY >= height then height - 1 else maxY) do + for x = (if minX < 0 then 0 else minX) to (if maxX >= width then width - 1 else maxX) do + let p = PointF (float32 x, float32 y) + if pixelOwnedByE p e neighbors then area <- area + 1 - if area < int minArea - then - e.Removed <- true + if area < int minArea then + e.State <- CellState.Removed + + // 5) Define non-rbc (peculiar) cells. + let darkStainData = parasites.darkStain.Data + ellipsesWithNeigbors + |> List.choose ( + fun (e, neighbors) -> + if e.State = CellState.Removed then + None + else + let mutable darkStainPixels = 0 + let mutable nbElement = 0 + let minX, minY, maxX, maxY = ellipseWindow e + for y = minY to maxY do + for x = minX to maxX do + let p = PointF (float32 x, float32 y) + if pixelOwnedByE p e neighbors then + nbElement <- nbElement + 1 + if darkStainData.[y, x, 0] > 0uy then + darkStainPixels <- darkStainPixels + 1 + + if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) then Some e else None + ) + + // We do not change the state during the process to avoid to have peculiar neighbors which change the behavior of 'pixelOwnedByE'. + |> List.iter (fun e -> e.State <- CellState.Peculiar) // 5) Define pixels associated to each ellipse and create the cells. - let radiusParasiteRatio = 0.4f - let radiusParasite = config.RBCRadius.Pixel * 0.5f - let perimeterParasiteSquared = (2.f * radiusParasite) ** 2.f |> roundInt - let parasiteOccupation = 0.08f // 8 % - let minimumParasiteArea = Const.PI * radiusParasite ** 2.f * parasiteOccupation |> roundInt - //let minimumStainArea = roundInt <| config.RBCRadius.Area * 0.02f // 1.5 % + let diameterParasiteSquared = (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 - then - None - else - let minX, minY, maxX, maxY = ellipseWindow e + |> List.choose ( + fun (e, neighbors) -> + if e.State = CellState.Removed then + None + else + let minX, minY, maxX, maxY = ellipseWindow e + + let nucleusPixels = List () + let parasitePixels = List () + + let mutable nbElement = 0 + + let elements = new Matrix (maxY - minY + 1, maxX - minX + 1) + for y = minY to maxY do + for x = minX to maxX do + let p = PointF (float32 x, float32 y) + if pixelOwnedByE p e neighbors then + elements.[y - minY, x - minX] <- 1uy + nbElement <- nbElement + 1 + + if nucleusData.[y, x, 0] > 0uy then + nucleusPixels.Add (Point (x, y)) + + if parasiteData.[y, x, 0] > 0uy then + parasitePixels.Add (Point (x, y)) + + let parasiteArea = + if nucleusPixels.Count > 0 then + seq { + for parasitePixel in parasitePixels do + if nucleusPixels.Exists (fun p -> pown (p.X - parasitePixel.X) 2 + pown (p.Y - parasitePixel.Y) 2 <= diameterParasiteSquared) then + yield 1 + } |> Seq.sum + else + 0 - let infectedPixels = List() - let stainPixels = 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.stain.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 - stainPixels.Add(Point(x, y)) - - if darkStain - then - darkStainPixels <- darkStainPixels + 1 - - let mutable stainArea = 0 - if infectedPixels.Count > 0 - then - for stainPixel in stainPixels do - if infectedPixels.Exists(fun p -> pown (p.X - stainPixel.X) 2 + pown (p.Y - stainPixel.Y) 2 <= perimeterParasiteSquared) - then - stainArea <- stainArea + 1 - - - let cellClass = - if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) - //|| float stainPixels > config.Parameters.maxStainRatio * (float nbElement) - then - Peculiar - - elif infectedPixels.Count > 0 && stainArea >= minimumParasiteArea - then - let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels - for p in infectionToRemove do - infection.Data.[p.Y, p.X, 0] <- 0uy - InfectedRBC + let cellClass = + if e.State = CellState.Peculiar then + Peculiar - else - HealthyRBC + elif nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea then + let infectionToRemove = Morpho.connectedComponents parasites.parasite nucleusPixels + for p in infectionToRemove do + nucleusData.[p.Y, p.X, 0] <- 0uy + InfectedRBC - Some { cellClass = cellClass - center = Point(roundInt e.Cx, roundInt e.Cy) - infectedArea = if cellClass = InfectedRBC then infectedPixels.Count else 0 - stainArea = stainArea - elements = elements }) + else + HealthyRBC + + Some + { + cellClass = cellClass + center = Point (roundInt e.Cx, roundInt e.Cy) + nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0 + parasiteArea = parasiteArea + elements = elements + } + )