X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FClassifier.fs;h=9b247f43db4599e702ce0b469659d5e881773765;hp=1db8b03e73d362b973e82d556d4bf174866a9571;hb=2d712781def419c9acc98368f7102b19b064f16d;hpb=1b8e45987bde692ab5602c281f878707f70459b7 diff --git a/Parasitemia/ParasitemiaCore/Classifier.fs b/Parasitemia/ParasitemiaCore/Classifier.fs index 1db8b03..9b247f4 100644 --- a/Parasitemia/ParasitemiaCore/Classifier.fs +++ b/Parasitemia/ParasitemiaCore/Classifier.fs @@ -12,7 +12,7 @@ open Utils type CellState = RBC = 1 | Removed = 2 | Peculiar = 3 -type private EllipseFlaggedKd (e: Ellipse) = +type private EllipseFlaggedKd (e : Ellipse) = inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha) member val State = CellState.RBC with get, set @@ -21,43 +21,47 @@ type private EllipseFlaggedKd (e: Ellipse) = member this.X = this.Cx member this.Y = this.Cy -let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (width: int) (height: int) (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 // 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 // Return 'true' if the point 'p' is owned by e. // The lines represents all intersections with other ellipses. - let pixelOwnedByE (p: PointF) (e: EllipseFlaggedKd) (neighbors: (EllipseFlaggedKd * PointF * PointF) 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 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 // Peculiar vs peculiar or RBC vs RBC. - then + 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 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 + 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) @@ -65,16 +69,14 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (widt 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 + 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 case1 - elif e.State = CellState.Peculiar // A peculiar always win against a RBC. - then + elif e.State = CellState.Peculiar then // A peculiar always win against a RBC. yield true else yield not <| e'.Contains p.X p.Y @@ -85,24 +87,24 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (widt // 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 e.State <> CellState.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.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])) - | _ -> + |> 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 - else - None) + ) else [] @@ -111,27 +113,25 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (widt // 2) Remove ellipses touching the edges. let widthF, heightF = float32 width, float32 height for e in ellipses do - if e.isOutside widthF heightF then e.State <- CellState.Removed + if e.IsOutside widthF heightF then e.State <- CellState.Removed // 3) Remove ellipses with a high standard deviation (high contrast). // Obsolete. It was useful when the ellipses result quality wasn't good. (* let imgData = img.Data - let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation(seq { + 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 @@ -140,44 +140,40 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (widt // 4) Remove ellipses with little area. let minArea = config.RBCRadius.MinArea for e, neighbors in ellipsesWithNeigbors do - if e.State <> CellState.Removed - then + if e.State <> CellState.Removed then let minX, minY, maxX, maxY = ellipseWindow e let mutable area = 0 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 + let p = PointF (float32 x, float32 y) + if pixelOwnedByE p e neighbors then area <- area + 1 - if area < int minArea - then + 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) + |> 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) @@ -191,62 +187,61 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (widt let darkStainData = parasites.darkStain.Data ellipsesWithNeigbors - |> 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 cellClass = - if e.State = CellState.Peculiar - then - Peculiar + |> 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 - 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 + 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) - nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0 - parasiteArea = parasiteArea - 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 + } + )