X-Git-Url: http://git.euphorik.ch/index.cgi?a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FClassifier.fs;h=f7c1bbb43052ad7d1e6ffca7c0e84e1fc71fbd8d;hb=b87b35b922551f122228df1fd9c530bbb807935a;hp=1db8b03e73d362b973e82d556d4bf174866a9571;hpb=2e3cd07dd099944059ef5e7a7f5ef57ffe3d677b;p=master-thesis.git diff --git a/Parasitemia/ParasitemiaCore/Classifier.fs b/Parasitemia/ParasitemiaCore/Classifier.fs index 1db8b03..f7c1bbb 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 + 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 + 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 @@ -85,14 +87,12 @@ 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 + if e <> otherE then match EEOver.EEOverlapArea e otherE with | Some (_, px, _) when px.Length > 2 -> otherE.State <- CellState.Removed @@ -102,7 +102,8 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (widt | _ -> None else - None) + None + ) else [] @@ -122,16 +123,14 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (widt 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 @@ -140,28 +139,24 @@ 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 + 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 + if e.State = CellState.Removed then None else let mutable darkStainPixels = 0 @@ -170,11 +165,9 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (widt 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 + if pixelOwnedByE p e neighbors then nbElement <- nbElement + 1 - if darkStainData.[y, x, 0] > 0uy - then + if darkStainData.[y, x, 0] > 0uy then darkStainPixels <- darkStainPixels + 1 if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) then Some e else None) @@ -191,62 +184,61 @@ 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 + |> 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 + let cellClass = + if e.State = CellState.Peculiar then + Peculiar - 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 + 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 - 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 }) + 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 + } + )