X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FClassifier.fs;h=0d2137545334091fc551d17610ff5f6f69d49243;hp=a12e595b372e90ea08ef95c04a6e4eea1dbe235f;hb=53440e757b4a4ab2a81b0f6a5dd1a2002c0133ba;hpb=6d99ab0dadc57e91cd846844b620fc90b52a2f96 diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs index a12e595..0d21375 100644 --- a/Parasitemia/Parasitemia/Classifier.fs +++ b/Parasitemia/Parasitemia/Classifier.fs @@ -21,7 +21,7 @@ type private EllipseFlaggedKd (e: Ellipse) = member this.Y = this.Cy -let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img: Image) (config: Config.Config) : Cell list = +let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: Image) (config: Config.Config) : Cell list = if ellipses.IsEmpty then [] @@ -29,10 +29,10 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img 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.RBCMaxRadius) * config.Parameters.scale - KdTree.maxX = e.Cx + (e.A + config.RBCMaxRadius) * config.Parameters.scale - KdTree.minY = e.Cy - (e.A + config.RBCMaxRadius) * config.Parameters.scale - KdTree.maxY = e.Cy + (e.A + config.RBCMaxRadius) * config.Parameters.scale } + let searchRegion (e: Ellipse) = { KdTree.minX = e.Cx - (e.A + config.RBCMaxRadius) + KdTree.maxX = e.Cx + (e.A + config.RBCMaxRadius) + KdTree.minY = e.Cy - (e.A + config.RBCMaxRadius) + KdTree.maxY = e.Cy + (e.A + config.RBCMaxRadius) } // The minimum window to contain a given ellipse. let ellipseWindow (e: Ellipse) = @@ -45,47 +45,86 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img let h = img.Height let h_f = float 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. + // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections. let tree = KdTree.Tree.BuildTree ellipses - let neighbors (e: Ellipse) : (EllipseFlaggedKd * PointD * PointD) list = - tree.Search (searchRegion e) - // We only keep the ellipses touching 'e'. - |> List.choose (fun otherE -> - match EEOver.EEOverlapArea e otherE with - | Some (area, px, py) when area > 0.0 && px.Length >= 2 && py.Length >= 2 -> - Some (otherE, PointD(px.[0], py.[0]), PointD(px.[1], py.[1])) - | _ -> - None ) - - let ellipsesWithNeigbors = ellipses |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e)) - - // 2) Remove ellipses with a lower percentage of foreground. (taken from the lower score to the highest). - (*for e, neighbors in List.rev ellipsesWithNeigbors do - let minX, minY, maxX, maxY = ellipseWindow e - - let mutable totalElement = 0 - let mutable fgElement = 0 - for y in (if minY < 0 then 0 else minY) .. (if maxY >= fg.Height then fg.Height - 1 else maxY) do - for x in (if minX < 0 then 0 else minX) .. (if maxX >= fg.Width then fg.Width - 1 else maxX) do - let yf, xf = float y, float x - if e.Contains xf yf && neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf) - then - totalElement <- totalElement + 1 - if fg.Data.[y, x, 0] > 0uy - then - fgElement <- fgElement + 1 - - if (float fgElement) / (float totalElement) < config.Parameters.percentageOfFgValidCell + let neighbors (e: EllipseFlaggedKd) : (EllipseFlaggedKd * PointD * PointD) list = + if not e.Removed then - e.Removed <- true*) + tree.Search (searchRegion e) + // We only keep the ellipses touching 'e'. + |> List.choose (fun otherE -> + match EEOver.EEOverlapArea e otherE with + | Some (_, px, _) when px.Length > 2 -> + otherE.Removed <- true + None + | Some (area, px, py) when area > 0.0 && px.Length = 2 -> + Some (otherE, PointD(px.[0], py.[0]), PointD(px.[1], py.[1])) + | _ -> + 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 - // 3) Remove ellipses touching the edges. + + // 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). + + // CvInvoke.Normalize(img, img, 0.0, 255.0, CvEnum.NormType.MinMax) // Not needed. + + let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation(seq { + for y in 0 .. h - 1 do + for x in 0 .. w - 1 do + yield float img.Data.[y, x, 0] }) + + for e in ellipses do + if not e.Removed + then + let shrinkedE = e.Scale 0.9 + 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 (float x) (float y) + then + yield float img.Data.[y, x, 0] }) + + if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then + e.Removed <- true + // 4) Remove ellipses with little area. + let minArea = config.RBCMinArea for e, neighbors in ellipsesWithNeigbors do if not e.Removed then @@ -94,34 +133,16 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.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 yf, xf = float y, float x - if e.Contains xf yf && - neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf) - then - area <- area + 1 + let p = PointD(float x, float 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 config.RBCMinArea + if area < int minArea then e.Removed <- true // 5) Define pixels associated to each ellipse and create the cells. - - // Return 'true' if the point 'p' is owned by e. - // The lines represents all intersections with other ellipses. - let pixelOwnedByE (p: PointD) (e: Ellipse) (lines: Line list) = - e.Contains p.X p.Y && - seq { - let c = PointD(e.Cx, e.Cy) - for d1 in lines do - let d2 = Utils.lineFromTwoPoints c p - if d2.Valid - then - let p' = Utils.pointFromTwoLines d1 d2 - yield sign (c.X - p.X) <> sign (c.X - p'.X) || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p // 'false' -> the point is owned by another ellipse. - else - yield true - } |> Seq.forall id - ellipsesWithNeigbors |> List.choose (fun (e, neighbors) -> if e.Removed @@ -135,24 +156,14 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img let mutable darkStainPixels = 0 let mutable nbElement = 0 - let mutable stain_x = 0.0 - let mutable stain_x2 = 0.0 - let mutable stain_y = 0.0 - let mutable stain_y2 = 0.0 - - let mutable sumCoords_y = 0 - let mutable sumCoords_x = 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(float x, float y) - if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (Utils.lineFromTwoPoints p1 p2))) + 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 - sumCoords_y <- sumCoords_y + y - sumCoords_x <- sumCoords_x + x if infection.Data.[y, x, 0] > 0uy then @@ -161,21 +172,18 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img if parasites.stain.Data.[y, x, 0] > 0uy then stainPixels <- stainPixels + 1 - stain_x <- stain_x + (float x) - stain_x2 <- stain_x2 + (float x) ** 2.0 - stain_y <- stain_y + (float y) - stain_y2 <- stain_y2 + (float y) ** 2.0 if parasites.darkStain.Data.[y, x, 0] > 0uy then darkStainPixels <- darkStainPixels + 1 let cellClass = - if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) (* || + if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) || + float stainPixels > config.Parameters.maxStainRatio * (float nbElement) (* || sqrt (((float sumCoords_x) / (float nbElement) - e.Cx) ** 2.0 + ((float sumCoords_y) / (float nbElement) - e.Cy) ** 2.0) > e.A * config.maxOffcenter *) then Peculiar - elif infectedPixels.Count > config.Parameters.parasitePixelsRequired + elif infectedPixels.Count >= 1 then let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels for p in infectionToRemove do