X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FClassifier.fs;h=0d2137545334091fc551d17610ff5f6f69d49243;hp=c54a3b1d27a3dd73548090dbbc51470f573fc0bb;hb=53440e757b4a4ab2a81b0f6a5dd1a2002c0133ba;hpb=21ce317bce2e1b58803bbb1be439161251478568 diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs index c54a3b1..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) = @@ -47,61 +47,82 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.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) (lines: Line list) = + 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 d1 in lines do + 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 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. + // 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 true + 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.map (fun e -> e, neighbors e) - - // 2) Remove ellipses with a high standard deviation (high contrast). - let globalStdDiviation = MathNet.Numerics.Statistics.StreamingStatistics.StandardDeviation(seq { - for y in 0 .. h - 1 do - for x in 0 .. w - 1 do - yield img.Data.[y, x, 0] |> float }) + let neighbors (e: EllipseFlaggedKd) : (EllipseFlaggedKd * PointD * PointD) list = + if not e.Removed + then + 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 + [] - for e, neighbors in List.rev ellipsesWithNeigbors do - let minX, minY, maxX, maxY = ellipseWindow e + // We reverse the list to get the lower score ellipses first. + let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) |> List.rev - let stdDiviation = MathNet.Numerics.Statistics.StreamingStatistics.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 - 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))) - then - yield img.Data.[y, x, 0] |> float }) - if stdDiviation > globalStdDiviation * config.Parameters.standardDeviationMaxRatio - then - e.Removed <- true - - // 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 @@ -113,7 +134,7 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img 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(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 area <- area + 1 @@ -139,7 +160,7 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img 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 @@ -157,11 +178,12 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img 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