X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FClassifier.fs;h=121a7f53d3bbfaddebee7ba2265602c9950d12e7;hp=0d2137545334091fc551d17610ff5f6f69d49243;hb=05be8164d308447b916544ae3ce4211500dfd8da;hpb=53440e757b4a4ab2a81b0f6a5dd1a2002c0133ba diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs index 0d21375..121a7f5 100644 --- a/Parasitemia/Parasitemia/Classifier.fs +++ b/Parasitemia/Parasitemia/Classifier.fs @@ -29,21 +29,21 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.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) - KdTree.maxX = e.Cx + (e.A + config.RBCMaxRadius) - KdTree.minY = e.Cy - (e.A + config.RBCMaxRadius) - KdTree.maxY = e.Cy + (e.A + config.RBCMaxRadius) } + 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 cx, cy = roundInt e.Cx, roundInt e.Cy - let a = int (e.A + 0.5) + let a = int (e.A + 0.5f) cx - a, cy - a, cx + a, cy + a let w = img.Width - let w_f = float w + let w_f = float32 w let h = img.Height - let h_f = float h + let h_f = float32 h // Return 'true' if the point 'p' is owned by e. // The lines represents all intersections with other ellipses. @@ -79,13 +79,17 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: 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])) - | _ -> + if e <> otherE + then + match EEOver.EEOverlapArea e otherE with + | Some (_, px, _) when px.Length > 2 -> + otherE.Removed <- true + None + | Some (area, px, py) when area > 0.f && px.Length = 2 -> + Some (otherE, PointD(px.[0], py.[0]), PointD(px.[1], py.[1])) + | _ -> + None + else None ) else [] @@ -93,38 +97,36 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: // We reverse the list to get the lower score ellipses first. let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) |> List.rev - // 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 { + 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 img.Data.[y, x, 0] }) + yield float imgData.[y, x, 0] }) for e in ellipses do if not e.Removed then - let shrinkedE = e.Scale 0.9 + 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 (float x) (float y) + if shrinkedE.Contains (float32 x) (float32 y) then - yield float img.Data.[y, x, 0] }) + yield float imgData.[y, x, 0] }) if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then e.Removed <- true + // 4) Remove ellipses with little area. - let minArea = config.RBCMinArea + let minArea = config.RBCRadius.MinArea for e, neighbors in ellipsesWithNeigbors do if not e.Removed then @@ -133,7 +135,7 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.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 p = PointD(float x, float y) + let p = PointD(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 area <- area + 1 @@ -159,7 +161,7 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: 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) + let p = PointD(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 @@ -179,8 +181,7 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: let cellClass = 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 *) + float stainPixels > config.Parameters.maxStainRatio * (float nbElement) then Peculiar elif infectedPixels.Count >= 1 @@ -194,4 +195,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: Some { cellClass = cellClass center = Point(roundInt e.Cx, roundInt e.Cy) + infectedArea = infectedPixels.Count + stainArea = stainPixels elements = elements })