X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FClassifier.fs;h=99b6edc0ad4d55518eee7096a8778d8b9b375937;hb=f9ee9f2c0c1194a6a8f7475ee2ca0b7076b32261;hp=52e7dc6ad880e6dd53f97d914fd9eee8d748b1dd;hpb=5b68d946369f998865d2dd330fd3b374b2b9a0ad;p=master-thesis.git diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs index 52e7dc6..99b6edc 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: ParasitesMarker.Result) (fg: 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: ParasitesMarker.Result) (fg: 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.maxRBCSize) * config.scale - KdTree.maxX = e.Cx + (e.A + config.maxRBCSize) * config.scale - KdTree.minY = e.Cy - (e.A + config.maxRBCSize) * config.scale - KdTree.maxY = e.Cy + (e.A + config.maxRBCSize) * config.scale } + 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 } // The minimum window to contain a given ellipse. let ellipseWindow (e: Ellipse) = @@ -40,13 +40,31 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg: let a = int (e.A + 0.5) cx - a, cy - a, cx + a, cy + a - // 1) Remove ellipses touching the edges. - let w = float fg.Width - let h = float fg.Height - let ellipsesInside = ellipses |> List.map (fun e -> EllipseFlaggedKd (e, Removed = e.isOutside w h)) + let w = img.Width + let w_f = float w + let h = img.Height + let h_f = float h - // 2) Associate touching ellipses with each ellipses. - let tree = KdTree.Tree.BuildTree ellipsesInside + // 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 + + let ellipses = ellipses |> List.map EllipseFlaggedKd + + // 1) Associate touching ellipses with each ellipses. + 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'. @@ -57,43 +75,53 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg: | _ -> None ) - let ellipsesWithNeigbors = ellipsesInside |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e)) + // 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 ellipse with a lower percentage of foreground. - for e, neighbors in ellipsesWithNeigbors do - let minX, minY, maxX, maxY = ellipseWindow 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 mutable totalElement = 0 - let mutable fgElement = 0 + for e in ellipses do + let minX, minY, maxX, maxY = ellipseWindow e - for y in minY .. maxY do - for x in minX .. maxX do - let yf, xf = float y, float x - if e.Contains xf yf && neighbors |> List.forall (fun (otherE, _, _) -> not <| otherE.Contains xf yf) - then - totalElement <- totalElement + 1 - if fg.Data.[y, x, 0] > 0uy + 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 + if e.Contains (float x) (float y) then - fgElement <- fgElement + 1 + yield img.Data.[y, x, 0] |> float }) - if totalElement < config.minimumCellArea || (float fgElement) / (float totalElement) < config.percentageOfFgValidCell + if stdDiviation > globalStdDiviation * config.Parameters.standardDeviationMaxRatio then e.Removed <- true - // 3) Define pixels associated to each ellipse and create the cells. + // 3) Remove ellipses touching the edges. + for e in ellipses do + if e.isOutside w_f h_f then e.Removed <- true - // 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 - 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. - } |> Seq.forall id + // 4) Remove ellipses with little area. + let minArea = config.RBCMinArea + for e, neighbors in ellipsesWithNeigbors do + if not e.Removed + then + let minX, minY, maxX, maxY = ellipseWindow e + + 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) + if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (Utils.lineFromTwoPoints p1 p2))) + then + area <- area + 1 + + if area < int minArea + then + e.Removed <- true + // 5) Define pixels associated to each ellipse and create the cells. ellipsesWithNeigbors |> List.choose (fun (e, neighbors) -> if e.Removed @@ -107,25 +135,14 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg: 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))) && - fg.Data.[y, x, 0] > 0uy + if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (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 @@ -134,21 +151,18 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg: 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.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.infectionPixelsRequired + elif infectedPixels.Count >= 1 then let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels for p in infectionToRemove do