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) (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.
| _ ->
None )
- let ellipsesWithNeigbors = ellipses |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e))
+ 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 })
- // 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
+ 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)
+ 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
- totalElement <- totalElement + 1
- if fg.Data.[y, x, 0] > 0uy
- then
- fgElement <- fgElement + 1
+ yield img.Data.[y, x, 0] |> float })
- if (float fgElement) / (float totalElement) < config.Parameters.percentageOfFgValidCell
+ if stdDiviation > globalStdDiviation * config.Parameters.standardDeviationMaxRatio
then
- e.Removed <- true*)
+ e.Removed <- true
// 3) Remove ellipses touching the edges.
for e in ellipses do
if e.isOutside w_f h_f 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
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 (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
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<byte>(maxY - minY + 1, maxX - minX + 1)
for y in minY .. maxY do
for x in minX .. maxX do
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
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
projects / master-thesis.git / commitdiff