member this.Y = this.Cy
-let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg: Image<Gray, byte>) (config: Config.Config) : Cell list =
+let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: Image<Gray, float32>) (config: Config.Config) : Cell list =
if ellipses.IsEmpty
then
[]
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)
+ 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) =
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))
-
- // 2) Associate touching ellipses with each ellipses.
- let tree = KdTree.Tree.BuildTree ellipsesInside
- 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 = ellipsesInside |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e))
-
- // 3) Remove ellipses with a lower percentage of foreground.
- for e, neighbors in 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, _, _) -> not <| otherE.Contains xf yf)
+ let w = img.Width
+ let w_f = float w
+ 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
- totalElement <- totalElement + 1
- if fg.Data.[y, x, 0] > 0uy
- then
- fgElement <- fgElement + 1
+ 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 and remove ellipse with more than two intersections.
+ let tree = KdTree.Tree.BuildTree ellipses
+ 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
+ []
+
+ // 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).
- if (float fgElement) / (float totalElement) < config.percentageOfFgValidCell
+ // 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
- e.Removed <- true
+ 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
let minX, minY, maxX, maxY = ellipseWindow e
let mutable area = 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 fg.Data.[y, x, 0] > 0uy &&
- e.Contains xf yf &&
- neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf)
- then
- area <- area + 1
+ 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 (otherE :> Ellipse, Utils.lineFromTwoPoints p1 p2)))
+ then
+ area <- area + 1
- if area < config.minimumCellArea
+ 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
- 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
-
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
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 (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
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
projects / master-thesis.git / blobdiff