open Types
open Utils
+type CellState = RBC = 1 | Removed = 2 | Peculiar = 3
-type private EllipseFlaggedKd (e: Ellipse) =
+type private EllipseFlaggedKd (e : Ellipse) =
inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha)
- member val Removed = false with get, set
+ member val State = CellState.RBC with get, set
interface KdTree.I2DCoords with
member this.X = this.Cx
member this.Y = this.Cy
-
-let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img: Image<Gray, float32>) (config: Config.Config) : Cell list =
- if ellipses.IsEmpty
- then
+let findCells (ellipses : Ellipse list) (parasites : ParasitesMarker.Result) (width : int) (height : int) (config : Config.Config) : Cell list =
+ if ellipses.IsEmpty then
[]
else
- 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.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) }
+ 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 ellipseWindow (e : Ellipse) =
let cx, cy = roundInt e.Cx, roundInt e.Cy
let a = int (e.A + 0.5f)
cx - a, cy - a, cx + a, cy + a
- let w = img.Width
- let w_f = float32 w
- let h = img.Height
- let h_f = float32 h
-
// Return 'true' if the point 'p' is owned by e.
// The lines represents all intersections with other ellipses.
- let pixelOwnedByE (p: PointF) (e: Ellipse) (others: (Ellipse * Line) list) =
+ let pixelOwnedByE (p : PointF) (e : EllipseFlaggedKd) (neighbors : (EllipseFlaggedKd * PointF * PointF) list) =
e.Contains p.X p.Y &&
seq {
- let c = PointF(e.Cx, e.Cy)
-
- for e', d1 in others do
- let d2 = lineFromTwoPoints c p
- let c' = PointF(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
- let delta, delta' =
- let d = c.X - p.X
- // To avoid rounding.
- if abs d < 0.001f then c.Y - p.Y, c.Y - p'.Y else d, c.X - p'.X
-
- // Yield 'false' when the point is owned by another ellipse.
- if case1
- then
- yield sign delta <> sign delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p
+ let c = PointF (e.Cx, e.Cy)
+
+ for e', d1 in
+ (neighbors
+ |> List.choose (
+ fun (otherE, p1, p2) ->
+ if otherE.State = CellState.Removed then
+ None
+ else
+ Some (otherE, Utils.lineFromTwoPoints p1 p2)
+ )) do
+ if e'.State = e.State then // Peculiar vs peculiar or RBC vs RBC.
+ let d2 = lineFromTwoPoints c p
+ let c' = PointF (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 not (Single.IsInfinity d2.A) then
+ let p' = Utils.pointFromTwoLines d1 d2
+ let delta, delta' =
+ let dx1, dx2 = (c.X - p.X), (c.X - p'.X)
+ // To avoid rounding issue.
+ if abs dx1 < 0.01f || abs dx2 < 0.01f then c.Y - p.Y, c.Y - p'.Y else dx1, dx2
+
+ // Yield 'false' when the point is owned by another ellipse.
+ if case1 then
+ yield sign delta <> sign delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p
+ else
+ yield sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p
else
- yield sign delta = sign delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints c p
+ yield case1
+
+ elif e.State = CellState.Peculiar then // A peculiar always win against a RBC.
+ yield true
else
- yield case1
+ yield not <| e'.Contains p.X p.Y
+
} |> 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 * PointF * PointF) list =
- if not e.Removed
- then
+ let neighbors (e : EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list =
+ if e.State <> CellState.Removed then
tree.Search (searchRegion e)
// We only keep the ellipses touching 'e'.
- |> List.choose (fun otherE ->
- 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, PointF(px.[0], py.[0]), PointF(px.[1], py.[1]))
- | _ ->
+ |> List.choose (
+ fun otherE ->
+ if e <> otherE then
+ match EEOver.EEOverlapArea e otherE with
+ | Some (_, px, _) when px.Length > 2 ->
+ otherE.State <- CellState.Removed
+ None
+ | Some (area, px, py) when area > 0.f && px.Length = 2 ->
+ Some (otherE, PointF (px.[0], py.[0]), PointF (px.[1], py.[1]))
+ | _ ->
+ None
+ else
None
- else
- 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
+ let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e)
// 2) Remove ellipses touching the edges.
+ let widthF, heightF = float32 width, float32 height
for e in ellipses do
- if e.isOutside w_f h_f then e.Removed <- true
+ if e.IsOutside widthF heightF then e.State <- CellState.Removed
// 3) Remove ellipses with a high standard deviation (high contrast).
- let imgData = img.Data
- let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation(seq {
+ // Obsolete. It was useful when the ellipses result quality wasn't good.
+ (* 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 imgData.[y, x, 0] })
for e in ellipses do
- if not e.Removed
- then
+ if not e.Removed then
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 (float32 x) (float32 y)
- then
+ if shrinkedE.Contains (float32 x) (float32 y) then
yield float imgData.[y, x, 0] })
if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
- e.Removed <- true
-
+ e.Removed <- true *)
// 4) Remove ellipses with little area.
let minArea = config.RBCRadius.MinArea
for e, neighbors in ellipsesWithNeigbors do
- if not e.Removed
- then
+ if e.State <> CellState.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 = PointF(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
+ for y = (if minY < 0 then 0 else minY) to (if maxY >= height then height - 1 else maxY) do
+ for x = (if minX < 0 then 0 else minX) to (if maxX >= width then width - 1 else maxX) do
+ let p = PointF (float32 x, float32 y)
+ if pixelOwnedByE p e neighbors then
area <- area + 1
- if area < int minArea
- then
- e.Removed <- true
+ if area < int minArea then
+ e.State <- CellState.Removed
+
+ // 5) Define non-rbc (peculiar) cells.
+ let darkStainData = parasites.darkStain.Data
+ ellipsesWithNeigbors
+ |> List.choose (
+ fun (e, neighbors) ->
+ if e.State = CellState.Removed then
+ None
+ else
+ let mutable darkStainPixels = 0
+ let mutable nbElement = 0
+ let minX, minY, maxX, maxY = ellipseWindow e
+ for y = minY to maxY do
+ for x = minX to maxX do
+ let p = PointF (float32 x, float32 y)
+ if pixelOwnedByE p e neighbors then
+ nbElement <- nbElement + 1
+ if darkStainData.[y, x, 0] > 0uy then
+ darkStainPixels <- darkStainPixels + 1
+
+ if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) then Some e else None
+ )
+
+ // We do not change the state during the process to avoid to have peculiar neighbors which change the behavior of 'pixelOwnedByE'.
+ |> List.iter (fun e -> e.State <- CellState.Peculiar)
// 5) Define pixels associated to each ellipse and create the cells.
+ let diameterParasiteSquared = (2.f * config.RBCRadius.ParasiteRadius) ** 2.f |> roundInt
+ let minimumParasiteArea = config.RBCRadius.MinimumParasiteArea |> roundInt
+
+ let nucleusData = parasites.nucleus.Copy().Data // Will be modified thus the copy.
+ let parasiteData = parasites.parasite.Data
+ let darkStainData = parasites.darkStain.Data
+
ellipsesWithNeigbors
- |> List.choose (fun (e, neighbors) ->
- if e.Removed
- then
- None
- else
- let minX, minY, maxX, maxY = ellipseWindow e
+ |> List.choose (
+ fun (e, neighbors) ->
+ if e.State = CellState.Removed then
+ None
+ else
+ let minX, minY, maxX, maxY = ellipseWindow e
+
+ let nucleusPixels = List<Point> ()
+ let parasitePixels = List<Point> ()
+
+ let mutable nbElement = 0
+
+ let elements = new Matrix<byte> (maxY - minY + 1, maxX - minX + 1)
+ for y = minY to maxY do
+ for x = minX to maxX do
+ let p = PointF (float32 x, float32 y)
+ if pixelOwnedByE p e neighbors then
+ elements.[y - minY, x - minX] <- 1uy
+ nbElement <- nbElement + 1
+
+ if nucleusData.[y, x, 0] > 0uy then
+ nucleusPixels.Add (Point (x, y))
+
+ if parasiteData.[y, x, 0] > 0uy then
+ parasitePixels.Add (Point (x, y))
+
+ let parasiteArea =
+ if nucleusPixels.Count > 0 then
+ seq {
+ for parasitePixel in parasitePixels do
+ if nucleusPixels.Exists (fun p -> pown (p.X - parasitePixel.X) 2 + pown (p.Y - parasitePixel.Y) 2 <= diameterParasiteSquared) then
+ yield 1
+ } |> Seq.sum
+ else
+ 0
- let infectedPixels = List<Point>()
- let mutable stainPixels = 0
- let mutable darkStainPixels = 0
- let mutable nbElement = 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 = PointF(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
- nbElement <- nbElement + 1
-
- if infection.Data.[y, x, 0] > 0uy
- then
- infectedPixels.Add(Point(x, y))
-
- if parasites.stain.Data.[y, x, 0] > 0uy
- then
- stainPixels <- stainPixels + 1
-
- if parasites.darkStain.Data.[y, x, 0] > 0uy
- then
- darkStainPixels <- darkStainPixels + 1
-
- let cellClass =
- if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) ||
- float stainPixels > config.Parameters.maxStainRatio * (float nbElement)
- then
- Peculiar
- elif infectedPixels.Count >= 1
- then
- let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
- for p in infectionToRemove do
- infection.Data.[p.Y, p.X, 0] <- 0uy
- InfectedRBC
- else
- HealthyRBC
+ let cellClass =
+ if e.State = CellState.Peculiar then
+ Peculiar
- Some { cellClass = cellClass
- center = Point(roundInt e.Cx, roundInt e.Cy)
- infectedArea = infectedPixels.Count
- stainArea = stainPixels
- elements = elements })
+ elif nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea then
+ let infectionToRemove = Morpho.connectedComponents parasites.parasite nucleusPixels
+ for p in infectionToRemove do
+ nucleusData.[p.Y, p.X, 0] <- 0uy
+ InfectedRBC
+
+ else
+ HealthyRBC
+
+ Some
+ {
+ cellClass = cellClass
+ center = Point (roundInt e.Cx, roundInt e.Cy)
+ nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0
+ parasiteArea = parasiteArea
+ elements = elements
+ }
+ )
projects / master-thesis.git / blobdiff