+++ /dev/null
-module Classifier
-
-open System
-open System.Collections.Generic
-open System.Drawing
-
-open Emgu.CV
-open Emgu.CV.Structure
-
-open Types
-open Utils
-
-
-type private EllipseFlaggedKd (e: Ellipse) =
- inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha)
-
- member val Removed = false 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
- []
- 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) }
-
- // 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 + 0.5f)
- 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: 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
- 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 ->
- 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
- []
-
- // 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).
- 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
- 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
- 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.RBCRadius.MinArea
- 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(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
-
- 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
- then
- None
- else
- let minX, minY, maxX, maxY = ellipseWindow e
-
- 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 = 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
- 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
-
- Some { cellClass = cellClass
- center = Point(roundInt e.Cx, roundInt e.Cy)
- infectedArea = infectedPixels.Count
- stainArea = stainPixels
- elements = elements })
projects / master-thesis.git / blobdiff