open Types
open Utils
-
type private EllipseFlaggedKd (e: Ellipse) =
inherit Ellipse (e.Cx, e.Cy, e.A, e.B, e.Alpha)
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 =
+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)
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) =
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
+ 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
let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e) |> List.rev
// 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.Removed <- true
// 3) Remove ellipses with a high standard deviation (high contrast).
- let imgData = img.Data
+ // 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] })
if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
- e.Removed <- true
-
+ e.Removed <- true *)
// 4) Remove ellipses with little area.
let minArea = config.RBCRadius.MinArea
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
+ for y in (if minY < 0 then 0 else minY) .. (if maxY >= height then height - 1 else maxY) do
+ for x in (if minX < 0 then 0 else minX) .. (if maxX >= width then width - 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
e.Removed <- true
// 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
else
let minX, minY, maxX, maxY = ellipseWindow e
- let infectedPixels = List<Point>()
- let mutable stainPixels = 0
+ let nucleusPixels = List<Point>()
+ let parasitePixels = List<Point>()
+
let mutable darkStainPixels = 0
let mutable nbElement = 0
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
+ elements.[y - minY, x - minX] <- 1uy
nbElement <- nbElement + 1
- if infection.Data.[y, x, 0] > 0uy
+ if nucleusData.[y, x, 0] > 0uy
then
- infectedPixels.Add(Point(x, y))
+ nucleusPixels.Add(Point(x, y))
- if parasites.stain.Data.[y, x, 0] > 0uy
+ if parasiteData.[y, x, 0] > 0uy
then
- stainPixels <- stainPixels + 1
+ parasitePixels.Add(Point(x, y))
- if parasites.darkStain.Data.[y, x, 0] > 0uy
+ if darkStainData.[y, x, 0] > 0uy
then
darkStainPixels <- darkStainPixels + 1
+ let mutable parasiteArea = 0
+ if nucleusPixels.Count > 0
+ then
+ for parasitePixel in parasitePixels do
+ if nucleusPixels.Exists(fun p -> pown (p.X - parasitePixel.X) 2 + pown (p.Y - parasitePixel.Y) 2 <= diameterParasiteSquared)
+ then
+ parasiteArea <- parasiteArea + 1
+
let cellClass =
- if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) ||
- float stainPixels > config.Parameters.maxStainRatio * (float nbElement)
+ if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement)
then
Peculiar
- elif infectedPixels.Count >= 1
+
+ elif nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea
then
- let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
+ let infectionToRemove = Morpho.connectedComponents parasites.parasite nucleusPixels
for p in infectionToRemove do
- infection.Data.[p.Y, p.X, 0] <- 0uy
+ nucleusData.[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
+ nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0
+ parasiteArea = parasiteArea
elements = elements })
projects / master-thesis.git / blobdiff