--- /dev/null
+module ParasitemiaCore.Ellipse
+
+open System
+open System.Collections.Generic
+open System.Drawing
+
+open MathNet.Numerics.LinearAlgebra
+
+open Emgu.CV
+open Emgu.CV.Structure
+
+open Utils
+open Config
+open MatchingEllipses
+open Const
+
+type private SearchExtremum = Minimum | Maximum
+
+let private goldenSectionSearch (f: float -> float) (nbIter: int) (xmin: float) (xmax: float) (searchExtremum: SearchExtremum) : (float * float) =
+ let gr = 1. / 1.6180339887498948482
+ let mutable a = xmin
+ let mutable b = xmax
+ let mutable c = b - gr * (b - a)
+ let mutable d = a + gr * (b - a)
+
+ for i in 1 .. nbIter do
+ let mutable fc = f c
+ let mutable fd = f d
+
+ if searchExtremum = Maximum
+ then
+ let tmp = fc
+ fc <- fd
+ fd <- tmp
+
+ if fc < fd
+ then
+ b <- d
+ d <- c
+ c <- b - gr * (b - a)
+ else
+ a <- c
+ c <- d
+ d <- a + gr * (b - a)
+
+ let x = (b + a) / 2.
+ x, f x
+
+// Ellipse.A is always equal or greater than Ellipse.B.
+// Ellipse.Alpha is between 0 and Pi.
+let ellipse (p1x: float) (p1y: float) (m1: float) (p2x: float) (p2y: float) (m2: float) (p3x: float) (p3y: float) : Types.Ellipse option =
+ let accuracy_extremum_search_1 = 10 // 3
+ let accuracy_extremum_search_2 = 10 // 4
+
+ // p3 as the referencial.
+ let p1x = p1x - p3x
+ let p1y = p1y - p3y
+
+ let p2x = p2x - p3x
+ let p2y = p2y - p3y
+
+ // Convert to polar coordinates.
+ let alpha1 = atan m1
+ let alpha2 = atan m2
+
+ let r1 = sqrt (p1x ** 2. + p1y ** 2.)
+ let theta1 = atan2 p1y p1x
+
+ let r2 = sqrt (p2x ** 2. + p2y ** 2.)
+ let theta2 = atan2 p2y p2x
+
+ let valid =
+ 4. * sin (alpha1 - theta1) * (-r1 * sin (alpha1 - theta1) + r2 * sin (alpha1 - theta2)) *
+ sin (alpha2 - theta2) * (-r1 * sin (alpha2 - theta1) + r2 * sin (alpha2 - theta2)) +
+ r1 * r2 * sin (alpha1 - alpha2) ** 2. * sin (theta1 - theta2) ** 2. < 0.
+
+ if valid
+ then
+ let r theta =
+ (r1 * r2 * (r1 * (cos (alpha2 + theta - theta1 - theta2) - cos (alpha2 - theta) * cos (theta1 - theta2)) * sin (alpha1 - theta1) + r2 * (-cos (alpha1 + theta - theta1 - theta2) + cos (alpha1 - theta) * cos (theta1 - theta2)) * sin (alpha2 - theta2)) * sin (theta1 - theta2)) /
+ (sin (alpha1 - theta1) * sin (alpha2 - theta2) * (r1 * sin (theta - theta1) - r2 * sin (theta - theta2)) ** 2. - r1 * r2 * sin (alpha1 - theta) * sin (alpha2 - theta) * sin (theta1 - theta2) ** 2.)
+
+ let rabs = r >> abs
+
+ // We search for an interval [theta_a, theta_b] and assume the function is unimodal in this interval.
+ let thetaTan, _ = goldenSectionSearch rabs accuracy_extremum_search_1 0. Math.PI Maximum
+ let rTan = r thetaTan
+
+ let PTanx = rTan * cos thetaTan
+ let PTany = rTan * sin thetaTan
+
+ let d1a = tan alpha1
+ let d1b = -d1a * p1x + p1y
+
+ let d2a = tan alpha2
+ let d2b = -d2a * p2x + p2y
+
+ let d3a = -1. / tan thetaTan
+ let d3b = -d3a * PTanx + PTany
+
+ let Ux = -(d1b - d2b) / (d1a - d2a)
+ let Uy = -(d2a * d1b - d1a * d2b) / (d1a - d2a)
+
+ let Vx = -(d1b - d3b) / (d1a - d3a)
+ let Vy = -(d3a * d1b - d1a * d3b) / (d1a - d3a)
+
+ let Wx = p1x + (p2x - p1x) / 2.
+ let Wy = p1y + (p2y - p1y) / 2.
+
+ let Zx = p1x + (PTanx - p1x) / 2.
+ let Zy = p1y + (PTany - p1y) / 2.
+
+ let va = -(-Vy + Zy) / (Vx - Zx)
+ let vb = -(Zx * Vy - Vx * Zy) / (Vx - Zx)
+
+ let ua = -(-Uy + Wy) / (Ux - Wx)
+ let ub = -(Wx * Uy - Ux * Wy) / (Ux - Wx)
+
+ let cx = -(vb - ub) / (va - ua)
+ let cy = -(ua * vb - va * ub) / (va - ua)
+
+ let rc = sqrt (cx ** 2. + cy ** 2.)
+ let psi = atan2 cy cx
+
+ let rellipse theta =
+ sqrt (
+ rc ** 2. + (r1 ** 2. * r2 ** 2. * (r1 * (cos (alpha2 + theta - theta1 - theta2) - cos (alpha2 - theta) * cos (theta1 - theta2)) * sin (alpha1 - theta1) + r2 * (-cos (alpha1 + theta - theta1 - theta2) + cos (alpha1 - theta) * cos (theta1 - theta2)) * sin (alpha2 - theta2)) ** 2. * sin (theta1 - theta2) ** 2.) /
+ (sin (alpha1 - theta1) * sin (alpha2 - theta2) * (r1 * sin (theta - theta1) - r2 * sin (theta - theta2)) ** 2. - r1 * r2 * sin (alpha1 - theta) * sin (alpha2 - theta) * sin (theta1 - theta2) ** 2.) ** 2. -
+ (2. * r1 * r2 * rc * cos (theta - psi) * (r1 * (cos (alpha2 + theta - theta1 - theta2) - cos (alpha2 - theta) * cos (theta1 - theta2)) * sin (alpha1 - theta1) + r2 * (-cos (alpha1 + theta - theta1 - theta2) + cos (alpha1 - theta) * cos (theta1 - theta2)) * sin (alpha2 - theta2)) * sin (theta1 - theta2)) /
+ (sin (alpha1 - theta1) * sin (alpha2 - theta2) * (r1 * sin (theta - theta1) - r2 * sin (theta - theta2)) ** 2. - r1 * r2 * sin (alpha1 - theta) * sin (alpha2 - theta) * sin (theta1 - theta2) ** 2.))
+
+ // We search for an interval [theta_a, theta_b] and assume the function is unimodal in this interval.
+ let r1eTheta, r1e = goldenSectionSearch rellipse accuracy_extremum_search_2 0. (Math.PI / 2.) Maximum // Pi/2 and not pi because the period is Pi.
+ let r2eTheta, r2e = goldenSectionSearch rellipse accuracy_extremum_search_2 0. (Math.PI / 2.) Minimum
+
+ let rr1e = r r1eTheta
+ let r1ex = rr1e * cos r1eTheta
+ let r1ey = rr1e * sin r1eTheta
+ let mutable alpha = atan ((r1ey - cy) / (r1ex - cx))
+ if alpha < 0.
+ then
+ alpha <- alpha + Math.PI
+
+ // Ride off the p3 referential.
+ let cx = cx + p3x
+ let cy = cy + p3y
+
+ Some (Types.Ellipse(float32 cx, float32 cy, float32 r1e, float32 r2e, float32 alpha))
+ else
+ None
+
+let ellipse2 (p1x: float) (p1y: float) (m1: float) (p2x: float) (p2y: float) (m2: float) (p3x: float) (p3y: float) : Types.Ellipse option =
+ let p0 = pointFromTwoLines (Types.Line(float32 m1, float32 (p1y - m1 * p1x))) (Types.Line(float32 m2, float32(p2y - m2 * p2x)))
+ let p0x, p0y = float p0.X, float p0.Y
+
+ let s = matrix [[ 1.; 0.; 0. ]
+ [ 0.; 0.; -0.5 ]
+ [ 0.; -0.5; 0. ]]
+
+ let v0 = matrix [[ 1.; p0x; p0y ]]
+ let v1 = matrix [[ 1.; p1x; p1y ]]
+ let v2 = matrix [[ 1.; p2x; p2y ]]
+ let v3 = matrix [[ 1.; p3x; p3y ]]
+
+ let p = (v3.Stack(v1).Stack(v2).Determinant() * v0).Stack(v0.Stack(v3).Stack(v2).Determinant() * v1).Stack(v0.Stack(v1).Stack(v3).Determinant() * v2).Transpose()
+ let conicMat = p * s.Inverse() * p.Transpose()
+ let a = conicMat.[0, 0]
+ let b = conicMat.[0, 1]
+ let c = conicMat.[1, 1]
+ let d = conicMat.[0, 2]
+ let e = conicMat.[1, 2]
+ let f = conicMat.[2, 2]
+
+ // Center.
+ let cx = b / a
+ let cy = d / a
+
+ let at = c * f - e ** 2. + (e * d - b * f) * cx + (b * e - c * d) * cy
+ if at = 0.
+ then
+ None
+ else
+ let q = (-1. / at) * (matrix [[ a * f - d ** 2.0; b * d - a * e ]; [ b * d - a * e; a * c - b ** 2.0 ]])
+ let eigen = q.Evd()
+ let eigenValues = eigen.EigenValues
+ let lambda = eigenValues.[1].Real
+ let mu = eigenValues.[0].Real
+
+ if lambda <= 0. || mu <= 0.
+ then
+ None
+ else
+ let r1, r2 = 1. / (sqrt lambda), 1. / (sqrt mu)
+
+ let eigenVectors = eigen.EigenVectors
+ let v_a = eigenVectors.[0, 0]
+ let v_b = eigenVectors.[1, 0] // [0, 1]
+
+ // Angle against the longest axis.
+ let phi = (if r2 > r1 then atan (v_b / v_a) else atan (v_a / v_b))
+
+ let phi' = if phi < 0. then phi + Math.PI else phi
+ let majorAxis, minorAxis = if r1 > r2 then r1, r2 else r2, r1
+
+ Some (Types.Ellipse(float32 cx, float32 cy, float32 majorAxis, float32 minorAxis, float32 phi'))
+
+
+let private vectorRotation (p1x: float32) (p1y: float32) (v1x: float32) (v1y: float32) (px: float32) (py: float32) : float32 =
+ let mutable rotation = 1.f
+ if p1y > py
+ then
+ if v1x > 0.f
+ then
+ rotation <- -1.f
+ elif p1y < py
+ then
+ if v1x < 0.f
+ then
+ rotation <- -1.f
+ elif p1x > px
+ then
+ if v1y < 0.f
+ then
+ rotation <- -1.f
+ elif p1x < px
+ then
+ if v1y > 0.f
+ then
+ rotation <- -1.f
+ rotation
+
+let private areVectorsValid (p1x: float32) (p1y: float32) (p2x: float32) (p2y: float32) (v1x: float32) (v1y: float32) (v2x: float32) (v2y: float32) : (float32 * float32) option =
+ let m1 = -v1x / v1y
+ let m2 = -v2x / v2y
+
+ let b1 = -m1 * p1x + p1y
+ let b2 = -m2 * p2x + p2y
+ let px = -((b1 - b2) / (m1 - m2))
+ let py = -((m2 * b1 - m1 * b2) / (m1 - m2))
+
+ let rot1 = vectorRotation p1x p1y v1x v1y px py
+ let rot2 = vectorRotation p2x p2y v2x v2y px py
+
+ if rot1 = rot2
+ then
+ None
+ else
+ let alpha1 = atan2 (p1y - py) (p1x - px)
+ let alpha2 = atan2 (p2y - py) (p2x - px)
+
+ let alpha1' = if alpha1 < 0.f then 2.f * PI + alpha1 else alpha1
+ let alpha2' = if alpha2 < 0.f then 2.f * PI + alpha2 else alpha2
+
+ let diff = rot1 * alpha1' + rot2 * alpha2'
+
+ if diff > PI || (diff < 0.f && diff > -PI)
+ then
+ None
+ else
+ Some (m1, m2)
+
+
+let find (edges: Matrix<byte>)
+ (xGradient: Image<Gray, float32>)
+ (yGradient: Image<Gray, float32>)
+ (config: Config) : MatchingEllipses =
+
+ let r1, r2 = config.RBCRadius.Min, config.RBCRadius.Max
+ let incrementWindowDivisor = 4.f
+
+ // We choose a window size for which the biggest ellipse can always be fitted in.
+ let windowSize = roundInt (2.f * r2 / (incrementWindowDivisor - 1.f) * incrementWindowDivisor)
+ let factorNbPick = config.Parameters.factorNbPick
+
+ let increment = windowSize / (int incrementWindowDivisor)
+
+ let radiusTolerance = (r2 - r1) * 0.2f
+
+ let squaredMinimumDistance = (float r2 / 1.5) ** 2.
+ let inline squaredDistance x1 y1 x2 y2 = (x1 - x2) ** 2. + (y1 - y2) ** 2.
+
+ let h = edges.Height
+ let w = edges.Width
+ let h_f = float32 h
+ let w_f = float32 w
+
+ let mutable last_i, last_j = Int32.MaxValue, Int32.MaxValue
+
+ let currentElements = List<Point>()
+
+ let edgesData = edges.Data
+ let xDirData = xGradient.Data
+ let yDirData = yGradient.Data
+
+ let rng = Random(42)
+
+ let ellipses = MatchingEllipses(config.RBCRadius.Pixel)
+
+ for window_i in -windowSize + increment .. increment .. h - increment do
+ for window_j in -windowSize + increment .. increment .. w - increment do
+
+ let window_i_begin = if window_i < 0 then 0 else window_i
+ let window_i_end = if window_i + windowSize - 1 >= h then h - 1 else window_i + windowSize - 1
+ let window_j_begin = if window_j < 0 then 0 else window_j
+ let window_j_end = if window_j + windowSize - 1 >= w then w - 1 else window_j + windowSize - 1
+
+ // Remove old elements.
+ let indexFirstElement = currentElements.FindIndex(fun p -> p.X >= window_j_begin)
+ if indexFirstElement > 0
+ then currentElements.RemoveRange(0, indexFirstElement)
+
+ // Add the new elements.
+ let newElemsBegin_j = window_j + windowSize - increment
+ let newElemsEnd_j = window_j + windowSize - 1
+ for j in (if newElemsBegin_j < 0 then 0 else newElemsBegin_j) .. (if newElemsEnd_j >= w then w - 1 else newElemsEnd_j) do
+ for i in window_i_begin .. window_i_end do
+ if edgesData.[i, j] = 1uy
+ then currentElements.Add(Point(j, i))
+
+ if currentElements.Count >= 10
+ then
+ let mutable nbOfPicks = (float currentElements.Count) * factorNbPick |> int
+ while nbOfPicks > 0 do
+ let p1 = currentElements.[rng.Next(currentElements.Count)]
+ let p2 = currentElements.[rng.Next(currentElements.Count)]
+ let p3 = currentElements.[rng.Next(currentElements.Count)]
+ if p1 <> p2 && p1 <> p3 && p2 <> p3
+ then
+ nbOfPicks <- nbOfPicks - 1
+ let p1yf, p1xf = float p1.Y, float p1.X
+ let p2yf, p2xf = float p2.Y, float p2.X
+ let p3yf, p3xf = float p3.Y, float p3.X
+ if squaredDistance p1xf p1yf p2xf p2yf >= squaredMinimumDistance &&
+ squaredDistance p1xf p1yf p3xf p3yf >= squaredMinimumDistance &&
+ squaredDistance p2xf p2yf p3xf p3yf >= squaredMinimumDistance
+ then
+ match areVectorsValid (float32 p1xf) (float32 p1yf) (float32 p2xf) (float32 p2yf) -xDirData.[p1.Y, p1.X, 0] -yDirData.[p1.Y, p1.X, 0] -xDirData.[p2.Y, p2.X, 0] -yDirData.[p2.Y, p2.X, 0] with
+ | Some (m1, m2) ->
+ //let pouet = ellipse2 p1xf p1yf (float m1) p2xf p2yf (float m2) p3xf p3yf
+ match ellipse2 p1xf p1yf (float m1) p2xf p2yf (float m2) p3xf p3yf with
+ | Some e when e.Cx > 0.f && e.Cx < w_f - 1.f && e.Cy > 0.f && e.Cy < h_f - 1.f &&
+ e.A >= r1 - radiusTolerance && e.A <= r2 + radiusTolerance && e.B >= r1 - radiusTolerance && e.B <= r2 + radiusTolerance ->
+ ellipses.Add e
+ | _ -> ()
+ | _ -> ()
+
+ currentElements.Clear()
+
+ ellipses
+
projects / master-thesis.git / blobdiff