4 open System.Collections.Generic
14 type private EllipseFlaggedKd (e
: Ellipse) =
15 inherit Ellipse (e
.Cx, e
.Cy, e
.A, e
.B, e
.Alpha)
17 member val Removed = false with get
, set
19 interface KdTree.I2DCoords with
20 member this
.X = this
.Cx
21 member this
.Y = this
.Cy
24 let findCells (ellipses
: Ellipse list) (parasites
: ParasitesMarker.Result) (img
: Image<Gray, float32
>) (config
: Config.Config) : Cell list =
29 let infection = parasites
.infection.Copy() // To avoid to modify the parameter.
31 // This is the minimum window size to check if other ellipses touch 'e'.
32 let searchRegion (e
: Ellipse) = { KdTree.minX
= e
.Cx - (e
.A + config
.RBCMaxRadius)
33 KdTree.maxX
= e
.Cx + (e
.A + config
.RBCMaxRadius)
34 KdTree.minY
= e
.Cy - (e
.A + config
.RBCMaxRadius)
35 KdTree.maxY
= e
.Cy + (e
.A + config
.RBCMaxRadius) }
37 // The minimum window to contain a given ellipse.
38 let ellipseWindow (e
: Ellipse) =
39 let cx, cy
= roundInt
e.Cx, roundInt
e.Cy
40 let a = int (e.A + 0.5)
41 cx - a, cy
- a, cx + a, cy
+ a
48 // Return 'true' if the point 'p' is owned by e.
49 // The lines represents all intersections with other ellipses.
50 let pixelOwnedByE (p
: PointD) (e: Ellipse) (others
: (Ellipse * Line) list) =
53 let c = PointD(e.Cx, e.Cy)
54 for e', d1 in others do
55 let d2 = Utils.lineFromTwoPoints c p
56 let c' = PointD(e'.Cx, e'.Cy)
57 let v = pointFromTwoLines
d1 (lineFromTwoPoints
c c')
58 let case1 = sign (v.X - c.X) <> sign (v.X - c'.X) || Utils.squaredDistanceTwoPoints
v c > Utils.squaredDistanceTwoPoints
v c'
61 let p' = Utils.pointFromTwoLines
d1 d2
62 // Yield 'false' when the point is owned by another ellipse.
65 yield sign
(c.X - p.X) <> sign
(c.X - p'.X) || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints
c p
67 yield sign
(c.X - p.X) = sign
(c.X - p'.X) && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints
c p
72 let ellipses = ellipses |> List.map
EllipseFlaggedKd
74 // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections.
75 let tree = KdTree.Tree.BuildTree ellipses
76 let neighbors (e: EllipseFlaggedKd) : (EllipseFlaggedKd * PointD * PointD) list =
79 tree.Search (searchRegion e)
80 // We only keep the ellipses touching 'e'.
81 |> List.choose
(fun otherE
->
82 match EEOver.EEOverlapArea e otherE with
83 | Some (_
, px
, _
) when px
.Length > 2 ->
84 otherE.Removed <- true
86 | Some (area
, px
, py
) when area
> 0.0 && px
.Length = 2 ->
87 Some (otherE, PointD(px
.[0], py
.[0]), PointD(px
.[1], py
.[1]))
93 // We reverse the list to get the lower score ellipses first.
94 let ellipsesWithNeigbors = ellipses |> List.map
(fun e -> e, neighbors e) |> List.rev
97 // 2) Remove ellipses touching the edges.
99 if e.isOutside
w_f h_f then e.Removed <- true
101 // 3) Remove ellipses with a high standard deviation (high contrast).
103 // CvInvoke.Normalize(img, img, 0.0, 255.0, CvEnum.NormType.MinMax) // Not needed.
105 let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation(seq
{
106 for y
in 0 .. h - 1 do
107 for x
in 0 .. w - 1 do
108 yield
float img.Data.[y
, x
, 0] })
113 let shrinkedE = e.Scale 0.9
114 let minX, minY
, maxX
, maxY
= ellipseWindow shrinkedE
116 let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq
{
117 for y
in (if minY
< 0 then 0 else minY) .. (if maxY
>= h then h - 1 else maxY) do
118 for x
in (if minX < 0 then 0 else minX) .. (if maxX
>= w then w - 1 else maxX) do
119 if shrinkedE.Contains (float x) (float y)
121 yield
float img.Data.[y, x, 0] })
123 if stdDeviation > globalStdDeviation * config
.Parameters.standardDeviationMaxRatio
then
126 // 4) Remove ellipses with little area.
127 let minArea = config
.RBCMinArea
128 for e, neighbors in ellipsesWithNeigbors do
131 let minX, minY, maxX, maxY = ellipseWindow e
134 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
135 for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
136 let p = PointD(float x, float y)
137 if pixelOwnedByE p e (neighbors |> List.choose
(fun (otherE, p1
, p2
) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints
p1 p2
)))
141 if area < int minArea
145 // 5) Define pixels associated to each ellipse and create the cells.
147 |> List.choose
(fun (e, neighbors) ->
152 let minX, minY, maxX, maxY = ellipseWindow e
154 let infectedPixels = List<Point>()
155 let mutable stainPixels = 0
156 let mutable darkStainPixels = 0
157 let mutable nbElement = 0
159 let elements = new Matrix<byte
>(maxY - minY + 1, maxX - minX + 1)
160 for y in minY .. maxY do
161 for x in minX .. maxX do
162 let p = PointD(float x, float y)
163 if pixelOwnedByE p e (neighbors |> List.choose
(fun (otherE, p1, p2
) -> if otherE.Removed then None else Some (otherE :> Ellipse, Utils.lineFromTwoPoints
p1 p2
)))
165 elements.[y-minY, x-minX] <- 1uy
166 nbElement <- nbElement + 1
168 if infection.Data.[y, x, 0] > 0uy
170 infectedPixels.Add(Point(x, y))
172 if parasites
.stain
.Data.[y, x, 0] > 0uy
174 stainPixels <- stainPixels + 1
176 if parasites
.darkStain
.Data.[y, x, 0] > 0uy
178 darkStainPixels <- darkStainPixels + 1
181 if float darkStainPixels > config
.Parameters.maxDarkStainRatio
* (float nbElement) ||
182 float stainPixels > config
.Parameters.maxStainRatio
* (float nbElement) (* ||
183 sqrt (((float sumCoords_x) / (float nbElement) - e.Cx) ** 2.0 + ((float sumCoords_y) / (float nbElement) - e.Cy) ** 2.0) > e.A * config.maxOffcenter *)
186 elif
infectedPixels.Count >= 1
188 let infectionToRemove = ImgTools.connectedComponents
parasites.stain
infectedPixels
189 for p in infectionToRemove do
190 infection.Data.[p.Y, p.X, 0] <- 0uy
195 Some { cellClass = cellClass
196 center
= Point(roundInt
e.Cx, roundInt
e.Cy)
197 elements = elements })