1
module ParasitemiaCore.Classifier
4 open System.Collections.Generic
13 type CellState = RBC = 1 | Removed = 2 | Peculiar = 3
15 type private EllipseFlaggedKd (e
: Ellipse) =
16 inherit Ellipse (e
.Cx, e
.Cy, e
.A, e
.B, e
.Alpha)
18 member val State = CellState.RBC with get
, set
20 interface KdTree.I2DCoords with
21 member this
.X = this
.Cx
22 member this
.Y = this
.Cy
24 let findCells (ellipses
: Ellipse list) (parasites
: ParasitesMarker.Result) (width
: int) (height
: int) (config
: Config.Config) : Cell list =
25 if ellipses
.IsEmpty then
28 // This is the minimum window size to check if other ellipses touch 'e'.
29 let searchRegion (e
: Ellipse) =
31 KdTree.minX
= e
.Cx - (e
.A + config
.RBCRadius.Max)
32 KdTree.maxX
= e
.Cx + (e
.A + config
.RBCRadius.Max)
33 KdTree.minY
= e
.Cy - (e
.A + config
.RBCRadius.Max)
34 KdTree.maxY
= e
.Cy + (e
.A + config
.RBCRadius.Max)
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 + 0.5f)
41 cx - a, cy
- a, cx + a, cy
+ a
43 // Return 'true' if the point 'p' is owned by e.
44 // The lines represents all intersections with other ellipses.
45 let pixelOwnedByE (p
: PointF) (e : EllipseFlaggedKd) (neighbors
: (EllipseFlaggedKd * PointF * PointF) list) =
48 let c = PointF(e.Cx, e.Cy)
53 fun (otherE, p1, p2) ->
54 if otherE.State = CellState.Removed then
57 Some (otherE, Utils.lineFromTwoPoints p1 p2)
59 if e'.State = e.State then // Peculiar vs peculiar or RBC vs RBC.
60 let d2 = lineFromTwoPoints
c p
61 let c' = PointF(e'.Cx, e'.Cy)
62 let v = pointFromTwoLines d1 (lineFromTwoPoints c c')
63 let case1 = sign
(v.X - c.X) <> sign
(v.X - c'.X) || Utils.squaredDistanceTwoPoints v c > Utils.squaredDistanceTwoPoints v c'
64 if not
(Single.IsInfinity d2.A) then
65 let p' = Utils.pointFromTwoLines d1 d2
67 let dx1, dx2
= (c.X - p.X), (c.X - p'.X)
68 // To avoid rounding issue.
69 if abs dx1 < 0.01f || abs dx2 < 0.01f then c.Y - p.Y, c.Y - p'.Y else dx1, dx2
71 // Yield 'false' when the point is owned by another ellipse.
73 yield sign
delta <> sign
delta' || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints
c p
75 yield sign
delta = sign
delta' && Utils.squaredDistanceTwoPoints c p' < Utils.squaredDistanceTwoPoints
c p
79 elif
e.State = CellState.Peculiar then // A peculiar always win against a RBC.
82 yield not
<| e'.Contains p.X p.Y
86 let ellipses = ellipses |> List.map EllipseFlaggedKd
88 // 1) Associate touching ellipses with each ellipses and remove ellipse with more than two intersections.
89 let tree = KdTree.Tree.BuildTree ellipses
90 let neighbors (e : EllipseFlaggedKd) : (EllipseFlaggedKd * PointF * PointF) list =
91 if e.State <> CellState.Removed then
92 tree.Search (searchRegion e)
93 // We only keep the ellipses touching 'e'.
94 |> List.choose (fun otherE ->
96 match EEOver.EEOverlapArea e otherE with
97 | Some (_, px, _) when px.Length > 2 ->
98 otherE.State <- CellState.Removed
100 | Some (area, px, py) when area > 0.f && px.Length = 2 ->
101 Some (otherE, PointF(px.[0], py.[0]), PointF(px.[1], py.[1]))
110 let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e)
112 // 2) Remove ellipses touching the edges.
113 let widthF, heightF = float32 width, float32 height
115 if e.isOutside widthF heightF then e.State <- CellState.Removed
117 // 3) Remove ellipses with a high standard deviation (high contrast).
118 // Obsolete. It was useful when the ellipses result quality wasn't
good.
119 (* let imgData = img.Data
120 let globalStdDeviation = MathNet.Numerics.Statistics.Statistics.PopulationStandardDeviation(seq {
121 for y in 0 .. h - 1 do
122 for x in 0 .. w - 1 do
123 yield float imgData.[y, x, 0] })
126 if not e.Removed then
127 let shrinkedE = e.Scale 0.9f
128 let minX, minY, maxX, maxY = ellipseWindow shrinkedE
130 let stdDeviation = MathNet.Numerics.Statistics.Statistics.StandardDeviation (seq {
131 for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
132 for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
133 if shrinkedE.Contains (float32 x) (float32 y) then
134 yield float imgData.[y, x, 0] })
136 if stdDeviation > globalStdDeviation * config.Parameters.standardDeviationMaxRatio then
139 // 4) Remove ellipses with little area.
140 let minArea = config
.RBCRadius.MinArea
141 for e, neighbors in ellipsesWithNeigbors do
142 if e.State <> CellState.Removed then
143 let minX, minY, maxX, maxY = ellipseWindow e
146 for y
= (if minY < 0 then 0 else minY) to (if maxY >= height
then height
- 1 else maxY) do
147 for x
= (if minX < 0 then 0 else minX) to (if maxX >= width
then width
- 1 else maxX) do
148 let p = PointF(float32 x
, float32 y
)
149 if pixelOwnedByE p e neighbors then
152 if area < int minArea then
153 e.State <- CellState.Removed
155 // 5) Define non-rbc (peculiar) cells.
156 let darkStainData = parasites
.darkStain
.Data
158 |> List.choose
(fun (e, neighbors) ->
159 if e.State = CellState.Removed then
162 let mutable darkStainPixels = 0
163 let mutable nbElement = 0
164 let minX, minY, maxX, maxY = ellipseWindow e
165 for y
= minY to maxY do
166 for x
= minX to maxX do
167 let p = PointF(float32 x
, float32 y
)
168 if pixelOwnedByE p e neighbors then
169 nbElement <- nbElement + 1
170 if darkStainData.[y
, x
, 0] > 0uy then
171 darkStainPixels <- darkStainPixels + 1
173 if float darkStainPixels > config
.Parameters.maxDarkStainRatio
* (float nbElement) then Some e else None)
175 // We do not change the state during the process to avoid to have peculiar neighbors which change the behavior of 'pixelOwnedByE'.
176 |> List.iter
(fun e -> e.State <- CellState.Peculiar)
178 // 5) Define pixels associated to each ellipse and create the cells.
179 let diameterParasiteSquared = (2.f
* config
.RBCRadius.ParasiteRadius) ** 2.f
|> roundInt
180 let minimumParasiteArea = config
.RBCRadius.MinimumParasiteArea |> roundInt
182 let nucleusData = parasites
.nucleus
.Copy().Data // Will be modified thus the copy.
183 let parasiteData = parasites
.parasite
.Data
184 let darkStainData = parasites
.darkStain
.Data
188 fun (e, neighbors) ->
189 if e.State = CellState.Removed then
192 let minX, minY, maxX, maxY = ellipseWindow e
194 let nucleusPixels = List<Point>()
195 let parasitePixels = List<Point>()
197 let mutable nbElement = 0
199 let elements = new Matrix<byte
>(maxY - minY + 1, maxX - minX + 1)
200 for y
= minY to maxY do
201 for x
= minX to maxX do
202 let p = PointF(float32 x
, float32 y
)
203 if pixelOwnedByE p e neighbors then
204 elements.[y
- minY, x
- minX] <- 1uy
205 nbElement <- nbElement + 1
207 if nucleusData.[y
, x
, 0] > 0uy then
208 nucleusPixels.Add(Point(x
, y
))
210 if parasiteData.[y
, x
, 0] > 0uy then
211 parasitePixels.Add(Point(x
, y
))
214 if nucleusPixels.Count > 0 then
216 for parasitePixel
in parasitePixels do
217 if nucleusPixels.Exists(fun p -> pown
(p.X - parasitePixel
.X) 2 + pown
(p.Y - parasitePixel
.Y) 2 <= diameterParasiteSquared) then
224 if e.State = CellState.Peculiar then
227 elif
nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea then
228 let infectionToRemove = Morpho.connectedComponents
parasites.parasite
nucleusPixels
229 for p in infectionToRemove do
230 nucleusData.[p.Y, p.X, 0] <- 0uy
238 cellClass = cellClass
239 center
= Point(roundInt
e.Cx, roundInt
e.Cy)
240 nucleusArea
= if cellClass = InfectedRBC then nucleusPixels.Count else 0
241 parasiteArea = parasiteArea