X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FClassifier.fs;h=f4b08446f9f6dc6b4762fc215f2c392152ec97d0;hb=3f8b0d281b3058faf23dbd0363de440bd04c6574;hp=c523790e9f70c4c80317cbfbede44e696c1f41a0;hpb=170abb893b9e6babbf93276e39e8c984cedbc68f;p=master-thesis.git

diff --git a/Parasitemia/ParasitemiaCore/Classifier.fs b/Parasitemia/ParasitemiaCore/Classifier.fs
index c523790..f4b0844 100644
--- a/Parasitemia/ParasitemiaCore/Classifier.fs
+++ b/Parasitemia/ParasitemiaCore/Classifier.fs
@@ -10,7 +10,6 @@ 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)
 
@@ -20,14 +19,11 @@ type private EllipseFlaggedKd (e: Ellipse) =
         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)
@@ -61,9 +57,9 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img:
                     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
@@ -130,7 +126,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img:
                 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
@@ -151,6 +146,13 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img:
                     e.Removed <- true
 
         // 5) Define pixels associated to each ellipse and create the cells.
+        let perimeterParasiteSquared = (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
@@ -159,8 +161,9 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img:
             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
 
@@ -170,37 +173,46 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img:
                         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 <= perimeterParasiteSquared)
+                        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 })