Cleaning + renaming.

[master-thesis.git] / Parasitemia / ParasitemiaCore / Classifier.fs

diff --git a/Parasitemia/ParasitemiaCore/Classifier.fs b/Parasitemia/ParasitemiaCore/Classifier.fs
index 2b6f3be..615840c 100644 (file)
--- a/Parasitemia/ParasitemiaCore/Classifier.fs
+++ b/Parasitemia/ParasitemiaCore/Classifier.fs
@@ -24,8 +24,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img:
     then
         []
     else
-        let infection = parasites.nucleus.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)
@@ -150,6 +148,11 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img:
         // 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
@@ -158,10 +161,9 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img:
             else
                 let minX, minY, maxX, maxY = ellipseWindow e
 
-                let infectedPixels = List<Point>()
-                let cytoplasmPixels = List<Point>()
+                let nucleusPixels = List<Point>()
+                let parasitePixels = List<Point>()
 
-                //let mutable stainPixels = 0
                 let mutable darkStainPixels = 0
                 let mutable nbElement = 0
 
@@ -171,45 +173,40 @@ 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
 
-                            let infected = infection.Data.[y, x, 0] > 0uy
-                            let stain = parasites.cytoplasm.Data.[y, x, 0] > 0uy
-                            let darkStain = parasites.darkStain.Data.[y, x, 0] > 0uy
-
-                            if infected
+                            if nucleusData.[y, x, 0] > 0uy
                             then
-                                infectedPixels.Add(Point(x, y))
+                                nucleusPixels.Add(Point(x, y))
 
-                            if stain
+                            if parasiteData.[y, x, 0] > 0uy
                             then
-                                cytoplasmPixels.Add(Point(x, y))
+                                parasitePixels.Add(Point(x, y))
 
-                            if darkStain
+                            if darkStainData.[y, x, 0] > 0uy
                             then
                                 darkStainPixels <- darkStainPixels + 1
 
-                let mutable cytoplasmArea = 0
-                if infectedPixels.Count > 0
+                let mutable parasiteArea = 0
+                if nucleusPixels.Count > 0
                 then
-                    for cytoplasmPixel in cytoplasmPixels do
-                        if infectedPixels.Exists(fun p -> pown (p.X - cytoplasmPixel.X) 2 + pown (p.Y - cytoplasmPixel.Y) 2 <= perimeterParasiteSquared)
+                    for parasitePixel in parasitePixels do
+                        if nucleusPixels.Exists(fun p -> pown (p.X - parasitePixel.X) 2 + pown (p.Y - parasitePixel.Y) 2 <= perimeterParasiteSquared)
                         then
-                            cytoplasmArea <- cytoplasmArea + 1
+                            parasiteArea <- parasiteArea + 1
 
 
                 let cellClass =
                     if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement)
-                       //|| float stainPixels > config.Parameters.maxStainRatio * (float nbElement)
                     then
                         Peculiar
 
-                    elif infectedPixels.Count > 0 && cytoplasmArea >= minimumParasiteArea
+                    elif nucleusPixels.Count > 0 && parasiteArea >= minimumParasiteArea
                     then
-                        let infectionToRemove = ImgTools.connectedComponents parasites.cytoplasm infectedPixels
+                        let infectionToRemove = ImgTools.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
@@ -217,6 +214,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (img:
 
                 Some { cellClass = cellClass
                        center = Point(roundInt e.Cx, roundInt e.Cy)
-                       nucleusArea = if cellClass = InfectedRBC then infectedPixels.Count else 0
-                       parasiteArea = cytoplasmArea
+                       nucleusArea = if cellClass = InfectedRBC then nucleusPixels.Count else 0
+                       parasiteArea = parasiteArea
                        elements = elements })