Change the parasite detection method.

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

diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs
index 3ed42f0..4c6cc56 100644 (file)
--- a/Parasitemia/Parasitemia/Classifier.fs
+++ b/Parasitemia/Parasitemia/Classifier.fs
@@ -21,7 +21,7 @@ type private EllipseFlaggedKd (e: Ellipse) =
         member this.Y = this.Cy
 
 
-let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg: Image<Gray, byte>) (config: Config.Config) : Cell list =
+let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img: Image<Gray, byte>) (config: Config.Config) : Cell list =
     if ellipses.IsEmpty
     then
         []
@@ -29,10 +29,10 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
         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.maxRBCSize) * config.scale
-                                          KdTree.maxX = e.Cx + (e.A + config.maxRBCSize) * config.scale
-                                          KdTree.minY = e.Cy - (e.A + config.maxRBCSize) * config.scale
-                                          KdTree.maxY = e.Cy + (e.A + config.maxRBCSize) * config.scale }
+        let searchRegion (e: Ellipse) = { KdTree.minX = e.Cx - (e.A + config.RBCMax) * config.Parameters.scale
+                                          KdTree.maxX = e.Cx + (e.A + config.RBCMax) * config.Parameters.scale
+                                          KdTree.minY = e.Cy - (e.A + config.RBCMax) * config.Parameters.scale
+                                          KdTree.maxY = e.Cy + (e.A + config.RBCMax) * config.Parameters.scale }
 
         // The minimum window to contain a given ellipse.
         let ellipseWindow (e: Ellipse) =
@@ -40,8 +40,10 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
             let a = int (e.A + 0.5)
             cx - a, cy - a, cx + a, cy + a
 
-        let w = float fg.Width
-        let h = float fg.Height
+        let w = img.Width
+        let w_f = float w
+        let h = img.Height
+        let h_f = float h
 
         let ellipses = ellipses |> List.map EllipseFlaggedKd
 
@@ -60,7 +62,7 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
         let ellipsesWithNeigbors = ellipses |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e))
 
         // 2) Remove ellipses with a lower percentage of foreground. (taken from the lower score to the highest).
-        for e, neighbors in List.rev ellipsesWithNeigbors do
+        (*for e, neighbors in List.rev ellipsesWithNeigbors do
             let minX, minY, maxX, maxY = ellipseWindow e
 
             let mutable totalElement = 0
@@ -75,13 +77,13 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
                             then
                                 fgElement <- fgElement + 1
 
-            if (float fgElement) / (float totalElement) < config.percentageOfFgValidCell
+            if (float fgElement) / (float totalElement) < config.Parameters.percentageOfFgValidCell
             then
-                e.Removed <- true
+                e.Removed <- true*)
 
         // 3) Remove ellipses touching the edges.
         for e in ellipses do
-            if e.isOutside w h then e.Removed <- true
+            if e.isOutside w_f h_f then e.Removed <- true
 
         // 4) Remove ellipses with little area.
         for e, neighbors in ellipsesWithNeigbors do
@@ -90,16 +92,15 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
                 let minX, minY, maxX, maxY = ellipseWindow e
 
                 let mutable area = 0
-                for y in (if minY < 0 then 0 else minY) .. (if maxY >= fg.Height then fg.Height - 1 else maxY) do
-                    for x in (if minX < 0 then 0 else minX) .. (if maxX >= fg.Width then fg.Width - 1 else maxX) do
+                for y in (if minY < 0 then 0 else minY) .. (if maxY >= h then h - 1 else maxY) do
+                    for x in (if minX < 0 then 0 else minX) .. (if maxX >= w then w - 1 else maxX) do
                         let yf, xf = float y, float x
-                        if fg.Data.[y, x, 0] > 0uy &&
-                           e.Contains xf yf &&
+                        if e.Contains xf yf &&
                            neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf)
                             then
                                 area <- area + 1
 
-                if area < config.minimumCellArea
+                if area < int config.RBCMinArea
                 then
                     e.Removed <- true
 
@@ -142,8 +143,7 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
                 for y in minY .. maxY do
                     for x in minX .. maxX do
                         let p = PointD(float x, float y)
-                        if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (Utils.lineFromTwoPoints p1 p2))) &&
-                           fg.Data.[y, x, 0] > 0uy
+                        if pixelOwnedByE p e (neighbors |> List.choose (fun (otherE, p1, p2) -> if otherE.Removed then None else Some (Utils.lineFromTwoPoints p1 p2)))
                         then
                             elements.[y-minY, x-minX] <- 1uy
                             nbElement <- nbElement + 1
@@ -167,11 +167,11 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
                                 darkStainPixels <- darkStainPixels + 1
 
                 let cellClass =
-                    if float darkStainPixels > config.MaxDarkStainRatio * (float nbElement) (* ||
+                    if float darkStainPixels > config.Parameters.maxDarkStainRatio * (float nbElement) (* ||
                         sqrt (((float sumCoords_x) / (float nbElement) - e.Cx) ** 2.0 + ((float sumCoords_y) / (float nbElement) - e.Cy) ** 2.0) > e.A * config.maxOffcenter *)
                     then
                         Peculiar
-                    elif infectedPixels.Count > config.infectionPixelsRequired
+                    elif infectedPixels.Count > config.Parameters.infectionPixelsRequired
                     then
                         let infectionToRemove = ImgTools.connectedComponents parasites.stain infectedPixels
                         for p in infectionToRemove do