X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FClassifier.fs;h=4c6cc564cfc621d9a121c1c43f6319c52435b2b3;hp=37507c5e927c1b685c5bd3a541afd4ec57821608;hb=84fdf7404133803fdf0dc867a4da68a144975191;hpb=e76da913cd58078ad2479357b2430ed62a6e0777

diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs
index 37507c5..4c6cc56 100644
--- 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) =
@@ -40,12 +40,15 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
             let a = int (e.A + 0.5)
             cx - a, cy - a, cx + a, cy + a
 
-        // 1) Remove ellipses touching the edges.
-        let ellipsesInside = ellipses |> List.map (fun e ->
-            EllipseFlaggedKd (e, Removed = e.isOutside (float fg.Width) (float fg.Height)))
+        let w = img.Width
+        let w_f = float w
+        let h = img.Height
+        let h_f = float h
 
-        // 2) Associate touching ellipses with each ellipses.
-        let tree = KdTree.Tree.BuildTree ellipsesInside
+        let ellipses = ellipses |> List.map EllipseFlaggedKd
+
+        // 1) Associate touching ellipses with each ellipses.
+        let tree = KdTree.Tree.BuildTree ellipses
         let neighbors (e: Ellipse) : (EllipseFlaggedKd * PointD * PointD) list =
             tree.Search (searchRegion e)
                 // We only keep the ellipses touching 'e'.
@@ -56,31 +59,52 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
                     | _ ->
                         None )
 
-        let ellipsesWithNeigbors = ellipsesInside |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e))
+        let ellipsesWithNeigbors = ellipses |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e))
 
-        // 3) Remove ellipse with a lower percentage of foreground.
-        let fgData = fg.Data
-        for e, neighbors in ellipsesWithNeigbors do
+        // 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
             let minX, minY, maxX, maxY = ellipseWindow e
 
             let mutable totalElement = 0
             let mutable fgElement = 0
-
-            for y in minY .. maxY do
-                for x in minX .. maxX do
+            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
                     let yf, xf = float y, float x
-                    if e.Contains xf yf && neighbors |> List.forall (fun (otherE, _, _) -> not <| otherE.Contains xf yf)
-                    then
-                        totalElement <- totalElement + 1
-                        if fgData.[y, x, 0] > 0uy
+                    if e.Contains xf yf && neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf)
                         then
-                            fgElement <- fgElement + 1
+                            totalElement <- totalElement + 1
+                            if fg.Data.[y, x, 0] > 0uy
+                            then
+                                fgElement <- fgElement + 1
+
+            if (float fgElement) / (float totalElement) < config.Parameters.percentageOfFgValidCell
+            then
+                e.Removed <- true*)
 
-            if totalElement < config.minimumCellArea || (float fgElement) / (float totalElement) < config.percentageOfFgValidCell
+        // 3) Remove ellipses touching the edges.
+        for e in ellipses do
+            if e.isOutside w_f h_f then e.Removed <- true
+
+        // 4) Remove ellipses with little area.
+        for e, neighbors in ellipsesWithNeigbors do
+            if not e.Removed
             then
-                e.Removed <- true
+                let minX, minY, maxX, maxY = ellipseWindow e
 
-        // 3) Define pixels associated to each ellipse and create the cells.
+                let mutable area = 0
+                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 e.Contains xf yf &&
+                           neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf)
+                            then
+                                area <- area + 1
+
+                if area < int config.RBCMinArea
+                then
+                    e.Removed <- true
+
+        // 5) Define pixels associated to each ellipse and create the cells.
 
         // Return 'true' if the point 'p' is owned by e.
         // The lines represents all intersections with other ellipses.
@@ -94,7 +118,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
                     yield sign (c.X - p.X) <> sign (c.X - p'.X) || Utils.squaredDistanceTwoPoints c p' > Utils.squaredDistanceTwoPoints c p // 'false' -> the point is owned by another ellipse.
             } |> Seq.forall id
 
-
         ellipsesWithNeigbors
         |> List.choose (fun (e, neighbors) ->
             if e.Removed
@@ -120,8 +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
@@ -145,11 +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