* Remove ellipses with a too high standard variation.

diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs
index a12e595..c54a3b1 100644 (file)
--- a/Parasitemia/Parasitemia/Classifier.fs
+++ b/Parasitemia/Parasitemia/Classifier.fs
@@ -45,6 +45,22 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img
         let h = img.Height
         let h_f = float h
 
         let h = img.Height
         let h_f = float h
 

+        // Return 'true' if the point 'p' is owned by e.
+        // The lines represents all intersections with other ellipses.
+        let pixelOwnedByE (p: PointD) (e: Ellipse) (lines: Line list) =
+            e.Contains p.X p.Y &&
+            seq {
+                let c = PointD(e.Cx, e.Cy)
+                for d1 in lines do
+                    let d2 = Utils.lineFromTwoPoints c p
+                    if d2.Valid
+                    then
+                        let p' = Utils.pointFromTwoLines d1 d2
+                        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.
+                    else
+                        yield true
+            } |> Seq.forall id
+

         let ellipses = ellipses |> List.map EllipseFlaggedKd
 
         // 1) Associate touching ellipses with each ellipses.
         let ellipses = ellipses |> List.map EllipseFlaggedKd
 
         // 1) Associate touching ellipses with each ellipses.


@@ -59,33 +75,35 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img
                     | _ ->
                         None )
 
                     | _ ->
                         None )
 

-        let ellipsesWithNeigbors = ellipses |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e))
+        let ellipsesWithNeigbors = ellipses |> List.map (fun e -> e, neighbors e)
+
+        // 2) Remove ellipses with a high standard deviation (high contrast).
+        let globalStdDiviation = MathNet.Numerics.Statistics.StreamingStatistics.StandardDeviation(seq {
+            for y in 0 .. h - 1 do
+                for x in 0 .. w - 1 do
+                    yield img.Data.[y, x, 0] |> float })

 
 

-        // 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 minX, minY, maxX, maxY = ellipseWindow e
 

-            let mutable totalElement = 0
-            let mutable fgElement = 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
-                    let yf, xf = float y, float x
-                    if e.Contains xf yf && neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf)
+            let stdDiviation = MathNet.Numerics.Statistics.StreamingStatistics.StandardDeviation(seq {
+                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 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)))

                         then
                         then

-                            totalElement <- totalElement + 1
-                            if fg.Data.[y, x, 0] > 0uy
-                            then
-                                fgElement <- fgElement + 1
+                            yield img.Data.[y, x, 0] |> float })

 
 

-            if (float fgElement) / (float totalElement) < config.Parameters.percentageOfFgValidCell
+            if stdDiviation > globalStdDiviation * config.Parameters.standardDeviationMaxRatio

             then
             then

-                e.Removed <- true*)
+                e.Removed <- true

 
         // 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.
 
         // 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.

+        let minArea = config.RBCMinArea

         for e, neighbors in ellipsesWithNeigbors do
             if not e.Removed
             then
         for e, neighbors in ellipsesWithNeigbors do
             if not e.Removed
             then


@@ -94,34 +112,16 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img
                 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 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
+                        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)))
+                        then
+                            area <- area + 1

 
 

-                if area < int config.RBCMinArea
+                if area < int minArea

                 then
                     e.Removed <- true
 
         // 5) Define pixels associated to each ellipse and create the cells.
                 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.
-        let pixelOwnedByE (p: PointD) (e: Ellipse) (lines: Line list) =
-            e.Contains p.X p.Y &&
-            seq {
-                let c = PointD(e.Cx, e.Cy)
-                for d1 in lines do
-                    let d2 = Utils.lineFromTwoPoints c p
-                    if d2.Valid
-                    then
-                        let p' = Utils.pointFromTwoLines d1 d2
-                        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.
-                    else
-                        yield true
-            } |> Seq.forall id
-

         ellipsesWithNeigbors
         |> List.choose (fun (e, neighbors) ->
             if e.Removed
         ellipsesWithNeigbors
         |> List.choose (fun (e, neighbors) ->
             if e.Removed


@@ -135,14 +135,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img
                 let mutable darkStainPixels = 0
                 let mutable nbElement = 0
 
                 let mutable darkStainPixels = 0
                 let mutable nbElement = 0
 

-                let mutable stain_x = 0.0
-                let mutable stain_x2 = 0.0
-                let mutable stain_y = 0.0
-                let mutable stain_y2 = 0.0
-
-                let mutable sumCoords_y = 0
-                let mutable sumCoords_x = 0
-

                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
                 for y in minY .. maxY do
                     for x in minX .. maxX do
                 let elements = new Matrix<byte>(maxY - minY + 1, maxX - minX + 1)
                 for y in minY .. maxY do
                     for x in minX .. maxX do


@@ -151,8 +143,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img
                         then
                             elements.[y-minY, x-minX] <- 1uy
                             nbElement <- nbElement + 1
                         then
                             elements.[y-minY, x-minX] <- 1uy
                             nbElement <- nbElement + 1

-                            sumCoords_y <- sumCoords_y + y
-                            sumCoords_x <- sumCoords_x + x

 
                             if infection.Data.[y, x, 0] > 0uy
                             then
 
                             if infection.Data.[y, x, 0] > 0uy
                             then


@@ -161,10 +151,6 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker2.Result) (img
                             if parasites.stain.Data.[y, x, 0] > 0uy
                             then
                                 stainPixels <- stainPixels + 1
                             if parasites.stain.Data.[y, x, 0] > 0uy
                             then
                                 stainPixels <- stainPixels + 1

-                                stain_x <- stain_x + (float x)
-                                stain_x2 <- stain_x2 + (float x) ** 2.0
-                                stain_y <- stain_y + (float y)
-                                stain_y2 <- stain_y2 + (float y) ** 2.0

 
                             if parasites.darkStain.Data.[y, x, 0] > 0uy
                             then
 
                             if parasites.darkStain.Data.[y, x, 0] > 0uy
                             then

diff --git a/Parasitemia/Parasitemia/Config.fs b/Parasitemia/Parasitemia/Config.fs
index a1b06e2..261d87b 100644 (file)
--- a/Parasitemia/Parasitemia/Config.fs
+++ b/Parasitemia/Parasitemia/Config.fs
@@ -30,6 +30,7 @@ type Parameters = {
 
     maxDarkStainRatio: float
 
 
     maxDarkStainRatio: float
 

+    standardDeviationMaxRatio: float // The standard deviation of the pixel values of a cell can't be greater than standardDeviationMaxRatio * global standard deviation

     minimumCellArea: float // Factor of RBC area.
 }
 
     minimumCellArea: float // Factor of RBC area.
 }
 

diff --git a/Parasitemia/Parasitemia/MatchingEllipses.fs b/Parasitemia/Parasitemia/MatchingEllipses.fs
index 2196122..7a4c51b 100644 (file)
--- a/Parasitemia/Parasitemia/MatchingEllipses.fs
+++ b/Parasitemia/Parasitemia/MatchingEllipses.fs
@@ -12,7 +12,7 @@ open Utils
 // Do not take in account matching score below this when two ellipses are matched.
 let matchingScoreThreshold1 = 0.6
 
 // Do not take in account matching score below this when two ellipses are matched.
 let matchingScoreThreshold1 = 0.6
 

-// All ellipsee with a score below this is removed.
+// All ellipses with a score below this are removed.

 let matchingScoreThreshold2 = 2.
 
 type private EllipseScoreFlaggedKd (matchingScore: float, e: Ellipse) =
 let matchingScoreThreshold2 = 2.
 
 type private EllipseScoreFlaggedKd (matchingScore: float, e: Ellipse) =

diff --git a/Parasitemia/Parasitemia/Program.fs b/Parasitemia/Parasitemia/Program.fs
index ac495b5..5b8c3e4 100644 (file)
--- a/Parasitemia/Parasitemia/Program.fs
+++ b/Parasitemia/Parasitemia/Program.fs
@@ -61,8 +61,8 @@ let main args =
             Config(
               { scale = 1.
 
             Config(
               { scale = 1.
 

-                minRbcRadius = -0.3
-                maxRbcRadius = 0.3
+                minRbcRadius = -0.35
+                maxRbcRadius = 0.35

 
                 preFilterSigma = 1.5
 
 
                 preFilterSigma = 1.5
 


@@ -80,7 +80,8 @@ let main args =
 
                 maxDarkStainRatio = 0.1
 
 
                 maxDarkStainRatio = 0.1
 

-                minimumCellArea = 0.3 })
+                standardDeviationMaxRatio = 0.65
+                minimumCellArea = 0.5 })

 
         match mode with
         | CmdLine (input, output) ->
 
         match mode with
         | CmdLine (input, output) ->