* Remove ellipses with too small area (improved).

* Draw all the ellipses in debug mode.

diff --git a/Parasitemia/Parasitemia/Classifier.fs b/Parasitemia/Parasitemia/Classifier.fs
index 52e7dc6..e0bbfa9 100644 (file)
--- a/Parasitemia/Parasitemia/Classifier.fs
+++ b/Parasitemia/Parasitemia/Classifier.fs
@@ -59,28 +59,47 @@ let findCells (ellipses: Ellipse list) (parasites: ParasitesMarker.Result) (fg:
 
         let ellipsesWithNeigbors = ellipsesInside |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e))
 
 
         let ellipsesWithNeigbors = ellipsesInside |> List.choose (fun e -> if e.Removed then None else Some (e, neighbors e))
 

-        // 3) Remove ellipse with a lower percentage of foreground.
+        // 3) Remove ellipses with a lower percentage of foreground.

         for e, neighbors in ellipsesWithNeigbors do
             let minX, minY, maxX, maxY = ellipseWindow e
 
             let mutable totalElement = 0
             let mutable fgElement = 0
         for e, neighbors in 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
                     let yf, xf = float y, float x
                     if e.Contains xf yf && neighbors |> List.forall (fun (otherE, _, _) -> not <| otherE.Contains xf yf)
             for y in minY .. maxY do
                 for x in minX .. 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 fg.Data.[y, x, 0] > 0uy

                         then
                         then

-                            fgElement <- fgElement + 1
+                            totalElement <- totalElement + 1
+                            if fg.Data.[y, x, 0] > 0uy
+                            then
+                                fgElement <- fgElement + 1

 
 

-            if totalElement < config.minimumCellArea || (float fgElement) / (float totalElement) < config.percentageOfFgValidCell
+            if (float fgElement) / (float totalElement) < config.percentageOfFgValidCell

             then
                 e.Removed <- true
 
             then
                 e.Removed <- true
 

-        // 3) Define pixels associated to each ellipse and create the cells.
+        // 4) Remove ellipses with little area.
+        for e, neighbors in ellipsesWithNeigbors do
+            if not e.Removed
+            then
+                let minX, minY, maxX, maxY = ellipseWindow e
+
+                let mutable area = 0
+                for y in minY .. maxY do
+                    for x in minX .. maxX do
+                        let yf, xf = float y, float x
+                        if fg.Data.[y, x, 0] > 0uy &&
+                           e.Contains xf yf &&
+                           neighbors |> List.forall (fun (otherE, _, _) -> otherE.Removed || not <| otherE.Contains xf yf)
+                            then
+                                area <- area + 1
+
+                if area < config.minimumCellArea
+                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.
 
         // Return 'true' if the point 'p' is owned by e.
         // The lines represents all intersections with other ellipses.

diff --git a/Parasitemia/Parasitemia/Config.fs b/Parasitemia/Parasitemia/Config.fs
index 8a172b8..464fd7e 100644 (file)
--- a/Parasitemia/Parasitemia/Config.fs
+++ b/Parasitemia/Parasitemia/Config.fs
@@ -16,6 +16,10 @@ type Config = {
     doGSigma2: float
     doGLowFreqPercentageReduction: float
 
     doGSigma2: float
     doGLowFreqPercentageReduction: float
 

+    // Ellipse.
+    factorNbPick: float
+    factorWindowSize: float // factor of 'maxRBCSize'.
+

     // Parasites detection.
     darkStainLevel: float
 
     // Parasites detection.
     darkStainLevel: float
 

diff --git a/Parasitemia/Parasitemia/Ellipse.fs b/Parasitemia/Parasitemia/Ellipse.fs
index 62c0936..128c823 100644 (file)
--- a/Parasitemia/Parasitemia/Ellipse.fs
+++ b/Parasitemia/Parasitemia/Ellipse.fs
@@ -7,28 +7,29 @@ open Emgu.CV
 open Emgu.CV.Structure
 
 open Utils
 open Emgu.CV.Structure
 
 open Utils

+open Config

 open MatchingEllipses
 
 
 type private SearchExtremum = Minimum | Maximum
 open MatchingEllipses
 
 
 type private SearchExtremum = Minimum | Maximum

-    
+

 let private goldenSectionSearch (f: float -> float) (nbIter: int) (xmin: float) (xmax: float) (searchExtremum: SearchExtremum) : (float * float) =
     let gr = 1.0 / 1.6180339887498948482
     let mutable a = xmin
     let mutable b = xmax
     let mutable c = b - gr * (b - a)
     let mutable d = a + gr * (b - a)
 let private goldenSectionSearch (f: float -> float) (nbIter: int) (xmin: float) (xmax: float) (searchExtremum: SearchExtremum) : (float * float) =
     let gr = 1.0 / 1.6180339887498948482
     let mutable a = xmin
     let mutable b = xmax
     let mutable c = b - gr * (b - a)
     let mutable d = a + gr * (b - a)

-    
+

     for i in 1 .. nbIter do
         let mutable fc = f c
         let mutable fd = f d
     for i in 1 .. nbIter do
         let mutable fc = f c
         let mutable fd = f d

-        
+

         if searchExtremum = Maximum
         then
             let tmp = fc
             fc <- fd
             fd <- tmp
         if searchExtremum = Maximum
         then
             let tmp = fc
             fc <- fd
             fd <- tmp

-        
+

         if fc < fd
         then
             b <- d
         if fc < fd
         then
             b <- d


@@ -38,7 +39,7 @@ let private goldenSectionSearch (f: float -> float) (nbIter: int) (xmin: float)
             a <- c
             c <- d
             d <- a + gr * (b - a)
             a <- c
             c <- d
             d <- a + gr * (b - a)

-    
+

     let x = (b + a) / 2.0
     x, f x
 
     let x = (b + a) / 2.0
     x, f x
 


@@ -51,92 +52,92 @@ let ellipse (p1x: float) (p1y: float) (m1: float) (p2x: float) (p2y: float) (m2:
     // p3 as the referencial.
     let p1x = p1x - p3x
     let p1y = p1y - p3y
     // p3 as the referencial.
     let p1x = p1x - p3x
     let p1y = p1y - p3y

-    
+

     let p2x = p2x - p3x
     let p2y = p2y - p3y
     let p2x = p2x - p3x
     let p2y = p2y - p3y

-        
+

     // Convert to polar coordinates.
     let alpha1 = atan m1
     let alpha2 = atan m2
     // Convert to polar coordinates.
     let alpha1 = atan m1
     let alpha2 = atan m2

-    
+

     let r1 = sqrt (p1x ** 2.0 + p1y ** 2.0)
     let theta1 = atan2 p1y p1x
 
     let r2 = sqrt (p2x**2.0 + p2y**2.0)
     let theta2 = atan2 p2y p2x
 
     let r1 = sqrt (p1x ** 2.0 + p1y ** 2.0)
     let theta1 = atan2 p1y p1x
 
     let r2 = sqrt (p2x**2.0 + p2y**2.0)
     let theta2 = atan2 p2y p2x
 

-    let valid = 
-        4.0 * sin (alpha1 - theta1) * (-r1 * sin (alpha1 - theta1) + r2 * sin (alpha1 - theta2)) * 
+    let valid =
+        4.0 * sin (alpha1 - theta1) * (-r1 * sin (alpha1 - theta1) + r2 * sin (alpha1 - theta2)) *

         sin (alpha2 - theta2) * (-r1 * sin (alpha2 - theta1) + r2 * sin (alpha2 - theta2)) +
         r1 * r2 * sin (alpha1 - alpha2) ** 2.0 * sin (theta1 - theta2) ** 2.0 < 0.0
         sin (alpha2 - theta2) * (-r1 * sin (alpha2 - theta1) + r2 * sin (alpha2 - theta2)) +
         r1 * r2 * sin (alpha1 - alpha2) ** 2.0 * sin (theta1 - theta2) ** 2.0 < 0.0

-    
+

     if valid
     then
     if valid
     then

-        let r theta = 
+        let r theta =

             (r1 * r2 * (r1 * (cos (alpha2 + theta - theta1 - theta2) - cos (alpha2 - theta) * cos (theta1 - theta2)) * sin (alpha1 - theta1) + r2 * (-cos (alpha1 + theta - theta1 - theta2) + cos (alpha1 - theta) * cos (theta1 - theta2)) * sin (alpha2 - theta2)) * sin (theta1 - theta2)) /
             (sin (alpha1 - theta1) * sin (alpha2 - theta2) * (r1 * sin (theta - theta1) - r2 * sin (theta - theta2)) ** 2.0 - r1 * r2 * sin (alpha1 - theta) * sin (alpha2 - theta) * sin (theta1 - theta2) ** 2.0)
             (r1 * r2 * (r1 * (cos (alpha2 + theta - theta1 - theta2) - cos (alpha2 - theta) * cos (theta1 - theta2)) * sin (alpha1 - theta1) + r2 * (-cos (alpha1 + theta - theta1 - theta2) + cos (alpha1 - theta) * cos (theta1 - theta2)) * sin (alpha2 - theta2)) * sin (theta1 - theta2)) /
             (sin (alpha1 - theta1) * sin (alpha2 - theta2) * (r1 * sin (theta - theta1) - r2 * sin (theta - theta2)) ** 2.0 - r1 * r2 * sin (alpha1 - theta) * sin (alpha2 - theta) * sin (theta1 - theta2) ** 2.0)

-                
+

         let rabs = r >> abs
         let rabs = r >> abs

-        
+

         // We search for an interval [theta_a, theta_b] and assume the function is unimodal in this interval.
         let thetaTan, _ = goldenSectionSearch rabs accuracy_extremum_search_1 0.0 Math.PI Maximum
         let rTan = r thetaTan
         // We search for an interval [theta_a, theta_b] and assume the function is unimodal in this interval.
         let thetaTan, _ = goldenSectionSearch rabs accuracy_extremum_search_1 0.0 Math.PI Maximum
         let rTan = r thetaTan

-                        
+

         let PTanx = rTan * cos thetaTan
         let PTany = rTan * sin thetaTan
         let PTanx = rTan * cos thetaTan
         let PTany = rTan * sin thetaTan

-        
+

         let d1a = tan alpha1
         let d1b = -d1a * p1x + p1y
         let d1a = tan alpha1
         let d1b = -d1a * p1x + p1y

-        
+

         let d2a = tan alpha2
         let d2b = -d2a * p2x + p2y
         let d2a = tan alpha2
         let d2b = -d2a * p2x + p2y

-        
+

         let d3a = -1.0 / tan thetaTan
         let d3b = -d3a * PTanx + PTany
         let d3a = -1.0 / tan thetaTan
         let d3b = -d3a * PTanx + PTany

-        
+

         let Ux = -(d1b - d2b) / (d1a - d2a)
         let Uy = -(d2a * d1b - d1a * d2b) / (d1a - d2a)
         let Ux = -(d1b - d2b) / (d1a - d2a)
         let Uy = -(d2a * d1b - d1a * d2b) / (d1a - d2a)

-        
+

         let Vx = -(d1b - d3b) / (d1a - d3a)
         let Vy = -(d3a * d1b - d1a * d3b) / (d1a - d3a)
         let Vx = -(d1b - d3b) / (d1a - d3a)
         let Vy = -(d3a * d1b - d1a * d3b) / (d1a - d3a)

-        
+

         let Wx = p1x + (p2x - p1x) / 2.0
         let Wy = p1y + (p2y - p1y) / 2.0
         let Wx = p1x + (p2x - p1x) / 2.0
         let Wy = p1y + (p2y - p1y) / 2.0

-        
+

         let Zx = p1x + (PTanx - p1x) / 2.0
         let Zy = p1y + (PTany - p1y) / 2.0
         let Zx = p1x + (PTanx - p1x) / 2.0
         let Zy = p1y + (PTany - p1y) / 2.0

-        
+

         let va = -(-Vy + Zy) / (Vx - Zx)
         let vb = -(Zx * Vy - Vx * Zy) / (Vx - Zx)
         let va = -(-Vy + Zy) / (Vx - Zx)
         let vb = -(Zx * Vy - Vx * Zy) / (Vx - Zx)

-        
+

         let ua = -(-Uy + Wy) / (Ux - Wx)
         let ub = -(Wx * Uy - Ux * Wy) / (Ux - Wx)
         let ua = -(-Uy + Wy) / (Ux - Wx)
         let ub = -(Wx * Uy - Ux * Wy) / (Ux - Wx)

-        
+

         let cx = -(vb - ub) / (va - ua)
         let cy = -(ua * vb - va * ub) / (va - ua)
         let cx = -(vb - ub) / (va - ua)
         let cy = -(ua * vb - va * ub) / (va - ua)

-        
+

         let rc = sqrt (cx**2.0 + cy**2.0)
         let psi = atan2 cy cx
         let rc = sqrt (cx**2.0 + cy**2.0)
         let psi = atan2 cy cx

-        
-        let rellipse theta = 
+
+        let rellipse theta =

             sqrt (
                 rc ** 2.0 + (r1 ** 2.0 * r2 ** 2.0 * (r1 * (cos (alpha2 + theta - theta1 - theta2) - cos (alpha2 - theta) * cos (theta1 - theta2)) * sin (alpha1 - theta1) + r2 * (-cos (alpha1 + theta - theta1 - theta2) + cos (alpha1 - theta) * cos (theta1 - theta2)) * sin (alpha2 - theta2)) ** 2.0 * sin (theta1 - theta2) ** 2.0) /
                 (sin (alpha1 - theta1) * sin (alpha2 - theta2) * (r1 * sin (theta - theta1) - r2 * sin (theta - theta2)) ** 2.0 - r1 * r2 * sin (alpha1 - theta) * sin (alpha2 - theta) * sin (theta1 - theta2) ** 2.0) ** 2.0 -
                 (2.0 * r1 * r2 * rc * cos (theta - psi) * (r1 * (cos (alpha2 + theta - theta1 - theta2) - cos (alpha2 - theta) * cos (theta1 - theta2)) * sin (alpha1 - theta1) + r2 * (-cos (alpha1 + theta - theta1 - theta2) + cos (alpha1 - theta) * cos (theta1 - theta2)) * sin (alpha2 - theta2)) * sin (theta1 - theta2)) /
                 (sin (alpha1 - theta1) * sin (alpha2 - theta2) * (r1 * sin (theta - theta1) - r2 * sin (theta - theta2)) ** 2.0 - r1 * r2 * sin (alpha1 - theta) * sin (alpha2 - theta) * sin (theta1 - theta2) ** 2.0))
             sqrt (
                 rc ** 2.0 + (r1 ** 2.0 * r2 ** 2.0 * (r1 * (cos (alpha2 + theta - theta1 - theta2) - cos (alpha2 - theta) * cos (theta1 - theta2)) * sin (alpha1 - theta1) + r2 * (-cos (alpha1 + theta - theta1 - theta2) + cos (alpha1 - theta) * cos (theta1 - theta2)) * sin (alpha2 - theta2)) ** 2.0 * sin (theta1 - theta2) ** 2.0) /
                 (sin (alpha1 - theta1) * sin (alpha2 - theta2) * (r1 * sin (theta - theta1) - r2 * sin (theta - theta2)) ** 2.0 - r1 * r2 * sin (alpha1 - theta) * sin (alpha2 - theta) * sin (theta1 - theta2) ** 2.0) ** 2.0 -
                 (2.0 * r1 * r2 * rc * cos (theta - psi) * (r1 * (cos (alpha2 + theta - theta1 - theta2) - cos (alpha2 - theta) * cos (theta1 - theta2)) * sin (alpha1 - theta1) + r2 * (-cos (alpha1 + theta - theta1 - theta2) + cos (alpha1 - theta) * cos (theta1 - theta2)) * sin (alpha2 - theta2)) * sin (theta1 - theta2)) /
                 (sin (alpha1 - theta1) * sin (alpha2 - theta2) * (r1 * sin (theta - theta1) - r2 * sin (theta - theta2)) ** 2.0 - r1 * r2 * sin (alpha1 - theta) * sin (alpha2 - theta) * sin (theta1 - theta2) ** 2.0))

-                        
-        // We search for an interval [theta_a, theta_b] and assume the function is unimodal in this interval.             
+
+        // We search for an interval [theta_a, theta_b] and assume the function is unimodal in this interval.

         let r1eTheta, r1e = goldenSectionSearch rellipse accuracy_extremum_search_2 0.0 (Math.PI / 2.0) Maximum // Pi/2 and not pi because the period is Pi.
         let r2eTheta, r2e = goldenSectionSearch rellipse accuracy_extremum_search_2 0.0 (Math.PI / 2.0) Minimum
         let r1eTheta, r1e = goldenSectionSearch rellipse accuracy_extremum_search_2 0.0 (Math.PI / 2.0) Maximum // Pi/2 and not pi because the period is Pi.
         let r2eTheta, r2e = goldenSectionSearch rellipse accuracy_extremum_search_2 0.0 (Math.PI / 2.0) Minimum

-                
+

         let rr1e = r r1eTheta
         let r1ex = rr1e * cos r1eTheta
         let r1ey = rr1e * sin r1eTheta
         let mutable alpha = atan ((r1ey - cy) / (r1ex - cx))
         if alpha < 0.0
         then
         let rr1e = r r1eTheta
         let r1ex = rr1e * cos r1eTheta
         let r1ey = rr1e * sin r1eTheta
         let mutable alpha = atan ((r1ey - cy) / (r1ex - cx))
         if alpha < 0.0
         then

-           alpha <- alpha + Math.PI 
-        
+           alpha <- alpha + Math.PI
+

         // Ride off the p3 referential.
         let cx = cx + p3x
         let cy = cy + p3y
         // Ride off the p3 referential.
         let cx = cx + p3x
         let cy = cy + p3y


@@ -153,9 +154,9 @@ let private vectorRotation (p1x: float) (p1y: float) (v1x: float) (v1y: float) (
         if v1x > 0.0
         then
             rotation <- -1.0
         if v1x > 0.0
         then
             rotation <- -1.0

-    elif p1y < py        
+    elif p1y < py

     then
     then

-        if v1x < 0.0 
+        if v1x < 0.0

         then
             rotation <- -1.0
     elif p1x > px
         then
             rotation <- -1.0
     elif p1x > px


@@ -163,9 +164,9 @@ let private vectorRotation (p1x: float) (p1y: float) (v1x: float) (v1y: float) (
         if v1y < 0.0
         then
             rotation <- -1.0
         if v1y < 0.0
         then
             rotation <- -1.0

-    elif p1x < px              
+    elif p1x < px

     then
     then

-        if v1y > 0.0 
+        if v1y > 0.0

         then
             rotation <- -1.0
     rotation
         then
             rotation <- -1.0
     rotation


@@ -174,15 +175,15 @@ let private vectorRotation (p1x: float) (p1y: float) (v1x: float) (v1y: float) (
 let private areVectorsValid (p1x: float) (p1y: float) (p2x: float) (p2y: float) (v1x: float) (v1y: float) (v2x: float) (v2y: float) : (float * float) option =
     let m1 = -v1x / v1y
     let m2 = -v2x / v2y
 let private areVectorsValid (p1x: float) (p1y: float) (p2x: float) (p2y: float) (v1x: float) (v1y: float) (v2x: float) (v2y: float) : (float * float) option =
     let m1 = -v1x / v1y
     let m2 = -v2x / v2y

-    
+

     let b1 = -m1 * p1x + p1y
     let b2 = -m2 * p2x + p2y
     let px = -((b1 - b2)/(m1 - m2))
     let py = -((m2 * b1 - m1 * b2)/(m1 - m2))
     let b1 = -m1 * p1x + p1y
     let b2 = -m2 * p2x + p2y
     let px = -((b1 - b2)/(m1 - m2))
     let py = -((m2 * b1 - m1 * b2)/(m1 - m2))

-    
+

     let rot1 = vectorRotation p1x p1y v1x v1y px py
     let rot2 = vectorRotation p2x p2y v2x v2y px py
     let rot1 = vectorRotation p1x p1y v1x v1y px py
     let rot2 = vectorRotation p2x p2y v2x v2y px py

-    
+

     if rot1 = rot2 || rot1 * atan2 (p1y - py) (p1x - px) + rot2 * atan2 (p2y - py) (p2x - px) <= 0.0
     then
         None
     if rot1 = rot2 || rot1 * atan2 (p1y - py) (p1x - px) + rot2 * atan2 (p2y - py) (p2x - px) <= 0.0
     then
         None


@@ -190,15 +191,16 @@ let private areVectorsValid (p1x: float) (p1y: float) (p2x: float) (p2y: float)
         Some (m1, m2)
 
 let find (edges: Matrix<byte>)
         Some (m1, m2)
 
 let find (edges: Matrix<byte>)

-         (xDir: Image<Gray, float>) 
-         (yDir: Image<Gray, float>) 
-         (radiusRange: float * float) 
-         (windowSize: int) 
-         (factorNbPick: float) : Types.Ellipse list =
+         (xDir: Image<Gray, float>)
+         (yDir: Image<Gray, float>)
+         (config: Config) : MatchingEllipses =
+
+    let r1, r2 = config.scale * config.minRBCSize, config.scale * config.maxRBCSize
+    let windowSize = roundInt (config.factorWindowSize * r2)
+    let factorNbPick = config.factorNbPick

 
     let increment = windowSize / 4
 
 
     let increment = windowSize / 4
 

-    let r1, r2 = radiusRange

     let radiusTolerance = (r2 - r1) * 0.2
 
     let minimumDistance = (r2 / 1.5) ** 2.0
     let radiusTolerance = (r2 - r1) * 0.2
 
     let minimumDistance = (r2 / 1.5) ** 2.0


@@ -206,7 +208,7 @@ let find (edges: Matrix<byte>)
 
     let h = edges.Height
     let w = edges.Width
 
     let h = edges.Height
     let w = edges.Width

-    
+

     let mutable last_i, last_j = Int32.MaxValue, Int32.MaxValue
 
     let currentElements = List<(int * int)>()
     let mutable last_i, last_j = Int32.MaxValue, Int32.MaxValue
 
     let currentElements = List<(int * int)>()


@@ -216,12 +218,12 @@ let find (edges: Matrix<byte>)
     let yDirData = yDir.Data
 
     let rng = Random(42)
     let yDirData = yDir.Data
 
     let rng = Random(42)

-    
+

     let ellipses = MatchingEllipses(r1)
     let ellipses = MatchingEllipses(r1)

-        
-    for window_i in -windowSize + increment .. increment .. h - increment do                                                  
-        for window_j in -windowSize + increment .. increment .. w - increment do            
-                
+
+    for window_i in -windowSize + increment .. increment .. h - increment do
+        for window_j in -windowSize + increment .. increment .. w - increment do
+

             let window_i_begin = if window_i < 0 then 0 else window_i
             let window_i_end = if window_i + windowSize - 1 >= h then h - 1 else window_i + windowSize - 1
             let window_j_begin = if window_j < 0 then 0 else window_j
             let window_i_begin = if window_i < 0 then 0 else window_i
             let window_i_end = if window_i + windowSize - 1 >= h then h - 1 else window_i + windowSize - 1
             let window_j_begin = if window_j < 0 then 0 else window_j


@@ -258,13 +260,13 @@ let find (edges: Matrix<byte>)
                             match areVectorsValid p1xf p1yf p2xf p2yf -xDirData.[p1y, p1x, 0] -yDirData.[p1y, p1x, 0] -xDirData.[p2y, p2x, 0] -yDirData.[p2y, p2x, 0] with
                             | Some (m1, m2) ->
                                 match ellipse p1xf p1yf m1 p2xf p2yf m2 p3xf p3yf with
                             match areVectorsValid p1xf p1yf p2xf p2yf -xDirData.[p1y, p1x, 0] -yDirData.[p1y, p1x, 0] -xDirData.[p2y, p2x, 0] -yDirData.[p2y, p2x, 0] with
                             | Some (m1, m2) ->
                                 match ellipse p1xf p1yf m1 p2xf p2yf m2 p3xf p3yf with

-                                | Some e when e.Cx > 0.0 && e.Cx < (float w) - 1.0 && e.Cy > 0.0 && e.Cy < (float h) - 1.0 && 
+                                | Some e when e.Cx > 0.0 && e.Cx < (float w) - 1.0 && e.Cy > 0.0 && e.Cy < (float h) - 1.0 &&

                                               e.A >= r1 - radiusTolerance && e.A <= r2 + radiusTolerance && e.B >= r1 - radiusTolerance && e.B <= r2 + radiusTolerance ->
                                      ellipses.Add e
                                 | _ -> ()
                             | _ -> ()
 
         currentElements.Clear()
                                               e.A >= r1 - radiusTolerance && e.A <= r2 + radiusTolerance && e.B >= r1 - radiusTolerance && e.B <= r2 + radiusTolerance ->
                                      ellipses.Add e
                                 | _ -> ()
                             | _ -> ()
 
         currentElements.Clear()

-        
-    ellipses.Ellipses
+
+    ellipses

 
 

diff --git a/Parasitemia/Parasitemia/ImgTools.fs b/Parasitemia/Parasitemia/ImgTools.fs
index f7e5a4a..7253390 100644 (file)
--- a/Parasitemia/Parasitemia/ImgTools.fs
+++ b/Parasitemia/Parasitemia/ImgTools.fs
@@ -156,41 +156,37 @@ let saveMat (mat: Matrix<'TDepth>) (filepath: string) =
     mat.CopyTo(img)
     saveImg img filepath
 
     mat.CopyTo(img)
     saveImg img filepath
 

-let drawLine (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: int) (y0: int) (x1: int) (y1: int) =
-    img.Draw(LineSegment2D(Point(x0, y0), Point(x1, y1)), color, 1);
+let drawLine (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: int) (y0: int) (x1: int) (y1: int) (thickness: int) =
+    img.Draw(LineSegment2D(Point(x0, y0), Point(x1, y1)), color, thickness);

 
 

-let drawLineF (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: float) (y0: float) (x1: float) (y1: float) =
-    let x0, y0, x1, y1 = roundInt(x0), roundInt(y0), roundInt(x1), roundInt(y1)
-    drawLine img color x0 y0 x1 y1
+let drawLineF (img: Image<'TColor, 'TDepth>) (color: 'TColor) (x0: float) (y0: float) (x1: float) (y1: float) (thickness: int) =
+    img.Draw(LineSegment2DF(PointF(float32 x0, float32 y0), PointF(float32 x1, float32 y1)), color, thickness, CvEnum.LineType.AntiAlias);

 
 

-let drawEllipse (img: Image<'TColor, 'TDepth>) (e: Types.Ellipse) (color: 'TColor) =
-    let cosAlpha = cos e.Alpha
-    let sinAlpha = sin e.Alpha
+let drawEllipse (img: Image<'TColor, 'TDepth>) (e: Types.Ellipse) (color: 'TColor) (alpha: float) =

 
 

-    let mutable x0 = 0.0
-    let mutable y0 = 0.0
-    let mutable first_iteration = true
+    if alpha >= 1.0
+    then
+        img.Draw(Ellipse(PointF(float32 e.Cx, float32 e.Cy), SizeF(2. * e.B |> float32, 2. * e.A |> float32), float32 <| e.Alpha / Math.PI * 180.), color, 1, CvEnum.LineType.AntiAlias)
+    else
+        let windowPosX = e.Cx - e.A - 5.0
+        let gapX = windowPosX - (float (int windowPosX))

 
 

-    let n = 40
-    let thetaIncrement = 2.0 * Math.PI / (float n)
+        let windowPosY = e.Cy - e.A - 5.0
+        let gapY = windowPosY - (float (int windowPosY))

 
 

-    for theta in 0.0 .. thetaIncrement .. 2.0 * Math.PI do
-        let cosTheta = cos theta
-        let sinTheta = sin theta
-        let x = e.Cx + cosAlpha * e.A * cosTheta - sinAlpha * e.B * sinTheta
-        let y = e.Cy + sinAlpha * e.A * cosTheta + cosAlpha * e.B * sinTheta
+        let roi = Rectangle(int windowPosX, int windowPosY, 2. * (e.A + 5.0) |> int, 2.* (e.A + 5.0) |> int)

 
 

-        if not first_iteration
+        img.ROI <- roi
+        if roi = img.ROI // We do not display ellipses touching the edges (FIXME)

         then
         then

-            drawLineF img color x0 y0 x y
-        else
-            first_iteration <- false
+            use i = new Image<'TColor, 'TDepth>(img.ROI.Size)
+            i.Draw(Ellipse(PointF(float32 <| (e.A + 5. + gapX) , float32 <| (e.A + 5. + gapY)), SizeF(2. * e.B |> float32, 2. * e.A |> float32), float32 <| e.Alpha / Math.PI * 180.), color, 1, CvEnum.LineType.AntiAlias)
+            CvInvoke.AddWeighted(img, 1.0, i, alpha, 0.0, img)
+        img.ROI <- Rectangle.Empty

 
 

-        x0 <- x
-        y0 <- y

 
 

-let drawEllipses (img: Image<'TColor, 'TDepth>) (ellipses: Types.Ellipse list) (color: 'TColor) =
-    List.iter (fun e -> drawEllipse img e color) ellipses
+let drawEllipses (img: Image<'TColor, 'TDepth>) (ellipses: Types.Ellipse list) (color: 'TColor) (alpha: float) =
+    List.iter (fun e -> drawEllipse img e color alpha) ellipses

 
 
 let rngCell =  System.Random()
 
 
 let rngCell =  System.Random()


@@ -213,13 +209,18 @@ let drawCell (img: Image<Bgr, byte>) (drawCellContent: bool) (c: Types.Cell) =
                     img.Data.[y + dy, x + dx, 1] <- if g + colorG > 255 then 255uy else byte (g + colorG)
                     img.Data.[y + dy, x + dx, 2] <- if r + colorR > 255 then 255uy else byte (r + colorR)
 
                     img.Data.[y + dy, x + dx, 1] <- if g + colorG > 255 then 255uy else byte (g + colorG)
                     img.Data.[y + dy, x + dx, 2] <- if r + colorR > 255 then 255uy else byte (r + colorR)
 

-    let crossColor = match c.cellClass with
-                     | Types.HealthyRBC -> Bgr(255.0, 0.0, 0.0)
-                     | Types.InfectedRBC -> Bgr(0.0, 0.0, 255.0)
-                     | Types.Peculiar -> Bgr(0.0, 0.0, 0.0)
+    let crossColor, crossColor2 =
+        match c.cellClass with
+        | Types.HealthyRBC -> Bgr(255., 0., 0.), Bgr(255., 255., 255.)
+        | Types.InfectedRBC -> Bgr(0., 0., 255.), Bgr(120., 120., 255.)
+        | Types.Peculiar -> Bgr(0., 0., 0.), Bgr(80., 80., 80.)
+
+    drawLine img crossColor2 (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 2
+    drawLine img crossColor2 c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 2
+
+    drawLine img crossColor (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y 1
+    drawLine img crossColor c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3) 1

 
 

-    drawLine img crossColor (c.center.X - 3) c.center.Y (c.center.X + 3) c.center.Y
-    drawLine img crossColor c.center.X (c.center.Y - 3) c.center.X (c.center.Y + 3)

 
 let drawCells (img: Image<Bgr, byte>) (drawCellContent: bool) (cells: Types.Cell list) =
     List.iter (fun c -> drawCell img drawCellContent c) cells
\ No newline at end of file
 
 let drawCells (img: Image<Bgr, byte>) (drawCellContent: bool) (cells: Types.Cell list) =
     List.iter (fun c -> drawCell img drawCellContent c) cells
\ No newline at end of file

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index c9e9422..9308780 100644 (file)
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -59,20 +59,15 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
     logTime "Finding edges" (fun() -> thin edges)
     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
 
     logTime "Finding edges" (fun() -> thin edges)
     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
 

-    (*

     let kmediansResults = KMedians.kmedians filteredGreen 1.0
 
     let parasites = ParasitesMarker.find green filteredGreen kmediansResults config
 
     let kmediansResults = KMedians.kmedians filteredGreen 1.0
 
     let parasites = ParasitesMarker.find green filteredGreen kmediansResults config
 

-    let radiusRange = config.scale * config.minRBCSize, config.scale * config.maxRBCSize
-    let windowSize = roundInt (1.6 * (snd radiusRange))
-    let factorNbPick = 1.5
-    let ellipses = logTime "Finding ellipses" (fun () ->
-        Ellipse.find edges xEdges yEdges radiusRange windowSize factorNbPick)
+    let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
+        let matchingEllipses = Ellipse.find edges xEdges yEdges config
+        matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )

 
     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
 
     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)

-    *)
-    let cells = []

 
     // Output pictures if debug flag is set.
     match config.debug with
 
     // Output pictures if debug flag is set.
     match config.debug with


@@ -80,12 +75,16 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         let buildFileName postfix = System.IO.Path.Combine(output, name + postfix)
         saveMat (edges * 255.0) (buildFileName " - edges.png")
 
         let buildFileName postfix = System.IO.Path.Combine(output, name + postfix)
         saveMat (edges * 255.0) (buildFileName " - edges.png")
 

-        (*saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
+        saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")

         saveImg parasites.stain (buildFileName " - parasites - stain.png")
         saveImg parasites.infection (buildFileName " - parasites - infection.png")
 
         saveImg parasites.stain (buildFileName " - parasites - stain.png")
         saveImg parasites.infection (buildFileName " - parasites - infection.png")
 

+        let imgAllEllipses = img.Copy()
+        drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
+        saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
+

         let imgEllipses = img.Copy()
         let imgEllipses = img.Copy()

-        drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0))
+        drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0

         saveImg imgEllipses (buildFileName " - ellipses.png")
 
         saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
         saveImg imgEllipses (buildFileName " - ellipses.png")
 
         saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")


@@ -96,7 +95,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
 
         let imgCells' = img.Copy()
         drawCells imgCells' true cells
 
         let imgCells' = img.Copy()
         drawCells imgCells' true cells

-        saveImg imgCells' (buildFileName " - cells - full.png")*)
+        saveImg imgCells' (buildFileName " - cells - full.png")

     | _ -> ()
 
     cells
     | _ -> ()
 
     cells

diff --git a/Parasitemia/Parasitemia/MatchingEllipses.fs b/Parasitemia/Parasitemia/MatchingEllipses.fs
index 8a1b4f8..da74c65 100644 (file)
--- a/Parasitemia/Parasitemia/MatchingEllipses.fs
+++ b/Parasitemia/Parasitemia/MatchingEllipses.fs
@@ -10,7 +10,7 @@ open Utils
 
 
 let matchingScoreThreshold1 = 0.6
 
 
 let matchingScoreThreshold1 = 0.6

-let matchingScoreThreshold2 = 1.0
+let matchingScoreThreshold2 = 1.

 
 type private EllipseScoreFlaggedKd (matchingScore: float, e: Ellipse) =
     let mutable matchingScore = matchingScore
 
 type private EllipseScoreFlaggedKd (matchingScore: float, e: Ellipse) =
     let mutable matchingScore = matchingScore


@@ -24,18 +24,21 @@ type private EllipseScoreFlaggedKd (matchingScore: float, e: Ellipse) =
     member val Processed = false with get, set
     member val Removed = false with get, set
 
     member val Processed = false with get, set
     member val Removed = false with get, set
 

-    interface KdTree.I2DCoords with    
+    interface KdTree.I2DCoords with

         member this.X = this.Ellipse.Cx
         member this.Y = this.Ellipse.Cy
 
         member this.X = this.Ellipse.Cx
         member this.Y = this.Ellipse.Cy
 

-        
+

 type MatchingEllipses (radiusMin: float) =
     let ellipses = List<EllipseScoreFlaggedKd>()
 type MatchingEllipses (radiusMin: float) =
     let ellipses = List<EllipseScoreFlaggedKd>()

-        
-    member this.Add (e: Ellipse) = 
+
+    member this.Add (e: Ellipse) =

         ellipses.Add(EllipseScoreFlaggedKd(0.0, e))
 
     member this.Ellipses : Ellipse list =
         ellipses.Add(EllipseScoreFlaggedKd(0.0, e))
 
     member this.Ellipses : Ellipse list =

+        List.ofSeq ellipses |> List.map (fun e -> e.Ellipse)
+
+    member this.PrunedEllipses : Ellipse list =

         if ellipses.Count = 0
         then
             []
         if ellipses.Count = 0
         then
             []


@@ -43,13 +46,13 @@ type MatchingEllipses (radiusMin: float) =
             // 1) Create a kd-tree from the ellipses list.
             let tree = KdTree.Tree.BuildTree (List.ofSeq ellipses)
 
             // 1) Create a kd-tree from the ellipses list.
             let tree = KdTree.Tree.BuildTree (List.ofSeq ellipses)
 

-            // 2) Compute the matching score of each ellipses.       
+            // 2) Compute the matching score of each ellipses.

             let windowSize = radiusMin
             for e in ellipses do
                 e.Processed <- true
                 let areaE = e.Ellipse.Area
                 let window = { KdTree.minX = e.Ellipse.Cx - windowSize / 2.0
             let windowSize = radiusMin
             for e in ellipses do
                 e.Processed <- true
                 let areaE = e.Ellipse.Area
                 let window = { KdTree.minX = e.Ellipse.Cx - windowSize / 2.0

-                               KdTree.maxX = e.Ellipse.Cx + windowSize / 2.0 
+                               KdTree.maxX = e.Ellipse.Cx + windowSize / 2.0

                                KdTree.minY = e.Ellipse.Cy - windowSize / 2.0
                                KdTree.maxY = e.Ellipse.Cy + windowSize / 2.0 }
                 for other in tree.Search window do
                                KdTree.minY = e.Ellipse.Cy - windowSize / 2.0
                                KdTree.maxY = e.Ellipse.Cy + windowSize / 2.0 }
                 for other in tree.Search window do


@@ -68,7 +71,7 @@ type MatchingEllipses (radiusMin: float) =
             // 3) Sort ellipses by their score.
             ellipses.Sort(fun e1 e2 -> e2.MatchingScore.CompareTo(e1.MatchingScore))
 
             // 3) Sort ellipses by their score.
             ellipses.Sort(fun e1 e2 -> e2.MatchingScore.CompareTo(e1.MatchingScore))
 

-            // 4) Remove ellipses wich have a low score. 
+            // 4) Remove ellipses wich have a low score.

             let i = ellipses.BinarySearch(EllipseScoreFlaggedKd(matchingScoreThreshold2, Ellipse(0.0, 0.0, 0.0, 0.0, 0.0)),
                                           { new IComparer<EllipseScoreFlaggedKd> with
                                                 member this.Compare(e1, e2) = e2.MatchingScore.CompareTo(e1.MatchingScore) }) |> abs
             let i = ellipses.BinarySearch(EllipseScoreFlaggedKd(matchingScoreThreshold2, Ellipse(0.0, 0.0, 0.0, 0.0, 0.0)),
                                           { new IComparer<EllipseScoreFlaggedKd> with
                                                 member this.Compare(e1, e2) = e2.MatchingScore.CompareTo(e1.MatchingScore) }) |> abs


@@ -84,12 +87,12 @@ type MatchingEllipses (radiusMin: float) =
                 if not e.Removed
                 then
                     let window = { KdTree.minX = e.Ellipse.Cx - e.Ellipse.A
                 if not e.Removed
                 then
                     let window = { KdTree.minX = e.Ellipse.Cx - e.Ellipse.A

-                                   KdTree.maxX = e.Ellipse.Cx + e.Ellipse.A 
+                                   KdTree.maxX = e.Ellipse.Cx + e.Ellipse.A

                                    KdTree.minY = e.Ellipse.Cy - e.Ellipse.A
                                    KdTree.maxY = e.Ellipse.Cy + e.Ellipse.A }
                     for other in tree.Search window do
                         if not other.Removed && other.MatchingScore < e.MatchingScore
                                    KdTree.minY = e.Ellipse.Cy - e.Ellipse.A
                                    KdTree.maxY = e.Ellipse.Cy + e.Ellipse.A }
                     for other in tree.Search window do
                         if not other.Removed && other.MatchingScore < e.MatchingScore

-                        then            
+                        then

                             if e.Ellipse.Contains other.Ellipse.Cx other.Ellipse.Cy
                             then
                                 other.Removed <- true
                             if e.Ellipse.Contains other.Ellipse.Cx other.Ellipse.Cy
                             then
                                 other.Removed <- true


@@ -97,5 +100,5 @@ type MatchingEllipses (radiusMin: float) =
 
             List.ofSeq ellipses |> List.map (fun e -> e.Ellipse)
 
 
             List.ofSeq ellipses |> List.map (fun e -> e.Ellipse)
 

-        
+

 
 

diff --git a/Parasitemia/Parasitemia/ParasitesMarker.fs b/Parasitemia/Parasitemia/ParasitesMarker.fs
index e422b04..9adf185 100644 (file)
--- a/Parasitemia/Parasitemia/ParasitesMarker.fs
+++ b/Parasitemia/Parasitemia/ParasitesMarker.fs
@@ -16,8 +16,6 @@ type Result = {
 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
 let find (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (kmediansResult: KMedians.Result) (config: Config.Config) : Result =
 
 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
 let find (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (kmediansResult: KMedians.Result) (config: Config.Config) : Result =
 

-    let green = ImgTools.gaussianFilter green 1.0
-

     // We use the filtered image to find the dark stain.
     let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResult
     let darkStain = d_fg.Cmp(median_bg * config.darkStainLevel, CvEnum.CmpType.GreaterThan)
     // We use the filtered image to find the dark stain.
     let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResult
     let darkStain = d_fg.Cmp(median_bg * config.darkStainLevel, CvEnum.CmpType.GreaterThan)


@@ -25,13 +23,12 @@ let find (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (km
     darkStain._And(fg)
 
     let fgFloat = (fg / 255.0).Convert<Gray, float32>()
     darkStain._And(fg)
 
     let fgFloat = (fg / 255.0).Convert<Gray, float32>()

-    let greenWithoutBg = green.Copy()
+    use greenWithoutBg = ImgTools.gaussianFilter green 1.0

     greenWithoutBg.SetValue(Gray(0.0), fg.Not())
 
     let findSmears (sigma: float) (level: float) : Image<Gray, byte> =
     greenWithoutBg.SetValue(Gray(0.0), fg.Not())
 
     let findSmears (sigma: float) (level: float) : Image<Gray, byte> =

-        let greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
-        let fgSmoothed = ImgTools.gaussianFilter fgFloat sigma
-
+        use greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
+        use fgSmoothed = ImgTools.gaussianFilter fgFloat sigma

         let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level), CvEnum.CmpType.LessThan)
         smears._And(fg)
         smears
         let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level), CvEnum.CmpType.LessThan)
         smears._And(fg)
         smears

diff --git a/Parasitemia/Parasitemia/Program.fs b/Parasitemia/Parasitemia/Program.fs
index 76fc244..f23cd39 100644 (file)
--- a/Parasitemia/Parasitemia/Program.fs
+++ b/Parasitemia/Parasitemia/Program.fs
@@ -71,7 +71,10 @@ let main args =
             doGSigma2 = 20.
             doGLowFreqPercentageReduction = 0.75
 
             doGSigma2 = 20.
             doGLowFreqPercentageReduction = 0.75
 

-            darkStainLevel = 0.5
+            factorNbPick = 2.0
+            factorWindowSize = 1.6
+
+            darkStainLevel = 0.4 // Lower -> more sensitive.

 
             stainSigma = 10.
             stainLevel = 0.9
 
             stainSigma = 10.
             stainLevel = 0.9


@@ -85,7 +88,7 @@ let main args =
 
             MaxDarkStainRatio = 0.1
 
 
             MaxDarkStainRatio = 0.1
 

-            minimumCellArea = 600. * scale ** 2. |> int
+            minimumCellArea = 1200. * scale ** 2. |> int

             maxOffcenter = 0.5 }
 
         match mode with
             maxOffcenter = 0.5 }
 
         match mode with