* Treat some special cases when ellipses intersecting.

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

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index c987e63..6111f06 100644 (file)
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -47,32 +47,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
     let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert<Gray, float32>()
     let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert<Gray, float32>()
 
-    use sobelKernel =
-        new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
-                                        [ 2.0f; 0.0f; -2.0f ]
-                                        [ 1.0f; 0.0f; -1.0f ]], Point(0, 0))
-
-    use xEdges = filteredGreenWhitoutStainFloat.Convolution(sobelKernel).Convert<Gray, float>()
-    use yEdges = filteredGreenWhitoutStainFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
-
-    let xEdgesData = xEdges.Data
-    let yEdgesData = yEdges.Data
-    for r in 0..xEdges.Rows-1 do
-        xEdgesData.[r, 0, 0] <- 0.0
-        xEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
-        yEdgesData.[r, 0, 0] <- 0.0
-        yEdgesData.[r, xEdges.Cols-1, 0] <- 0.0
-
-    for c in 0..xEdges.Cols-1 do
-        xEdgesData.[0, c, 0] <- 0.0
-        xEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
-        yEdgesData.[0, c, 0] <- 0.0
-        yEdgesData.[xEdges.Rows-1, c, 0] <- 0.0
-
-    use magnitudes = new Matrix<float>(xEdges.Size)
-    CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles).
-
-    let min = ref 0.0
+    (*let min = ref 0.0
     let minLocation = ref <| Point()
     let max = ref 0.0
     let maxLocation = ref <| Point()
@@ -82,11 +57,14 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
     use edges = new Matrix<byte>(xEdges.Size)
     CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
 
-    logTime "Finding edges" (fun() -> thin edges)
+    logTime "Finding edges" (fun() -> thin edges)*)
+
+    let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStainFloat
+
     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
 
     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
-        let matchingEllipses = Ellipse.find edges xEdges yEdges config
+        let matchingEllipses = Ellipse.find edges xGradient yGradient config
         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
 
     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
@@ -106,7 +84,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         saveImg parasites.infection (buildFileName " - parasites - infection.png")
 
         let imgAllEllipses = img.Copy()
-        drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1
+        drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 
         let imgEllipses = img.Copy()