Use float32 images instead of byte to improve the edge detection precision.

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

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index ff82b8b..a240878 100644 (file)
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -20,7 +20,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
 
     let greenFloat = green.Convert<Gray, float32>()
 
 
     let greenFloat = green.Convert<Gray, float32>()
 

-    let filteredGreen = gaussianFilter green config.Parameters.preFilterSigma
+    let filteredGreen = gaussianFilter greenFloat config.Parameters.preFilterSigma

 
     (*let maximaImg = filteredGreen.Copy()
     let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
 
     (*let maximaImg = filteredGreen.Copy()
     let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)


@@ -31,37 +31,19 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
     logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
 
     let initialAreaOpen = 2000
     logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
 
     let initialAreaOpen = 2000

-    logTime "areaOpen 1" (fun () -> ImgTools.areaOpen filteredGreen 2000)
+    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpen)

 
     config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
 
     let secondAreaOpen = int <| config.RBCArea / 3.
     if secondAreaOpen > initialAreaOpen
     then
 
     config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
 
     let secondAreaOpen = int <| config.RBCArea / 3.
     if secondAreaOpen > initialAreaOpen
     then

-        logTime "areaOpen 2" (fun () -> ImgTools.areaOpen filteredGreen secondAreaOpen)
+        logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)

 
 

-    let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
-
-    let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen filteredGreenFloat config
+    let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config

     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config

-    let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert<Gray, float32>()
-    let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert<Gray, float32>()
-
-    let canny = green.Canny(60., 40.)
-
-    (*let min = ref 0.0
-    let minLocation = ref <| Point()
-    let max = ref 0.0
-    let maxLocation = ref <| Point()
-    magnitudes.MinMax(min, max, minLocation, maxLocation)
-
-    use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
-    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)*)
-
-    let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStainFloat
+    let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain

 
     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
 
 
     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
 


@@ -79,7 +61,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
 
         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 
 
         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 

-        saveImg canny (buildFileName " - canny.png")
+        //saveImg canny (buildFileName " - canny.png")

 
         saveMat (edges * 255.0) (buildFileName " - edges.png")
 
 
         saveMat (edges * 255.0) (buildFileName " - edges.png")
 


@@ -95,8 +77,6 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
         saveImg imgEllipses (buildFileName " - ellipses.png")
 
         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")
-

         let imgCells = img.Copy()
         drawCells imgCells false cells
         saveImg imgCells (buildFileName " - cells.png")
         let imgCells = img.Copy()
         drawCells imgCells false cells
         saveImg imgCells (buildFileName " - cells.png")


@@ -105,18 +85,15 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         drawCells imgCells' true cells
         saveImg imgCells' (buildFileName " - cells - full.png")
 
         drawCells imgCells' true cells
         saveImg imgCells' (buildFileName " - cells - full.png")
 

-        let filteredGreenMaxima = gaussianFilter green config.Parameters.preFilterSigma
+        let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma

         for m in ImgTools.findMaxima filteredGreenMaxima do
         for m in ImgTools.findMaxima filteredGreenMaxima do

-            ImgTools.drawPoints filteredGreenMaxima m 255uy
+            ImgTools.drawPoints filteredGreenMaxima m 255.f

         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 
         saveImg filteredGreen (buildFileName " - filtered.png")
         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
         saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 
         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 
         saveImg filteredGreen (buildFileName " - filtered.png")
         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
         saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 

-        (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png")
-        saveImg stainMarker (buildFileName " - stain (area closing).png")*)
-

         saveImg green (buildFileName " - green.png")
 
         use blue  = scaledImg.Item(0)
         saveImg green (buildFileName " - green.png")
 
         use blue  = scaledImg.Item(0)