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 6f78b7c..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 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)
@@ -30,58 +30,25 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
     let greenOpen1 = filteredGreen.Copy()
     logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
 
-    logTime "areaOpen" (fun () -> ImgTools.areaOpen filteredGreen 2000)
+    let initialAreaOpen = 2000
+    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpen)
 
     config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
 
-    let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
+    let secondAreaOpen = int <| config.RBCArea / 3.
+    if secondAreaOpen > initialAreaOpen
+    then
+        logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
 
-    let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreenFloat 1.0)
+    let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
+    //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
 
-    let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker2.find filteredGreen filteredGreenFloat kmediansResults config
-    let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert<Gray, float32>()
-    let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert<Gray, float32>()
+    let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
 
-    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 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)
     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)
@@ -94,6 +61,8 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
 
         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
 
+        //saveImg canny (buildFileName " - canny.png")
+
         saveMat (edges * 255.0) (buildFileName " - edges.png")
 
         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
@@ -101,15 +70,13 @@ 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()
         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")
@@ -118,16 +85,14 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         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
-            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.png")
-
-        (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png")
-        saveImg stainMarker (buildFileName " - stain (area closing).png")*)
+        saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
+        saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 
         saveImg green (buildFileName " - green.png")