Cleaning, micro-optimizations.

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

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index 6111f06..fdae997 100644 (file)
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -17,50 +17,22 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
     use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
 
     use green = scaledImg.Item(1)
-
     let greenFloat = green.Convert<Gray, float32>()
+    let filteredGreen = gaussianFilter greenFloat config.Parameters.preFilterSigma
 
-    let filteredGreen = gaussianFilter green config.Parameters.preFilterSigma
-
-    (*let maximaImg = filteredGreen.Copy()
-    let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
-    for m in maxima do
-        ImgTools.drawPoints maximaImg m 255uy
-
-    let greenOpen1 = filteredGreen.Copy()
-    logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
+    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
 
-    let initialAreaOpen = 2000
-    logTime "areaOpen 1" (fun () -> ImgTools.areaOpen filteredGreen 2000)
-
-    config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
+    config.RBCRadius <- logTime "Granulometry" (fun() -> Granulometry.findRadius (filteredGreen.Convert<Gray, byte>()) (10, 100) 0.3 |> float)
 
     let secondAreaOpen = int <| config.RBCArea / 3.
-    if secondAreaOpen > initialAreaOpen
+    if secondAreaOpen > config.Parameters.initialAreaOpen
     then
-        logTime "areaOpen 2" (fun () -> ImgTools.areaOpen filteredGreen secondAreaOpen)
-
-    let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
+        logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
 
-    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 filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert<Gray, float32>()
-    let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert<Gray, float32>()
-
-    (*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 = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
 
     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
@@ -77,6 +49,8 @@ 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")
@@ -91,8 +65,6 @@ 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")
 
-        // saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
-
         let imgCells = img.Copy()
         drawCells imgCells false cells
         saveImg imgCells (buildFileName " - cells.png")
@@ -101,18 +73,15 @@ 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 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)