X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FMainAnalysis.fs;h=043eb739cd6dcaba1805a62f7e43f885f4373685;hb=3ddaf64dc5ba6a7066a279ad75b9a1ee72194639;hp=a240878a6cd133153fdb2b76827f0a2ca8f8b62a;hpb=d0c85068bb98a7999ed994f02669befa70edd5f9;p=master-thesis.git

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index a240878..043eb73 100644
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -13,43 +13,32 @@ open Types
 
 
 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
-
-    use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
-
-    use green = scaledImg.Item(1)
-
+    use green = img.Item(1)
     let greenFloat = green.Convert<Gray, float32>()
+    let filteredGreen = gaussianFilter greenFloat (float config.Parameters.preFilterSigma)
 
-    let filteredGreen = gaussianFilter greenFloat 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
+    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
 
-    let greenOpen1 = filteredGreen.Copy()
-    logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
+    let r1 = logTime "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) (10, 80) 0.5 |> float32)
+    // let r2 = logTime "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen (10, 80) |> float32)
+    // log (sprintf "r1: %A, r2: %A" r1 r2)
+    config.RBCRadius <- r1
 
-    let initialAreaOpen = 2000
-    logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpen)
+    let secondAreaOpen = int <| config.RBCArea / 3.f
 
-    config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
-
-    let secondAreaOpen = int <| config.RBCArea / 3.
-    if secondAreaOpen > initialAreaOpen
+    if secondAreaOpen > config.Parameters.initialAreaOpen
     then
         logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
 
-    let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
+    let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
 
-    let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
-
-    logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
+    let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
+    logTime "Removing small connected components from thinning" (fun () -> removeArea edges (config.RBCRadius ** 2.f / 50.f |> int))
 
     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
         let matchingEllipses = Ellipse.find edges xGradient yGradient config
-        matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
+        matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
 
     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
 
@@ -61,8 +50,6 @@ 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")
@@ -73,7 +60,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
 
-        let imgEllipses = img.Copy()
+        let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
         saveImg imgEllipses (buildFileName " - ellipses.png")
 
@@ -92,14 +79,14 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
 
         saveImg filteredGreen (buildFileName " - filtered.png")
         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
-        saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
+        //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 
         saveImg green (buildFileName " - green.png")
 
-        use blue  = scaledImg.Item(0)
+        use blue = img.Item(0)
         saveImg blue (buildFileName " - blue.png")
 
-        use red = scaledImg.Item(2)
+        use red = img.Item(2)
         saveImg red (buildFileName " - red.png")
     | _ -> ()