Simplification of the parasite marker.

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

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index d959624..c987e63 100644 (file)
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -30,24 +30,30 @@ 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.areaOpen filteredGreen 2000)
 
-    config.RBCSize <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
+    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.areaOpen filteredGreen secondAreaOpen)
 
-    let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreenFloat 1.0)
+    let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
 
-    let parasites, filteredGreenWhitoutParasites, filteredGreenWhitoutStain = ParasitesMarker2.find filteredGreen filteredGreenFloat kmediansResults config
-    let filteredGreenWhitoutParasitesFloat = filteredGreenWhitoutParasites.Convert<Gray, float32>()
+    let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen filteredGreenFloat config
+    //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
+    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 = filteredGreenWhitoutParasitesFloat.Convolution(sobelKernel).Convert<Gray, float>()
-    use yEdges = filteredGreenWhitoutParasitesFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
+    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
@@ -83,7 +89,7 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         let matchingEllipses = Ellipse.find edges xEdges yEdges config
         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
 
-    let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutParasites config)
+    let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
 
     // Output pictures if debug flag is set.
     match config.Debug with
@@ -107,7 +113,7 @@ 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")
+        // saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
 
         let imgCells = img.Copy()
         drawCells imgCells false cells
@@ -123,7 +129,8 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 
         saveImg filteredGreen (buildFileName " - filtered.png")
-        saveImg filteredGreenWhitoutParasites (buildFileName " - filtered closed.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")*)