Change the parasite detection method.

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

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index 155bfcc..d959624 100644 (file)
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -14,52 +14,40 @@ open Types
 
 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
 
-    use scaledImg = if config.scale = 1.0 then img else img.Resize(config.scale, CvEnum.Inter.Area)
+    use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
 
-    use blue  = scaledImg.Item(0)
     use green = scaledImg.Item(1)
-    use red = scaledImg.Item(2)
-
 
     let greenFloat = green.Convert<Gray, float32>()
 
-    let green = gaussianFilter green 1.5
+    let filteredGreen = gaussianFilter green config.Parameters.preFilterSigma
 
-    // let RBCSize = Granulometry.findRadius green (10, 100) 0.5
+    (*let maximaImg = filteredGreen.Copy()
+    let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
+    for m in maxima do
+        ImgTools.drawPoints maximaImg m 255uy
 
-    match config.debug with
-    | DebugOn output ->
-        let dirPath = System.IO.Path.Combine(output, name)
-        System.IO.Directory.CreateDirectory dirPath |> ignore
-        let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
+    let greenOpen1 = filteredGreen.Copy()
+    logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
 
-        saveImg green (buildFileName " - green.png")
-
-        let greenMaxima = green.Copy()
-        let maxima = ImgTools.findMaxima greenMaxima
-        for m in maxima do
-            for p in m do
-                greenMaxima.Data.[p.Y, p.X, 0] <- 255uy
+    logTime "areaOpen" (fun () -> ImgTools.areaOpen filteredGreen 2000)
 
-        saveImg greenMaxima (buildFileName " - maxima.png")
+    config.RBCSize <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
 
-        logTime "areaOpen" (fun () -> ImgTools.areaOpen green 800)
-        saveImg green (buildFileName " - green opened.png")
-
-    | _ -> ()
+    let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
 
-    []
-    (*
+    let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreenFloat 1.0)
 
-    use filteredGreen = (gaussianFilter greenFloat config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter greenFloat config.doGSigma2)
+    let parasites, filteredGreenWhitoutParasites, filteredGreenWhitoutStain = ParasitesMarker2.find filteredGreen filteredGreenFloat kmediansResults config
+    let filteredGreenWhitoutParasitesFloat = filteredGreenWhitoutParasites.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 = filteredGreen.Convolution(sobelKernel).Convert<Gray, float>()
-    use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
+    use xEdges = filteredGreenWhitoutParasitesFloat.Convolution(sobelKernel).Convert<Gray, float>()
+    use yEdges = filteredGreenWhitoutParasitesFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
 
     let xEdgesData = xEdges.Data
     let yEdgesData = yEdges.Data
@@ -91,18 +79,14 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
     logTime "Finding edges" (fun() -> thin edges)
     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
 
-    let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
-
-    let parasites = ParasitesMarker.find greenFloat filteredGreen kmediansResults config
-
     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
         let matchingEllipses = Ellipse.find edges xEdges yEdges config
         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
 
-    let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config)
+    let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutParasites config)
 
     // Output pictures if debug flag is set.
-    match config.debug with
+    match config.Debug with
     | DebugOn output ->
         let dirPath = System.IO.Path.Combine(output, name)
         System.IO.Directory.CreateDirectory dirPath |> ignore
@@ -133,10 +117,24 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
         drawCells imgCells' true cells
         saveImg imgCells' (buildFileName " - cells - full.png")
 
-        saveImg (normalizeAndConvert filteredGreen) (buildFileName " - filtered.png")
-        saveImg blue (buildFileName " - blue.png")
+        let filteredGreenMaxima = gaussianFilter green config.Parameters.preFilterSigma
+        for m in ImgTools.findMaxima filteredGreenMaxima do
+            ImgTools.drawPoints filteredGreenMaxima m 255uy
+        saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
+
+        saveImg filteredGreen (buildFileName " - filtered.png")
+        saveImg filteredGreenWhitoutParasites (buildFileName " - filtered closed.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 blue (buildFileName " - blue.png")
+
+        use red = scaledImg.Item(2)
         saveImg red (buildFileName " - red.png")
     | _ -> ()
 
-    cells*)
+    cells