* Remove the 'DoG' filter.

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

diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs
index 155bfcc..39383fc 100644 (file)
--- a/Parasitemia/Parasitemia/MainAnalysis.fs
+++ b/Parasitemia/Parasitemia/MainAnalysis.fs
@@ -20,46 +20,25 @@ let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell li
     use green = scaledImg.Item(1)
     use red = scaledImg.Item(2)
 
-
     let greenFloat = green.Convert<Gray, float32>()
 
-    let green = gaussianFilter green 1.5
-
-    // let RBCSize = Granulometry.findRadius green (10, 100) 0.5
+    let filteredGreen = gaussianFilter green config.preFilterSigma
+    logTime "areaOpen" (fun () -> ImgTools.areaOpen filteredGreen 2000)
 
-    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 RBCSize = Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
+    let RBCSizeDelta = RBCSize / 3.0
 
-        saveImg green (buildFileName " - green.png")
+    let config = { config with minRBCSize = RBCSize - RBCSizeDelta ; maxRBCSize = RBCSize + RBCSizeDelta }
 
-        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
-
-        saveImg greenMaxima (buildFileName " - maxima.png")
-
-        logTime "areaOpen" (fun () -> ImgTools.areaOpen green 800)
-        saveImg green (buildFileName " - green opened.png")
-
-    | _ -> ()
-
-    []
-    (*
-
-    use filteredGreen = (gaussianFilter greenFloat config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter greenFloat config.doGSigma2)
+    let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
 
     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 = filteredGreenFloat.Convolution(sobelKernel).Convert<Gray, float>()
+    use yEdges = filteredGreenFloat.Convolution(sobelKernel.Transpose()).Convert<Gray, float>()
 
     let xEdgesData = xEdges.Data
     let yEdgesData = yEdges.Data
@@ -91,9 +70,9 @@ 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 kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreenFloat 1.0)
 
-    let parasites = ParasitesMarker.find greenFloat filteredGreen kmediansResults config
+    let parasites = ParasitesMarker.find greenFloat filteredGreenFloat kmediansResults config
 
     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
         let matchingEllipses = Ellipse.find edges xEdges yEdges config
@@ -133,10 +112,15 @@ 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")
+        let filteredGreenMaxima = gaussianFilter green config.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 blue (buildFileName " - blue.png")
         saveImg green (buildFileName " - green.png")
         saveImg red (buildFileName " - red.png")
     | _ -> ()
 
-    cells*)
+    cells