Remove ellipses touching the edges.

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

diff --git a/Parasitemia/Parasitemia/ImageAnalysis.fs b/Parasitemia/Parasitemia/ImageAnalysis.fs
index 1215965..feb427d 100644 (file)
--- a/Parasitemia/Parasitemia/ImageAnalysis.fs
+++ b/Parasitemia/Parasitemia/ImageAnalysis.fs
@@ -11,13 +11,13 @@ open ImgTools
 open Config
 open Types
 
-type Result = {
+(*type Result = {
     RBCPositions : Point list
     infectedRBCPositions : Point list
     img: Image<Bgr, byte>
-}
+}*)
 
-let doAnalysis (img: Image<Bgr, byte>) (config: Config) : Result =
+let doAnalysis (img: Image<Bgr, byte>) (config: Config) : Classifier.Cell list =
 
     let imgFloat = img.Convert<Bgr, float32>()
     use scaledImg = if config.scale = 1.0 then imgFloat else imgFloat.Resize(config.scale, CvEnum.Inter.Area)
@@ -41,7 +41,7 @@ let doAnalysis (img: Image<Bgr, byte>) (config: Config) : Result =
     //let test = greenMatrix.[10, 10]
 
     use filteredGreen = (gaussianFilter green config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter green config.doGSigma2)
-
+    
     use sobelKernel = 
         new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ]
                                         [ 2.0f; 0.0f; -2.0f ]
@@ -75,21 +75,38 @@ let doAnalysis (img: Image<Bgr, byte>) (config: Config) : Result =
 
     use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
     use edges = new Matrix<byte>(xEdges.Size)    
-    let threshold = CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary)        
-    thin edges    
-    removeArea edges 12
+    CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
+        
+    logTime "Finding edges" (fun() ->
+        thin edges)
+
+    logTime "Removing small connected components" (fun () -> 
+        removeArea edges 12)
     
     saveMat (edges * 255.0) "edges.png" 
 
+
+    let kmediansResults = KMedians.kmedians filteredGreen 1.0
+
+    let parasites = ParasitesMarker.find green filteredGreen kmediansResults config
+    
+    saveImg parasites.darkStain "parasites_dark_stain.png"
+    saveImg parasites.stain "parasites_stain.png"
+    saveImg parasites.infection "parasites_infection.png"
+
     let radiusRange = config.scale * 20.0, config.scale * 40.0
     let windowSize = roundInt (1.6 * (snd radiusRange))
-    let factorNbPick = 1.0;
-    let ellipses = Ellipse.find edges xEdges yEdges radiusRange windowSize factorNbPick
-        
-    drawEllipse img (List.head ellipses) (Bgr(0.0, 255.0, 255.0))
-    saveImg img "ellipses.png" 
-
-    { RBCPositions = []; infectedRBCPositions = []; img = img }
+    let factorNbPick = 1.5
+    let ellipses = logTime "Finding ellipses" (fun () ->
+        Ellipse.find edges xEdges yEdges radiusRange windowSize factorNbPick) |> List.filter (fun e -> not (e.CutAVericalLine 0.0) &&
+                                                                                                       not (e.CutAVericalLine (float img.Width)) &&
+                                                                                                       not (e.CutAnHorizontalLine 0.0) &&
+                                                                                                       not (e.CutAnHorizontalLine (float img.Height)))
+                
+    drawEllipses img ellipses (Bgr(0.0, 255.0, 255.0))
+    //saveImg img "ellipses.png"
+
+    Classifier.findCells ellipses parasites kmediansResults.fg
 
     //