X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FMainAnalysis.fs;h=ff82b8b710ca44387aaae075f237ef5664526f73;hb=dcf3645b3426991237567e90bab9806a9c111cd1;hp=d959624b8b2b7ded61e54a2342b70056a11c8965;hpb=84fdf7404133803fdf0dc867a4da68a144975191;p=master-thesis.git diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs index d959624..ff82b8b 100644 --- a/Parasitemia/Parasitemia/MainAnalysis.fs +++ b/Parasitemia/Parasitemia/MainAnalysis.fs @@ -30,43 +30,26 @@ let doAnalysis (img: Image) (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() // Is it neccessary? - - let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreenFloat 1.0) - - let parasites, filteredGreenWhitoutParasites, filteredGreenWhitoutStain = ParasitesMarker2.find filteredGreen filteredGreenFloat kmediansResults config - let filteredGreenWhitoutParasitesFloat = filteredGreenWhitoutParasites.Convert() - - 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() - use yEdges = filteredGreenWhitoutParasitesFloat.Convolution(sobelKernel.Transpose()).Convert() + let secondAreaOpen = int <| config.RBCArea / 3. + if secondAreaOpen > initialAreaOpen + then + logTime "areaOpen 2" (fun () -> ImgTools.areaOpen filteredGreen secondAreaOpen) - let xEdgesData = xEdges.Data - let yEdgesData = yEdges.Data - for r in 0..xEdges.Rows-1 do - xEdgesData.[r, 0, 0] <- 0.0 - xEdgesData.[r, xEdges.Cols-1, 0] <- 0.0 - yEdgesData.[r, 0, 0] <- 0.0 - yEdgesData.[r, xEdges.Cols-1, 0] <- 0.0 + let filteredGreenFloat = filteredGreen.Convert() // Is it neccessary? - for c in 0..xEdges.Cols-1 do - xEdgesData.[0, c, 0] <- 0.0 - xEdgesData.[xEdges.Rows-1, c, 0] <- 0.0 - yEdgesData.[0, c, 0] <- 0.0 - yEdgesData.[xEdges.Rows-1, c, 0] <- 0.0 + let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen filteredGreenFloat config + //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config + let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert() + let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert() - use magnitudes = new Matrix(xEdges.Size) - CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles). + let canny = green.Canny(60., 40.) - let min = ref 0.0 + (*let min = ref 0.0 let minLocation = ref <| Point() let max = ref 0.0 let maxLocation = ref <| Point() @@ -76,14 +59,17 @@ let doAnalysis (img: Image) (name: string) (config: Config) : Cell li use edges = new Matrix(xEdges.Size) CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore - logTime "Finding edges" (fun() -> thin edges) + logTime "Finding edges" (fun() -> thin edges)*) + + let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStainFloat + logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12) let allEllipses, ellipses = logTime "Finding ellipses" (fun () -> - let matchingEllipses = Ellipse.find edges xEdges yEdges config + let matchingEllipses = Ellipse.find edges xGradient yGradient 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 @@ -93,6 +79,8 @@ let doAnalysis (img: Image) (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") @@ -100,14 +88,14 @@ let doAnalysis (img: Image) (name: string) (config: Config) : Cell li saveImg parasites.infection (buildFileName " - parasites - infection.png") let imgAllEllipses = img.Copy() - drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1 + drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05 saveImg imgAllEllipses (buildFileName " - ellipses - all.png") let imgEllipses = img.Copy() 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 +111,8 @@ let doAnalysis (img: Image) (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")*)