X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FMainAnalysis.fs;h=6111f06fcbc507bbc2edf8e6a70776db2618d753;hb=bef2e9f0bf1bba21d4c988fdf654c2dc303ec34a;hp=155bfcce65df5fd359522dc72c3ae87aa5059b1d;hpb=b070295cf67b2025164a34b6594e84f0d771cdc9;p=master-thesis.git diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs index 155bfcc..6111f06 100644 --- a/Parasitemia/Parasitemia/MainAnalysis.fs +++ b/Parasitemia/Parasitemia/MainAnalysis.fs @@ -14,71 +14,40 @@ open Types let doAnalysis (img: Image) (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() - let green = gaussianFilter green 1.5 - - // let RBCSize = Granulometry.findRadius green (10, 100) 0.5 - - 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) - - 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 - - saveImg greenMaxima (buildFileName " - maxima.png") + let filteredGreen = gaussianFilter green config.Parameters.preFilterSigma - logTime "areaOpen" (fun () -> ImgTools.areaOpen green 800) - saveImg green (buildFileName " - green opened.png") + (*let maximaImg = filteredGreen.Copy() + let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg) + for m in maxima do + ImgTools.drawPoints maximaImg m 255uy - | _ -> () + let greenOpen1 = filteredGreen.Copy() + logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*) - [] - (* + let initialAreaOpen = 2000 + logTime "areaOpen 1" (fun () -> ImgTools.areaOpen filteredGreen 2000) - use filteredGreen = (gaussianFilter greenFloat config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter greenFloat config.doGSigma2) + config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float - 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)) + let secondAreaOpen = int <| config.RBCArea / 3. + if secondAreaOpen > initialAreaOpen + then + logTime "areaOpen 2" (fun () -> ImgTools.areaOpen filteredGreen secondAreaOpen) - use xEdges = filteredGreen.Convolution(sobelKernel).Convert() - use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert() + let filteredGreenFloat = filteredGreen.Convert() // Is it neccessary? - 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 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() - 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 - - use magnitudes = new Matrix(xEdges.Size) - CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles). - - let min = ref 0.0 + (*let min = ref 0.0 let minLocation = ref <| Point() let max = ref 0.0 let maxLocation = ref <| Point() @@ -88,21 +57,20 @@ 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 "Removing small connected components from thinning" (fun () -> removeArea edges 12) + logTime "Finding edges" (fun() -> thin edges)*) - let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0) + let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStainFloat - let parasites = ParasitesMarker.find greenFloat filteredGreen kmediansResults config + 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 kmediansResults.fg config) + let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain 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 @@ -116,14 +84,14 @@ 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 @@ -133,10 +101,25 @@ let doAnalysis (img: Image) (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 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")*) + 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