X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FMainAnalysis.fs;h=fdae99748bfb385f0635aa8f9141fdcfebae1b87;hp=3a38c4e95ab41e38f1bc919c010381da0424264e;hb=53440e757b4a4ab2a81b0f6a5dd1a2002c0133ba;hpb=e76da913cd58078ad2479357b2430ed62a6e0777 diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs index 3a38c4e..fdae997 100644 --- a/Parasitemia/Parasitemia/MainAnalysis.fs +++ b/Parasitemia/Parasitemia/MainAnalysis.fs @@ -14,77 +14,57 @@ open Types let doAnalysis (img: Image) (name: string) (config: Config) : Cell list = - let imgFloat = img.Convert() - use scaledImg = if config.scale = 1.0 then imgFloat else imgFloat.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 green = scaledImg.Item(1) + let greenFloat = green.Convert() + let filteredGreen = gaussianFilter greenFloat config.Parameters.preFilterSigma - use filteredGreen = (gaussianFilter green config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter green config.doGSigma2) + logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen) - 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)) + config.RBCRadius <- logTime "Granulometry" (fun() -> Granulometry.findRadius (filteredGreen.Convert()) (10, 100) 0.3 |> float) - use xEdges = filteredGreen.Convolution(sobelKernel).Convert() - use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert() + let secondAreaOpen = int <| config.RBCArea / 3. + if secondAreaOpen > config.Parameters.initialAreaOpen + then + logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF 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 parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config + //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config - 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 minLocation = ref <| Point() - let max = ref 0.0 - let maxLocation = ref <| Point() - magnitudes.MinMax(min, max, minLocation, maxLocation) - - use magnitudesByte = ((magnitudes / !max) * 255.0).Convert() // Otsu from OpenCV only support 'byte'. - 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) + let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain) logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12) - let kmediansResults = KMedians.kmedians filteredGreen 1.0 + let allEllipses, ellipses = logTime "Finding ellipses" (fun () -> + let matchingEllipses = Ellipse.find edges xGradient yGradient config + matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses ) - let parasites = ParasitesMarker.find green filteredGreen kmediansResults config + let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config) - let radiusRange = config.scale * config.minRBCSize, config.scale * config.maxRBCSize - let windowSize = roundInt (1.6 * (snd radiusRange)) - let factorNbPick = 1.5 - let ellipses = logTime "Finding ellipses" (fun () -> - Ellipse.find edges xEdges yEdges radiusRange windowSize factorNbPick) + // Output pictures if debug flag is set. + match config.Debug with + | DebugOn output -> + let dirPath = System.IO.Path.Combine(output, name) + System.IO.Directory.CreateDirectory dirPath |> ignore - let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config) + let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix) + + //saveImg canny (buildFileName " - canny.png") - match config.debug with - | DebugOn output -> - let buildFileName postfix = System.IO.Path.Combine(output, name + postfix) saveMat (edges * 255.0) (buildFileName " - edges.png") + saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png") saveImg parasites.stain (buildFileName " - parasites - stain.png") saveImg parasites.infection (buildFileName " - parasites - infection.png") + let imgAllEllipses = img.Copy() + 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)) + 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") - let imgCells = img.Copy() drawCells imgCells false cells saveImg imgCells (buildFileName " - cells.png") @@ -92,6 +72,23 @@ let doAnalysis (img: Image) (name: string) (config: Config) : Cell li let imgCells' = img.Copy() drawCells imgCells' true cells saveImg imgCells' (buildFileName " - cells - full.png") + + let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma + for m in ImgTools.findMaxima filteredGreenMaxima do + ImgTools.drawPoints filteredGreenMaxima m 255.f + 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 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