X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FMainAnalysis.fs;h=926aeac5523dcf734cab8660809337e8eb8a6b32;hp=7b8b066306d50a012032da29d9f0c945e93aa819;hb=e588f9c954a54cb259b2c1f6f9e8d9dbd4639269;hpb=074d6b0377f51e868deb1c427891c722d0270deb diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs index 7b8b066..926aeac 100644 --- a/Parasitemia/ParasitemiaCore/MainAnalysis.fs +++ b/Parasitemia/ParasitemiaCore/MainAnalysis.fs @@ -12,6 +12,7 @@ open Emgu.CV.Structure open Logger open Utils +open Morpho open ImgTools open Config open Types @@ -50,23 +51,26 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr logWithName "Starting analysis ..." - use green = img.Item(1) - let greenFloat = green.Convert() - let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation + use img_float = img.Convert() - logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution) + use img_RBC = img_float.[1] // mergeChannelsWithProjection img_float config.Parameters.averageColor_RBC config.Parameters.averageColor_BG 255. + use img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC - let initialAreaOpening = int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter * 1.2f // We do an area opening a little larger to avoid to do a second one in the case the radius found is near the initial one. - do! logTimeWithName "First area opening" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening; report 10) + use img_parasites = img_float.[2] // mergeChannelsWithProjection img_float config.Parameters.averageColor_Parasite config.Parameters.averageColor_RBC 255. + use img_parasites_filtered = gaussianFilter img_parasites config.LPFStandardDeviationParasite + + logWithName (sprintf "Nominal erythrocyte diameter: %A" config.RBCRadiusByResolution) + + let initialAreaOpening = int <| config.RBCRadiusByResolution.Area * config.Parameters.ratioAreaPaleCenter * 1.1f // We do an area opening a little larger to avoid to do a second one in the case the radius found is near the initial one. + do! logTimeWithName "First area opening" (fun () -> areaOpenF img_RBC_filtered initialAreaOpening; report 10) let range = let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta - //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert()) range 1.0 |> float32) - let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)) + let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32)) config.SetRBCRadius <| radius - logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius) + logWithName (sprintf "Found erythrocyte diameter: %A" config.RBCRadius) do! report 20 @@ -74,23 +78,26 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter if secondAreaOpening > initialAreaOpening then - logTimeWithName "Second area opening" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening; report 30) + logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30) else report 30 - let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config - //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config + // Removing parasites. + areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f) + + let! parasites, imgWhitoutParasite, imgWithoutNucleus = + logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config)) let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () -> - let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain + let edges, xGradient, yGradient = Edges.find img_RBC_filtered removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int) - reportWithVal 40 (edges, xGradient, yGradient)) + reportWithVal 50 (edges, xGradient, yGradient)) let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config)) let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses)) - let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config)) + let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config)) logWithName "Analysis finished" @@ -103,44 +110,43 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix) - saveMat (edges * 255.0) (buildFileName " - edges.png") + IO.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") + IO.saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png") + IO.saveImg parasites.parasite (buildFileName " - parasites - stain.png") + IO.saveImg parasites.nucleus (buildFileName " - parasites - infection.png") let imgAllEllipses = img.Copy() - drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04 - saveImg imgAllEllipses (buildFileName " - ellipses - all.png") + Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04 + IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png") - let imgEllipses = filteredGreenWhitoutStain.Convert() - drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0 - saveImg imgEllipses (buildFileName " - ellipses.png") + let imgEllipses = img_RBC_filtered.Convert() + Drawing.drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0 + IO.saveImg imgEllipses (buildFileName " - ellipses.png") let imgCells = img.Copy() - drawCells imgCells false cells - saveImg imgCells (buildFileName " - cells.png") + Drawing.drawCells imgCells false cells + IO.saveImg imgCells (buildFileName " - cells.png") let imgCells' = img.Copy() - drawCells imgCells' true cells - saveImg imgCells' (buildFileName " - cells - full.png") - - let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation - for m in ImgTools.findMaxima filteredGreenMaxima do - ImgTools.drawPoints filteredGreenMaxima m 255.f - saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png") + Drawing.drawCells imgCells' true cells + IO.saveImg imgCells' (buildFileName " - cells - full.png") - saveImg filteredGreen (buildFileName " - filtered.png") - saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png") - //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png") + let filteredGreenMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC + for m in findMaxima filteredGreenMaxima do + Drawing.drawPoints filteredGreenMaxima m 255.f + IO.saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png") - saveImg green (buildFileName " - green.png") + IO.saveImg img_RBC_filtered (buildFileName " - filtered.png") + IO.saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png") + IO.saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.png") - use blue = img.Item(0) - saveImg blue (buildFileName " - blue.png") + IO.saveImg img_RBC (buildFileName " - source - RBC.png") + IO.saveImg img_parasites (buildFileName " - source - parasites.png") - use red = img.Item(2) - saveImg red (buildFileName " - red.png") + IO.saveImg (normalize img_float.[2] 255.) (buildFileName " - source - red.png") + IO.saveImg (normalize img_float.[1] 255.) (buildFileName " - source - green.png") + IO.saveImg (normalize img_float.[0] 255.) (buildFileName " - source - blue.png") | _ -> () return cells }