X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FMainAnalysis.fs;h=926aeac5523dcf734cab8660809337e8eb8a6b32;hp=9c85c7b1169b1ec906c0bca4985862884a548510;hb=e588f9c954a54cb259b2c1f6f9e8d9dbd4639269;hpb=e3842630f4d36c5ea8c8a0c3d4762684e1c510f4 diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs index 9c85c7b..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 @@ -58,7 +59,7 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr 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 erytrocyte diameter: %A" config.RBCRadiusByResolution) + 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) @@ -69,7 +70,7 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr 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 @@ -88,7 +89,7 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config)) let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () -> - let edges, xGradient, yGradient = findEdges img_RBC_filtered + let edges, xGradient, yGradient = Edges.find img_RBC_filtered removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int) reportWithVal 50 (edges, xGradient, yGradient)) @@ -109,43 +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.parasite (buildFileName " - parasites - stain.png") - saveImg parasites.nucleus (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 = img_RBC_filtered.Convert() - drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0 - saveImg imgEllipses (buildFileName " - ellipses.png") + 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") + Drawing.drawCells imgCells' true cells + IO.saveImg imgCells' (buildFileName " - cells - full.png") let filteredGreenMaxima = gaussianFilter img_RBC config.LPFStandardDeviationRBC for m in findMaxima filteredGreenMaxima do - drawPoints filteredGreenMaxima m 255.f - saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png") + Drawing.drawPoints filteredGreenMaxima m 255.f + IO.saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png") - saveImg img_RBC_filtered (buildFileName " - filtered.png") - saveImg imgWhitoutParasite (buildFileName " - filtered closed stain.png") - saveImg imgWithoutNucleus (buildFileName " - filtered closed infection.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") - saveImg img_RBC (buildFileName " - source - RBC.png") - saveImg img_parasites (buildFileName " - source - parasites.png") + IO.saveImg img_RBC (buildFileName " - source - RBC.png") + IO.saveImg img_parasites (buildFileName " - source - parasites.png") - saveImg (normalize img_float.[2] 255.) (buildFileName " - source - red.png") - saveImg (normalize img_float.[1] 255.) (buildFileName " - source - green.png") - saveImg (normalize img_float.[0] 255.) (buildFileName " - source - blue.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 }