X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FMainAnalysis.fs;h=be72a2b34a05e08542f31a1e40fa911e4960b076;hp=0f368d812442c458314862fb90e6fcb028182fc3;hb=6c70577f0bcc17881c753f7a527d2ff4672bb6aa;hpb=3990946e49fe34e9adcf0e04b0418cd16676e6fe diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs index 0f368d8..be72a2b 100644 --- a/Parasitemia/ParasitemiaCore/MainAnalysis.fs +++ b/Parasitemia/ParasitemiaCore/MainAnalysis.fs @@ -16,123 +16,135 @@ open ImgTools open Config open Types -let doAnalysis (img: Image) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list = +let doAnalysis (img: Image) (name: string) (config: Config) (reportProgress: (int -> bool) option) : Cell list option = // To report the progress of this function from 0 to 100. - let inline report (percent: int) = + let reportWithVal (percent: int) (value: 'a) : 'a option = match reportProgress with - | Some f -> f percent - | _ -> () + | Some f -> + if f percent + then Some value + else None + | _ -> Some value + + let report (percent: int) : unit option = + reportWithVal percent () let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text let logWithName mess = Log.User(buildLogWithName mess) - let inline logTimeWithName (text: string) (f: unit -> 'a) : 'a = Log.LogWithTime((buildLogWithName text), Severity.USER, f) - - logWithName "Starting analysis ..." + let inline logTimeWithName (text: string) (f: unit -> 'a option) : 'a option = Log.LogWithTime((buildLogWithName text), Severity.USER, f) - use green = img.Item(1) - let greenFloat = green.Convert() - let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation + maybe { + do! report 0 - logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution) + logWithName "Starting analysis ..." - 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. - logTimeWithName "First area opening" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening) + use green = img.Item(1) + let greenFloat = green.Convert() + let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation - report 10 + logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution) - 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) - config.SetRBCRadius <| logTimeWithName "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32) + 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) - logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius) + //do! report 10 - report 20 + 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)) + config.SetRBCRadius <| radius - let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter - if secondAreaOpening > initialAreaOpening - then - logTimeWithName "Second area opening" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening) + logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius) - let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config - //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config + do! report 20 - let edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () -> - let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain - removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int) - edges, xGradient, yGradient) + do! + let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter + if secondAreaOpening > initialAreaOpening + then + logTimeWithName "Second area opening" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening; report 30) + else + report 30 - let matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config) + let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config + //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config - report 60 + let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () -> + let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain + removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int) + reportWithVal 40 (edges, xGradient, yGradient)) - let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses) + let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config)) - report 80 + let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses)) - let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config) + let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config)) - report 100 + logWithName "Analysis finished" - logWithName "Analysis finished" + do + // 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 - // 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 buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix) - let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix) + saveMat (edges * 255.0) (buildFileName " - edges.png") - 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") - 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 matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04 + saveImg imgAllEllipses (buildFileName " - ellipses - all.png") - let imgAllEllipses = img.Copy() - drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04 - 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 = filteredGreenWhitoutStain.Convert() - drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0 - saveImg imgEllipses (buildFileName " - ellipses.png") + let imgCells = img.Copy() + drawCells imgCells false cells + saveImg imgCells (buildFileName " - cells.png") - let imgCells = img.Copy() - drawCells imgCells false cells - saveImg imgCells (buildFileName " - cells.png") + let imgCells' = img.Copy() + drawCells imgCells' true cells + saveImg imgCells' (buildFileName " - cells - full.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") - 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") + saveImg filteredGreen (buildFileName " - filtered.png") + saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png") + //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.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") - saveImg green (buildFileName " - green.png") + use blue = img.Item(0) + saveImg blue (buildFileName " - blue.png") - use blue = img.Item(0) - saveImg blue (buildFileName " - blue.png") + use red = img.Item(2) + saveImg red (buildFileName " - red.png") + | _ -> () - use red = img.Item(2) - saveImg red (buildFileName " - red.png") - | _ -> () + return cells } - cells - -// ID * cell list. -let doMultipleAnalysis (imgs: (string * Config * Image) list) (reportProgress: (int -> unit) option) : (string * Cell list) list = - let inline report (percent: int) = +/// +/// Do multiple analyses on the same time. The number of concurrent process depends if the number of the core. +/// +/// +/// An optional function to report progress. The process is aborted if the returned value is false +let doMultipleAnalysis (imgs: (string * Config * Image) list) (reportProgress: (int -> bool) option) : (string * Cell list) list option = + let report (percent: int) : bool = match reportProgress with | Some f -> f percent - | _ -> () + | _ -> true let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary() let nbImgs = List.length imgs @@ -143,7 +155,18 @@ let doMultipleAnalysis (imgs: (string * Config * Image) list) (report let n = Environment.ProcessorCount - imgs - |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p))) - |> PSeq.withDegreeOfParallelism n - |> PSeq.toList + let results = + imgs + |> PSeq.choose ( + fun (id, config, img) -> + match doAnalysis img id config (Some (fun p -> reportProgressImg id p)) with + | Some result -> Some (id, result) + | None -> None) + |> PSeq.withDegreeOfParallelism n + |> PSeq.toList + + // If one of the analyses has been aborted we return 'None'. + if List.length results <> List.length imgs + then None + else Some results +