X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FMainAnalysis.fs;h=cae64279bf0b8f3b71c2c066ee13adf8285535bf;hb=3b645f8ff5259f88a33ffbd9a63b10a8640c439f;hp=846c067b8fee42ae3b2643361c2c9ddd1bb200bc;hpb=4bfa3cbdc6145e6944f02e24829ab2ef3a851ac1;p=master-thesis.git diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs index 846c067..cae6427 100644 --- a/Parasitemia/ParasitemiaCore/MainAnalysis.fs +++ b/Parasitemia/ParasitemiaCore/MainAnalysis.fs @@ -16,123 +16,151 @@ open ImgTools open Config open Types -let doAnalysis (img: Image) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list = +/// +/// Analyze the given image and detect reb blood cell (RBC) in it. +/// +/// The image +/// The name, used during logging +/// The configuration, must not be shared with another analysis +/// An optional function to report progress and/or cancel the process. +/// The first call returning 'false' will cancel the analysis. +/// The 'int' parameter correspond to the progression from 0 to 100 +/// A list of detected cells or nothing if the process has been cancelled +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) = + // Return 'None' if the process must be aborted. + 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) + let inline logTimeWithName (text: string) (f: unit -> 'a option) : 'a option = Log.LogWithTime((buildLogWithName text), Severity.USER, f) - logWithName "Starting analysis ..." + maybe { + do! report 0 - use green = img.Item(1) - let greenFloat = green.Convert() - let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation + logWithName "Starting analysis ..." - logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution) + use img_float = img.Convert() - 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 "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening) + // use img_RBC = mergeChannels img_float config.Parameters.colorContribution_BG_RBC + use img_RBC = mergeChannelsWithProjection img_float (94.7f, 80.7f, 99.3f) (113.3f, 135.3f, 150.3f) 255. + let img_RBC_filtered = gaussianFilter img_RBC config.LPFStandardDeviationRBC - report 10 + //use img_parasites = mergeChannels img_float config.Parameters.colorContribution_RBC_parasite + use img_parasites = mergeChannelsWithProjection img_float (76.f, 58.f, 94.f) (94.7f, 80.7f, 99.3f) 255. - 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) + logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution) - logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius) + 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 () -> ImgTools.areaOpenF img_RBC_filtered initialAreaOpening; 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 img_RBC_filtered range |> float32)) + config.SetRBCRadius <| radius - let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter - if secondAreaOpening > initialAreaOpening - then - logTimeWithName "Area opening number two" (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 img_RBC_filtered secondAreaOpening; report 30) + else + report 30 - let matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config) + // Removing of parasites. + ImgTools.areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f) - report 60 + let parasites, filteredGreenWhitoutStain, filteredGreenWithoutInfection = ParasitesMarker.find img_parasites config + //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config - let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses) + let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () -> + let edges, xGradient, yGradient = ImgTools.findEdges img_RBC_filtered + removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int) + reportWithVal 40 (edges, xGradient, yGradient)) - report 80 + let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config)) - let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config) + let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses)) - report 100 + let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config)) - logWithName "Analysis finished" + logWithName "Analysis finished" - // 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 + 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 - 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 = img_RBC_filtered.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 img_RBC config.LPFStandardDeviationRBC + 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 img_RBC_filtered (buildFileName " - filtered.png") + saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png") + saveImg filteredGreenWithoutInfection (buildFileName " - filtered closed infection.png") - saveImg green (buildFileName " - green.png") + saveImg img_RBC (buildFileName " - source - RBC.png") + saveImg img_parasites (buildFileName " - source - parasites.png") + | _ -> () - use blue = img.Item(0) - saveImg blue (buildFileName " - blue.png") + return cells } - use red = img.Item(2) - saveImg red (buildFileName " - red.png") - | _ -> () - - 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. +/// +/// The images: (name * configuration * image) +/// An optional function to report progress and/or cancel the process. +/// The first call returning 'false' will cancel the analysis. +/// The 'int' parameter correspond to the progression from 0 to 100 +/// 'None' if the process has been cancelled or the list of result as (name * cells), 'name' corresponds to the given name +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 +171,18 @@ 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 +