X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FMainAnalysis.fs;h=926aeac5523dcf734cab8660809337e8eb8a6b32;hp=0f368d812442c458314862fb90e6fcb028182fc3;hb=e588f9c954a54cb259b2c1f6f9e8d9dbd4639269;hpb=97c24aa168f06f507fdff79429038d78a2c33326 diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs index 0f368d8..926aeac 100644 --- a/Parasitemia/ParasitemiaCore/MainAnalysis.fs +++ b/Parasitemia/ParasitemiaCore/MainAnalysis.fs @@ -12,127 +12,158 @@ open Emgu.CV.Structure open Logger open Utils +open Morpho 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 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 report (percent: int) : unit option = + reportWithVal percent () - logWithName "Starting analysis ..." + 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 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 img_float = img.Convert() - report 10 + 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 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) + 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 "Found erytrocyte diameter: %A" config.RBCRadius) + logWithName (sprintf "Nominal erythrocyte diameter: %A" config.RBCRadiusByResolution) - report 20 + 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 secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter - if secondAreaOpening > initialAreaOpening - then - logTimeWithName "Second area opening" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening) + let range = + let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel + int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta + let! radius = logTimeWithName "Granulometry (area)" (fun() -> reportWithVal 10 (Granulometry.findRadiusByAreaClosing img_RBC_filtered range |> float32)) + config.SetRBCRadius <| radius - let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config - //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config + logWithName (sprintf "Found erythrocyte diameter: %A" config.RBCRadius) - 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! report 20 - let matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config) + do! + let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter + if secondAreaOpening > initialAreaOpening + then + logTimeWithName "Second area opening" (fun () -> areaOpenF img_RBC_filtered secondAreaOpening; report 30) + else + report 30 - report 60 + // Removing parasites. + areaCloseF img_RBC_filtered (roundInt <| Const.PI * config.RBCRadius.ParasiteRadius ** 2.f) - let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses) + let! parasites, imgWhitoutParasite, imgWithoutNucleus = + logTimeWithName "Parasites segmentation" (fun () -> reportWithVal 40 (ParasitesMarker.find img_parasites_filtered config)) - report 80 + let! edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () -> + let edges, xGradient, yGradient = Edges.find img_RBC_filtered + removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int) + reportWithVal 50 (edges, xGradient, yGradient)) - let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config) + let! matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> reportWithVal 60 (Ellipse.find edges xGradient yGradient config)) - report 100 + let! prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> reportWithVal 80 (matchingEllipses.PrunedEllipses)) - logWithName "Analysis finished" + let! cells = logTimeWithName "Classifier" (fun () -> reportWithVal 100 (Classifier.findCells prunedEllipses parasites img_RBC_filtered config)) - // 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 + logWithName "Analysis finished" - let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix) + 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 - saveMat (edges * 255.0) (buildFileName " - edges.png") + let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix) - saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png") - saveImg parasites.stain (buildFileName " - parasites - stain.png") - saveImg parasites.infection (buildFileName " - parasites - infection.png") + IO.saveMat (edges * 255.0) (buildFileName " - edges.png") - let imgAllEllipses = img.Copy() - drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04 - saveImg imgAllEllipses (buildFileName " - ellipses - all.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 imgEllipses = filteredGreenWhitoutStain.Convert() - drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0 - saveImg imgEllipses (buildFileName " - ellipses.png") + let imgAllEllipses = img.Copy() + Drawing.drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04 + IO.saveImg imgAllEllipses (buildFileName " - ellipses - all.png") - let imgCells = img.Copy() - drawCells imgCells false cells - saveImg imgCells (buildFileName " - cells.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' true cells - saveImg imgCells' (buildFileName " - cells - full.png") + let imgCells = img.Copy() + Drawing.drawCells imgCells false cells + IO.saveImg imgCells (buildFileName " - cells.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 imgCells' = img.Copy() + 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") + | _ -> () - cells + return 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 +174,18 @@ 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 +