X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FMainAnalysis.fs;h=8f595141c638a57ca6dd727a18bb9b1d2c282fe7;hp=2be9be151c4cf70b1f9240ad9de12222694df2f4;hb=05be8164d308447b916544ae3ce4211500dfd8da;hpb=807437584bdd3d7b7b33be8282472f81f8cce606 diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs index 2be9be1..8f59514 100644 --- a/Parasitemia/Parasitemia/MainAnalysis.fs +++ b/Parasitemia/Parasitemia/MainAnalysis.fs @@ -1,6 +1,7 @@ module ImageAnalysis open System +open System.Linq open System.Drawing open FSharp.Collections.ParallelSeq @@ -13,46 +14,66 @@ open ImgTools open Config open Types - let doAnalysis (img: Image) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list = + // To report the progress of this function from 0 to 100. let inline report (percent: int) = match reportProgress with | Some f -> f percent | _ -> () + let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text + let logWithName = buildLogWithName >> log + let inline logTimeWithName (text: string) (f: unit -> 'a) : 'a = logTime (buildLogWithName text) f + + logWithName "Starting analysis ..." + use green = img.Item(1) let greenFloat = green.Convert() - let filteredGreen = gaussianFilter greenFloat (float config.Parameters.preFilterSigma) + let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation + + logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution) + + 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) - logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen) report 8 - let r1 = logTime "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert()) (10, 80) 0.5 |> float32) - // let r2 = logTime "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen (10, 80) |> float32) + 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) // log (sprintf "r1: %A, r2: %A" r1 r2) - config.RBCRadius <- r1 - report 24 - let secondAreaOpen = int <| config.RBCArea * config.Parameters.ratioSecondAreaOpen + logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius) - if secondAreaOpen > config.Parameters.initialAreaOpen + report 24 + + let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter + if secondAreaOpening > initialAreaOpening then - logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen) + logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening) let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config - let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain) - logTime "Removing small connected components from thinning" (fun () -> removeArea edges (config.RBCRadius ** 2.f / 50.f |> int)) + 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) - let allEllipses, ellipses = logTime "Finding ellipses" (fun () -> + let allEllipses, ellipses = logTimeWithName "Finding ellipses" (fun () -> let matchingEllipses = Ellipse.find edges xGradient yGradient config matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses) + report 80 - let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config) + let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config) + report 100 + logWithName "Analysis finished" + // Output pictures if debug flag is set. match config.Debug with | DebugOn output -> @@ -83,7 +104,7 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr drawCells imgCells' true cells saveImg imgCells' (buildFileName " - cells - full.png") - let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma + 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") @@ -103,29 +124,24 @@ let doAnalysis (img: Image) (name: string) (config: Config) (reportPr cells - -// ID * cell radius * cell list. -let doMultipleAnalysis (imgs: (string * Image) list) (config : Config) (reportProgress: (int -> unit) option) : (string * float * Cell list) list = +// ID * cell list. +let doMultipleAnalysis (imgs: (string * Config * Image) list) (reportProgress: (int -> unit) option) : (string * Cell list) list = let inline report (percent: int) = match reportProgress with | Some f -> f percent | _ -> () - let monitor = Object() - let mutable total = 0 + let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary() let nbImgs = List.length imgs - let reportProgressImg = - (fun progress -> - lock monitor (fun () -> total <- total + progress) - report (total / nbImgs)) - let nbConcurrentTaskLimit = 4 + let reportProgressImg (id: string) (progress: int) = + progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore + report (progressPerAnalysis.Values.Sum() / nbImgs) + + let nbConcurrentTaskLimit = 4 // To reduce the memory taken. let n = Environment.ProcessorCount imgs - |> PSeq.map (fun (id, img) -> - let localConfig = config.Copy() - let cells = doAnalysis img id localConfig (Some reportProgressImg) - id, float localConfig.RBCRadius, cells) + |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p))) |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n) |> PSeq.toList