X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FMainAnalysis.fs;h=8f595141c638a57ca6dd727a18bb9b1d2c282fe7;hp=a240878a6cd133153fdb2b76827f0a2ca8f8b62a;hb=05be8164d308447b916544ae3ce4211500dfd8da;hpb=d0c85068bb98a7999ed994f02669befa70edd5f9 diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs index a240878..8f59514 100644 --- a/Parasitemia/Parasitemia/MainAnalysis.fs +++ b/Parasitemia/Parasitemia/MainAnalysis.fs @@ -1,8 +1,11 @@ module ImageAnalysis open System +open System.Linq open System.Drawing +open FSharp.Collections.ParallelSeq + open Emgu.CV open Emgu.CV.Structure @@ -11,47 +14,65 @@ 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 doAnalysis (img: Image) (name: string) (config: Config) : Cell list = - - use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area) + 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 - use green = scaledImg.Item(1) + logWithName "Starting analysis ..." + use green = img.Item(1) let greenFloat = green.Convert() + let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation - let filteredGreen = gaussianFilter greenFloat config.Parameters.preFilterSigma + logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution) - (*let maximaImg = filteredGreen.Copy() - let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg) - for m in maxima do - ImgTools.drawPoints maximaImg m 255uy + 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) - let greenOpen1 = filteredGreen.Copy() - logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*) + report 8 - let initialAreaOpen = 2000 - logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpen) + 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 <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float + logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius) - let secondAreaOpen = int <| config.RBCArea / 3. - if secondAreaOpen > 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, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config + let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config - let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain - - logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12) + 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 ) + matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses) + + report 80 + + let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config) + + report 100 - let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config) + logWithName "Analysis finished" // Output pictures if debug flag is set. match config.Debug with @@ -61,8 +82,6 @@ let doAnalysis (img: Image) (name: string) (config: Config) : Cell li let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix) - //saveImg canny (buildFileName " - canny.png") - saveMat (edges * 255.0) (buildFileName " - edges.png") saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png") @@ -73,7 +92,7 @@ let doAnalysis (img: Image) (name: string) (config: Config) : Cell li drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05 saveImg imgAllEllipses (buildFileName " - ellipses - all.png") - let imgEllipses = img.Copy() + let imgEllipses = filteredGreenWhitoutStain.Convert() drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0 saveImg imgEllipses (buildFileName " - ellipses.png") @@ -85,22 +104,44 @@ let doAnalysis (img: Image) (name: string) (config: Config) : Cell li 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") saveImg filteredGreen (buildFileName " - filtered.png") saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png") - saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png") + //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png") saveImg green (buildFileName " - green.png") - use blue = scaledImg.Item(0) + use blue = img.Item(0) saveImg blue (buildFileName " - blue.png") - use red = scaledImg.Item(2) + 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) = + match reportProgress with + | Some f -> f percent + | _ -> () + + let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary() + let nbImgs = List.length imgs + + 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, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p))) + |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n) + |> PSeq.toList