X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FMainAnalysis.fs;h=8f595141c638a57ca6dd727a18bb9b1d2c282fe7;hp=6f78b7cc1229a75edd2ef68f9a28decfc37e7932;hb=05be8164d308447b916544ae3ce4211500dfd8da;hpb=6d99ab0dadc57e91cd846844b620fc90b52a2f96 diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs index 6f78b7c..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 @@ -11,80 +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 green config.Parameters.preFilterSigma - - (*let maximaImg = filteredGreen.Copy() - let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg) - for m in maxima do - ImgTools.drawPoints maximaImg m 255uy - - let greenOpen1 = filteredGreen.Copy() - logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*) + logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution) - logTime "areaOpen" (fun () -> ImgTools.areaOpen filteredGreen 2000) + 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) - config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float + report 8 - let filteredGreenFloat = filteredGreen.Convert() // Is it neccessary? + 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) - let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreenFloat 1.0) + logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius) - let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker2.find filteredGreen filteredGreenFloat kmediansResults config - let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert() - let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert() + report 24 - use sobelKernel = - new ConvolutionKernelF(array2D [[ 1.0f; 0.0f; -1.0f ] - [ 2.0f; 0.0f; -2.0f ] - [ 1.0f; 0.0f; -1.0f ]], Point(0, 0)) + let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter + if secondAreaOpening > initialAreaOpening + then + logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening) - use xEdges = filteredGreenWhitoutStainFloat.Convolution(sobelKernel).Convert() - use yEdges = filteredGreenWhitoutStainFloat.Convolution(sobelKernel.Transpose()).Convert() + let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config + //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config - let xEdgesData = xEdges.Data - let yEdgesData = yEdges.Data - for r in 0..xEdges.Rows-1 do - xEdgesData.[r, 0, 0] <- 0.0 - xEdgesData.[r, xEdges.Cols-1, 0] <- 0.0 - yEdgesData.[r, 0, 0] <- 0.0 - yEdgesData.[r, xEdges.Cols-1, 0] <- 0.0 + 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) - for c in 0..xEdges.Cols-1 do - xEdgesData.[0, c, 0] <- 0.0 - xEdgesData.[xEdges.Rows-1, c, 0] <- 0.0 - yEdgesData.[0, c, 0] <- 0.0 - yEdgesData.[xEdges.Rows-1, c, 0] <- 0.0 + let allEllipses, ellipses = logTimeWithName "Finding ellipses" (fun () -> + let matchingEllipses = Ellipse.find edges xGradient yGradient config + matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses) - use magnitudes = new Matrix(xEdges.Size) - CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles). + report 80 - let min = ref 0.0 - let minLocation = ref <| Point() - let max = ref 0.0 - let maxLocation = ref <| Point() - magnitudes.MinMax(min, max, minLocation, maxLocation) + let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config) - use magnitudesByte = ((magnitudes / !max) * 255.0).Convert() // Otsu from OpenCV only support 'byte'. - use edges = new Matrix(xEdges.Size) - CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore + report 100 - logTime "Finding edges" (fun() -> thin edges) - logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12) - - let allEllipses, ellipses = logTime "Finding ellipses" (fun () -> - let matchingEllipses = Ellipse.find edges xEdges yEdges config - matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses ) - - 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 @@ -101,15 +89,13 @@ let doAnalysis (img: Image) (name: string) (config: Config) : Cell li saveImg parasites.infection (buildFileName " - parasites - infection.png") let imgAllEllipses = img.Copy() - drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.1 + 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") - saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png") - let imgCells = img.Copy() drawCells imgCells false cells saveImg imgCells (buildFileName " - cells.png") @@ -118,24 +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 green config.Parameters.preFilterSigma + let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation for m in ImgTools.findMaxima filteredGreenMaxima do - ImgTools.drawPoints filteredGreenMaxima m 255uy + ImgTools.drawPoints filteredGreenMaxima m 255.f saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png") saveImg filteredGreen (buildFileName " - filtered.png") - saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed.png") - - (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png") - saveImg stainMarker (buildFileName " - stain (area closing).png")*) + saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.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