X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FMainAnalysis.fs;h=7f55c7ca324449f65f26b1616e124db941b88d0c;hb=4147bfad3c85dcf4fe7d291abf7d356379d88b4f;hp=3f35fb7ce4cbf03748306078f579d82c619f2437;hpb=8cf3b0a302943312c588690b4e4c90af17b3e87a;p=master-thesis.git diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs index 3f35fb7..7f55c7c 100644 --- a/Parasitemia/Parasitemia/MainAnalysis.fs +++ b/Parasitemia/Parasitemia/MainAnalysis.fs @@ -3,6 +3,8 @@ open System open System.Drawing +open FSharp.Collections.ParallelSeq + open Emgu.CV open Emgu.CV.Structure @@ -11,68 +13,57 @@ open ImgTools open Config open Types - -let doAnalysis (img: Image) (name: string) (config: Config) : Cell list = - - let imgFloat = img.Convert() - use scaledImg = if config.scale = 1.0 then imgFloat else imgFloat.Resize(config.scale, CvEnum.Inter.Area) - - use green = scaledImg.Item(1) - - use filteredGreen = (gaussianFilter green config.doGSigma1) - config.doGLowFreqPercentageReduction * (gaussianFilter green config.doGSigma2) - - 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)) - - use xEdges = filteredGreen.Convolution(sobelKernel).Convert() - use yEdges = filteredGreen.Convolution(sobelKernel.Transpose()).Convert() - - 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 - - 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 - - use magnitudes = new Matrix(xEdges.Size) - CvInvoke.CartToPolar(xEdges, yEdges, magnitudes, new Mat()) // Compute the magnitudes (without angles). - - let min = ref 0.0 - let minLocation = ref <| Point() - let max = ref 0.0 - let maxLocation = ref <| Point() - magnitudes.MinMax(min, max, minLocation, maxLocation) - - 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 - - logTime "Finding edges" (fun() -> thin edges) - logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12) - - let kmediansResults = logTime "Finding foreground (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0) - - let parasites = ParasitesMarker.find green filteredGreen kmediansResults config +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 + | _ -> () + + use green = img.Item(1) + let greenFloat = green.Convert() + let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation + + let initialAreaOpening = int<| config.RBCArea * config.Parameters.ratioAreaPaleCenter + logTime "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening) + report 8 + + let range = + let delta = config.Parameters.granulometryRange * config.RBCRadius + int <| config.RBCRadius - delta, int <| config.RBCRadius + delta + //let r1 = logTime "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert()) range 1.0 |> float32) + let r2 = logTime "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32) + // log (sprintf "r1: %A, r2: %A" r1 r2) + config.RBCRadius <- r2 + report 24 + + let secondAreaOpening = int <| config.RBCArea * config.Parameters.ratioAreaPaleCenter + if secondAreaOpening > initialAreaOpening + then + logTime "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 allEllipses, ellipses = logTime "Finding ellipses" (fun () -> - let matchingEllipses = Ellipse.find edges xEdges yEdges config - matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses ) + let matchingEllipses = Ellipse.find edges xGradient yGradient config + matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses) + report 80 - let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites kmediansResults.fg config) + let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config) + report 100 // Output pictures if debug flag is set. - match config.debug with + match config.Debug with | DebugOn output -> - let buildFileName postfix = System.IO.Path.Combine(output, name + postfix) + let dirPath = System.IO.Path.Combine(output, name) + System.IO.Directory.CreateDirectory dirPath |> ignore + + let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix) + saveMat (edges * 255.0) (buildFileName " - edges.png") saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png") @@ -80,15 +71,13 @@ 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") @@ -96,6 +85,49 @@ let doAnalysis (img: Image) (name: string) (config: Config) : Cell li 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") + + saveImg filteredGreen (buildFileName " - filtered.png") + saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png") + //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png") + + saveImg green (buildFileName " - green.png") + + use blue = img.Item(0) + saveImg blue (buildFileName " - blue.png") + + use red = img.Item(2) + saveImg red (buildFileName " - red.png") | _ -> () cells + +// ID * cell radius * cell list. +let doMultipleAnalysis (imgs: (string * Image) list) (config : Config) (reportProgress: (int -> unit) option) : (string * float * Cell list) list = + let inline report (percent: int) = + match reportProgress with + | Some f -> f percent + | _ -> () + + let monitor = Object() + let mutable total = 0 + let nbImgs = List.length imgs + let reportProgressImg = + (fun progress -> + lock monitor (fun () -> total <- total + progress) + report (total / nbImgs)) + + let nbConcurrentTaskLimit = 4 + 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.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n) + |> PSeq.toList