X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FMainAnalysis.fs;fp=Parasitemia%2FParasitemia%2FMainAnalysis.fs;h=0000000000000000000000000000000000000000;hp=53429b234dd8589ea3423d149e0ed17cb386deaa;hb=4bfa3cbdc6145e6944f02e24829ab2ef3a851ac1;hpb=48ecdfc43001c444eff6ad442986049384674af2 diff --git a/Parasitemia/Parasitemia/MainAnalysis.fs b/Parasitemia/Parasitemia/MainAnalysis.fs deleted file mode 100644 index 53429b2..0000000 --- a/Parasitemia/Parasitemia/MainAnalysis.fs +++ /dev/null @@ -1,147 +0,0 @@ -module ImageAnalysis - -open System -open System.Linq -open System.Drawing - -open FSharp.Collections.ParallelSeq - -open Emgu.CV -open Emgu.CV.Structure - -open Utils -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 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) - - report 10 - - 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) - - logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius) - - report 20 - - let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter - if secondAreaOpening > initialAreaOpening - then - 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 = 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 matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config) - - report 60 - - let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses) - - report 80 - - let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config) - - report 100 - - logWithName "Analysis finished" - - // 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 - - 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") - saveImg parasites.stain (buildFileName " - parasites - stain.png") - saveImg parasites.infection (buildFileName " - parasites - infection.png") - - let imgAllEllipses = img.Copy() - drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04 - saveImg imgAllEllipses (buildFileName " - ellipses - all.png") - - let imgEllipses = filteredGreenWhitoutStain.Convert() - drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0 - saveImg imgEllipses (buildFileName " - ellipses.png") - - let imgCells = img.Copy() - drawCells imgCells false cells - saveImg imgCells (buildFileName " - cells.png") - - 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 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 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