X-Git-Url: http://git.euphorik.ch/?a=blobdiff_plain;f=Parasitemia%2FParasitemiaCore%2FMainAnalysis.fs;fp=Parasitemia%2FParasitemiaCore%2FMainAnalysis.fs;h=846c067b8fee42ae3b2643361c2c9ddd1bb200bc;hb=4bfa3cbdc6145e6944f02e24829ab2ef3a851ac1;hp=0000000000000000000000000000000000000000;hpb=48ecdfc43001c444eff6ad442986049384674af2;p=master-thesis.git

diff --git a/Parasitemia/ParasitemiaCore/MainAnalysis.fs b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
new file mode 100644
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+++ b/Parasitemia/ParasitemiaCore/MainAnalysis.fs
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+module ParasitemiaCore.Analysis
+
+open System
+open System.Linq
+open System.Drawing
+
+open FSharp.Collections.ParallelSeq
+
+open Emgu.CV
+open Emgu.CV.Structure
+
+open Logger
+
+open Utils
+open ImgTools
+open Config
+open Types
+
+let doAnalysis (img: Image<Bgr, byte>) (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 mess = Log.User(buildLogWithName mess)
+    let inline logTimeWithName (text: string) (f: unit -> 'a) : 'a = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
+
+    logWithName "Starting analysis ..."
+
+    use green = img.Item(1)
+    let greenFloat = green.Convert<Gray, float32>()
+    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<Gray, byte>()) 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<Bgr, byte>()
+        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<Bgr, byte>) 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<string, int>()
+    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