Parasitemia/ParasitemiaCore/MainAnalysis.fs

   1 module ParasitemiaCore.Analysis
   2
   3 open System
   4 open System.Linq
   5 open System.Drawing
   6
   7 open FSharp.Collections.ParallelSeq
   8
   9 open Emgu.CV
  10 open Emgu.CV.Structure
  11
  12 open Logger
  13
  14 open Utils
  15 open ImgTools
  16 open Config
  17 open Types
  18
  19 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list =
  20     // To report the progress of this function from 0 to 100.
  21     let inline report (percent: int) =
  22         match reportProgress with
  23         | Some f -> f percent
  24         | _ -> ()
  25
  26     let inline buildLogWithName (text:  string) = sprintf "(%s) %s" name text
  27     let logWithName mess = Log.User(buildLogWithName mess)
  28     let inline logTimeWithName (text: string) (f: unit -> 'a) : 'a = Log.LogWithTime((buildLogWithName text), Severity.USER, f)
  29
  30     logWithName "Starting analysis ..."
  31
  32     use green = img.Item(1)
  33     let greenFloat = green.Convert<Gray, float32>()
  34     let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
  35
  36     logWithName (sprintf "Nominal erytrocyte diameter: %A" config.RBCRadiusByResolution)
  37
  38     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.
  39     logTimeWithName "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening)
  40
  41     report 10
  42
  43     let range =
  44         let delta = config.Parameters.granulometryRange * config.RBCRadiusByResolution.Pixel
  45         int <| config.RBCRadiusByResolution.Pixel - delta, int <| config.RBCRadiusByResolution.Pixel + delta
  46     //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
  47     config.SetRBCRadius <| logTimeWithName "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)
  48
  49     logWithName (sprintf "Found erytrocyte diameter: %A" config.RBCRadius)
  50
  51     report 20
  52
  53     let secondAreaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
  54     if secondAreaOpening > initialAreaOpening
  55     then
  56         logTimeWithName "Area opening number two" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpening)
  57
  58     let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
  59     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  60
  61     let edges, xGradient, yGradient = logTimeWithName "Finding edges" (fun () ->
  62         let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
  63         removeArea edges (config.RBCRadius.Pixel ** 2.f / 50.f |> int)
  64         edges, xGradient, yGradient)
  65
  66     let matchingEllipses = logTimeWithName "Finding ellipses" (fun () -> Ellipse.find edges xGradient yGradient config)
  67
  68     report 60
  69
  70     let prunedEllipses = logTimeWithName "Ellipses pruning" (fun () -> matchingEllipses.PrunedEllipses)
  71
  72     report 80
  73
  74     let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells prunedEllipses parasites filteredGreenWhitoutStain config)
  75
  76     report 100
  77
  78     logWithName "Analysis finished"
  79
  80     // Output pictures if debug flag is set.
  81     match config.Debug with
  82     | DebugOn output ->
  83         let dirPath = System.IO.Path.Combine(output, name)
  84         System.IO.Directory.CreateDirectory dirPath |> ignore
  85
  86         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  87
  88         saveMat (edges * 255.0) (buildFileName " - edges.png")
  89
  90         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  91         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  92         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  93
  94         let imgAllEllipses = img.Copy()
  95         drawEllipses imgAllEllipses matchingEllipses.Ellipses (Bgr(255.0, 255.0, 255.0)) 0.04
  96         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  97
  98         let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
  99         drawEllipses imgEllipses prunedEllipses (Bgr(0.0, 240.0, 240.0)) 1.0
 100         saveImg imgEllipses (buildFileName " - ellipses.png")
 101
 102         let imgCells = img.Copy()
 103         drawCells imgCells false cells
 104         saveImg imgCells (buildFileName " - cells.png")
 105
 106         let imgCells' = img.Copy()
 107         drawCells imgCells' true cells
 108         saveImg imgCells' (buildFileName " - cells - full.png")
 109
 110         let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
 111         for m in ImgTools.findMaxima filteredGreenMaxima do
 112             ImgTools.drawPoints filteredGreenMaxima m 255.f
 113         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 114
 115         saveImg filteredGreen (buildFileName " - filtered.png")
 116         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
 117         //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 118
 119         saveImg green (buildFileName " - green.png")
 120
 121         use blue = img.Item(0)
 122         saveImg blue (buildFileName " - blue.png")
 123
 124         use red = img.Item(2)
 125         saveImg red (buildFileName " - red.png")
 126     | _ -> ()
 127
 128     cells
 129
 130 // ID * cell list.
 131 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> unit) option) : (string * Cell list) list =
 132     let inline report (percent: int) =
 133         match reportProgress with
 134         | Some f -> f percent
 135         | _ -> ()
 136
 137     let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
 138     let nbImgs = List.length imgs
 139
 140     let reportProgressImg (id: string) (progress: int) =
 141         progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
 142         report (progressPerAnalysis.Values.Sum() / nbImgs)
 143
 144     let n = Environment.ProcessorCount
 145
 146     imgs
 147     |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p)))
 148     |> PSeq.withDegreeOfParallelism n
 149     |> PSeq.toList