Parasitemia/Parasitemia/MainAnalysis.fs

   1 module ImageAnalysis
   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 Utils
  13 open ImgTools
  14 open Config
  15 open Types
  16
  17 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) (reportProgress: (int -> unit) option) : Cell list =
  18     // To report the progress of this function from 0 to 100.
  19     let inline report (percent: int) =
  20         match reportProgress with
  21         | Some f -> f percent
  22         | _ -> ()
  23
  24     let inline buildLogWithName (text: string) = sprintf "(%s) %s" name text
  25     let logWithName = buildLogWithName >> log
  26     let inline logTimeWithName (text: string) (f: unit -> 'a) : 'a = logTime (buildLogWithName text) f
  27
  28     logWithName "Starting analysis ..."
  29
  30     use green = img.Item(1)
  31     let greenFloat = green.Convert<Gray, float32>()
  32     let filteredGreen = gaussianFilter greenFloat config.LPFStandardDeviation
  33
  34     logWithName (sprintf "Nominal erytrocyte diameter: %s" config.FormattedRadius)
  35
  36     let initialAreaOpening = int<| config.RBCArea * 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.
  37     logTimeWithName "Area opening number one" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpening)
  38
  39     report 8
  40
  41     let range =
  42         let delta = config.Parameters.granulometryRange * config.RBCRadius
  43         int <| config.RBCRadius - delta, int <| config.RBCRadius + delta
  44     //let r1 = log "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) range 1.0 |> float32)
  45     let r2 = logTimeWithName "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen range |> float32)
  46     // log (sprintf "r1: %A, r2: %A" r1 r2)
  47     config.RBCRadius <- r2
  48
  49     logWithName (sprintf "Found erytrocyte diameter: %s" config.FormattedRadius)
  50
  51     report 24
  52
  53     let secondAreaOpening = int <| config.RBCArea * 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 ** 2.f / 50.f |> int)
  64         edges, xGradient, yGradient)
  65
  66     let allEllipses, ellipses = logTimeWithName "Finding ellipses" (fun () ->
  67         let matchingEllipses = Ellipse.find edges xGradient yGradient config
  68         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
  69
  70     report 80
  71
  72     let cells = logTimeWithName "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  73
  74     report 100
  75
  76     logWithName "Analysis finished"
  77
  78     // Output pictures if debug flag is set.
  79     match config.Debug with
  80     | DebugOn output ->
  81         let dirPath = System.IO.Path.Combine(output, name)
  82         System.IO.Directory.CreateDirectory dirPath |> ignore
  83
  84         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  85
  86         saveMat (edges * 255.0) (buildFileName " - edges.png")
  87
  88         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  89         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  90         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  91
  92         let imgAllEllipses = img.Copy()
  93         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
  94         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  95
  96         let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
  97         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
  98         saveImg imgEllipses (buildFileName " - ellipses.png")
  99
 100         let imgCells = img.Copy()
 101         drawCells imgCells false cells
 102         saveImg imgCells (buildFileName " - cells.png")
 103
 104         let imgCells' = img.Copy()
 105         drawCells imgCells' true cells
 106         saveImg imgCells' (buildFileName " - cells - full.png")
 107
 108         let filteredGreenMaxima = gaussianFilter greenFloat config.LPFStandardDeviation
 109         for m in ImgTools.findMaxima filteredGreenMaxima do
 110             ImgTools.drawPoints filteredGreenMaxima m 255.f
 111         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 112
 113         saveImg filteredGreen (buildFileName " - filtered.png")
 114         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
 115         //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 116
 117         saveImg green (buildFileName " - green.png")
 118
 119         use blue = img.Item(0)
 120         saveImg blue (buildFileName " - blue.png")
 121
 122         use red = img.Item(2)
 123         saveImg red (buildFileName " - red.png")
 124     | _ -> ()
 125
 126     cells
 127
 128 // ID * cell list.
 129 let doMultipleAnalysis (imgs: (string * Config * Image<Bgr, byte>) list) (reportProgress: (int -> unit) option) : (string * Cell list) list =
 130     let inline report (percent: int) =
 131         match reportProgress with
 132         | Some f -> f percent
 133         | _ -> ()
 134
 135     let progressPerAnalysis = System.Collections.Concurrent.ConcurrentDictionary<string, int>()
 136     let nbImgs = List.length imgs
 137
 138     let reportProgressImg (id: string) (progress: int) =
 139         progressPerAnalysis.AddOrUpdate(id, progress, (fun _ _ -> progress)) |> ignore
 140         report (progressPerAnalysis.Values.Sum() / nbImgs)
 141
 142     let nbConcurrentTaskLimit = 4
 143     let n = Environment.ProcessorCount
 144
 145     imgs
 146     |> PSeq.map (fun (id, config, img) -> id, doAnalysis img id config (Some (fun p -> reportProgressImg id p)))
 147     |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
 148     |> PSeq.toList