Parasitemia/Parasitemia/MainAnalysis.fs

   1 module ImageAnalysis
   2
   3 open System
   4 open System.Drawing
   5
   6 open Emgu.CV
   7 open Emgu.CV.Structure
   8
   9 open Utils
  10 open ImgTools
  11 open Config
  12 open Types
  13
  14
  15 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
  16
  17     use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
  18
  19     use green = scaledImg.Item(1)
  20
  21     let greenFloat = green.Convert<Gray, float32>()
  22
  23     let filteredGreen = gaussianFilter greenFloat config.Parameters.preFilterSigma
  24
  25     (*let maximaImg = filteredGreen.Copy()
  26     let maxima = logTime "maxima" (fun () -> ImgTools.findMaxima maximaImg)
  27     for m in maxima do
  28         ImgTools.drawPoints maximaImg m 255uy
  29
  30     let greenOpen1 = filteredGreen.Copy()
  31     logTime "areaOpen1" (fun () -> ImgTools.areaOpen greenOpen1 2000)*)
  32
  33     let initialAreaOpen = 2000
  34     logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen initialAreaOpen)
  35
  36     config.RBCRadius <- Granulometry.findRadius filteredGreen (10, 100) 0.5 |> float
  37
  38     let secondAreaOpen = int <| config.RBCArea / 3.
  39     if secondAreaOpen > initialAreaOpen
  40     then
  41         logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
  42
  43     let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
  44     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  45
  46     let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStain
  47
  48     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
  49
  50     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  51         let matchingEllipses = Ellipse.find edges xGradient yGradient config
  52         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
  53
  54     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  55
  56     // Output pictures if debug flag is set.
  57     match config.Debug with
  58     | DebugOn output ->
  59         let dirPath = System.IO.Path.Combine(output, name)
  60         System.IO.Directory.CreateDirectory dirPath |> ignore
  61
  62         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  63
  64         //saveImg canny (buildFileName " - canny.png")
  65
  66         saveMat (edges * 255.0) (buildFileName " - edges.png")
  67
  68         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  69         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  70         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  71
  72         let imgAllEllipses = img.Copy()
  73         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
  74         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  75
  76         let imgEllipses = img.Copy()
  77         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
  78         saveImg imgEllipses (buildFileName " - ellipses.png")
  79
  80         let imgCells = img.Copy()
  81         drawCells imgCells false cells
  82         saveImg imgCells (buildFileName " - cells.png")
  83
  84         let imgCells' = img.Copy()
  85         drawCells imgCells' true cells
  86         saveImg imgCells' (buildFileName " - cells - full.png")
  87
  88         let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
  89         for m in ImgTools.findMaxima filteredGreenMaxima do
  90             ImgTools.drawPoints filteredGreenMaxima m 255.f
  91         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
  92
  93         saveImg filteredGreen (buildFileName " - filtered.png")
  94         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
  95         saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
  96
  97         saveImg green (buildFileName " - green.png")
  98
  99         use blue  = scaledImg.Item(0)
 100         saveImg blue (buildFileName " - blue.png")
 101
 102         use red = scaledImg.Item(2)
 103         saveImg red (buildFileName " - red.png")
 104     | _ -> ()
 105
 106     cells