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 green 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.areaOpen filteredGreen 2000)
  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.areaOpen filteredGreen secondAreaOpen)
  42
  43     let filteredGreenFloat = filteredGreen.Convert<Gray, float32>() // Is it neccessary?
  44
  45     let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen filteredGreenFloat config
  46     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  47     let filteredGreenWhitoutInfectionFloat = filteredGreenWhitoutInfection.Convert<Gray, float32>()
  48     let filteredGreenWhitoutStainFloat = filteredGreenWhitoutStain.Convert<Gray, float32>()
  49
  50     (*let min = ref 0.0
  51     let minLocation = ref <| Point()
  52     let max = ref 0.0
  53     let maxLocation = ref <| Point()
  54     magnitudes.MinMax(min, max, minLocation, maxLocation)
  55
  56     use magnitudesByte = ((magnitudes / !max) * 255.0).Convert<byte>() // Otsu from OpenCV only support 'byte'.
  57     use edges = new Matrix<byte>(xEdges.Size)
  58     CvInvoke.Threshold(magnitudesByte, edges, 0.0, 1.0, CvEnum.ThresholdType.Otsu ||| CvEnum.ThresholdType.Binary) |> ignore
  59
  60     logTime "Finding edges" (fun() -> thin edges)*)
  61
  62     let edges, xGradient, yGradient = ImgTools.findEdges filteredGreenWhitoutStainFloat
  63
  64     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
  65
  66     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  67         let matchingEllipses = Ellipse.find edges xGradient yGradient config
  68         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
  69
  70     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  71
  72     // Output pictures if debug flag is set.
  73     match config.Debug with
  74     | DebugOn output ->
  75         let dirPath = System.IO.Path.Combine(output, name)
  76         System.IO.Directory.CreateDirectory dirPath |> ignore
  77
  78         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  79
  80         saveMat (edges * 255.0) (buildFileName " - edges.png")
  81
  82         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  83         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  84         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  85
  86         let imgAllEllipses = img.Copy()
  87         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
  88         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  89
  90         let imgEllipses = img.Copy()
  91         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
  92         saveImg imgEllipses (buildFileName " - ellipses.png")
  93
  94         // saveImg (kmediansResults.fg * 255.0) (buildFileName " - foreground.png")
  95
  96         let imgCells = img.Copy()
  97         drawCells imgCells false cells
  98         saveImg imgCells (buildFileName " - cells.png")
  99
 100         let imgCells' = img.Copy()
 101         drawCells imgCells' true cells
 102         saveImg imgCells' (buildFileName " - cells - full.png")
 103
 104         let filteredGreenMaxima = gaussianFilter green config.Parameters.preFilterSigma
 105         for m in ImgTools.findMaxima filteredGreenMaxima do
 106             ImgTools.drawPoints filteredGreenMaxima m 255uy
 107         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
 108
 109         saveImg filteredGreen (buildFileName " - filtered.png")
 110         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
 111         saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
 112
 113         (*saveImg parasitesMarker (buildFileName " - parasites (area closing).png")
 114         saveImg stainMarker (buildFileName " - stain (area closing).png")*)
 115
 116         saveImg green (buildFileName " - green.png")
 117
 118         use blue  = scaledImg.Item(0)
 119         saveImg blue (buildFileName " - blue.png")
 120
 121         use red = scaledImg.Item(2)
 122         saveImg red (buildFileName " - red.png")
 123     | _ -> ()
 124
 125     cells