Parasitemia/ParasitemiaCore/ParasitesMarker.fs

   1 module ParasitemiaCore.ParasitesMarker
   2
   3 open System.Drawing
   4 open System.Linq
   5
   6 open Emgu.CV
   7 open Emgu.CV.Structure
   8
   9 open Utils
  10
  11 type Result = {
  12     darkStain: Image<Gray, byte>
  13     infection: Image<Gray, byte>
  14     stain: Image<Gray, byte> }
  15
  16 // Create three binary markers :
  17 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
  18 // * 'Stain' corresponds to the stain around the parasites.
  19 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
  20 let findMa (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
  21     // We use the filtered image to find the dark stain.
  22     let kmediansResults = KMedians.kmedians filteredGreen
  23     let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResults
  24     let darkStain = d_fg.Cmp(median_bg * float config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
  25     darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))
  26     darkStain._And(fg)
  27
  28     let fgFloat = (fg / 255.0).Convert<Gray, float32>()
  29     use greenWithoutBg = ImgTools.gaussianFilter green 1.0
  30     greenWithoutBg.SetValue(Gray(0.0), fg.Not())
  31
  32     let findSmears (sigma: float) (level: float) : Image<Gray, byte> =
  33         use greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
  34         use fgSmoothed = ImgTools.gaussianFilter fgFloat sigma
  35         let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level), CvEnum.CmpType.LessThan)
  36         smears._And(fg)
  37         smears
  38
  39     let tmp = filteredGreen.Convert<Gray, byte>()
  40
  41     { darkStain = darkStain;
  42       stain = findSmears 10. 0.9
  43       infection = findSmears 2.2 0.87 },
  44     tmp,
  45     tmp
  46
  47 // Create three binary markers :
  48 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
  49 // * 'Stain' corresponds to the stain around the parasites.
  50 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
  51 let find (img: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
  52
  53     let imgFilteredInfection = ImgTools.gaussianFilter img config.LPFStandardDeviationParasite
  54     let filteredGreenWithoutInfection = imgFilteredInfection.Copy()
  55     ImgTools.areaCloseF filteredGreenWithoutInfection (roundInt config.RBCRadius.NucleusArea)
  56
  57     (*
  58     let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
  59     ImgTools.areaCloseF filteredGreenWithoutStain (int config.RBCRadius.StainArea) *)
  60
  61     let darkStain =
  62         // We use the filtered image to find the dark stain.
  63         let _, mean_fg, mean_bg =
  64             let hist = ImgTools.histogramImg filteredGreenWithoutInfection 300
  65             ImgTools.otsu hist
  66         filteredGreenWithoutInfection.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel + (float mean_fg), CvEnum.CmpType.LessThan)
  67
  68     let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
  69         let diff = img.Copy()
  70         diff._Mul(level)
  71         CvInvoke.Subtract(closed, diff, diff)
  72         diff._ThresholdBinary(Gray(0.0), Gray(255.))
  73         diff.Convert<Gray, byte>()
  74
  75     let infectionMarker = marker imgFilteredInfection filteredGreenWithoutInfection (1. / config.Parameters.infectionSensitivity)
  76
  77     let imgFilteredStain = ImgTools.gaussianFilter img config.LPFStandardDeviationStain
  78     let areaOpening = int <| config.RBCRadius.Area * config.Parameters.ratioAreaPaleCenter
  79     //ImgTools.areaOpenF imgFilteredStain areaOpening
  80
  81     let filteredGreenWithoutStain = imgFilteredStain.CopyBlank()
  82     let kernelSize =
  83         let size = roundInt (config.RBCRadius.Pixel / 5.f)
  84         if size % 2 = 0 then size + 1 else size
  85     use kernel =
  86         if kernelSize <= 3
  87         then
  88             CvInvoke.GetStructuringElement(CvEnum.ElementShape.Rectangle, Size(3, 3), Point(-1, -1))
  89         else
  90             CvInvoke.GetStructuringElement(CvEnum.ElementShape.Ellipse, Size(kernelSize, kernelSize), Point(-1, -1))
  91
  92     CvInvoke.MorphologyEx(imgFilteredStain, filteredGreenWithoutStain, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
  93     let stainMarker = marker (*filteredGreenWithoutInfection*) imgFilteredStain filteredGreenWithoutStain (1. / config.Parameters.cytoplasmSensitivity)
  94
  95     //
  96     (*let blackTopHat = filteredGreenWithoutStain.CopyBlank()
  97     CvInvoke.Subtract(filteredGreenWithoutStain, imgFilteredStain, blackTopHat)
  98     ImgTools.saveImg blackTopHat "blackTopHat.png"*)
  99
 100     { darkStain = darkStain
 101       infection = infectionMarker
 102       stain = stainMarker },
 103     filteredGreenWithoutStain,
 104     filteredGreenWithoutInfection
 105
 106