Parasitemia/Parasitemia/ParasitesMarker.fs

   1 module ParasitesMarker
   2
   3 open System.Drawing
   4 open System.Linq
   5
   6 open Emgu.CV
   7 open Emgu.CV.Structure
   8 open Utils
   9
  10 type Result = {
  11     darkStain: Image<Gray, byte>
  12     infection: Image<Gray, byte>
  13     stain: Image<Gray, byte> }
  14
  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
  22     // We use the filtered image to find the dark stain.
  23     let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians filteredGreen 1.0)
  24     let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResults
  25     let darkStain = d_fg.Cmp(median_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
  26     darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))
  27     darkStain._And(fg)
  28
  29     let fgFloat = (fg / 255.0).Convert<Gray, float32>()
  30     use greenWithoutBg = ImgTools.gaussianFilter green 1.0
  31     greenWithoutBg.SetValue(Gray(0.0), fg.Not())
  32
  33     let findSmears (sigma: float) (level: float) : Image<Gray, byte> =
  34         use greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
  35         use fgSmoothed = ImgTools.gaussianFilter fgFloat sigma
  36         let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level), CvEnum.CmpType.LessThan)
  37         smears._And(fg)
  38         smears
  39
  40     let tmp = filteredGreen.Convert<Gray, byte>()
  41
  42     { darkStain = darkStain;
  43       stain = findSmears 10. 0.9
  44       infection = findSmears 2.2 0.87 },
  45     tmp,
  46     tmp
  47
  48
  49 // Create three binary markers :
  50 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
  51 // * 'Stain' corresponds to the stain around the parasites.
  52 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
  53 let find (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
  54
  55     let filteredGreenWithoutInfection = filteredGreen.Copy()
  56     ImgTools.areaCloseF filteredGreenWithoutInfection (int config.InfectionArea)
  57
  58     let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
  59     ImgTools.areaCloseF filteredGreenWithoutStain (int config.StainArea)
  60
  61     // We use the filtered image to find the dark stain.
  62
  63     // With K-Means.
  64     let kmeansResults = logTime "Finding fg/bg (k-means)" (fun () -> KMeans.kmeans (filteredGreenWithoutInfection) 1.0)
  65     let { KMeans.mean_bg = value_bg; KMeans.mean_fg = value_fg; KMeans.d_fg = d_fg } = kmeansResults
  66
  67     // With K-Medians.
  68     (* let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection) 1.0) // FIXME: avoid converting this again in MainAnalysis
  69     let { KMedians.median_bg = value_bg; KMedians.median_fg = value_fg; KMedians.d_fg = d_fg } = kmediansResults *)
  70
  71     let darkStain = d_fg.Cmp(value_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
  72     darkStain._And(filteredGreenWithoutInfection.Cmp(value_fg, CvEnum.CmpType.LessThan))
  73
  74     let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
  75         let diff = closed - (img * level)
  76         diff._ThresholdBinary(Gray(0.0), Gray(255.))
  77         diff.Convert<Gray, byte>()
  78
  79     let infectionMarker = marker filteredGreen filteredGreenWithoutInfection config.Parameters.infectionLevel
  80     let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel
  81
  82     { darkStain = darkStain
  83       infection = infectionMarker
  84       stain = stainMarker },
  85     filteredGreenWithoutInfection,
  86     filteredGreenWithoutStain
  87
  88