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     // We use the filtered image to find the dark stain.
  22     let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> 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
  48 // Create three binary markers :
  49 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
  50 // * 'Stain' corresponds to the stain around the parasites.
  51 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
  52 let find (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> =
  53     use filteredGreenWithoutInfection = filteredGreen.Copy()
  54     ImgTools.areaCloseF filteredGreenWithoutInfection (int config.InfectionArea)
  55
  56     let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
  57     ImgTools.areaCloseF filteredGreenWithoutStain (int config.StainArea)
  58
  59     let darkStain =
  60         // We use the filtered image to find the dark stain.
  61         let _, mean_fg, mean_bg =
  62             let hist = ImgTools.histogramImg filteredGreenWithoutInfection 300
  63             ImgTools.otsu hist
  64         filteredGreenWithoutInfection.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel + (float mean_fg), CvEnum.CmpType.LessThan)
  65
  66     let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
  67         let diff = img.Copy()
  68         diff._Mul(level)
  69         CvInvoke.Subtract(closed, diff, diff)
  70         diff._ThresholdBinary(Gray(0.0), Gray(255.))
  71         diff.Convert<Gray, byte>()
  72
  73     let infectionMarker = marker filteredGreen filteredGreenWithoutInfection config.Parameters.infectionLevel
  74     let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel
  75
  76     // TODO: comprendre pourquoi des valeurs sont negatives!?!?
  77     let blackTopHat = filteredGreen.CopyBlank()
  78     CvInvoke.Subtract(filteredGreenWithoutInfection, filteredGreen, blackTopHat)
  79     ImgTools.saveImg (ImgTools.normalizeAndConvert blackTopHat) "BottomHat.png"
  80
  81     { darkStain = darkStain
  82       infection = infectionMarker
  83       stain = stainMarker },
  84     filteredGreenWithoutStain
  85
  86