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 Logger
  10
  11 open Utils
  12
  13 type Result = {
  14     darkStain: Image<Gray, byte>
  15     infection: Image<Gray, byte>
  16     stain: Image<Gray, byte> }
  17
  18 // Create three binary markers :
  19 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
  20 // * 'Stain' corresponds to the stain around the parasites.
  21 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
  22 let findMa (green: Image<Gray, float32>) (filteredGreen: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
  23     // We use the filtered image to find the dark stain.
  24     let kmediansResults = Log.LogWithTime("Finding fg/bg (k-medians)", Severity.USER, (fun () -> KMedians.kmedians filteredGreen))
  25     let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResults
  26     let darkStain = d_fg.Cmp(median_bg * float config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
  27     darkStain._And(filteredGreen.Cmp(median_fg, CvEnum.CmpType.LessThan))
  28     darkStain._And(fg)
  29
  30     let fgFloat = (fg / 255.0).Convert<Gray, float32>()
  31     use greenWithoutBg = ImgTools.gaussianFilter green 1.0
  32     greenWithoutBg.SetValue(Gray(0.0), fg.Not())
  33
  34     let findSmears (sigma: float) (level: float) : Image<Gray, byte> =
  35         use greenWithoutBgSmoothed = ImgTools.gaussianFilter greenWithoutBg sigma
  36         use fgSmoothed = ImgTools.gaussianFilter fgFloat sigma
  37         let smears = (greenWithoutBg.Mul(fgSmoothed)).Cmp(greenWithoutBgSmoothed.Mul(level), CvEnum.CmpType.LessThan)
  38         smears._And(fg)
  39         smears
  40
  41     let tmp = filteredGreen.Convert<Gray, byte>()
  42
  43     { darkStain = darkStain;
  44       stain = findSmears 10. 0.9
  45       infection = findSmears 2.2 0.87 },
  46     tmp,
  47     tmp
  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> =
  54     use filteredGreenWithoutInfection = filteredGreen.Copy()
  55     ImgTools.areaCloseF filteredGreenWithoutInfection (int config.RBCRadius.InfectionArea)
  56
  57     let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
  58     ImgTools.areaCloseF filteredGreenWithoutStain (int config.RBCRadius.StainArea)
  59
  60     let darkStain =
  61         // We use the filtered image to find the dark stain.
  62         let _, mean_fg, mean_bg =
  63             let hist = ImgTools.histogramImg filteredGreenWithoutInfection 300
  64             ImgTools.otsu hist
  65         filteredGreenWithoutInfection.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel + (float mean_fg), CvEnum.CmpType.LessThan)
  66
  67     let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
  68         let diff = img.Copy()
  69         diff._Mul(level)
  70         CvInvoke.Subtract(closed, diff, diff)
  71         diff._ThresholdBinary(Gray(0.0), Gray(255.))
  72         diff.Convert<Gray, byte>()
  73
  74     let infectionMarker = marker filteredGreen filteredGreenWithoutInfection (1. / config.Parameters.infectionSensitivity)
  75     let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain (1. / config.Parameters.stainSensitivity)
  76
  77     // TODO: comprendre pourquoi des valeurs sont negatives!?!?
  78     (*
  79     let blackTopHat = filteredGreen.CopyBlank()
  80     CvInvoke.Subtract(filteredGreenWithoutInfection, filteredGreen, blackTopHat)
  81     ImgTools.saveImg (ImgTools.normalizeAndConvert blackTopHat) "BottomHat.png"
  82     *)
  83
  84     { darkStain = darkStain
  85       infection = infectionMarker
  86       stain = stainMarker },
  87     filteredGreenWithoutStain
  88
  89