Parasitemia/Parasitemia/ParasitesMarker2.fs

   1 module ParasitesMarker2
   2
   3 open System.Drawing
   4
   5 open Emgu.CV
   6 open Emgu.CV.Structure
   7
   8 open Utils
   9
  10 type Result = {
  11     darkStain: Image<Gray, byte>
  12     infection: Image<Gray, byte>
  13     stain: Image<Gray, byte> }
  14
  15 // Create three binary markers :
  16 // * 'Dark stain' corresponds to the colored pixel, it's independent of the size of the areas.
  17 // * 'Stain' corresponds to the stain around the parasites.
  18 // * 'Infection' corresponds to the parasite. It shouldn't contain thrombocytes.
  19 let find (filteredGreen: Image<Gray, byte>) (filteredGreenFloat: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
  20
  21     let filteredGreenWithoutInfection = filteredGreen.Copy()
  22     ImgTools.areaClose filteredGreenWithoutInfection (int config.InfectionArea)
  23
  24     let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
  25     ImgTools.areaClose filteredGreenWithoutStain (int config.StainArea)
  26
  27     // We use the filtered image to find the dark stain.
  28     let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0) // FIXME: avoid converting again this in MainAnalysis
  29     let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResults
  30     let darkStain = d_fg.Cmp(median_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
  31     darkStain._And(filteredGreenWithoutInfection.Cmp(median_fg, CvEnum.CmpType.LessThan))
  32
  33     let marker (img: Image<Gray, byte>) (closed: Image<Gray, byte>) (threshold: float) : Image<Gray, byte> =
  34         let diff = closed - img
  35
  36         let min = ref [| 0. |]
  37         let minLocation = ref <| [| Point() |]
  38         let max = ref [| 0. |]
  39         let maxLocation = ref <| [| Point() |]
  40         diff.MinMax(min, max, minLocation, maxLocation)
  41         let max = (!max).[0]
  42
  43         let limitThreshold = 0.1
  44         let valueThreshold = (*if max < limitThreshold * (median_bg - median_fg) then max / 2. else *) max * threshold
  45
  46         diff._ThresholdBinary(Gray(valueThreshold), Gray(255.))
  47         diff
  48
  49     let infectionMarker = marker filteredGreen filteredGreenWithoutInfection config.Parameters.infectionLevel
  50     let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel
  51
  52     { darkStain = darkStain
  53       infection = infectionMarker
  54       stain = stainMarker },
  55     filteredGreenWithoutInfection,
  56     filteredGreenWithoutStain
  57
  58
  59
  60
  61