Parasitemia/Parasitemia/ParasitesMarker2.fs

   1 module ParasitesMarker2
   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 find (filteredGreen: Image<Gray, byte>) (filteredGreenFloat: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, byte> * Image<Gray, byte> =
  21
  22     let filteredGreenWithoutInfection = filteredGreen.Copy()
  23     ImgTools.areaClose filteredGreenWithoutInfection (int config.InfectionArea)
  24
  25     let filteredGreenWithoutStain = filteredGreenWithoutInfection.Copy()
  26     ImgTools.areaClose filteredGreenWithoutStain (int config.StainArea)
  27
  28     // We use the filtered image to find the dark stain.
  29     let kmediansResults = logTime "Finding fg/bg (k-medians)" (fun () -> KMedians.kmedians (filteredGreenWithoutInfection.Convert<Gray, float32>()) 1.0) // FIXME: avoid converting again this in MainAnalysis
  30     let { KMedians.fg = fg; KMedians.median_bg = median_bg; KMedians.median_fg = median_fg; KMedians.d_fg = d_fg } = kmediansResults
  31     let darkStain = d_fg.Cmp(median_bg * config.Parameters.darkStainLevel, CvEnum.CmpType.GreaterThan)
  32     darkStain._And(filteredGreenWithoutInfection.Cmp(median_fg, CvEnum.CmpType.LessThan))
  33
  34     let marker (img: Image<Gray, byte>) (closed: Image<Gray, byte>) (level: float) : Image<Gray, byte> =
  35         let diff = closed - img
  36
  37         let min = ref [| 0. |]
  38         let minLocation = ref <| [| Point() |]
  39         let max = ref [| 0. |]
  40         let maxLocation = ref <| [| Point() |]
  41         diff.MinMax(min, max, minLocation, maxLocation)
  42         let max = (!max).[0]
  43
  44         let threshold = 0.2 * max
  45         let diff' = diff - threshold
  46
  47         let m = MathNet.Numerics.Statistics.StreamingStatistics.Mean(seq {
  48                 for m in ImgTools.findMaxima diff' do
  49                     let p = m.First()
  50                     yield diff'.Data.[p.Y, p.X, 0] |> float }) + threshold
  51
  52         let valueThreshold = m * level
  53
  54         diff._ThresholdBinary(Gray(valueThreshold), Gray(255.))
  55         diff
  56
  57     let infectionMarker = marker filteredGreen filteredGreenWithoutInfection config.Parameters.infectionLevel
  58     let stainMarker = marker filteredGreenWithoutInfection filteredGreenWithoutStain config.Parameters.stainLevel
  59
  60     { darkStain = darkStain
  61       infection = infectionMarker
  62       stain = stainMarker },
  63     filteredGreenWithoutInfection,
  64     filteredGreenWithoutStain
  65
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