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 Utils
  10
  11 type Result = {
  12     darkStain: Image<Gray, byte> // Colored pixel, it's independent of the size of the areas. It corresponds to white cells, schizontes, gametocytes, throphozoites.
  13     nucleus: Image<Gray, byte> // Parasite nucleus. It may contain some debris. It shouldn't contain thrombocytes or larger elements.
  14     cytoplasm: Image<Gray, byte> } // Parasite cytoplasm.
  15
  16 let find (img: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
  17
  18     let imgFilteredParasite = ImgTools.gaussianFilter img config.LPFStandardDeviationParasite
  19
  20     let filteredGreenWithoutNucleus = imgFilteredParasite.Copy()
  21     ImgTools.areaCloseF filteredGreenWithoutNucleus (roundInt config.RBCRadius.NucleusArea)
  22
  23     let darkStain =
  24         // We use the filtered image to find the dark stain.
  25         let _, mean_fg, mean_bg =
  26             let hist = ImgTools.histogramImg filteredGreenWithoutNucleus 300
  27             ImgTools.otsu hist
  28         filteredGreenWithoutNucleus.Cmp(-(float mean_bg) * config.Parameters.darkStainLevel + (float mean_fg), CvEnum.CmpType.LessThan)
  29
  30     let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
  31         let diff = img.Copy()
  32         diff._Mul(level)
  33         CvInvoke.Subtract(closed, diff, diff)
  34         diff._ThresholdBinary(Gray(0.0), Gray(255.))
  35         diff.Convert<Gray, byte>()
  36
  37     let nucleusMarker = marker imgFilteredParasite filteredGreenWithoutNucleus (1. / config.Parameters.infectionSensitivity)
  38
  39     let filteredGreenWithoutCytoplasm = imgFilteredParasite.CopyBlank()
  40     let kernelSize =
  41         let size = roundInt (config.RBCRadius.Pixel / 5.f)
  42         if size % 2 = 0 then size + 1 else size
  43     use kernel =
  44         if kernelSize <= 3
  45         then
  46             CvInvoke.GetStructuringElement(CvEnum.ElementShape.Rectangle, Size(3, 3), Point(-1, -1))
  47         else
  48             CvInvoke.GetStructuringElement(CvEnum.ElementShape.Ellipse, Size(kernelSize, kernelSize), Point(-1, -1))
  49
  50     CvInvoke.MorphologyEx(imgFilteredParasite, filteredGreenWithoutCytoplasm, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
  51     let cytoplasmMarker = marker imgFilteredParasite filteredGreenWithoutCytoplasm (1. / config.Parameters.cytoplasmSensitivity)
  52
  53     { darkStain = darkStain
  54       nucleus = nucleusMarker
  55       cytoplasm = cytoplasmMarker },
  56     filteredGreenWithoutCytoplasm,
  57     filteredGreenWithoutNucleus
  58
  59