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