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 Histogram
  11 open Otsu
  12 open Morpho
  13 open ImgTools
  14
  15 type Result = {
  16     darkStain: Image<Gray, byte> // Colored pixel, it's independent of the size of the areas. It corresponds to white cells, schizontes, gametocytes, throphozoites.
  17     nucleus: Image<Gray, byte> // Parasite nucleus. It may contain some debris. It shouldn't contain thrombocytes or larger elements.
  18     parasite: Image<Gray, byte> } // The whole parasites.
  19
  20 let find (img: Image<Gray, float32>) (config: Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
  21
  22     let imgWithoutNucleus = img.Copy()
  23     areaCloseF imgWithoutNucleus (roundInt config.RBCRadius.NucleusArea)
  24
  25     let darkStain =
  26         // We use the filtered image to find the dark stain.
  27         let _, mean_fg, mean_bg =
  28             let hist = histogramImg imgWithoutNucleus 300
  29             otsu hist
  30         imgWithoutNucleus.Cmp(float mean_fg - config.Parameters.darkStainLevel * float (mean_bg - mean_fg), CvEnum.CmpType.LessThan)
  31
  32     let marker (img: Image<Gray, float32>) (closed: Image<Gray, float32>) (level: float) : Image<Gray, byte> =
  33         let diff = img.Copy()
  34         diff._Mul(level)
  35         CvInvoke.Subtract(closed, diff, diff)
  36         diff._ThresholdBinary(Gray(0.0), Gray(255.))
  37         diff.Convert<Gray, byte>()
  38
  39     // Nucleus.
  40     let nucleusMarker = marker img imgWithoutNucleus (1. / config.Parameters.infectionSensitivity)
  41
  42     // Cytoplasm.
  43     let imgWithoutParasite = img.CopyBlank()
  44     let kernelSize =
  45         let size = roundInt config.RBCRadius.CytoplasmSize
  46         if size % 2 = 0 then size + 1 else size
  47     use kernel =
  48         if kernelSize <= 3
  49         then
  50             CvInvoke.GetStructuringElement(CvEnum.ElementShape.Rectangle, Size(3, 3), Point(-1, -1))
  51         else
  52             CvInvoke.GetStructuringElement(CvEnum.ElementShape.Ellipse, Size(kernelSize, kernelSize), Point(-1, -1))
  53
  54     CvInvoke.MorphologyEx(img, imgWithoutParasite, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
  55     let parasiteMarker = marker img imgWithoutParasite (1. / config.Parameters.cytoplasmSensitivity)
  56
  57     { darkStain = darkStain
  58       nucleus = nucleusMarker
  59       parasite = parasiteMarker },
  60     imgWithoutParasite,
  61     imgWithoutNucleus
  62
  63