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     {
  17         darkStain : Image<Gray, byte> // Colored pixel, it's independent of the size of the areas. It corresponds to white cells, schizontes, gametocytes, throphozoites.
  18         nucleus : Image<Gray, byte> // Parasite nucleus. It may contain some debris. It shouldn't contain thrombocytes or larger elements.
  19         parasite : Image<Gray, byte> // The whole parasites.
  20     }
  21
  22 let find (img : Image<Gray, float32>) (config : Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
  23
  24     let imgWithoutNucleus = img.Copy ()
  25     areaCloseF imgWithoutNucleus (roundInt config.RBCRadius.NucleusArea)
  26
  27     let darkStain =
  28         // We use the filtered image to find the dark stain.
  29         let _, mean_fg, mean_bg =
  30             let hist = histogramImg imgWithoutNucleus 300
  31             otsu hist
  32         imgWithoutNucleus.Cmp (float mean_fg - config.Parameters.darkStainLevel * float (mean_bg - mean_fg), CvEnum.CmpType.LessThan)
  33
  34     let marker (img : Image<Gray, float32>) (closed : Image<Gray, float32>) (level : float) : Image<Gray, byte> =
  35         let diff = img.Copy ()
  36         diff._Mul level
  37         CvInvoke.Subtract (closed, diff, diff)
  38         diff._ThresholdBinary (Gray 0.0, Gray 255.)
  39         diff.Convert<Gray, byte> ()
  40
  41     // Nucleus.
  42     let nucleusMarker = marker img imgWithoutNucleus (1. / config.Parameters.infectionSensitivity)
  43
  44     // Cytoplasm.
  45     let imgWithoutParasite = img.CopyBlank ()
  46     let kernelSize =
  47         let size = roundInt config.RBCRadius.CytoplasmSize
  48         if size % 2 = 0 then size + 1 else size
  49     use kernel =
  50         if kernelSize <= 3 then
  51             CvInvoke.GetStructuringElement (CvEnum.ElementShape.Rectangle, Size (3, 3), Point (-1, -1))
  52         else
  53             CvInvoke.GetStructuringElement (CvEnum.ElementShape.Ellipse, Size (kernelSize, kernelSize), Point (-1, -1))
  54
  55     CvInvoke.MorphologyEx (img, imgWithoutParasite, CvEnum.MorphOp.Close, kernel, Point(-1, -1), 1, CvEnum.BorderType.Replicate, MCvScalar())
  56     let parasiteMarker = marker img imgWithoutParasite (1. / config.Parameters.cytoplasmSensitivity)
  57
  58     {
  59         darkStain = darkStain
  60         nucleus = nucleusMarker
  61         parasite = parasiteMarker
  62     },
  63     imgWithoutParasite,
  64     imgWithoutNucleus
  65
  66