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
  14 type Result =
  15     {
  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
  21 let find (img : Image<Gray, float32>) (config : Config.Config) : Result * Image<Gray, float32> * Image<Gray, float32> =
  22
  23     let imgWithoutNucleus = img.Copy ()
  24     areaCloseF imgWithoutNucleus (roundInt config.RBCRadius.NucleusArea)
  25
  26     let darkStain =
  27         // We use the filtered image to find the dark stain.
  28         let _, mean_fg, mean_bg =
  29             let hist = histogramImg imgWithoutNucleus 300
  30             otsu hist
  31         imgWithoutNucleus.Cmp (float mean_fg - config.Parameters.darkStainLevel * float (mean_bg - mean_fg), CvEnum.CmpType.LessThan)
  32
  33     let marker (img : Image<Gray, float32>) (closed : Image<Gray, float32>) (level : float) : Image<Gray, byte> =
  34         let diff = img.Copy ()
  35         diff._Mul level
  36         CvInvoke.Subtract (closed, diff, diff)
  37         diff._ThresholdBinary (Gray 0.0, Gray 255.)
  38         diff.Convert<Gray, byte> ()
  39
  40     // Nucleus.
  41     let nucleusMarker = marker img imgWithoutNucleus (1. / config.Parameters.infectionSensitivity)
  42
  43     // Cytoplasm.
  44     let imgWithoutParasite = img.CopyBlank ()
  45     let kernelSize =
  46         let size = roundInt config.RBCRadius.CytoplasmSize
  47         if size % 2 = 0 then size + 1 else size
  48     use kernel =
  49         if kernelSize <= 3 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     {
  58         darkStain = darkStain
  59         nucleus = nucleusMarker
  60         parasite = parasiteMarker
  61     },
  62     imgWithoutParasite,
  63     imgWithoutNucleus
  64
  65