Parasitemia/Parasitemia/MainAnalysis.fs

   1 module ImageAnalysis
   2
   3 open System
   4 open System.Drawing
   5
   6 open Emgu.CV
   7 open Emgu.CV.Structure
   8
   9 open Utils
  10 open ImgTools
  11 open Config
  12 open Types
  13
  14
  15 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
  16     let scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
  17
  18     use green = scaledImg.Item(1)
  19     let greenFloat = green.Convert<Gray, float32>()
  20     let filteredGreen = gaussianFilter greenFloat (float config.Parameters.preFilterSigma)
  21
  22     logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
  23
  24     config.RBCRadius <- logTime "Granulometry" (fun() -> Granulometry.findRadius (filteredGreen.Convert<Gray, byte>()) (10, 100) 0.3 |> float32)
  25
  26     let secondAreaOpen = int <| config.RBCArea / 3.f
  27     if secondAreaOpen > config.Parameters.initialAreaOpen
  28     then
  29         logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
  30
  31     let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
  32     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  33
  34     let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
  35     logTime "Removing small connected components from thinning" (fun () -> removeArea edges (config.RBCRadius ** 2.f / 50.f |> int))
  36
  37     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  38         let matchingEllipses = Ellipse.find edges xGradient yGradient config
  39         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
  40
  41     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  42
  43     // Output pictures if debug flag is set.
  44     match config.Debug with
  45     | DebugOn output ->
  46         let dirPath = System.IO.Path.Combine(output, name)
  47         System.IO.Directory.CreateDirectory dirPath |> ignore
  48
  49         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  50
  51         saveMat (edges * 255.0) (buildFileName " - edges.png")
  52
  53         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  54         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  55         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  56
  57         let imgAllEllipses = img.Copy()
  58         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
  59         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  60
  61         let imgEllipses = img.Copy()
  62         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
  63         saveImg imgEllipses (buildFileName " - ellipses.png")
  64
  65         let imgCells = img.Copy()
  66         drawCells imgCells false cells
  67         saveImg imgCells (buildFileName " - cells.png")
  68
  69         let imgCells' = img.Copy()
  70         drawCells imgCells' true cells
  71         saveImg imgCells' (buildFileName " - cells - full.png")
  72
  73         let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
  74         for m in ImgTools.findMaxima filteredGreenMaxima do
  75             ImgTools.drawPoints filteredGreenMaxima m 255.f
  76         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
  77
  78         saveImg filteredGreen (buildFileName " - filtered.png")
  79         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
  80         //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
  81
  82         saveImg green (buildFileName " - green.png")
  83
  84         use blue  = scaledImg.Item(0)
  85         saveImg blue (buildFileName " - blue.png")
  86
  87         use red = scaledImg.Item(2)
  88         saveImg red (buildFileName " - red.png")
  89     | _ -> ()
  90
  91     cells