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
  17     use scaledImg = if config.Parameters.scale = 1.0 then img else img.Resize(config.Parameters.scale, CvEnum.Inter.Area)
  18
  19     use green = scaledImg.Item(1)
  20     let greenFloat = green.Convert<Gray, float32>()
  21     let filteredGreen = gaussianFilter greenFloat config.Parameters.preFilterSigma
  22
  23     logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
  24
  25     config.RBCRadius <- logTime "Granulometry" (fun() -> Granulometry.findRadius (filteredGreen.Convert<Gray, byte>()) (10, 100) 0.5 |> float)
  26
  27     let secondAreaOpen = int <| config.RBCArea / 3.
  28     if secondAreaOpen > config.Parameters.initialAreaOpen
  29     then
  30         logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
  31
  32     let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
  33     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  34
  35     let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
  36     logTime "Removing small connected components from thinning" (fun () -> removeArea edges 12)
  37
  38     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  39         let matchingEllipses = Ellipse.find edges xGradient yGradient config
  40         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses )
  41
  42     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  43
  44     // Output pictures if debug flag is set.
  45     match config.Debug with
  46     | DebugOn output ->
  47         let dirPath = System.IO.Path.Combine(output, name)
  48         System.IO.Directory.CreateDirectory dirPath |> ignore
  49
  50         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  51
  52         //saveImg canny (buildFileName " - canny.png")
  53
  54         saveMat (edges * 255.0) (buildFileName " - edges.png")
  55
  56         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  57         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  58         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  59
  60         let imgAllEllipses = img.Copy()
  61         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
  62         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  63
  64         let imgEllipses = img.Copy()
  65         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
  66         saveImg imgEllipses (buildFileName " - ellipses.png")
  67
  68         let imgCells = img.Copy()
  69         drawCells imgCells false cells
  70         saveImg imgCells (buildFileName " - cells.png")
  71
  72         let imgCells' = img.Copy()
  73         drawCells imgCells' true cells
  74         saveImg imgCells' (buildFileName " - cells - full.png")
  75
  76         let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
  77         for m in ImgTools.findMaxima filteredGreenMaxima do
  78             ImgTools.drawPoints filteredGreenMaxima m 255.f
  79         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
  80
  81         saveImg filteredGreen (buildFileName " - filtered.png")
  82         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
  83         saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
  84
  85         saveImg green (buildFileName " - green.png")
  86
  87         use blue  = scaledImg.Item(0)
  88         saveImg blue (buildFileName " - blue.png")
  89
  90         use red = scaledImg.Item(2)
  91         saveImg red (buildFileName " - red.png")
  92     | _ -> ()
  93
  94     cells