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     use green = img.Item(1)
  17     let greenFloat = green.Convert<Gray, float32>()
  18     let filteredGreen = gaussianFilter greenFloat (float config.Parameters.preFilterSigma)
  19
  20     logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
  21
  22     let r1 = logTime "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) (10, 80) 0.5 |> float32)
  23     // let r2 = logTime "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen (10, 80) |> float32)
  24     // log (sprintf "r1: %A, r2: %A" r1 r2)
  25     config.RBCRadius <- r1
  26
  27     let secondAreaOpen = int <| config.RBCArea / 3.f
  28
  29     if secondAreaOpen > config.Parameters.initialAreaOpen
  30     then
  31         logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
  32
  33     let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
  34     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  35
  36     let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
  37     logTime "Removing small connected components from thinning" (fun () -> removeArea edges (config.RBCRadius ** 2.f / 50.f |> int))
  38
  39     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  40         let matchingEllipses = Ellipse.find edges xGradient yGradient config
  41         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
  42
  43     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  44
  45     // Output pictures if debug flag is set.
  46     match config.Debug with
  47     | DebugOn output ->
  48         let dirPath = System.IO.Path.Combine(output, name)
  49         System.IO.Directory.CreateDirectory dirPath |> ignore
  50
  51         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  52
  53         saveMat (edges * 255.0) (buildFileName " - edges.png")
  54
  55         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  56         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  57         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  58
  59         let imgAllEllipses = img.Copy()
  60         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
  61         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  62
  63         let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
  64         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
  65         saveImg imgEllipses (buildFileName " - ellipses.png")
  66
  67         let imgCells = img.Copy()
  68         drawCells imgCells false cells
  69         saveImg imgCells (buildFileName " - cells.png")
  70
  71         let imgCells' = img.Copy()
  72         drawCells imgCells' true cells
  73         saveImg imgCells' (buildFileName " - cells - full.png")
  74
  75         let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
  76         for m in ImgTools.findMaxima filteredGreenMaxima do
  77             ImgTools.drawPoints filteredGreenMaxima m 255.f
  78         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
  79
  80         saveImg filteredGreen (buildFileName " - filtered.png")
  81         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
  82         //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
  83
  84         saveImg green (buildFileName " - green.png")
  85
  86         use blue = img.Item(0)
  87         saveImg blue (buildFileName " - blue.png")
  88
  89         use red = img.Item(2)
  90         saveImg red (buildFileName " - red.png")
  91     | _ -> ()
  92
  93     cells