Parasitemia/Parasitemia/MainAnalysis.fs

   1 module ImageAnalysis
   2
   3 open System
   4 open System.Drawing
   5
   6 open FSharp.Collections.ParallelSeq
   7
   8 open Emgu.CV
   9 open Emgu.CV.Structure
  10
  11 open Utils
  12 open ImgTools
  13 open Config
  14 open Types
  15
  16
  17 let doAnalysis (img: Image<Bgr, byte>) (name: string) (config: Config) : Cell list =
  18     use green = img.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     let r1 = logTime "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) (10, 80) 0.5 |> float32)
  25     // let r2 = logTime "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen (10, 80) |> float32)
  26     // log (sprintf "r1: %A, r2: %A" r1 r2)
  27     config.RBCRadius <- r1
  28
  29     let secondAreaOpen = int <| config.RBCArea / 3.f
  30
  31     if secondAreaOpen > config.Parameters.initialAreaOpen
  32     then
  33         logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
  34
  35     let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
  36     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  37
  38     let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
  39     logTime "Removing small connected components from thinning" (fun () -> removeArea edges (config.RBCRadius ** 2.f / 50.f |> int))
  40
  41     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  42         let matchingEllipses = Ellipse.find edges xGradient yGradient config
  43         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
  44
  45     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  46
  47     // Output pictures if debug flag is set.
  48     match config.Debug with
  49     | DebugOn output ->
  50         let dirPath = System.IO.Path.Combine(output, name)
  51         System.IO.Directory.CreateDirectory dirPath |> ignore
  52
  53         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  54
  55         saveMat (edges * 255.0) (buildFileName " - edges.png")
  56
  57         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  58         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  59         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  60
  61         let imgAllEllipses = img.Copy()
  62         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
  63         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  64
  65         let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
  66         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
  67         saveImg imgEllipses (buildFileName " - ellipses.png")
  68
  69         let imgCells = img.Copy()
  70         drawCells imgCells false cells
  71         saveImg imgCells (buildFileName " - cells.png")
  72
  73         let imgCells' = img.Copy()
  74         drawCells imgCells' true cells
  75         saveImg imgCells' (buildFileName " - cells - full.png")
  76
  77         let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
  78         for m in ImgTools.findMaxima filteredGreenMaxima do
  79             ImgTools.drawPoints filteredGreenMaxima m 255.f
  80         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
  81
  82         saveImg filteredGreen (buildFileName " - filtered.png")
  83         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
  84         //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
  85
  86         saveImg green (buildFileName " - green.png")
  87
  88         use blue = img.Item(0)
  89         saveImg blue (buildFileName " - blue.png")
  90
  91         use red = img.Item(2)
  92         saveImg red (buildFileName " - red.png")
  93     | _ -> ()
  94
  95     cells
  96
  97
  98 let doMultipleAnalysis (imgs: (string * Image<Bgr, byte>) list) (config : Config) : (string * Cell list) list =
  99     let nbConcurrentTaskLimit = 4
 100     let n = Environment.ProcessorCount
 101
 102     imgs
 103     |> PSeq.map (fun (id, img) -> id, doAnalysis img id (config.Copy()))
 104     |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
 105     |> PSeq.toList