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) (reportProgress: (int -> unit) option) : Cell list =
  18     let inline report (percent: int) =
  19         match reportProgress with
  20         | Some f -> f percent
  21         | _ -> ()
  22
  23     use green = img.Item(1)
  24     let greenFloat = green.Convert<Gray, float32>()
  25     let filteredGreen = gaussianFilter greenFloat (float config.Parameters.preFilterSigma)
  26
  27     logTime "areaOpen 1" (fun () -> ImgTools.areaOpenF filteredGreen config.Parameters.initialAreaOpen)
  28     report 8
  29
  30     let r1 = logTime "Granulometry (morpho)" (fun() -> Granulometry.findRadiusByClosing (filteredGreen.Convert<Gray, byte>()) (10, 80) 0.5 |> float32)
  31     // let r2 = logTime "Granulometry (area)" (fun() -> Granulometry.findRadiusByAreaClosing filteredGreen (10, 80) |> float32)
  32     // log (sprintf "r1: %A, r2: %A" r1 r2)
  33     config.RBCRadius <- r1
  34     report 24
  35
  36     let secondAreaOpen = int <| config.RBCArea * config.Parameters.ratioSecondAreaOpen
  37
  38     if secondAreaOpen > config.Parameters.initialAreaOpen
  39     then
  40         logTime "areaOpen 2" (fun () -> ImgTools.areaOpenF filteredGreen secondAreaOpen)
  41
  42     let parasites, filteredGreenWhitoutStain = ParasitesMarker.find filteredGreen config
  43     //let parasites, filteredGreenWhitoutInfection, filteredGreenWhitoutStain = ParasitesMarker.findMa greenFloat filteredGreenFloat config
  44
  45     let edges, xGradient, yGradient = logTime "Finding edges" (fun () -> ImgTools.findEdges filteredGreenWhitoutStain)
  46     logTime "Removing small connected components from thinning" (fun () -> removeArea edges (config.RBCRadius ** 2.f / 50.f |> int))
  47
  48     let allEllipses, ellipses = logTime "Finding ellipses" (fun () ->
  49         let matchingEllipses = Ellipse.find edges xGradient yGradient config
  50         matchingEllipses.Ellipses, matchingEllipses.PrunedEllipses)
  51     report 80
  52
  53     let cells = logTime "Classifier" (fun () -> Classifier.findCells ellipses parasites filteredGreenWhitoutStain config)
  54     report 100
  55
  56     // Output pictures if debug flag is set.
  57     match config.Debug with
  58     | DebugOn output ->
  59         let dirPath = System.IO.Path.Combine(output, name)
  60         System.IO.Directory.CreateDirectory dirPath |> ignore
  61
  62         let buildFileName postfix = System.IO.Path.Combine(dirPath, name + postfix)
  63
  64         saveMat (edges * 255.0) (buildFileName " - edges.png")
  65
  66         saveImg parasites.darkStain (buildFileName " - parasites - dark stain.png")
  67         saveImg parasites.stain (buildFileName " - parasites - stain.png")
  68         saveImg parasites.infection (buildFileName " - parasites - infection.png")
  69
  70         let imgAllEllipses = img.Copy()
  71         drawEllipses imgAllEllipses allEllipses (Bgr(0.0, 240.0, 240.0)) 0.05
  72         saveImg imgAllEllipses (buildFileName " - ellipses - all.png")
  73
  74         let imgEllipses = filteredGreenWhitoutStain.Convert<Bgr, byte>()
  75         drawEllipses imgEllipses ellipses (Bgr(0.0, 240.0, 240.0)) 1.0
  76         saveImg imgEllipses (buildFileName " - ellipses.png")
  77
  78         let imgCells = img.Copy()
  79         drawCells imgCells false cells
  80         saveImg imgCells (buildFileName " - cells.png")
  81
  82         let imgCells' = img.Copy()
  83         drawCells imgCells' true cells
  84         saveImg imgCells' (buildFileName " - cells - full.png")
  85
  86         let filteredGreenMaxima = gaussianFilter greenFloat config.Parameters.preFilterSigma
  87         for m in ImgTools.findMaxima filteredGreenMaxima do
  88             ImgTools.drawPoints filteredGreenMaxima m 255.f
  89         saveImg filteredGreenMaxima (buildFileName " - filtered - maxima.png")
  90
  91         saveImg filteredGreen (buildFileName " - filtered.png")
  92         saveImg filteredGreenWhitoutStain (buildFileName " - filtered closed stain.png")
  93         //saveImg filteredGreenWhitoutInfection (buildFileName " - filtered closed infection.png")
  94
  95         saveImg green (buildFileName " - green.png")
  96
  97         use blue = img.Item(0)
  98         saveImg blue (buildFileName " - blue.png")
  99
 100         use red = img.Item(2)
 101         saveImg red (buildFileName " - red.png")
 102     | _ -> ()
 103
 104     cells
 105
 106
 107 // ID * cell radius * cell list.
 108 let doMultipleAnalysis (imgs: (string * Image<Bgr, byte>) list) (config : Config) (reportProgress: (int -> unit) option) : (string * float * Cell list) list =
 109     let inline report (percent: int) =
 110         match reportProgress with
 111         | Some f -> f percent
 112         | _ -> ()
 113
 114     let monitor = Object()
 115     let mutable total = 0
 116     let nbImgs = List.length imgs
 117     let reportProgressImg =
 118         (fun progress ->
 119             lock monitor (fun () -> total <- total + progress)
 120             report (total / nbImgs))
 121
 122     let nbConcurrentTaskLimit = 4
 123     let n = Environment.ProcessorCount
 124
 125     imgs
 126     |> PSeq.map (fun (id, img) ->
 127         let localConfig = config.Copy()
 128         let cells = doAnalysis img id localConfig (Some reportProgressImg)
 129         id, float localConfig.RBCRadius, cells)
 130     |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
 131     |> PSeq.toList