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