Parasitemia/Parasitemia/Program.fs

   1 module Parasitemia.Main
   2
   3 open System
   4 open System.IO
   5 open System.Windows
   6 open System.Windows.Media
   7 open System.Windows.Markup
   8 open System.Windows.Shapes
   9 open System.Windows.Controls
  10 open System.Drawing
  11 open System.Diagnostics
  12
  13 open Emgu.CV
  14 open Emgu.CV.Structure
  15 open Emgu.CV.WPF
  16
  17 open Config
  18
  19 let display (window : Views.MainWindow) (img : IImage) =
  20    let imgControl = window.Root.FindName("img") :?> Controls.Image
  21    imgControl.Source <- BitmapSourceConvert.ToBitmapSource(img)
  22
  23 let log (window : Views.MainWindow) (mess : string) =
  24    let txtLog = window.Root.FindName("txtLog") :?> Controls.TextBlock
  25    txtLog.Text <- txtLog.Text + mess + "\n"
  26
  27
  28 type Input =
  29     | File of string
  30     | Dir of string
  31
  32 type RunningMode =
  33     | CmdLine of Input * string
  34     | Window
  35
  36 type Arguments = RunningMode * bool
  37
  38 let parseArgs (args: string[]) : Arguments =
  39
  40     let output = Array.tryFindIndex ((=) "--output") args
  41
  42     let runningMode =
  43         match Array.tryFindIndex ((=) "--folder") args, output with
  44         | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 ->
  45             CmdLine ((Dir args.[i+1]), args.[i_output + 1])
  46         | _ ->
  47             match Array.tryFindIndex ((=) "--file") args, output with
  48             | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 ->
  49                 CmdLine ((File args.[i+1]), args.[i_output + 1])
  50             |_ ->
  51                 Window
  52
  53     runningMode, Array.exists ((=) "--debug") args
  54
  55
  56 [<EntryPoint>]
  57 let main args =
  58     match parseArgs args with
  59     | mode, debug ->
  60         let config =
  61             Config(
  62               { scale = 1.
  63
  64                 minRbcRadius = -0.32
  65                 maxRbcRadius = 0.32
  66
  67                 preFilterSigma = 1.7 // 1.5
  68
  69                 factorNbPick = 1.0
  70                 factorWindowSize = 2.0
  71
  72                 darkStainLevel = 0.25 // Lower -> more sensitive. 0.3
  73                 maxDarkStainRatio = 0.1
  74
  75                 infectionArea = 0.012 // 1.2 %
  76                 infectionLevel = 1.12 // Lower -> more sensitive.
  77
  78                 stainArea = 0.08 // 8 %
  79                 stainLevel = 1.1 // Lower -> more sensitive.
  80                 maxStainRatio = 0.12 // 12 %
  81
  82                 standardDeviationMaxRatio = 0.58 // 0.55
  83                 minimumCellArea = 0.5 })
  84
  85         match mode with
  86         | CmdLine (input, output) ->
  87             if debug
  88             then
  89                 config.Debug <- DebugOn output
  90
  91             Directory.CreateDirectory output |> ignore
  92
  93             use logFile = new StreamWriter(new FileStream(Path.Combine(output, "log.txt"), FileMode.Append, FileAccess.Write))
  94             Utils.log <- (fun m -> logFile.WriteLine(m))
  95             Utils.log (sprintf "=== New run : %A %A ===" DateTime.Now  (if debug then "[DEBUG]" else "[RELEASE]"))
  96
  97             let files = match input with
  98                         | File file -> [ file ]
  99                         | Dir dir -> Directory.EnumerateFiles dir |> List.ofSeq
 100
 101             use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
 102
 103             for file in files do
 104                 try
 105                     use img = new Image<Bgr, byte>(file)
 106                     Utils.log (sprintf "== File: %A" file)
 107
 108                     let cells = Utils.logTime "Whole analyze" (fun () -> ImageAnalysis.doAnalysis img (Path.GetFileNameWithoutExtension(FileInfo(file).Name)) config)
 109                     let total, infected = Utils.countCells cells
 110                     fprintf resultFile "File: %s %d %d %.2f\n" file total infected (100. * (float infected) / (float total))
 111                 with
 112                 | :? IOException as ex -> Utils.log (sprintf "Unable to open the image '%A': %A" file ex)
 113             0
 114
 115         | Window ->
 116             let app = new Application()
 117             let mainWindow = Views.MainWindow()
 118
 119             if debug
 120             then
 121                 config.Debug <- DebugOn "."
 122
 123             Utils.log <- (fun m -> log mainWindow m)
 124
 125             //display mainWindow img
 126             mainWindow.Root.Show()
 127             app.Run()