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 scale = 1.
  61         let config = {
  62             debug = if debug then DebugOn "." else DebugOff
  63
  64             scale = scale
  65
  66             // RBC size range in px at scale = 1.0.
  67             minRBCSize = 20.
  68             maxRBCSize = 40.
  69
  70             doGSigma1 = 1.5
  71             doGSigma2 = 20.
  72             doGLowFreqPercentageReduction = 0.75
  73
  74             factorNbPick = 2.0
  75             factorWindowSize = 1.6
  76
  77             darkStainLevel = 0.4 // Lower -> more sensitive.
  78
  79             stainSigma = 10.
  80             stainLevel = 0.9
  81             stainSpreadRequired = 3.0
  82
  83             infectionSigma = 2.2
  84             infectionLevel = 0.85
  85             infectionPixelsRequired = 1
  86
  87             percentageOfFgValidCell = 0.4
  88
  89             MaxDarkStainRatio = 0.1
  90
  91             minimumCellArea = 1200. * scale ** 2. |> int
  92             maxOffcenter = 0.5 }
  93
  94         match mode with
  95         | CmdLine (input, output) ->
  96             let config = { config with debug = DebugOn output }
  97
  98             Directory.CreateDirectory output |> ignore
  99
 100             use logFile = new StreamWriter(new FileStream(Path.Combine(output, "log.txt"), FileMode.Append, FileAccess.Write))
 101             Utils.log <- (fun m -> logFile.WriteLine(m))
 102             Utils.log (sprintf "=== New run : %A ===" DateTime.Now)
 103
 104             let files = match input with
 105                         | File file -> [ file ]
 106                         | Dir dir -> Directory.EnumerateFiles dir |> List.ofSeq
 107
 108             use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
 109
 110             for file in files do
 111                 try
 112                     use img = new Image<Bgr, byte>(file)
 113                     Utils.log (sprintf "== File: %A" file)
 114                     let cells = Utils.logTime "Whole analyze" (fun () -> ImageAnalysis.doAnalysis img (FileInfo(file).Name) config)
 115                     let total, infected = Utils.countCells cells
 116                     fprintf resultFile "File: %s %d %d %.2f\n" file total infected (100. * (float infected) / (float total))
 117                 with
 118                 | :? IOException as ex -> Utils.log (sprintf "Unable to open the image '%A': %A" file ex)
 119             0
 120
 121         | Window ->
 122             let app = new Application()
 123             let mainWindow = Views.MainWindow()
 124
 125             Utils.log <- (fun m -> log mainWindow m)
 126
 127             //display mainWindow img
 128             mainWindow.Root.Show()
 129             app.Run()