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 open System.Threading
  13
  14 open FSharp.Collections.ParallelSeq
  15
  16 open Emgu.CV
  17 open Emgu.CV.Structure
  18 open Emgu.CV.WPF
  19
  20 open Config
  21
  22 let display (window : Views.MainWindow) (img : IImage) =
  23    let imgControl = window.Root.FindName("img") :?> Controls.Image
  24    imgControl.Source <- BitmapSourceConvert.ToBitmapSource(img)
  25
  26 let log (window : Views.MainWindow) (mess : string) =
  27    let txtLog = window.Root.FindName("txtLog") :?> Controls.TextBlock
  28    txtLog.Text <- txtLog.Text + mess + "\n"
  29
  30
  31 type Input =
  32     | File of string
  33     | Dir of string
  34
  35 type RunningMode =
  36     | CmdLine of Input * string
  37     | Window
  38
  39 type Arguments = RunningMode * bool
  40
  41 let parseArgs (args: string[]) : Arguments =
  42
  43     let output = Array.tryFindIndex ((=) "--output") args
  44
  45     let runningMode =
  46         match Array.tryFindIndex ((=) "--folder") args, output with
  47         | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 ->
  48             CmdLine ((Dir args.[i+1]), args.[i_output + 1])
  49         | _ ->
  50             match Array.tryFindIndex ((=) "--file") args, output with
  51             | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 ->
  52                 CmdLine ((File args.[i+1]), args.[i_output + 1])
  53             |_ ->
  54                 Window
  55
  56     runningMode, Array.exists ((=) "--debug") args
  57
  58
  59 [<EntryPoint>]
  60 let main args =
  61     match parseArgs args with
  62     | mode, debug ->
  63         let config =
  64             Config(
  65               { scale = 1.
  66
  67                 initialAreaOpen = 2000
  68
  69                 minRbcRadius = -0.32f
  70                 maxRbcRadius = 0.32f
  71
  72                 preFilterSigma = 1.7 // 1.5
  73
  74                 factorNbPick = 1.0
  75
  76                 darkStainLevel = 0.22 // Lower -> more sensitive. 0.3. Careful about illumination on the borders.
  77                 maxDarkStainRatio = 0.1 // 10 %
  78
  79                 infectionArea = 0.012f // 1.2 %
  80                 infectionLevel = 1.12 // Lower -> more sensitive.
  81
  82                 stainArea = 0.08f // 8 %
  83                 stainLevel = 1.1 // Lower -> more sensitive.
  84                 maxStainRatio = 0.12 // 12 %
  85
  86                 standardDeviationMaxRatio = 0.5 // 0.55
  87                 minimumCellArea = 0.5f })
  88
  89         match mode with
  90         | CmdLine (input, output) ->
  91             if debug
  92             then
  93                 config.Debug <- DebugOn output
  94
  95             Directory.CreateDirectory output |> ignore
  96
  97             use logFile = new StreamWriter(new FileStream(Path.Combine(output, "log.txt"), FileMode.Append, FileAccess.Write))
  98             Utils.log <- (fun m -> logFile.WriteLine(m))
  99             Utils.log (sprintf "=== New run : %A %A ===" DateTime.Now  (if debug then "[DEBUG]" else "[RELEASE]"))
 100
 101             let files = match input with
 102                         | File file -> [ file ]
 103                         | Dir dir -> Directory.EnumerateFiles dir |> List.ofSeq
 104
 105             use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
 106
 107             //try
 108             let images = seq { for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), new Image<Bgr, byte>(file) }
 109
 110             let nbConcurrentTaskLimit = 4
 111             let n = Environment.ProcessorCount
 112
 113             Utils.logTime "Whole analyze" (fun () ->
 114                 let results =
 115                     images
 116                     |> PSeq.map (fun (id, img) -> id, ImageAnalysis.doAnalysis img id (config.Copy()))
 117                     |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
 118
 119                 for id, cells in results do
 120                     let total, infected = Utils.countCells cells
 121                     fprintf resultFile "File: %s %d %d %.2f\n" id total infected (100. * (float infected) / (float total)))
 122
 123             //Utils.log (sprintf "== File: %A" file)
 124             //with
 125             //| :? IOException as ex -> Utils.log (sprintf "Unable to open the image '%A': %A" file ex)
 126             0
 127
 128         | Window ->
 129             let app = new Application()
 130             let mainWindow = Views.MainWindow()
 131
 132             if debug
 133             then
 134                 config.Debug <- DebugOn "."
 135
 136             Utils.log <- (fun m -> log mainWindow m)
 137
 138             //display mainWindow img
 139             mainWindow.Root.Show()
 140             app.Run()