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               {
  66                 initialAreaOpen = 2000
  67
  68                 minRbcRadius = -0.32f
  69                 maxRbcRadius = 0.32f
  70
  71                 preFilterSigma = 1.7 // 1.5
  72
  73                 factorNbPick = 1.0
  74
  75                 darkStainLevel = 0.25 // Lower -> more sensitive. 0.3. Careful about illumination on the borders.
  76                 maxDarkStainRatio = 0.1 // 10 %
  77
  78                 infectionArea = 0.012f // 1.2 %
  79                 infectionLevel = 1.12 // Lower -> more sensitive.
  80
  81                 stainArea = 0.08f // 8 %
  82                 stainLevel = 1.1 // Lower -> more sensitive.
  83                 maxStainRatio = 0.12 // 12 %
  84
  85                 standardDeviationMaxRatio = 0.5 // 0.55
  86                 minimumCellArea = 0.5f })
  87
  88         match mode with
  89         | CmdLine (input, output) ->
  90             if debug
  91             then
  92                 config.Debug <- DebugOn output
  93
  94             Directory.CreateDirectory output |> ignore
  95
  96             use logFile = new StreamWriter(new FileStream(Path.Combine(output, "log.txt"), FileMode.Append, FileAccess.Write))
  97             Utils.log <- (fun m -> logFile.WriteLine(m))
  98             Utils.log (sprintf "=== New run : %A %A ===" DateTime.Now  (if debug then "[DEBUG]" else "[RELEASE]"))
  99
 100             let files = match input with
 101                         | File file -> [ file ]
 102                         | Dir dir -> Directory.EnumerateFiles dir |> List.ofSeq
 103
 104             use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
 105
 106             //try
 107             let images = seq { for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), new Image<Bgr, byte>(file) }
 108
 109             let nbConcurrentTaskLimit = 4
 110             let n = Environment.ProcessorCount
 111
 112             Utils.logTime "Whole analyze" (fun () ->
 113                 let results =
 114                     images
 115                     |> PSeq.map (fun (id, img) -> id, ImageAnalysis.doAnalysis img id (config.Copy()))
 116                     |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
 117
 118                 for id, cells in results do
 119                     let total, infected = Utils.countCells cells
 120                     fprintf resultFile "File: %s %d %d %.2f\n" id total infected (100. * (float infected) / (float total)))
 121
 122             //Utils.log (sprintf "== File: %A" file)
 123             //with
 124             //| :? IOException as ex -> Utils.log (sprintf "Unable to open the image '%A': %A" file ex)
 125             0
 126
 127         | Window ->
 128             let app = new Application()
 129             let mainWindow = Views.MainWindow()
 130
 131             if debug
 132             then
 133                 config.Debug <- DebugOn "."
 134
 135             Utils.log <- (fun m -> log mainWindow m)
 136
 137             //display mainWindow img
 138             mainWindow.Root.Show()
 139             app.Run()