Parasitemia/Parasitemia/Program.fs

   1 module Parasitemia.Main
   2
   3 open System
   4 open System.IO
   5 open System.Threading
   6
   7 open Emgu.CV
   8 open Emgu.CV.Structure
   9
  10 open Config
  11
  12 type Input =
  13     | File of string
  14     | Dir of string
  15
  16 type RunningMode =
  17     | CmdLine of Input * string
  18     | Window
  19
  20 type Arguments = RunningMode * bool
  21
  22 let parseArgs (args: string[]) : Arguments =
  23
  24     let output = Array.tryFindIndex ((=) "--output") args
  25
  26     let runningMode =
  27         match Array.tryFindIndex ((=) "--folder") args, output with
  28         | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 ->
  29             CmdLine ((Dir args.[i+1]), args.[i_output + 1])
  30         | _ ->
  31             match Array.tryFindIndex ((=) "--file") args, output with
  32             | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 ->
  33                 CmdLine ((File args.[i+1]), args.[i_output + 1])
  34             |_ ->
  35                 Window
  36
  37     runningMode, Array.exists ((=) "--debug") args
  38
  39
  40 [<EntryPoint>]
  41 [<STAThread()>]
  42 let main args =
  43     match parseArgs args with
  44     | mode, debug ->
  45         let config =
  46             Config(
  47               {
  48                 initialAreaOpen = 2000
  49                 ratioSecondAreaOpen = 1.f / 3.f
  50
  51                 minRbcRadius = -0.3f
  52                 maxRbcRadius = 0.3f
  53
  54                 preFilterSigma = 1.7 // 1.5
  55
  56                 factorNbPick = 1.0
  57
  58                 darkStainLevel = 0.25 // 0.3
  59                 maxDarkStainRatio = 0.1 // 10 %
  60
  61                 infectionArea = 0.012f // 1.2 %
  62                 infectionLevel = 1.12 // Lower -> more sensitive.
  63
  64                 stainArea = 0.08f // 8 %
  65                 stainLevel = 1.1 // Lower -> more sensitive.
  66                 maxStainRatio = 0.12 // 12 %
  67
  68                 standardDeviationMaxRatio = 0.5 // 0.55
  69                 minimumCellAreaFactor = 0.5f })
  70
  71         match mode with
  72         | CmdLine (input, output) ->
  73             if debug
  74             then
  75                 config.Debug <- DebugOn output
  76
  77             Directory.CreateDirectory output |> ignore
  78
  79             use logFile = new StreamWriter(new FileStream(Path.Combine(output, "log.txt"), FileMode.Append, FileAccess.Write))
  80             Utils.log <- (fun m -> logFile.WriteLine(m))
  81             Utils.log (sprintf "=== New run : %A %A ===" DateTime.Now  (if debug then "[DEBUG]" else "[RELEASE]"))
  82
  83             let files = match input with
  84                         | File file -> [ file ]
  85                         | Dir dir -> Directory.EnumerateFiles dir |> List.ofSeq
  86
  87             use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
  88
  89             //try
  90             let images = [ for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), new Image<Bgr, byte>(file) ]
  91
  92
  93             Utils.logTime "Whole analyze" (fun () ->
  94                 let results = ImageAnalysis.doMultipleAnalysis images config None
  95
  96                 for id, _, cells in results do
  97                     let total, infected = Utils.countCells cells
  98                     fprintf resultFile "File: %s %d %d %.2f\n" id total infected (100. * (float infected) / (float total)))
  99
 100             //Utils.log (sprintf "== File: %A" file)
 101             //with
 102             //| :? IOException as ex -> Utils.log (sprintf "Unable to open the image '%A': %A" file ex)
 103             0
 104
 105         | Window ->
 106             (*let display (window : Views.MainWindow) (img : IImage) =
 107                let imgControl = window.Root.FindName("img") :?> Controls.Image
 108                imgControl.Source <- BitmapSourceConvert.ToBitmapSource(img)
 109
 110             let log (window : Views.MainWindow) (mess : string) =
 111                let txtLog = window.Root.FindName("txtLog") :?> Controls.TextBlock
 112                txtLog.Text <- txtLog.Text + mess + "\n"*)
 113
 114             if debug then config.Debug <- DebugOn "."
 115             GUI.Main.run config