Parasitemia/Parasitemia/Program.fs

   1 module Parasitemia.Main
   2
   3 open System
   4 open System.IO
   5 open System.Threading
   6
   7 open FSharp.Collections.ParallelSeq
   8
   9 open Emgu.CV
  10 open Emgu.CV.Structure
  11
  12 open Config
  13
  14 type Input =
  15     | File of string
  16     | Dir of string
  17
  18 type RunningMode =
  19     | CmdLine of Input * string
  20     | Window
  21
  22 type Arguments = RunningMode * bool
  23
  24 let parseArgs (args: string[]) : Arguments =
  25
  26     let output = Array.tryFindIndex ((=) "--output") args
  27
  28     let runningMode =
  29         match Array.tryFindIndex ((=) "--folder") args, output with
  30         | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 ->
  31             CmdLine ((Dir args.[i+1]), args.[i_output + 1])
  32         | _ ->
  33             match Array.tryFindIndex ((=) "--file") args, output with
  34             | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 ->
  35                 CmdLine ((File args.[i+1]), args.[i_output + 1])
  36             |_ ->
  37                 Window
  38
  39     runningMode, Array.exists ((=) "--debug") args
  40
  41
  42 [<EntryPoint>]
  43 [<STAThread()>]
  44 let main args =
  45     match parseArgs args with
  46     | mode, debug ->
  47         let config =
  48             Config(
  49               {
  50                 initialAreaOpen = 2000
  51
  52                 minRbcRadius = -0.3f
  53                 maxRbcRadius = 0.3f
  54
  55                 preFilterSigma = 1.7 // 1.5
  56
  57                 factorNbPick = 1.0
  58
  59                 darkStainLevel = 0.25 // Lower -> more sensitive. 0.3. Careful about illumination on the borders.
  60                 maxDarkStainRatio = 0.1 // 10 %
  61
  62                 infectionArea = 0.012f // 1.2 %
  63                 infectionLevel = 1.12 // Lower -> more sensitive.
  64
  65                 stainArea = 0.08f // 8 %
  66                 stainLevel = 1.1 // Lower -> more sensitive.
  67                 maxStainRatio = 0.12 // 12 %
  68
  69                 standardDeviationMaxRatio = 0.5 // 0.55
  70                 minimumCellArea = 0.5f })
  71
  72         match mode with
  73         | CmdLine (input, output) ->
  74             if debug
  75             then
  76                 config.Debug <- DebugOn output
  77
  78             Directory.CreateDirectory output |> ignore
  79
  80             use logFile = new StreamWriter(new FileStream(Path.Combine(output, "log.txt"), FileMode.Append, FileAccess.Write))
  81             Utils.log <- (fun m -> logFile.WriteLine(m))
  82             Utils.log (sprintf "=== New run : %A %A ===" DateTime.Now  (if debug then "[DEBUG]" else "[RELEASE]"))
  83
  84             let files = match input with
  85                         | File file -> [ file ]
  86                         | Dir dir -> Directory.EnumerateFiles dir |> List.ofSeq
  87
  88             use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
  89
  90             //try
  91             let images = seq { for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), new Image<Bgr, byte>(file) }
  92
  93             let nbConcurrentTaskLimit = 4
  94             let n = Environment.ProcessorCount
  95
  96             Utils.logTime "Whole analyze" (fun () ->
  97                 let results =
  98                     images
  99                     |> PSeq.map (fun (id, img) -> id, ImageAnalysis.doAnalysis img id (config.Copy()))
 100                     |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
 101
 102                 for id, cells in results do
 103                     let total, infected = Utils.countCells cells
 104                     fprintf resultFile "File: %s %d %d %.2f\n" id total infected (100. * (float infected) / (float total)))
 105
 106             //Utils.log (sprintf "== File: %A" file)
 107             //with
 108             //| :? IOException as ex -> Utils.log (sprintf "Unable to open the image '%A': %A" file ex)
 109             0
 110
 111         | Window ->
 112             (*let display (window : Views.MainWindow) (img : IImage) =
 113                let imgControl = window.Root.FindName("img") :?> Controls.Image
 114                imgControl.Source <- BitmapSourceConvert.ToBitmapSource(img)
 115
 116             let log (window : Views.MainWindow) (mess : string) =
 117                let txtLog = window.Root.FindName("txtLog") :?> Controls.TextBlock
 118                txtLog.Text <- txtLog.Text + mess + "\n"*)
 119
 120             if debug then config.Debug <- DebugOn "."
 121             GUI.Main.run config