open System
open System.IO
-open System.Windows
-open System.Windows.Media
-open System.Windows.Markup
-open System.Windows.Shapes
-open System.Windows.Controls
-open System.Drawing
-open System.Diagnostics
+open System.Threading
+
+open FSharp.Collections.ParallelSeq
open Emgu.CV
open Emgu.CV.Structure
-open Emgu.CV.WPF
open Config
-let display (window : Views.MainWindow) (img : IImage) =
- let imgControl = window.Root.FindName("img") :?> Controls.Image
- imgControl.Source <- BitmapSourceConvert.ToBitmapSource(img)
-
-let log (window : Views.MainWindow) (mess : string) =
- let txtLog = window.Root.FindName("txtLog") :?> Controls.TextBlock
- txtLog.Text <- txtLog.Text + mess + "\n"
-
-
type Input =
| File of string
| Dir of string
[<EntryPoint>]
+[<STAThread()>]
let main args =
match parseArgs args with
| mode, debug ->
- let scale = 1.
- let config = {
- debug = if debug then DebugOn "." else DebugOff
-
- scale = scale
-
- // RBC size range in px at scale = 1.0.
- minRBCSize = 20.
- maxRBCSize = 40.
+ let config =
+ Config(
+ {
+ initialAreaOpen = 2000
- doGSigma1 = 1.5
- doGSigma2 = 20.
- doGLowFreqPercentageReduction = 0.75
+ minRbcRadius = -0.3f
+ maxRbcRadius = 0.3f
- factorNbPick = 2.0
- factorWindowSize = 1.6
+ preFilterSigma = 1.7 // 1.5
- darkStainLevel = 0.4 // Lower -> more sensitive.
+ factorNbPick = 1.0
- stainSigma = 10.
- stainLevel = 0.9
- stainSpreadRequired = 3.0
+ darkStainLevel = 0.25 // Lower -> more sensitive. 0.3. Careful about illumination on the borders.
+ maxDarkStainRatio = 0.1 // 10 %
- infectionSigma = 2.2
- infectionLevel = 0.85
- infectionPixelsRequired = 1
+ infectionArea = 0.012f // 1.2 %
+ infectionLevel = 1.12 // Lower -> more sensitive.
- percentageOfFgValidCell = 0.4
+ stainArea = 0.08f // 8 %
+ stainLevel = 1.1 // Lower -> more sensitive.
+ maxStainRatio = 0.12 // 12 %
- MaxDarkStainRatio = 0.1
-
- minimumCellArea = 1200. * scale ** 2. |> int
- maxOffcenter = 0.5 }
+ standardDeviationMaxRatio = 0.5 // 0.55
+ minimumCellArea = 0.5f })
match mode with
| CmdLine (input, output) ->
- let config = { config with debug = DebugOn output }
+ if debug
+ then
+ config.Debug <- DebugOn output
Directory.CreateDirectory output |> ignore
use logFile = new StreamWriter(new FileStream(Path.Combine(output, "log.txt"), FileMode.Append, FileAccess.Write))
Utils.log <- (fun m -> logFile.WriteLine(m))
- Utils.log (sprintf "=== New run : %A ===" DateTime.Now)
+ Utils.log (sprintf "=== New run : %A %A ===" DateTime.Now (if debug then "[DEBUG]" else "[RELEASE]"))
let files = match input with
| File file -> [ file ]
use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
- for file in files do
- try
- use img = new Image<Bgr, byte>(file)
- Utils.log (sprintf "== File: %A" file)
- let cells = Utils.logTime "Whole analyze" (fun () -> ImageAnalysis.doAnalysis img (FileInfo(file).Name) config)
+ //try
+ let images = seq { for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), new Image<Bgr, byte>(file) }
+
+ let nbConcurrentTaskLimit = 4
+ let n = Environment.ProcessorCount
+
+ Utils.logTime "Whole analyze" (fun () ->
+ let results =
+ images
+ |> PSeq.map (fun (id, img) -> id, ImageAnalysis.doAnalysis img id (config.Copy()))
+ |> PSeq.withDegreeOfParallelism (if n > nbConcurrentTaskLimit then nbConcurrentTaskLimit else n)
+
+ for id, cells in results do
let total, infected = Utils.countCells cells
- fprintf resultFile "File: %s %d %d %.2f\n" file total infected (100. * (float infected) / (float total))
- with
- | _ as ex -> Utils.log (sprintf "Unable to open the image '%A': %A" file ex)
+ fprintf resultFile "File: %s %d %d %.2f\n" id total infected (100. * (float infected) / (float total)))
+
+ //Utils.log (sprintf "== File: %A" file)
+ //with
+ //| :? IOException as ex -> Utils.log (sprintf "Unable to open the image '%A': %A" file ex)
0
| Window ->
- let app = new Application()
- let mainWindow = Views.MainWindow()
+ (*let display (window : Views.MainWindow) (img : IImage) =
+ let imgControl = window.Root.FindName("img") :?> Controls.Image
+ imgControl.Source <- BitmapSourceConvert.ToBitmapSource(img)
- Utils.log <- (fun m -> log mainWindow m)
+ let log (window : Views.MainWindow) (mess : string) =
+ let txtLog = window.Root.FindName("txtLog") :?> Controls.TextBlock
+ txtLog.Text <- txtLog.Text + mess + "\n"*)
- //display mainWindow img
- mainWindow.Root.Show()
- app.Run()
+ if debug then config.Debug <- DebugOn "."
+ GUI.run config