X-Git-Url: http://git.euphorik.ch/?p=master-thesis.git;a=blobdiff_plain;f=Parasitemia%2FParasitemia%2FProgram.fs;h=09f43126106c852a7f65209546448e8db679f893;hp=b44c65f0855e47537579219803863d07bd78d72e;hb=044b0ae69df3ac565432545b2fa934589016f9bd;hpb=d9a6e072ecf299db691c05bb559a71265f812ba3 diff --git a/Parasitemia/Parasitemia/Program.fs b/Parasitemia/Parasitemia/Program.fs index b44c65f..09f4312 100644 --- a/Parasitemia/Parasitemia/Program.fs +++ b/Parasitemia/Parasitemia/Program.fs @@ -1,5 +1,6 @@ module Parasitemia.Main +open System open System.IO open System.Windows open System.Windows.Media @@ -8,6 +9,9 @@ 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 @@ -15,58 +19,122 @@ open Emgu.CV.WPF open Config -let display (window : Views.MainWindow) (img : IImage) = +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" - -[] -do - Utils.dprintfn "OpenCV test" - - let app = new Application() - let mainWindow = Views.MainWindow() - - Utils.log <- (fun m -> log mainWindow m) - - let config = { - scale = 1.0 - - doGSigma1 = 1.5 - doGSigma2 = 20.0 - doGLowFreqPercentageReduction = 0.9 - - darkStainLevel = 0.839 - - stainSigma = 10.0 - stainLevel = 0.9 - stainSpreadRequired = 3.0 - - infectionSigma = 2.0 - infectionLevel = 0.762 - infectionPixelsRequired = 1 } - - ///// ELLIPSES ///// - //use img = new Image("../../../../src/Tests_hough/images/1508133543-7-4-120-0001.png") - //use img = new Image("../../../../src/Tests_hough/images/rbc_single.png") - //use img = new Image("../../../../src/Tests_hough/images/rbc_single_oblong_4.png") - //use img = new Image("../../../../src/Tests_hough/images/strange_rbc_1.png") - //use img = new Image("../../../../src/Tests_hough/images/rbc_single_blurred.png") - use img = new Image("../../../../src/Tests_hough/images/lot.png") - - - ///// PARASITES ///// - //use img = new Image("../../../../src/Parasites/images/1.png") - -// KdTree.test3 () -// Utils.dprintfn "area: %A" area - - let result = Utils.logTime "Total" (fun () -> - ImageAnalysis.doAnalysis img config ) - - display mainWindow img - mainWindow.Root.Show() - app.Run() |> ignore + + +type Input = + | File of string + | Dir of string + +type RunningMode = + | CmdLine of Input * string + | Window + +type Arguments = RunningMode * bool + +let parseArgs (args: string[]) : Arguments = + + let output = Array.tryFindIndex ((=) "--output") args + + let runningMode = + match Array.tryFindIndex ((=) "--folder") args, output with + | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 -> + CmdLine ((Dir args.[i+1]), args.[i_output + 1]) + | _ -> + match Array.tryFindIndex ((=) "--file") args, output with + | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 -> + CmdLine ((File args.[i+1]), args.[i_output + 1]) + |_ -> + Window + + runningMode, Array.exists ((=) "--debug") args + + +[] +let main args = + match parseArgs args with + | mode, debug -> + let config = + Config( + { scale = 1. + + initialAreaOpen = 2000 + + minRbcRadius = -0.32f + maxRbcRadius = 0.32f + + preFilterSigma = 1.7 // 1.5 + + factorNbPick = 1.0 + + darkStainLevel = 0.22 // Lower -> more sensitive. 0.3. Careful about illumination on the borders. + maxDarkStainRatio = 0.1 // 10 % + + infectionArea = 0.012f // 1.2 % + infectionLevel = 1.12 // Lower -> more sensitive. + + stainArea = 0.08f // 8 % + stainLevel = 1.1 // Lower -> more sensitive. + maxStainRatio = 0.12 // 12 % + + standardDeviationMaxRatio = 0.5 // 0.55 + minimumCellArea = 0.5f }) + + match mode with + | CmdLine (input, 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 %A ===" DateTime.Now (if debug then "[DEBUG]" else "[RELEASE]")) + + let files = match input with + | File file -> [ file ] + | Dir dir -> Directory.EnumerateFiles dir |> List.ofSeq + + use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write)) + + //try + let images = seq { for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), new Image(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" 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() + + if debug + then + config.Debug <- DebugOn "." + + Utils.log <- (fun m -> log mainWindow m) + + //display mainWindow img + mainWindow.Root.Show() + app.Run()