module Parasitemia.Main open System open System.IO open System.Threading open FSharp.Collections.ParallelSeq open Emgu.CV open Emgu.CV.Structure open Config 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( { initialAreaOpen = 2000 minRbcRadius = -0.3f maxRbcRadius = 0.3f preFilterSigma = 1.7 // 1.5 factorNbPick = 1.0 darkStainLevel = 0.25 // 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 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"*) if debug then config.Debug <- DebugOn "." GUI.run config