open ParasitemiaCore.Utils
open ParasitemiaCore.Config
-type Input =
- | File of string
- | Dir of string
-
-type RunningMode =
- | CmdLine of Input * string // A file or a directory to process and the output directory.
- | Window of string option // An optional path to a file to open can be given in window mode.
-
-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 (if args.Length > 0 && not (args.[0].StartsWith("--")) then Some args.[0] else None)
-
- runningMode, Array.exists ((=) "--debug") args
-
-let showArgsHelp () =
- printfn "Usage of Parasitemia :"
- printfn "Non-interactive mode:"
- printfn " %s (--folder <folder>|--file <file>) --output <folder> [--debug]" System.AppDomain.CurrentDomain.FriendlyName
- printfn " --folder <folder> : an input folder containing images to analyze"
- printfn " --file <file> : an image file to be analyzed"
- printfn " --output <folder> : a folder to put the results"
- printfn " --debug : output more information like intermediate images if set"
-
- printfn "Interactive mode:"
- printfn " %s [<document-file>] [--debug]" System.AppDomain.CurrentDomain.FriendlyName
- printfn " <document-file> : a PIAZ file to automatically open at startup"
- printfn " --debug : output information like intermediate images if set in the current directory"
-
-[<System.Runtime.InteropServices.DllImport("kernel32.dll")>]
-extern bool AttachConsole(int dwProcessId)
+[<System.Runtime.InteropServices.DllImport "kernel32.dll">]
+extern bool AttachConsole (int dwProcessId)
[<EntryPoint>]
-[<STAThread()>]
+[<STAThread ()>]
let main args =
// To redirect stdout to the attached console.
- AttachConsole(-1) |> ignore // -1 to attach to the parent process.
+ AttachConsole -1 |> ignore // -1 to attach to the parent process.
+
+ Log.LogDirectory <- Constants.USER_DIRECTORY_LOG
+
+#if DEBUG
+ Log.ClearLogFiles ()
+#endif
+
+ Log.AvoidRepeatingIdenticalMessages <- true
if Array.exists (fun e -> e = "--help" || e = "-h") args then
- showArgsHelp ()
+ Args.showArgsHelp ()
0
else
try
- Log.Info "Starting of Parasitemia UI ..."
+ Log.Info ">>>>> Starting of Parasitemia UI ..."
+ // Log.Info "UI Version: %s" Utils.UIVersion TODO
let result =
- match parseArgs args with
+ match Args.parse args with
| mode, debug ->
- let config = Config(defaultParameters)
+ let config = Config defaultParameters
+
+#if DEBUG
+ Log.DebugLoggingEnabled <- true
+#else
+ Log.DebugLoggingEnabled <- debug
+#endif
+
+ Log.Info "Command line arguments: %s" (args |> String.concat " ")
+ Log.Info "Configuration: %O" config
+ // Log.Info "Settings from %s:\n%s" Settings.Instance.Path Settings.Instance.AsJson TODO
match mode with
- | CmdLine (input, output) ->
+ | Args.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))
- let listener = { new IListener with member this.NewEntry severity header mess = logFile.WriteLine(header + " : " + mess) }
- Log.AddListener(listener)
+ use logFile = new StreamWriter (new FileStream (Path.Combine(output, "log.txt"), FileMode.Append, FileAccess.Write))
+ let listener = { new IListener with member this.NewEntry severity header mess = logFile.WriteLine (header + " : " + mess) }
+ Log.AddListener listener
Log.Info "=== New run : %O %s ===" 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))
-
- let images = [ for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), config.Copy(), new Image<Bgr, byte>(file) ]
-
- Log.LogWithTime Severity.INFO (fun () ->
- match ParasitemiaCore.Analysis.doMultipleAnalysis images None with
- | Some results ->
- for id, cells in results do
- let config, img = images |> List.pick (fun (id', config', img') -> if id' = id then Some (config', img') else None)
- img.Dispose()
- let total, infected = countCells cells
- fprintf resultFile "File: %s %d %d %.2f (diameter: %O)\n" id total infected (100. * (float infected) / (float total)) config.RBCRadius
- | None ->
- fprintf resultFile "Analysis aborted"
- Some ()) "Whole analyze" |> ignore
-
- Log.RmListener(listener)
+ let files =
+ match input with
+ | Args.File file -> [ file ]
+ | Args.Dir dir -> Directory.EnumerateFiles dir |> List.ofSeq
+
+ use resultFile = new StreamWriter (new FileStream (Path.Combine (output, "results.txt"), FileMode.Append, FileAccess.Write))
+
+ let images = [ for file in files -> Path.GetFileNameWithoutExtension (FileInfo(file).Name), config.Copy (), new Image<Bgr, byte> (file) ]
+
+ Log.LogWithTime Types.Severity.INFO (
+ fun () ->
+ match ParasitemiaCore.Analysis.doMultipleAnalysis images None with
+ | Some results ->
+ for id, result in results do
+ let config, img = images |> List.pick (fun (id', config', img') -> if id' = id then Some (config', img') else None)
+ img.Dispose ()
+ let total, infected = countCells result.Cells
+ fprintf resultFile "File: %s %d %d %.2f (diameter: %O)\n" id total infected (100. * (float infected) / (float total)) config.RBCRadius
+ | None ->
+ fprintf resultFile "Analysis aborted"
+ Some ()
+ ) "Whole analyze" |> ignore
+
+ Log.RemoveListener listener
0
- | Window fileToOpen ->
+ | Args.Window fileToOpen ->
if debug then config.Debug <- DebugOn "."
GUI.run config fileToOpen
- Log.Info "Parasitemia UI closed"
+ Log.Info "<<<<< Parasitemia UI closed"
+ Log.Close ()
result
with
| ex ->
Log.Fatal "Error: %A" ex
+ Log.Close ()
1
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projects / master-thesis.git / blobdiff