module Parasitemia.Main
+open System
open System.IO
open System.Windows
open System.Windows.Media
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 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"
-
-[<System.STAThreadAttribute>]
-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<Bgr, byte>("../../../../src/Tests_hough/images/1508133543-7-4-120-0001.png")
- //use img = new Image<Bgr, byte>("../../../../src/Tests_hough/images/rbc_single.png")
- //use img = new Image<Bgr, byte>("../../../../src/Tests_hough/images/rbc_single_oblong_4.png")
- //use img = new Image<Bgr, byte>("../../../../src/Tests_hough/images/strange_rbc_1.png")
- //use img = new Image<Bgr, byte>("../../../../src/Tests_hough/images/rbc_single_blurred.png")
- use img = new Image<Bgr, byte>("../../../../src/Tests_hough/images/lot.png")
-
-
- ///// PARASITES /////
- //use img = new Image<Bgr, byte>("../../../../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
+
+
+[<EntryPoint>]
+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<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" 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()
projects / master-thesis.git / blobdiff