open System.IO
open System.Threading
-open FSharp.Collections.ParallelSeq
-
open Emgu.CV
open Emgu.CV.Structure
| Dir of string
type RunningMode =
- | CmdLine of Input * string
- | Window
+ | 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
| 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
+ Window (if args.Length > 0 && not (args.[0].StartsWith("--")) then Some args.[0] else None)
runningMode, Array.exists ((=) "--debug") args
-
[<EntryPoint>]
[<STAThread()>]
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
+ let e = Ellipse.ellipse2 -11.4 -7.8 -0.169811 -23.75 0.8 -3.885714 -19. 1.5
- 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 parseArgs args with
+ | mode, debug ->
+ let config = Config(defaultParameters)
match mode with
| CmdLine (input, output) ->
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 images = [ for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), config.Copy(), 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)
+ let results = ImageAnalysis.doMultipleAnalysis images None
for id, cells in results do
+ let config = images |> List.pick (fun (id', config', _) -> if id' = id then Some config' else None)
let total, infected = Utils.countCells cells
- fprintf resultFile "File: %s %d %d %.2f\n" id total infected (100. * (float infected) / (float total)))
+ fprintf resultFile "File: %s %d %d %.2f (diameter: %A)\n" id total infected (100. * (float infected) / (float total)) config.RBCRadius)
//Utils.log (sprintf "== File: %A" file)
//with
//| :? IOException as ex -> Utils.log (sprintf "Unable to open the image '%A': %A" file ex)
0
- | Window ->
+ | Window fileToOpen ->
(*let display (window : Views.MainWindow) (img : IImage) =
let imgControl = window.Root.FindName("img") :?> Controls.Image
imgControl.Source <- BitmapSourceConvert.ToBitmapSource(img)
txtLog.Text <- txtLog.Text + mess + "\n"*)
if debug then config.Debug <- DebugOn "."
- GUI.Main.run config
+ GUI.Main.run config fileToOpen