* Add the analysis window.

[master-thesis.git] / Parasitemia / Parasitemia / Program.fs

diff --git a/Parasitemia/Parasitemia/Program.fs b/Parasitemia/Parasitemia/Program.fs
index 76fc244..038f827 100644 (file)
--- a/Parasitemia/Parasitemia/Program.fs
+++ b/Parasitemia/Parasitemia/Program.fs
@@ -2,29 +2,13 @@
 
 open System
 open System.IO
-open System.Windows
-open System.Windows.Media
-open System.Windows.Markup
-open System.Windows.Shapes
-open System.Windows.Controls
-open System.Drawing
-open System.Diagnostics
+open System.Threading
 
 open Emgu.CV
 open Emgu.CV.Structure
-open Emgu.CV.WPF
 
 open Config
 
-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"
-
-
 type Input =
     | File of string
     | Dir of string
@@ -54,49 +38,47 @@ let parseArgs (args: string[]) : Arguments =
 
 
 [<EntryPoint>]
+[<STAThread()>]
 let main args =
     match parseArgs args with
     | mode, debug ->
-        let scale = 1.
-        let config = {
-            debug = if debug then DebugOn "." else DebugOff
-
-            scale = scale
-
-            // RBC size range in px at scale = 1.0.
-            minRBCSize = 20.
-            maxRBCSize = 40.
+        let config =
+            Config(
+              {
+                initialAreaOpen = 2000
+                ratioSecondAreaOpen = 1.f / 3.f
 
-            doGSigma1 = 1.5
-            doGSigma2 = 20.
-            doGLowFreqPercentageReduction = 0.75
+                minRbcRadius = -0.3f
+                maxRbcRadius = 0.3f
 
-            darkStainLevel = 0.5
+                preFilterSigma = 1.7 // 1.5
 
-            stainSigma = 10.
-            stainLevel = 0.9
-            stainSpreadRequired = 3.0
+                factorNbPick = 1.0
 
-            infectionSigma = 2.2
-            infectionLevel = 0.85
-            infectionPixelsRequired = 1
+                darkStainLevel = 0.25 // 0.3
+                maxDarkStainRatio = 0.1 // 10 %
 
-            percentageOfFgValidCell = 0.4
+                infectionArea = 0.012f // 1.2 %
+                infectionLevel = 1.12 // Lower -> more sensitive.
 
-            MaxDarkStainRatio = 0.1
+                stainArea = 0.08f // 8 %
+                stainLevel = 1.1 // Lower -> more sensitive.
+                maxStainRatio = 0.12 // 12 %
 
-            minimumCellArea = 600. * scale ** 2. |> int
-            maxOffcenter = 0.5 }
+                standardDeviationMaxRatio = 0.5 // 0.55
+                minimumCellAreaFactor = 0.5f })
 
         match mode with
         | CmdLine (input, output) ->
-            let config = { config with debug = DebugOn 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 ===" DateTime.Now)
+            Utils.log (sprintf "=== New run : %A %A ===" DateTime.Now  (if debug then "[DEBUG]" else "[RELEASE]"))
 
             let files = match input with
                         | File file -> [ file ]
@@ -104,23 +86,30 @@ let main args =
 
             use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
 
-            for file in files do
-                try
-                    use img = new Image<Bgr, byte>(file)
-                    Utils.log (sprintf "== File: %A" file)
-                    let cells = Utils.logTime "Whole analyze" (fun () -> ImageAnalysis.doAnalysis img (FileInfo(file).Name) config)
+            //try
+            let images = [ for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), new Image<Bgr, byte>(file) ]
+
+
+            Utils.logTime "Whole analyze" (fun () ->
+                let results = ImageAnalysis.doMultipleAnalysis images config None
+
+                for id, _, cells in results do
                     let total, infected = Utils.countCells cells
-                    fprintf resultFile "File: %s %d %d %.2f\n" file total infected (100. * (float infected) / (float total))
-                with
-                | _ as ex -> Utils.log (sprintf "Unable to open the image '%A': %A" file ex)
+                    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()
+            (*let display (window : Views.MainWindow) (img : IImage) =
+               let imgControl = window.Root.FindName("img") :?> Controls.Image
+               imgControl.Source <- BitmapSourceConvert.ToBitmapSource(img)
 
-            Utils.log <- (fun m -> log mainWindow m)
+            let log (window : Views.MainWindow) (mess : string) =
+               let txtLog = window.Root.FindName("txtLog") :?> Controls.TextBlock
+               txtLog.Text <- txtLog.Text + mess + "\n"*)
 
-            //display mainWindow img
-            mainWindow.Root.Show()
-            app.Run()
+            if debug then config.Debug <- DebugOn "."
+            GUI.Main.run config