Change the parasite detection method.

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

diff --git a/Parasitemia/Parasitemia/Program.fs b/Parasitemia/Parasitemia/Program.fs
index ac17c82..103596a 100644 (file)
--- a/Parasitemia/Parasitemia/Program.fs
+++ b/Parasitemia/Parasitemia/Program.fs
@@ -57,65 +57,69 @@ let parseArgs (args: string[]) : Arguments =
 let main args =
     match parseArgs args with
     | mode, debug ->
-        let scale = 1.
-        let config = {
-            debug = if debug then DebugOn "." else DebugOff
+        let config =
+            Config(
+              { scale = 1.
 
-            scale = scale
+                minRbcRadius = -0.3
+                maxRbcRadius = 0.3
 
-            // RBC size range in px at scale = 1.0.
-            minRBCSize = 20.
-            maxRBCSize = 40.
+                preFilterSigma = 1.5
 
-            doGSigma1 = 1.5
-            doGSigma2 = 20.
-            doGLowFreqPercentageReduction = 0.75
+                factorNbPick = 1.0
+                factorWindowSize = 2.0
 
-            darkStainLevel = 0.5
+                darkStainLevel = 0.4 // Lower -> more sensitive.
 
-            stainSigma = 10.
-            stainLevel = 0.9
-            stainSpreadRequired = 3.0
+                stainArea = 0.02
+                stainLevel = 0.2
 
-            infectionSigma = 2.2
-            infectionLevel = 0.85
-            infectionPixelsRequired = 1
+                infectionArea = 0.06
+                infectionLevel = 0.2
+                infectionPixelsRequired = 1
 
-            percentageOfFgValidCell = 0.4
+                maxDarkStainRatio = 0.1
 
-            MaxDarkStainRatio = 0.1
-
-            minimumCellArea = 600. * scale ** 2. |> int
-            maxOffcenter = 0.5 }
+                minimumCellArea = 0.3 })
 
         match mode with
         | CmdLine (input, output) ->
-            let config = { config with debug = DebugOn output }
-            Utils.log <- (fun m -> Console.WriteLine m)
+            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.Create, FileAccess.Write))
+            use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
 
             for file in files do
                 try
-                    let fileInfo = FileInfo(file)
                     use img = new Image<Bgr, byte>(file)
-                    let cells = Utils.logTime "Whole analyze" (fun () -> ImageAnalysis.doAnalysis img fileInfo.Name config)
+                    Utils.log (sprintf "== File: %A" file)
+
+                    let cells = Utils.logTime "Whole analyze" (fun () -> ImageAnalysis.doAnalysis img (Path.GetFileNameWithoutExtension(FileInfo(file).Name)) config)
                     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)
+                | :? 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