Add functions to apply an area opening and to compute granulometry.

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

diff --git a/Parasitemia/Parasitemia/Program.fs b/Parasitemia/Parasitemia/Program.fs
index d7348cf..fdbc908 100644 (file)
--- a/Parasitemia/Parasitemia/Program.fs
+++ b/Parasitemia/Parasitemia/Program.fs
@@ -65,14 +65,14 @@ let main args =
 
             // RBC size range in px at scale = 1.0.
             minRBCSize = 20.
-            maxRBCSize = 40.
+            maxRBCSize = 42.
 
             doGSigma1 = 1.5
-            doGSigma2 = 20.
+            doGSigma2 = 30.
             doGLowFreqPercentageReduction = 0.75
 
-            factorNbPick = 2.0
-            factorWindowSize = 1.6
+            factorNbPick = 1.0
+            factorWindowSize = 2.0
 
             darkStainLevel = 0.4 // Lower -> more sensitive.
 
@@ -88,18 +88,18 @@ let main args =
 
             MaxDarkStainRatio = 0.1
 
-            minimumCellArea = 1200. * scale ** 2. |> int
+            minimumCellArea = 1000. * scale ** 2. |> int
             maxOffcenter = 0.5 }
 
         match mode with
         | CmdLine (input, output) ->
-            let config = { config with debug = DebugOn output }
+            let config = if debug then { config with debug = DebugOn output } else config
 
             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 ]
@@ -111,7 +111,8 @@ let main args =
                 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)
+
+                    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