New implementation of maximum amplitude classification and implemention of island search

src/main/java/fr/pasteur/ida/zellige/main/Main.java

@@ -57,10 +57,11 @@ public class Main
 
         // Input of the image.
         final String imagePath =
-//        "doc/STK.tif";
+        "doc/STK.tif";
 //        "C:\\Users\\ctrebeau\\Desktop\\MoucheAile\\STK\\STK_Mouche_c01_f0001_p005.tif";
-        "C:\\Users\\ctrebeau\\Downloads\\phantom3b_combined.tif";
+//        "C:\\Users\\ctrebeau\\Downloads\\phantom3b_combined.tif";
 //                "C:\\Users\\ctrebeau\\Desktop\\HighRes\\STK_170706_Vangl2-Lp-wt_E14.5_Phall_cochlea_01bHighRes_c01_f0001_p005.tif";
+//       "C:\\Users\\ctrebeau\\Desktop\\HighRes\\STK_170706_Vangl2-Lp-wt_E14.5_Phall_cochlea_01bHighRes_c01_f0001_p002.tif";
         System.out.println(imagePath);
         // Creation of the image : version with unsigned type. */
         /* JY version for opening files. */
@@ -72,7 +73,7 @@ public class Main
         /* User Parameters AKA arguments to run the program*/
         double amplitude = Double.parseDouble( args[ 0 ] );
         double otsu = Double.parseDouble( args[ 1 ] );
-        int sigmas = Integer.parseInt( args[ 2 ] );
+        double sigmas = Double.parseDouble( args[ 2 ] );
         int k1 = Integer.parseInt( args[ 3 ] );
         double percent1 = Double.parseDouble( args[ 4 ] );
         int k2 = Integer.parseInt( args[ 5 ] );
@@ -96,7 +97,7 @@ public class Main
         if ( stackImage.numDimensions() == 3 )// Is it a stack ?
         {
             ImageJFunctions.show( stackImage, "original" );
-            ImageJFunctions.show( TestMIP.findMIP( stackImage, stackImage.factory() ), "MIP" );
+//            ImageJFunctions.show( TestMIP.findMIP( stackImage, stackImage.factory() ), "MIP" );
             ReferenceSurfaceExtraction rse = new ReferenceSurfaceExtraction<>( stackImage, stackImage.factory(),userParameters, advancedUserParameters );
             rse.extract();
             rse.project();