genericity enforcement

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

@@ -31,7 +31,7 @@ import org.slf4j.LoggerFactory;
 
 import java.util.ArrayList;
 
-import static fr.pasteur.ida.zellige.constructionMethods.pixelSelection.util.Derivative.FORWARD;
+import static fr.pasteur.ida.zellige.constructionMethods.pixelSelection.util.Derivative.CENTRAL;
 
 
 public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T > >
@@ -61,7 +61,8 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
     private int SS_OS_count;
     private int SS_smallSurfaces;
     private int SS_goodSurfaces;
-    private static final String derivativeMethod = FORWARD;
+    private static final String derivativeMethod = CENTRAL;
+
 
     public ReferenceSurfaceExtraction( RandomAccessibleInterval< T > input, ImgFactory< T > factory,
                                        PixelSelectionParameters parameters, ProjectionParameters projectionParameters,
@@ -133,6 +134,7 @@ public class ReferenceSurfaceExtraction< T extends RealType< T > & NativeType< T
         {
 //            displaySurface( surface );
             Img< UnsignedShortType > processedZMap = processedZMap( surface );
+//            ImageJFunctions.show(processedZMap, "process z map "+ index);
             ReferenceSurface< T > referenceSurface = new ReferenceSurface<>( input, factory, processedZMap, index++ );
             referenceSurfaces.add( referenceSurface );
         }

src/test/java/fr/pasteur/ida/zellige/behavior/ParameterSweep.java

@@ -10,7 +10,8 @@ import fr.pasteur.ida.zellige.utils.ZelligePipelineAnalyse;
 import ij.ImageJ;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.Img;
-import net.imglib2.type.numeric.real.FloatType;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
 import org.junit.Ignore;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeAll;
@@ -24,16 +25,15 @@ import java.io.IOException;
 import java.util.ArrayList;
 
 
-public class ParameterSweep
+public class ParameterSweep< T extends RealType< T > & NativeType< T >, R extends RealType< R > & NativeType< R > >
 {
 
     private final static Logger LOGGER = LoggerFactory.getLogger( ParameterSweep.class );
-    static ArrayList< Img< FloatType > > ref;
-    static Img< FloatType > tested;
+    ArrayList< Img< T > > ref;
+    Img< R > tested;
     private static CSVWriter writer;
 
-    @BeforeAll
-    static void init() throws IOException
+    public ParameterSweep() throws IOException
     {
         String imagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\STK_Mouche_c01_f0001_p013.tif";
         final String[] refImagePath = new String[]{
@@ -42,7 +42,7 @@ public class ParameterSweep
                 "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\GT\\Ground truth Height map_3.tif",
                 "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\GT\\Ground truth Height map_4.tif"
         };
-        ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "centralDerivative_noSmooth_STK_Mouche_c01_f0001_p013" );
+        ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "test_mouche" );
         ref = files.getRefs();
         tested = files.getTested();
         writer = new CSVWriter( files.getPath() );
@@ -53,7 +53,31 @@ public class ParameterSweep
                 "FS_good", "FS_small", "FS_finalised",
                 "SS_good", "SS_small", "SS_finalised", "OptimizedSet" };
         writer.writeToFile( header );
-        RMSEAndCoverageComputation.setSubtract( - 1 );
+        RMSEAndCoverageComputation.setSubtract( 0 );
+    }
+
+    @BeforeAll
+    static void init() throws IOException
+    {
+//        String imagePath = "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\STK_Mouche_c01_f0001_p013.tif";
+//        final String[] refImagePath = new String[]{
+//                "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\GT\\Ground truth Height map_1.tif",
+//                "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\GT\\Ground truth Height map_2.tif",
+//                "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\GT\\Ground truth Height map_3.tif",
+//                "C:\\Users\\ctrebeau\\Desktop\\Zellige analysis\\files\\Mouche_c01_f0001_p013\\GT\\Ground truth Height map_4.tif"
+//        };
+//        ParameterSweepFiles files = new ParameterSweepFiles( refImagePath, imagePath, "test_mouche" );
+//        ref = files.getRefs();
+//        tested = files.getTested();
+//        writer = new CSVWriter( files.getPath() );
+//        String[] header = { "Parameter1", "Parameter1Value",
+//                "GroundTruthNb", "SelectedPixelNb", "RMSE", "Coverage", "SelectionPT", "ConstructionPT",
+//                "FS_OS_PT", "FS_surface_PT", "SS_OS_PT", "SS_surface_PT", "Total_PT",
+//                "FS_OS_count", "FS_startingOS_count", "SS_OS_count", "SS_startingOS_count",
+//                "FS_good", "FS_small", "FS_finalised",
+//                "SS_good", "SS_small", "SS_finalised", "OptimizedSet" };
+//        writer.writeToFile( header );
+//        RMSEAndCoverageComputation.setSubtract( 0 );
     }
 
     @AfterAll
@@ -81,7 +105,7 @@ public class ParameterSweep
         double adequacy = 1;
         ReferenceSurfaceExtraction.setAdequacy( adequacy );
         parameters.print();
-        ZelligePipelineAnalyse analyse = new ZelligePipelineAnalyse();
+        ZelligePipelineAnalyse< T, R > analyse = new ZelligePipelineAnalyse();
         analyse.run( parameters, tested, ref );
         for ( RMSEAndCoverageComputation r : analyse.getErrorList() )
         {
@@ -110,7 +134,7 @@ public class ParameterSweep
 
     @Ignore
     @ParameterizedTest
-    @CsvSource( value = "Amplitude;0.2;GaussianBlur;2;0.8;0.1;4;10;5;1;0.7;10;0.8;0.1;10;0.9;YES",
+    @CsvSource( value = "Amplitude;0.2;GaussianBlur;2;0.8;0.1;4;30;5;1;0.7;10;0.8;0.1;10;0.9;YES",
             delimiterString = ";" )
     void parameterSweepSingle( String testedParameter, String testedParameterValue, String filter, int filterParameter,
                                double amplitudeThreshold, double otsuThreshold,
@@ -130,7 +154,7 @@ public class ParameterSweep
         double adequacy = 1;
         ReferenceSurfaceExtraction.setAdequacy( adequacy );
         parameters.print();
-        ZelligePipelineAnalyse analyse = new ZelligePipelineAnalyse();
+        ZelligePipelineAnalyse< T, R > analyse = new ZelligePipelineAnalyse();
         analyse.run( parameters, tested, ref );
         for ( RMSEAndCoverageComputation r : analyse.getErrorList() )
         {