Feature : batch mode

src/main/java/fr/pasteur/ida/zellige/utils/test/ZelligePipelineAnalyse.java

@@ -61,69 +61,69 @@ public class ZelligePipelineAnalyse< T extends RealType< T > & NativeType< T >,
     }
 
     @SuppressWarnings( { "unchecked", "rawtypes" } )
-    public void run( final ZParameters parameters, final Img< R > tested, final ArrayList< Img > GT ) throws Exception
-    {
-        long startTime = System.currentTimeMillis();
-        ImgFactory< R > factory = tested.factory();
-
-        extraction = new ReferenceSurfaceExtraction<>();
-        long extractionStartTime = System.currentTimeMillis();
-        extraction.select(tested, parameters.getPretreatmentParameters(), parameters.getClassificationParameters(), parameters.getPostTreatmentParameters() );
-        long extractionStopTime = System.currentTimeMillis();
-        selectionProcessingTime = extractionStopTime - extractionStartTime;
-        LOGGER.debug( "Extraction processing time : {} ms", selectionProcessingTime );
-        selectedPixelNumber = getPixelNumber( extraction.getMaximums() );
-        int index = 0;
-        long stopTime = 0;
-        try
-        {
-            extractionStartTime = System.currentTimeMillis();
-            extraction.construct(tested, factory, parameters.getConstructionParameters() );
-            stopTime = System.currentTimeMillis();
-            constructionProcessingTime = stopTime - extractionStartTime;
-            LOGGER.debug( "Construction processing time : {} ms", constructionProcessingTime );
-            ArrayList< ReferenceSurface< R > > surfaces = extraction.getReferenceSurfaces();
-
-            for ( Img refImage : GT )// Parsing of GT list.
-            {
-                index++;
-                ArrayList< RMSEAndCoverageComputation< T, UnsignedShortType > > tempList = new ArrayList<>();
-                for ( ReferenceSurface< R > rf : surfaces )// Test of each reconstructed surface
-                {
-                    RMSEAndCoverageComputation< T, UnsignedShortType > errors =
-                            new RMSEAndCoverageComputation<>( refImage, index, rf.getzMap() );
-                    errors.compute();
-                    tempList.add( errors );
-                }
-                RMSEAndCoverageComputation< T, UnsignedShortType > finalError = findRightSurface( tempList );
-                this.errorList.add( finalError );
-            }
-        }
-        catch ( NotAnHeightMapException h )
-        {
-            LOGGER.debug( " Exception raised for ref n°{} " , index );
-        }
-
-        catch ( NoSurfaceFoundException s )
-        {
-            stopTime = System.currentTimeMillis();
-            LOGGER.debug( "An NoSurfaceFoundException was raised" );
-            constructionProcessingTime = stopTime - extractionStartTime;
-            for ( int i = 0; i < GT.size(); i++ )
-            {
-                index++;
-                RMSEAndCoverageComputation< T, UnsignedShortType > errors =
-                        new RMSEAndCoverageComputation<>( index );
-                this.errorList.add( errors );
-            }
-            LOGGER.debug( "Construction processing time : {} ms", constructionProcessingTime );
-        }
-        catch ( Exception n )
-        {
-            LOGGER.debug( "An {} was raised", n.getClass() );
-        }
-        this.processingTime = ( stopTime - startTime );
-    }
+//    public void run( final ZParameters parameters, final Img< R > tested, final ArrayList< Img > GT ) throws Exception
+//    {
+//        long startTime = System.currentTimeMillis();
+//        ImgFactory< R > factory = tested.factory();
+//
+//        extraction = new ReferenceSurfaceExtraction<>();
+//        long extractionStartTime = System.currentTimeMillis();
+//        extraction.select(tested, parameters.getPretreatmentParameters(), parameters.getClassificationParameters(), parameters.getPostTreatmentParameters() );
+//        long extractionStopTime = System.currentTimeMillis();
+//        selectionProcessingTime = extractionStopTime - extractionStartTime;
+//        LOGGER.debug( "Extraction processing time : {} ms", selectionProcessingTime );
+//        selectedPixelNumber = getPixelNumber( extraction.getMaximums() );
+//        int index = 0;
+//        long stopTime = 0;
+//        try
+//        {
+//            extractionStartTime = System.currentTimeMillis();
+//            extraction.construct(tested, factory, parameters.getConstructionParameters() );
+//            stopTime = System.currentTimeMillis();
+//            constructionProcessingTime = stopTime - extractionStartTime;
+//            LOGGER.debug( "Construction processing time : {} ms", constructionProcessingTime );
+//            ArrayList< ReferenceSurface< R > > surfaces = extraction.getReferenceSurfaces();
+//
+//            for ( Img refImage : GT )// Parsing of GT list.
+//            {
+//                index++;
+//                ArrayList< RMSEAndCoverageComputation< T, UnsignedShortType > > tempList = new ArrayList<>();
+//                for ( ReferenceSurface< R > rf : surfaces )// Test of each reconstructed surface
+//                {
+//                    RMSEAndCoverageComputation< T, UnsignedShortType > errors =
+//                            new RMSEAndCoverageComputation<>( refImage, index, rf.getzMap() );
+//                    errors.compute();
+//                    tempList.add( errors );
+//                }
+//                RMSEAndCoverageComputation< T, UnsignedShortType > finalError = findRightSurface( tempList );
+//                this.errorList.add( finalError );
+//            }
+//        }
+//        catch ( NotAnHeightMapException h )
+//        {
+//            LOGGER.debug( " Exception raised for ref n°{} " , index );
+//        }
+//
+//        catch ( NoSurfaceFoundException s )
+//        {
+//            stopTime = System.currentTimeMillis();
+//            LOGGER.debug( "An NoSurfaceFoundException was raised" );
+//            constructionProcessingTime = stopTime - extractionStartTime;
+//            for ( int i = 0; i < GT.size(); i++ )
+//            {
+//                index++;
+//                RMSEAndCoverageComputation< T, UnsignedShortType > errors =
+//                        new RMSEAndCoverageComputation<>( index );
+//                this.errorList.add( errors );
+//            }
+//            LOGGER.debug( "Construction processing time : {} ms", constructionProcessingTime );
+//        }
+//        catch ( Exception n )
+//        {
+//            LOGGER.debug( "An {} was raised", n.getClass() );
+//        }
+//        this.processingTime = ( stopTime - startTime );
+//    }
 
     private int getPixelNumber( Img<FloatType> maximumCoordinates )
     {

src/main/resources/fr.pasteur.ida.zellige.gui.view/BatchModeDialog.fxml

@@ -13,12 +13,16 @@
 
     <HBox prefHeight="26.0" prefWidth="399.0" spacing="10">
         <TextField fx:id="filePathField" editable="false" prefWidth="300" />
-        <Button onAction="#handleBrowse" text="Browse" />
+        <Button text="Browse" >
+            <onAction>#handleBrowse</onAction>
+        </Button>
       <padding>
          <Insets left="10.0" right="10.0" />
       </padding>
     </HBox>
 
-    <Button onAction="#handleRun" text="Run" />
+    <Button text="Run" >
+        <onAction>#handleRun</onAction>
+    </Button>
 
 </fx:root>