diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionRound.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionRound.java index 67dbe696254fa424401997d2fd60c43a734610b0..34212160c9a1a4318c281f8e599fa8b6d3f9dbf1 100644 --- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionRound.java +++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ConstructionRound.java @@ -86,7 +86,7 @@ public abstract class ConstructionRound } else { - LOGGER.debug( this.getClass().toGenericString() + " : No Surface Found in {}", this.getClass() ); + LOGGER.debug( "{} : No Surface Found in {}", this.getClass().toGenericString(), this.getClass() ); throw new NoSurfaceFoundException(); } } @@ -98,7 +98,7 @@ public abstract class ConstructionRound */ void mergeSurface( ArrayList< Surface > surfaces ) { - LOGGER.debug( this.getClass().toGenericString() + " : Merging step..." ); + LOGGER.debug( "{} : Merging step...", this.getClass().toGenericString() ); // Merging step. ArrayList< Surface > toRemoved = new ArrayList<>(); for ( int i = surfaces.size() - 1; i > 0; i-- ) @@ -115,7 +115,7 @@ public abstract class ConstructionRound } else { - LOGGER.debug( "Not the same : " + two.overlappingRate( one ) * 10 / 10.00 ); + LOGGER.debug( "Not the same : {}", two.overlappingRate( one ) * 10 / 10.00 ); } } } diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstruction.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstruction.java index f64eee6f5944065cda26e39f069c262eac5f1182..1f83954a3ea9a1424385fafcc11df749d62101aa 100644 --- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstruction.java +++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/rounds/ose/OseConstruction.java @@ -65,7 +65,7 @@ public abstract class OseConstruction oseListArray.set(i, findOSE( maximums[ i ] )); } startingStatus.setStartingStatus(); - LOGGER.debug( "Starting size = " + startingStatus.getStartingSize() ); + LOGGER.debug( "Starting size = {}", startingStatus.getStartingSize() ); LOGGER.debug( "Ose construction complete. All sections processed." ); } diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages.java index 44c7aa8ce8bce9f71deb2aefa767119fb5455d53..1cba1553ebca5cd9be79b2859200bb5673835d36 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages.java @@ -166,8 +166,8 @@ public class HM_black_GT_distanceDisplay_realImages< T extends RealType< T > & N } } } - LOGGER.debug( "GTCount =" + GTCount ); - LOGGER.debug( "HMCount =" + HMCount ); + LOGGER.debug( "GTCount ={}", GTCount ); + LOGGER.debug( "HMCount ={}", HMCount ); } Scatter scatter = new Scatter( points, colors ); scatter.setWidth( 2 ); diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages_2D.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages_2D.java index 397e89a4e00f4b2767eb5a1c8ad33b79bb07565d..50bb84744cfe0dd6d75308df89fe407888eb1c19 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages_2D.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/HM_black_GT_distanceDisplay_realImages_2D.java @@ -165,8 +165,8 @@ public class HM_black_GT_distanceDisplay_realImages_2D< T extends RealType< T > } } } - LOGGER.debug( "GTCount =" + GTCount ); - LOGGER.debug( "HMCount =" + HMCount ); + LOGGER.debug( "GTCount ={}", GTCount ); + LOGGER.debug( "HMCount ={}", HMCount ); } Scatter scatter = new Scatter( points, colors ); scatter.setWidth( 2 ); diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/OSEDisplay.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/OSEDisplay.java index 08efb3e52f1b5b24973d01d359a38e7b47020552..a5f53b7c76df2e5e68ead9104c960151ab480c6e 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/OSEDisplay.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/OSEDisplay.java @@ -87,7 +87,7 @@ public class OSEDisplay extends AbstractAnalysis } Coord3d[] points = new Coord3d[ count ]; Color[] colors = new Color[ count ]; - LOGGER.debug( "count : " + count ); + LOGGER.debug( "count : {}", count ); Random r = new Random(); r.setSeed( 50 ); @@ -108,7 +108,7 @@ public class OSEDisplay extends AbstractAnalysis int z = coordinate.getZ(); if ( z == 6 || z == 7 ) { - LOGGER.debug( osID + " : " + coordinate ); + LOGGER.debug( "{} : {}", osID, coordinate ); } points[ index ] = new Coord3d( x, y, z ); colors[ index ] = Color.BLACK; diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/OSEListDisplay.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/OSEListDisplay.java index 9fda4d804d73e18ccad2aab84f5b2bab935934bb..b5f4be514ba6528c5f08decf8fe310e04511bef8 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/OSEListDisplay.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/OSEListDisplay.java @@ -88,7 +88,7 @@ public class OSEListDisplay extends AbstractAnalysis } Coord3d[] points = new Coord3d[ count ]; Color[] colors = new Color[ count ]; - LOGGER.debug( "count : " + count ); + LOGGER.debug( "count : {}", count ); Random r = new Random(); r.setSeed( 50 ); float x; diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/SurfaceDisplay.java b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/SurfaceDisplay.java index 8ad932615ef78ad3b1f22e8969869d3c46ba3dc6..9b2c0e777fa8ef23221d178eaf0387e5e1ca46b9 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/SurfaceDisplay.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/jzy3D/SurfaceDisplay.java @@ -121,7 +121,7 @@ public class SurfaceDisplay extends AbstractAnalysis } } LOGGER.debug( System.lineSeparator() ); - LOGGER.debug( "Number of duplicate = " + size ); + LOGGER.debug( "Number of duplicate = {}", size ); Scatter scatter = new Scatter( points, colors ); scatter.setWidth( 1 ); chart = AWTChartComponentFactory.chart( Quality.Advanced, "newt" ); diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/test/CSVWriter.java b/src/main/java/fr/pasteur/ida/zellige/utils/test/CSVWriter.java index c4e7d0c778d5a7e65dbc90bd1dd4a3661e78ae01..64bafa9591a18e9881ec3a0e4f292e96b6e4877b 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/test/CSVWriter.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/test/CSVWriter.java @@ -54,7 +54,7 @@ public class CSVWriter try { bw = new BufferedWriter( new FileWriter( csvOutputFile, true ) ); - LOGGER.debug( "CSV location : " + "target/" + testedFileName + EXTENSION ); + LOGGER.debug( "CSV location : target/{}" + EXTENSION, testedFileName ); } catch ( IOException ioException ) { diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/test/RMSEAndCoverageComputation.java b/src/main/java/fr/pasteur/ida/zellige/utils/test/RMSEAndCoverageComputation.java index 6d5d2078eef724d037b8243a0bd534f0b1a15d8f..d46dbff5fd9d582233deed6302d1d77833f6debc 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/test/RMSEAndCoverageComputation.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/test/RMSEAndCoverageComputation.java @@ -217,8 +217,8 @@ public class RMSEAndCoverageComputation< T extends RealType< T > & NativeType< T ImageJFunctions.show( HM ); RMSEAndCoverageComputation< FloatType, FloatType > computation = new RMSEAndCoverageComputation<>( GT, 0, HM ); computation.compute(); - LOGGER.debug( "RMSE = " + computation.RMSE ); - LOGGER.debug( "Coverage = " + computation.coverage ); + LOGGER.debug( "RMSE = {}", computation.RMSE ); + LOGGER.debug( "Coverage = {}", computation.coverage ); } } diff --git a/src/main/java/fr/pasteur/ida/zellige/utils/test/ZParameters.java b/src/main/java/fr/pasteur/ida/zellige/utils/test/ZParameters.java index bd518093b6054c55ae99f205b560f0ae03228d68..a03c18eb2d32237d148830e76b8c52698ef43d79 100644 --- a/src/main/java/fr/pasteur/ida/zellige/utils/test/ZParameters.java +++ b/src/main/java/fr/pasteur/ida/zellige/utils/test/ZParameters.java @@ -96,21 +96,21 @@ public class ZParameters public void print() { - LOGGER.debug( "method : " + pretreatmentParameters.getMethod() ); - LOGGER.debug( "parameter : " + pretreatmentParameters.getRadius() ); - LOGGER.debug( "amplitude : " + classificationParameters.getAmplitudeThreshold() ); - LOGGER.debug( "threshold : " + classificationParameters.getOtsuThreshold() ); - LOGGER.debug( "connexity : " + postTreatmentParameters.getConnexity() ); - LOGGER.debug( "island size : " + postTreatmentParameters.getIslandSize() ); - LOGGER.debug( "sigmaXY : " + postTreatmentParameters.getSigmaXY() ); - LOGGER.debug( "sigmaZ : " + postTreatmentParameters.getSigmaZ() ); - LOGGER.debug( "starting os size1 : " + constructionParameters[ 0 ].getStartingSizeThreshold() ); - LOGGER.debug( "overlap1 :" + constructionParameters[ 0 ].getOverlap() ); - LOGGER.debug( "percent1 :" + constructionParameters[ 0 ].getConnexityRate() ); - LOGGER.debug( "starting os size2 : " + constructionParameters[ 1 ].getStartingSizeThreshold() ); - LOGGER.debug( "overlap2 :" + constructionParameters[ 1 ].getOverlap() ); - LOGGER.debug( "percent2 :" + constructionParameters[ 1 ].getConnexityRate() ); - LOGGER.debug( "adequacy : " + ReferenceSurfaceExtraction.getAdequacy() ); - LOGGER.debug( " Delta : " + projectionParameters.getDelta() ); + LOGGER.debug( "method : {}", pretreatmentParameters.getMethod() ); + LOGGER.debug( "parameter : {}", pretreatmentParameters.getRadius() ); + LOGGER.debug( "amplitude : {}", classificationParameters.getAmplitudeThreshold() ); + LOGGER.debug( "threshold : {}", classificationParameters.getOtsuThreshold() ); + LOGGER.debug( "connexity : {}", postTreatmentParameters.getConnexity() ); + LOGGER.debug( "island size : {}", postTreatmentParameters.getIslandSize() ); + LOGGER.debug( "sigmaXY : {}", postTreatmentParameters.getSigmaXY() ); + LOGGER.debug( "sigmaZ : {}", postTreatmentParameters.getSigmaZ() ); + LOGGER.debug( "starting os size1 : {}", constructionParameters[ 0 ].getStartingSizeThreshold() ); + LOGGER.debug( "overlap1 :{}", constructionParameters[ 0 ].getOverlap() ); + LOGGER.debug( "percent1 :{}", constructionParameters[ 0 ].getConnexityRate() ); + LOGGER.debug( "starting os size2 : {}", constructionParameters[ 1 ].getStartingSizeThreshold() ); + LOGGER.debug( "overlap2 :{}", constructionParameters[ 1 ].getOverlap() ); + LOGGER.debug( "percent2 :{}", constructionParameters[ 1 ].getConnexityRate() ); + LOGGER.debug( "adequacy : {}", ReferenceSurfaceExtraction.getAdequacy() ); + LOGGER.debug( " Delta : {}", projectionParameters.getDelta() ); } } diff --git a/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java b/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java index f6e695779ddcab21292c30c7c8a51cca33e36321..e79dade0611950544a0e8cf6cd4821d5832913b6 100644 --- a/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java +++ b/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java @@ -99,14 +99,14 @@ public class StartingOSESameSurfaceTest ArrayList< AbstractOSE > list2 = findAllStartingOSE( oseLists ); osePartOfSurface.removeAll( list2 ); - LOGGER.debug( "surface starting ose : " + osePartOfSurface.size() ); + LOGGER.debug( "surface starting ose : {}", osePartOfSurface.size() ); TreeMap< Double, Integer > uniqueSurface = new TreeMap<>(); for ( AbstractOSE ose : osePartOfSurface ) { oseLists.reset(); Surface s = SurfaceConstruction.run( oseLists, ose, width, overlap, connexity ); double overlappingRate = overlappingRate( reference, s ); - LOGGER.debug( " This surface has an overlap rate of " + overlappingRate + " with the reference surface" ); + LOGGER.debug( " This surface has an overlap rate of {} with the reference surface", overlappingRate ); Integer j = uniqueSurface.get(overlappingRate); uniqueSurface.put( overlappingRate, ( j == null ) ? 1 : j + 1 ); }