diff --git a/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java b/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java index b0c2fdc5d6c945d72d49f587904f602179b86e40..4bb0426aca7cb5fea923e121521219d93c27e308 100644 --- a/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java +++ b/src/main/java/fr/pasteur/ida/zellige/command/Zellige.java @@ -50,7 +50,7 @@ public class Zellige extends ContextCommand .getPath( "" ) .toAbsolutePath() .toString(); - String imageFilePath = "doc/Mouche.tif"; + String imageFilePath = "doc/Scan1_volume_crop.tif"; // Launch ImageJ. ImageJ ij = new ImageJ(); diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java index 875bcfa28f6db53bcf1fd8b0ac7f8418d36eea2e..d803581738f93fe12bcbc9ce4ff8bfeee3cebdaa 100644 --- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java +++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/pretreatment/Pretreatment.java @@ -77,7 +77,7 @@ public class Pretreatment< T extends RealType< T > & NativeType< T > > LOGGER.debug( "Starting process..." ); try { - Img< T > temp = Binning.binning( input, getBin() ); // Binning op + Img< T > temp = Binning.run( input, getBin() ); // Binning op if (temp == null) { throw new BinningFailedException(); @@ -151,7 +151,7 @@ public class Pretreatment< T extends RealType< T > & NativeType< T > > ImageJFunctions.show( kernel, "original" ); double time1 = System.currentTimeMillis(); int bin = 1; - Img< UnsignedByteType > output = Binning.binning( kernel, bin ); + Img< UnsignedByteType > output = Binning.run( kernel, bin ); double time2 = System.currentTimeMillis(); LOGGER.debug( "Multithreading time = {}s", ( time2 - time1 ) / 1000 ); assert output != null; 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 b3eb2ad0563227b205bd62497e9cdb726b24c260..3a0d83a4b43de4369edea46e4f5feab13f47bb91 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 @@ -58,7 +58,7 @@ public class ZParameters double startingThreshold2, int overlap2, double connexityRate2, double surfaceMinSizeFactor, int delta ) throws DataValidationException { - pretreatmentParameters = new PretreatmentParameters( filter, filterParameter ); + pretreatmentParameters = new PretreatmentParameters( filter, filterParameter, 2); classificationParameters = new ClassificationParameters( amplitudeThreshold, otsuThreshold ); postTreatmentParameters = new PostTreatmentParameters( XYSmoothing, ZSmoothing, ISSize, ISConnexity ); @@ -97,7 +97,7 @@ public class ZParameters public void print() { LOGGER.debug( "method : " + pretreatmentParameters.getMethod() ); - LOGGER.debug( "parameter : " + pretreatmentParameters.getParameter() ); + LOGGER.debug( "parameter : " + pretreatmentParameters.getRadius() ); LOGGER.debug( "amplitude : " + classificationParameters.getAmplitudeThreshold() ); LOGGER.debug( "threshold : " + classificationParameters.getOtsuThreshold() ); LOGGER.debug( "connexity : " + postTreatmentParameters.getConnexity() ); 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 72553f2cf12f7363e5d7bc6499fd75dbe00cae9b..8ec2228443fab09c0535e87d5cb67cf703a75674 100644 --- a/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java +++ b/src/test/java/fr/pasteur/ida/zellige/behavior/StartingOSESameSurfaceTest.java @@ -74,7 +74,7 @@ public class StartingOSESameSurfaceTest double startingSizeThreshold = 0.9; int overlap = 10; double connexity = 0.5; - PretreatmentParameters pretreatmentParameters = new PretreatmentParameters( "GaussianBlur", 2 ); + PretreatmentParameters pretreatmentParameters = new PretreatmentParameters( "GaussianBlur", 2,1 ); ClassificationParameters classificationParameters = new ClassificationParameters( amplitude, otsu ); PostTreatmentParameters postTreatmentParameters = new PostTreatmentParameters( sigmaXY, sigmaZ, 5, 8 ); @@ -83,7 +83,7 @@ public class StartingOSESameSurfaceTest @SuppressWarnings( "unchecked" ) final Img< T > source = ( Img< T > ) imgPlus.getImg(); - Pixels[][] maximums = Selection.run( source, pretreatmentParameters, classificationParameters, postTreatmentParameters ); + Pixels[][] maximums = Selection.run( source, source.factory(), pretreatmentParameters, classificationParameters, postTreatmentParameters ); OSEListArray oseLists = OseConstructionXZ.run( maximums, startingSizeThreshold ); int width = maximums[ 0 ].length; diff --git a/src/test/java/fr/pasteur/ida/zellige/parameters/PretreatmentParametersTest.java b/src/test/java/fr/pasteur/ida/zellige/parameters/PretreatmentParametersTest.java index 843e968ac7eb2918239c126be724479dac2a0f91..8b78c35745dff8544769ab98306b8e546090c0d2 100644 --- a/src/test/java/fr/pasteur/ida/zellige/parameters/PretreatmentParametersTest.java +++ b/src/test/java/fr/pasteur/ida/zellige/parameters/PretreatmentParametersTest.java @@ -50,7 +50,7 @@ public class PretreatmentParametersTest @CsvSource( { GAUSSIAN_BLUR + ", 1" } ) void rightMethodWithRightParameterValue_whenChecked_doesntRaiseAnyException( String method, double value ) { - assertDoesNotThrow( () -> new PretreatmentParameters( method, value ) ); + assertDoesNotThrow( () -> new PretreatmentParameters( method, value,1 ) ); } @DisplayName( "A wrong method should raise DataValidationException for any method" ) @@ -58,7 +58,7 @@ public class PretreatmentParametersTest void wrongDenoisingMethod_whenChecked_RaisesADataValidationException() { DataValidationException exception = assertThrows( DataValidationException.class, () -> - new PretreatmentParameters( "Wrong method", 15 ) ); + new PretreatmentParameters( "Wrong method", 15, 1) ); assertThat( exception ).hasMessageContaining( NOT_IMPLEMENTED ); } @@ -68,7 +68,7 @@ public class PretreatmentParametersTest void gaussianBlurMethodWithLessThanThreeParameter_whenChecked_RaisesAnException( String method ) { double value = - 1; - DataValidationException exception = assertThrows( DataValidationException.class, () -> new PretreatmentParameters( method, value ) ); + DataValidationException exception = assertThrows( DataValidationException.class, () -> new PretreatmentParameters( method, value, 1) ); assertThat( exception ).hasMessageContaining( "parameter value" ); } @@ -77,7 +77,7 @@ public class PretreatmentParametersTest void parameterValueSuperiorTo10_whenChecked_RaisesADataValidationException() { DataValidationException exception = assertThrows( DataValidationException.class, () -> - new PretreatmentParameters( GAUSSIAN_BLUR, 15 ) ); + new PretreatmentParameters( GAUSSIAN_BLUR, 15, 1) ); assertThat( exception ).hasMessageContaining( "parameter value" ); }