From b734bbeca7108e4b99d2986d6d4adf8eba60ef99 Mon Sep 17 00:00:00 2001
From: ctrebeau <ctrebeau@pasteur.fr>
Date: Tue, 19 Nov 2024 14:39:03 +0100
Subject: [PATCH] feature : Binning - testing parameters
---
src/main/java/fr/pasteur/ida/zellige/command/Zellige.java | 2 +-
.../steps/selection/pretreatment/Pretreatment.java | 4 ++--
.../fr/pasteur/ida/zellige/utils/test/ZParameters.java | 4 ++--
.../ida/zellige/behavior/StartingOSESameSurfaceTest.java | 4 ++--
.../zellige/parameters/PretreatmentParametersTest.java | 8 ++++----
5 files changed, 11 insertions(+), 11 deletions(-)
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 b0c2fdc..4bb0426 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 875bcfa..d803581 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 b3eb2ad..3a0d83a 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 72553f2..8ec2228 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 843e968..8b78c35 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" );
}
--
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