From 31ff6aa80cd76dea00c62b490d0dc269cd1cc2be Mon Sep 17 00:00:00 2001
From: ctrebeau <ctrebeau@pasteur.fr>
Date: Tue, 22 Oct 2024 17:08:00 +0200
Subject: [PATCH] Bug fix : memory isssue - the function
"factory.create(input)" is replaced by
"factory.create(input.dimensionAsLongArray)" to avoid using too much memory.
---
.../ida/zellige/steps/construction/Interpolation.java | 2 +-
.../steps/projection/ReferenceSurfaceProjection.java | 4 ++--
.../selection/classification/AmplitudeClassification.java | 4 ++--
.../steps/selection/classification/Classification.java | 2 +-
.../selection/classification/OtsuClassification.java | 8 ++++----
.../steps/selection/postTreatment/PostTreatment.java | 2 +-
.../postTreatment/islandSearch/IslandSearch.java | 2 +-
.../steps/selection/pretreatment/Pretreatment.java | 2 +-
.../zellige/steps/selection/util/ExtremaDetection.java | 2 +-
.../zellige/steps/selection/util/ExtremaDetection2D.java | 2 +-
10 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/construction/Interpolation.java b/src/main/java/fr/pasteur/ida/zellige/steps/construction/Interpolation.java
index 78a3590..877defc 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/construction/Interpolation.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/construction/Interpolation.java
@@ -170,7 +170,7 @@ public class Interpolation
private Img< UnsignedShortType > execute( RandomAccessibleInterval< UnsignedShortType > input, int dimension )
{
ImgFactory< UnsignedShortType > factory = new ArrayImgFactory<>( new UnsignedShortType() );
- Img< UnsignedShortType > interpolated = factory.create( input );
+ Img< UnsignedShortType > interpolated = factory.create( input.dimensionsAsLongArray() );
ImgUtil.copy( input, interpolated );
RandomAccess< UnsignedShortType > interpolatedAccess = interpolated.randomAccess();
RandomAccess< UnsignedShortType > zMapAccess = input.randomAccess();
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java b/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java
index a1a88f2..e30c964 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/projection/ReferenceSurfaceProjection.java
@@ -194,7 +194,7 @@ public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T
public static < T extends RealType< T > & NativeType< T > > Img< BitType > getSegmentedSurfaceMask
( IterableInterval< T > segmentedSurface, int delta )
{
- Img< BitType > segmentedSurfaceMask = new ArrayImgFactory<>( new BitType() ).create( segmentedSurface );
+ Img< BitType > segmentedSurfaceMask = new ArrayImgFactory<>( new BitType() ).create( segmentedSurface.dimensionsAsLongArray() );
Cursor< T > surfaceAccess = segmentedSurface.cursor();
RandomAccess< BitType > mapAccess = segmentedSurfaceMask.randomAccess();
while ( surfaceAccess.hasNext() )
@@ -223,7 +223,7 @@ public class ReferenceSurfaceProjection< T extends RealType< T > & NativeType< T
public static < T extends RealType< T > & NativeType< T > > Img< T > getSegmentedSurface
( Img< UnsignedShortType > extractedHeightMap, RandomAccessibleInterval< T > originalInput, ImgFactory< T > factory )
{
- Img< T > segmentedSurface = factory.create( originalInput );
+ Img< T > segmentedSurface = factory.create( originalInput.dimensionsAsLongArray() );
RandomAccess< T > surfaceAccess = segmentedSurface.randomAccess();
RandomAccess< T > inputAccess = originalInput.randomAccess();
Cursor< UnsignedShortType > heightMapCursor = extractedHeightMap.cursor();
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/AmplitudeClassification.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/AmplitudeClassification.java
index ac6e9de..badccd5 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/AmplitudeClassification.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/AmplitudeClassification.java
@@ -82,7 +82,7 @@ public class AmplitudeClassification< T extends RealType< T > & NativeType< T >
final ImgFactory< T > factory, double amplitudeThreshold ) throws DataValidationException
{
long start = System.currentTimeMillis();
- Img< BitType > amplitude = new ArrayImgFactory<>( new BitType() ).create( input );
+ Img< BitType > amplitude = new ArrayImgFactory<>( new BitType() ).create( input.dimensionsAsLongArray() );
AmplitudeClassification< T > classification =
new AmplitudeClassification<>( input, factory, amplitude, amplitudeThreshold );
classification.run();
@@ -132,7 +132,7 @@ public class AmplitudeClassification< T extends RealType< T > & NativeType< T >
private Img< T > getAmplitude(
RandomAccessibleInterval< T > max, ImgFactory< T > factory, RandomAccessibleInterval< T > min )
{
- Img< T > amp = factory.create( max );
+ Img< T > amp = factory.create( max.dimensionsAsLongArray() );
RandomAccess< T > maxAccess = max.randomAccess();
RandomAccess< T > minAccess = min.randomAccess();
RandomAccess< T > ampAccess = amp.randomAccess();
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/Classification.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/Classification.java
index 8934c3b..c16a3a2 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/Classification.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/Classification.java
@@ -153,7 +153,7 @@ public class Classification< T extends RealType< T > & NativeType< T > >
ImgFactory< BitType > factory,
RandomAccessibleInterval< BitType > thresholds )
{
- Img< BitType > output = factory.create( thresholds );
+ Img< BitType > output = factory.create( thresholds.dimensionsAsLongArray() );
Cursor< BitType > amplitudeCursor = amplitude.localizingCursor();
RandomAccess< BitType > thresholdAccess
= thresholds.randomAccess();
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/OtsuClassification.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/OtsuClassification.java
index 15561a8..47ac18f 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/OtsuClassification.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/classification/OtsuClassification.java
@@ -64,7 +64,7 @@ public class OtsuClassification< T extends RealType< T > & NativeType< T > >
this.input = input;
this.output = output;
this.userThreshold = userThreshold;
- this.grid = factory.create( input );
+ this.grid = factory.create( input.dimensionsAsLongArray() );
}
/**
@@ -74,7 +74,7 @@ public class OtsuClassification< T extends RealType< T > & NativeType< T > >
private OtsuClassification( final RandomAccessibleInterval< T > input, final ImgFactory< T > factory )
{
this.input = input;
- this.grid = factory.create( input );
+ this.grid = factory.create( input.dimensionsAsLongArray() );
}
/**
@@ -91,7 +91,7 @@ public class OtsuClassification< T extends RealType< T > & NativeType< T > >
long start = System.currentTimeMillis();
// Prepare output.
final ImgFactory< BitType > bitTypeImgFactory = net.imglib2.util.Util.getArrayOrCellImgFactory( input, new BitType() );
- Img< BitType > binary = bitTypeImgFactory.create( input );
+ Img< BitType > binary = bitTypeImgFactory.create( input.dimensionsAsLongArray() );
OtsuClassification< T > classification = new OtsuClassification<>( input, factory, binary, userThreshold );
classification.run();
long stop = System.currentTimeMillis();
@@ -131,7 +131,7 @@ public class OtsuClassification< T extends RealType< T > & NativeType< T > >
{
long start = System.currentTimeMillis();
final ImgFactory< BitType > bitTypeImgFactory = net.imglib2.util.Util.getArrayOrCellImgFactory( input, new BitType() );
- Img< BitType > output = bitTypeImgFactory.create( input );
+ Img< BitType > output = bitTypeImgFactory.create( input.dimensionsAsLongArray() );
Cursor< T > sourceCursor = input.localizingCursor();
Cursor< T > gridCursor = grid.cursor();
RandomAccess< BitType > randomAccess = output.randomAccess();
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/PostTreatment.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/PostTreatment.java
index a9db304..e5863da 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/PostTreatment.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/PostTreatment.java
@@ -82,7 +82,7 @@ public class PostTreatment
public static Img< FloatType > convertBitTypeIntoFloatType( IterableInterval< BitType > image )
{
final ImgFactory< FloatType > imgFactory = new ArrayImgFactory<>( new FloatType() );
- final Img< FloatType > copy = imgFactory.create( image );
+ final Img< FloatType > copy = imgFactory.create( image.dimensionsAsLongArray() );
Cursor< BitType > bitTypeCursor = image.cursor();
Cursor< FloatType > floatTypeCursor = copy.cursor();
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/islandSearch/IslandSearch.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/islandSearch/IslandSearch.java
index 39d9d09..b0c5b03 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/islandSearch/IslandSearch.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/postTreatment/islandSearch/IslandSearch.java
@@ -79,7 +79,7 @@ public class IslandSearch
{
long start = System.currentTimeMillis();
ImgFactory< BitType > factory = new ArrayImgFactory<>( new BitType() );
- Img< BitType > output = factory.create( classifiedImage );
+ Img< BitType > output = factory.create( classifiedImage.dimensionsAsLongArray() );
ImgUtil.copy( classifiedImage, output );
new IslandSearch( classifiedImage, output, islandSize, connectivityType );
long stop = System.currentTimeMillis();
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 c257cb2..24c51b3 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
@@ -103,7 +103,7 @@ public class Pretreatment< T extends RealType< T > & NativeType< T > >
RandomAccessibleInterval< T > image, ImgFactory< T > factory )
{
LOGGER.debug( "Staring normalization." );
- Img< T > normalizedImage = factory.create( image );
+ Img< T > normalizedImage = factory.create( image.dimensionsAsLongArray() );
ImgUtil.copy( image, normalizedImage );
T min = normalizedImage.firstElement().createVariable();
min.setReal( 0 );
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection.java
index e2a32d5..6d1cd56 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection.java
@@ -59,7 +59,7 @@ public class ExtremaDetection< T extends RealType< T > & NativeType< T > >
parameterCheck( input, factory, type, method );
this.input = input;
this.factory = factory;
- this.extrema = factory.create( input );
+ this.extrema = factory.create( input.dimensionsAsLongArray() );
this.type = type;
LOGGER.debug( "Partial derivative is : {}", method );
}
diff --git a/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection2D.java b/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection2D.java
index 1ae97bb..e4507dc 100644
--- a/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection2D.java
+++ b/src/main/java/fr/pasteur/ida/zellige/steps/selection/util/ExtremaDetection2D.java
@@ -79,7 +79,7 @@ public class ExtremaDetection2D< T extends RealType< T > & NativeType< T > >
{
{
// Output for partial derivative.
- RandomAccessibleInterval< T > sectionDerivative = factory.create( inputSection );
+ RandomAccessibleInterval< T > sectionDerivative = factory.create( inputSection.dimensionsAsLongArray() );
// Partial derivative computation */
Derivative.run( inputSection, sectionDerivative, method );
computeExtrema( inputSection, sectionDerivative );
--
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