From 187ddbeedbc77ccdcd201a76c1c8b53113b8354a Mon Sep 17 00:00:00 2001
From: ctrebeau <ctrebeau@pasteur.fr>
Date: Tue, 12 Nov 2024 11:12:45 +0100
Subject: [PATCH] Bug fix - Avoid NPE when the ImfFactory is a CellIMgFactory
with null reader (https://github.com/scifio/scifio/issues/476)
---
.../zellige/steps/selection/pretreatment/Pretreatment.java | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
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 c373350..c951595 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
@@ -44,6 +44,7 @@ import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.util.ImgUtil;
+import net.imglib2.util.Util;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -134,7 +135,8 @@ public class Pretreatment< T extends RealType< T > & NativeType< T > >
*/
private static < T extends RealType< T > & NativeType< T > > Img< FloatType > gaussianBlurFilterDenoising( RandomAccessibleInterval< T > input, ImgFactory< T > factory, double radius )
{
- ImgFactory< FloatType > newImgFactory = factory.imgFactory( new FloatType() );
+ Dimensions dimensions = new FinalDimensions( input.dimension( 0 ), input.dimension( 1 ), input.dimension( 2 ) );
+ ImgFactory< FloatType > newImgFactory = Util.getArrayOrCellImgFactory(dimensions, new FloatType());
Img< FloatType > output = newImgFactory.create( input.dimensionsAsLongArray() );
Utils.gaussianConvolution_( input, output, new double[]{ radius, radius, 1 } );
return output;
@@ -168,7 +170,7 @@ public class Pretreatment< T extends RealType< T > & NativeType< T > >
}
}
- Img< UnsignedByteType > output_unbinned = Unbinning.run( i, i.factory(), bin );
+ Img< UnsignedByteType > output_unbinned = Unbinning.run( i, bin );
ImageJFunctions.show( output_unbinned, "unbinned 1" );
}
}
--
GitLab