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Exception in thread "main" java.lang.NoSuchMethodError: net.imglib2.cache.queue.BlockingFetchQueues.<init>(I)V
at bdv.img.hdf5.Hdf5ImageLoader.open(Hdf5ImageLoader.java:215)
at bdv.img.hdf5.Hdf5ImageLoader.<init>(Hdf5ImageLoader.java:166)
at bdv.img.hdf5.Hdf5ImageLoader.<init>(Hdf5ImageLoader.java:152)
at bdv.img.hdf5.Hdf5ImageLoader.<init>(Hdf5ImageLoader.java:147)
at bdv.img.hdf5.XmlIoHdf5ImageLoader.fromXml(XmlIoHdf5ImageLoader.java:71)
at bdv.img.hdf5.XmlIoHdf5ImageLoader.fromXml(XmlIoHdf5ImageLoader.java:50)
at mpicbg.spim.data.generic.sequence.XmlIoAbstractSequenceDescription.fromXml(XmlIoAbstractSequenceDescription.java:111)
at mpicbg.spim.data.generic.XmlIoAbstractSpimData.fromXml(XmlIoAbstractSpimData.java:153)
at bdv.spimdata.XmlIoSpimDataMinimal.load(XmlIoSpimDataMinimal.java:86)
at bdv.util.ExampleSpimData.main(ExampleSpimData.java:15)
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-core</artifactId>
<version>7.0.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2</artifactId>
<!--<version>5.8.1-SNAPSHOT</version>-->
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2-cache</artifactId>
<version>1.0.0-beta-14-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2-realtransform</artifactId>
<version>2.2.2-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
<artifactId>imglib2-ui</artifactId>
<version>2.0.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>ui-behaviour</artifactId>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
BdvFunctions
: Source
when required and possible according to the functionVolatileViews.wrapAsVolatile
] (BIOP/bigdataviewer-vistools@17eeeaa). There are issues, notably regarding the way the cache is handled I guess. It's working for my use case, but I'd like to hear from you regarding what should be improved. Maybe the whole approach is wrong.SourceAndConverter
can also return a Volatile
version of itself! Given that's the case it seems to me to be the object of choice to work with for multi-resolution image analysis and display in imglib2 land. @hanslovsky Do you see any advantages of using your DataSource
instead? https://github.com/saalfeldlab/paintera/blob/master/src/main/java/org/janelia/saalfeldlab/paintera/data/DataSource.java
to work with for multi-resolution image analysis and display
SourceState< T > extends SourceAndConverter< T >
Bdv
. Currently I am using BigDataServer with bdv.h5 files. This works well, however our IT-department wants to store the data as S3. Is there something useable in terms of n5/S3 for Bdv?
n5-aws-s3
should not be any different than any other N5Reader
or N5Writer
. Maybe n5-spark, n5-utils, n5-imglib2, or the paintera conversion helper have some inspiration for you.
SharedQueue
beeing passed when using VolatileViews.wrapAsVolatile(final RandomAccessibleInterval< T > rai,
final SharedQueue queue,
final CacheHints hints )
and the CacheControl
that I see a bit everywhere when Volatile
type are involved. My main issue is to make a class that makes a VolatileSource
from a non-volatile source (see here), but I don't know how to deal properly with the cache.
bigdataviewer-vistools
which allows for some bdv.viewer.Source
to be wrapped as Volatile. (bigdataviewer/bigdataviewer-vistools#38) Probably not optimal, but I think it exposes a current limitation of BdvFunctions.show(Souce src)
: it does wrap sources that could be wrapped as volatile. I put an example of such limitation being overcomed in this small video : https://www.youtube.com/watch?v=SdngXeEatqA. Maybe it's the wrong way to solve the limitation (exposing the SourceAndConverter is probably more general), but here it is if you want to have a look.
fly.mpi-cbg.de
server?