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)
Is it a problem of Java version ? Do you have any idea how I could solve this ?
Simple examples work however
What versions of those are you using?
My forked repo is here actually : https://github.com/BIOP/bigdataviewer-vistools
Ok, like this it works:
<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>
Thanks @hanslovsky !
So I don't know if that's the place to share that, but I've made some modifications on
BdvFunctions: - [a helper class to download and cache datasets for testing] (BIOP/bigdataviewer-vistools@a4e414c)
- [a way to wrap
Sourcewhen 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.
@tpietzsch @NicoKiaru Very interesting that
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
for display, yes
for image analysis probably not, because you will not care about converting to ARGB, and also not about volatile access
for that the non-volatile Source is enough
@hanslovsky same idea in BDV. BDV's
SourceState< T > extends SourceAndConverter< T >
@hanslovsky @bogovicj @tpietzsch Some other topic: I need to serve a TB sized volume EM data set via http, streaming it into
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?
(he's away this week, though, maybe poke again on this topic next week if you haven't already made something work)
Using
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.
yea, but the "other" stuff you do will be more involved (all the aws cli stuff) https://docs.aws.amazon.com/cli/latest/userguide/cli-chap-configure.html#cli-quick-configuration
is it 1 TB or many?
because for many TB, you will probably want to do it on a cluster. And for that @igorpisarev stuff might be perfect
Otherwise, if it is 1TB it might still be possible from Fiji/BDV locally
Awesome that you have done the work for the Bdv! It is 8 TB if you naively load it into RAM, but since there are many black pixels, lossless compressed it is 2.5 TB. @tpietzsch would your code also support export to and reading from n5-aws-s3 or only to the standard file based n5?
I have a hard time understanding the link between the
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.
@hanslovsky @NicoKiaru @bogovicj Does any of you maybe have an idea about this issue? tischi/bdv-utils#2
Hi, http://fly.mpi-cbg.de:8081 do not seem to be alive. Is it temporary ? Is there another bigdataserver that can be used for testing ?
I've just pull a PR in
bigdataviewer-vistools which allows for some bdv.viewer.Sourceto 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.
Oh wait, I am talking about a different server I think. The 3D Viewer docs.
@turekg Do you have power/influence over the
fly.mpi-cbg.de server?