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  • Dec 10 19:40

    bnorthan on master

    Lower DefaultPadInputFFT priori… (compare)

  • Dec 10 14:41

    tinevez on jungle

    Color the table text depending … Fixed bug in Table views preven… Also close table windows when c… and 4 more (compare)

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    tinevez on master-view-table3

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  • Dec 09 15:10

    tinevez on jungle

    Avoid keyboard clashes with BDV… Merge remote-tracking branch 'o… (compare)

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    tinevez on harness-2d

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    tinevez on jungle

    Harness 2D datasets in BDV view… Merge remote-tracking branch 'o… (compare)

  • Dec 05 16:04

    ctrueden on display-priority

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  • Dec 05 07:23
    imagejan commented #368
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    frauzufall closed #368
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    frauzufall on display-priority

    DefaultDisplayService: If multi… Adds test for DefaultDisplaySer… (compare)

  • Dec 03 18:42
    ctrueden commented #368
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  • Dec 03 14:51
    imagejan commented #368
tpietzsch
@tpietzsch
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
Philipp Hanslovsky
@hanslovsky
Yes, @tpietzsch is right. DataSource still requires a converter (which is part of a SourceState (not the same as in BDV) in Paintera).
tpietzsch
@tpietzsch
but in general, yes, if you want something for both display AND analysis, then SourceAndConverter is the thing
@hanslovsky same idea in BDV. BDV's SourceState< T > extends SourceAndConverter< T >
Philipp Hanslovsky
@hanslovsky
:plus1:
Christian "Tischi" Tischer
@tischi

@tpietzsch @hanslovsky Thanks! Sounds great! I could look into

(1) make a way to expose adding SourceAndConverter in the vistools BdvFunctions

unless someone else wants to do it?

@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?
Philipp Hanslovsky
@hanslovsky
John Bogovic
@bogovicj
:+1:
Christian "Tischi" Tischer
@tischi
@hanslovsky @bogovicj Thanks! Do you also have examples that writes a pyramid to n5-s3 from an RandomAccessibleInterval and reads it back, e.g., into a Source (CachedCellImg backed). Or something like that?
John Bogovic
@bogovicj
I don't, but @igorpisarev might
(he's away this week, though, maybe poke again on this topic next week if you haven't already made something work)
Philipp Hanslovsky
@hanslovsky
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.
John Bogovic
@bogovicj
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
Philipp Hanslovsky
@hanslovsky
:plus1:
tpietzsch
@tpietzsch
bdv will soon have export to N5, just needs to be merged
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
Christian "Tischi" Tischer
@tischi
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?
Christian "Tischi" Tischer
@tischi
@bogovicj I guess I wait until Igor is back in case he already has some practical experience with aws-s3. And thanks for the pointers regarding the aws user guide. We would have the data stored locally, so I have to look at this with our IT guys.
NicoKiaru
@NicoKiaru
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.
Christian "Tischi" Tischer
@tischi
Not sure that helps, but for me, when the RandomAccessibleInterval rai is backed by a CachedCellImg it was working fine automagically just using VolatileViews.wrapAsVolatile( rai ) without specifying any of the Queues and CacheHints..
Christian "Tischi" Tischer
@tischi
@hanslovsky @NicoKiaru @bogovicj Does any of you maybe have an idea about this issue? tischi/bdv-utils#2
Christian "Tischi" Tischer
@tischi
@NicoKiaru Thanks for posting in the issue. I think you found the "bug".
NicoKiaru
@NicoKiaru
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 ?
NicoKiaru
@NicoKiaru
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.
Curtis Rueden
@ctrueden
@NicoKiaru Bene knows. He says (via private mail) that server is permanently down, but he is working on restoring it somewhere.
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?
Christian "Tischi" Tischer
@tischi
@NicoKiaru Here is a BigDataServer running, but many images, takes a while: http://cbb-bigdata01.embl.de/0.6.0
NicoKiaru
@NicoKiaru
thanks @tischi and @ctrueden !
Stephan Saalfeld
@axtimwalde
@tomancak @tpietzsch I think fly.mpi-cbg.de is not very alive, can you resurrect it?
(oh, and because there might still be some useful stuff, is it possible to get a copy of my home directory there?)
...probably asking too late...
Igor Pisarev
@igorpisarev
Hi @tischi! I'm back and can help with setting up n5-s3 if you have any questions. As @hanslovsky and @bogovicj suggested, you can use n5-spark to generate multiscale exports using an instance of N5AmazonS3Writer. The best examples would probably be the tests in n5-spark and n5-aws-s3 repositories
Igor Pisarev
@igorpisarev
n5-spark can run either locally or on a cluster, including Amazon's EMR platform (elastic map-reduce) that supports Spark. There is a wiki page in https://github.com/saalfeldlab/n5-spark/wiki that shows how to run a Spark application on AWS
turekg
@turekg
@ctrueden @axtimwalde I never heard of this machine, but I can look into it if you want...
Christian "Tischi" Tischer
@tischi
Hi @igorpisarev, thanks for offering help! Just to get started, do I need a cluster and n5-spark or could I also do it one a single machine for a small test data set?
Stephan Saalfeld
@axtimwalde
@turekg this is the old @tomancak lab application server. It used to run the original CATMAID, some databases maintained by Pavel and Radek, and the personal home-pages of @StephanPreibisch and @axtimwalde
Igor Pisarev
@igorpisarev
@tischi the n5 downsampling code is in n5-spark, but you can run it on your machine. Take a look at n5-spark repo, there are scripts for building the shaded jar and running it on a local machine. When you run locally, Spark emulates the cluster environment by using threads, and it comes as a self-contained maven dependency so you don't need to install anything extra. You can also run it in your IDE by supplying the following JVM variable: -Dspark.master=local[1] that sets the number of threads to use, or -Dspark.master=local[*] for using all cores
Christian "Tischi" Tischer
@tischi
@igorpisarev Check! I will try asap. Thanks again!!
Jan Eglinger
@imagejan
An imglib2-roi question: is it possible to sample (random) points on a sphere by taking some GeomMasks.closedSphere(...).xor(GeomMasks.openSphere(…))? And/or to get a full list of points representing the sphere surface by some Bresenham-like algorithm?
Or is using imglib2-roi for this a bad idea, and I should rather take a math function of a sphere and sample points “manually” ?
(I was thinking in the direction of ImgLib2 Example 4a, but taking a sphere surface instead of the full volume…)
turekg
@turekg
@axtimwalde must be tomancak-srv1. It is not available outside MPI-CBG. I can see CATMAID in /srv/www .
I am due to retire this machine, after moving some stuff over to bds.mpi-cbg.de and archiving the rest. Tell me where I can upload your stuff and I can get a tarball of your dir to you
Stephan Saalfeld
@axtimwalde
oh---that's great
Stephan Preibisch
@StephanPreibisch
@turekg would be great to have this of my directory as well … shouldn’t be too big, maybe just put it on google drive or so? Thank you so much!!
turekg
@turekg
@StephanPreibisch will put in on ownCloud and send you a link. It’s 39G so it will have to wait until @axtimwalde grabs his last directory off it. I’ll let you know when ready