Hdf5 Reader Fiji Source Code

@ctrueden @imagejan @joshmoore

Do you know where the source code for Fiji’s hdf5 reader is?
I could only find the homepage, but no link to the source…

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To find these things in the future… type what you are looking for into the search bar. In this case typing hdf5 should work. Then in the Commands that match, look for “Location”—which here is plugins/HDF5_Vibez-1.0.2.jar as of this writing—as well as the “Source” button which should open your web browser to the source code on GitHub.

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type what you are looking for into the search bar

Wow! Tried it! Worked! Great!

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Are you considering taking up the maintenance of the plugin?

…in fact we had a one day mini-hackathon with a couple of people to see what could be done about hdf5 support in ImageJ / java. I think @joshmoore will soon post something about this here in the forum…

may I ask, why you ask :slight_smile:
are you one of the developers of the plugin?

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Note that @radoslaw.ejsmont is the current maintainer of HDF5_Vibez, if you have any questions or issues with it.

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No, I’m just a humble user who sometimes need to use the plugin and I have had some issues with it in the past. That’s why I’m hoping for someone to start maintaining it again :slight_smile:

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Did @radoslaw.ejsmont take over the sites.imagej.net/Ronneber Update Site, so if I install the plugin via the Updater do I get the vanilla version from Olaf or the github version? Don’t mind, I just checked the site, you will get the old version. I will checkout your github version and overwrite the version from the updater.

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@falk No, he did not. AFAIK @ctrueden is putting new releases from GitHub there. This could change.

@Christian_Tischer cool that you are making a hackathon. Would be really good to integrate HDF5 with scifio - I started working on that, but I recently started my own lab and have more pressing issues. I am happy though to review and accept pull requests that come out of your work!

@BThorsted have you solved the ArrayIndexOutOfBoundsException issue? I could not reproduce it, so it’s quite hard to fix something I cannot take a look at.

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So which update site should I enable to obtain the latest HDF5_Vibez plugin?

Finally I found it. The HDF5 update site and the “U-Net Segmentation” update site shadowed the HDF5_Vibez plugin from the Java8 update site. I removed HDF5_Vibez from the “U-Net segmentation” update site in favor of your version and I will keep the HDF5 update site disabled to avoid shadowing in the future.

I also edited the HDF5 plugin project page to guide others to the maintained version.

Thanks for maintaining the hdf5 plugin!

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The latest HDF5_Vibez is published on the Java-8 update site, as part of Fiji. You should not need to enable any third party update sites to receive it.

Great.

No, I decided to work around the bug by using a different file format. It was not the best solution for me, but it gets the job done. I just realized that my issue might be because I use the hdf5 update site and it might be that I am using a bugged version rather than the latest java-8 version. I will look into this tomorrow.

…in fact we had a one day mini-hackathon with a couple of people to see what could be done about hdf5 support in ImageJ / java. I think @joshmoore will soon post something about this here in the forum… (@Christian_Tischer)

:+1: I’ll start a new thread. From my point of view, what we were hacking on was one-level lower, and so far, focused on writing (multifile) H5 but would eventually include reading as well as support for N5, etc. My interest is in having a library in Java that we trust as much as say libtiff for reading and writing these ndim files. I’d then think that HDF5_Vibez and/or a scifio plugin etc could use that as a common dependency (which may re-raise discussions around the likes of https://github.com/scijava/nar-hdf5)

cool that you are making a hackathon. Would be really good to integrate HDF5 with scifio - I started working on that, but I recently started my own lab and have more pressing issues. I am happy though to review and accept pull requests that come out of your work! (@radoslaw.ejsmont)

Cheers, Radoslaw. Certainly https://github.com/fiji/HDF5_Vibez/pull/4/files#diff-fb86d26ad759026ecd66fad73f45484dR54 looks like a similar effort with the design difference that API methods were restricted to net.imglib2.* rather than ij.*.

~Josh

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