Bug 1609549 - Update ImageJ to v1.53a
Summary: Update ImageJ to v1.53a
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: imagej
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Ben Beasley
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2018-07-29 10:13 UTC by Alexander Ploumistos
Modified: 2022-06-09 12:24 UTC (History)
4 users (show)

Fixed In Version: imagej-1.53r-1.fc37 imagej-1.53r-3.fc36 imagej-1.53r-3.fc35
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2022-05-31 11:16:41 UTC
Type: Bug
Embargoed:


Attachments (Terms of Use)

Description Alexander Ploumistos 2018-07-29 10:13:42 UTC
Hello Adam,

Would it be possible to update ImageJ to the latest version? There have been quite a few bugfixes and new features introduced since 1.50h.

Best regards
Alex

Comment 1 Ben Cotton 2019-05-02 19:22:07 UTC
This message is a reminder that Fedora 28 is nearing its end of life.
On 2019-May-28 Fedora will stop maintaining and issuing updates for
Fedora 28. It is Fedora's policy to close all bug reports from releases
that are no longer maintained. At that time this bug will be closed as
EOL if it remains open with a Fedora 'version' of '28'.

Package Maintainer: If you wish for this bug to remain open because you
plan to fix it in a currently maintained version, simply change the 'version' 
to a later Fedora version.

Thank you for reporting this issue and we are sorry that we were not 
able to fix it before Fedora 28 is end of life. If you would still like 
to see this bug fixed and are able to reproduce it against a later version 
of Fedora, you are encouraged  change the 'version' to a later Fedora 
version prior this bug is closed as described in the policy above.

Although we aim to fix as many bugs as possible during every release's 
lifetime, sometimes those efforts are overtaken by events. Often a 
more recent Fedora release includes newer upstream software that fixes 
bugs or makes them obsolete.

Comment 2 Ben Cotton 2019-05-02 21:14:45 UTC
This message is a reminder that Fedora 28 is nearing its end of life.
On 2019-May-28 Fedora will stop maintaining and issuing updates for
Fedora 28. It is Fedora's policy to close all bug reports from releases
that are no longer maintained. At that time this bug will be closed as
EOL if it remains open with a Fedora 'version' of '28'.

Package Maintainer: If you wish for this bug to remain open because you
plan to fix it in a currently maintained version, simply change the 'version' 
to a later Fedora version.

Thank you for reporting this issue and we are sorry that we were not 
able to fix it before Fedora 28 is end of life. If you would still like 
to see this bug fixed and are able to reproduce it against a later version 
of Fedora, you are encouraged  change the 'version' to a later Fedora 
version prior this bug is closed as described in the policy above.

Although we aim to fix as many bugs as possible during every release's 
lifetime, sometimes those efforts are overtaken by events. Often a 
more recent Fedora release includes newer upstream software that fixes 
bugs or makes them obsolete.

Comment 3 Ben Cotton 2019-05-28 21:59:02 UTC
Fedora 28 changed to end-of-life (EOL) status on 2019-05-28. Fedora 28 is
no longer maintained, which means that it will not receive any further
security or bug fix updates. As a result we are closing this bug.

If you can reproduce this bug against a currently maintained version of
Fedora please feel free to reopen this bug against that version. If you
are unable to reopen this bug, please file a new report against the
current release. If you experience problems, please add a comment to this
bug.

Thank you for reporting this bug and we are sorry it could not be fixed.

Comment 4 Alexander Ploumistos 2019-05-29 07:09:03 UTC
Given the recent java package mayhem and the upstream transition to newer java versions, I do not suppose the update is trivial, but I'm reopening the bug to keep track of things.

Comment 5 Ankur Sinha (FranciscoD) 2020-04-03 11:01:46 UTC
Adam, Alexander: ImageJ is quite important in neuroscience related image processing. What can the NeuroFedora SIG do to help here?

(Yes, the Java situation is a tough one, we have other packages stuck because of gradle and so on too :/)

Comment 6 Ankur Sinha (FranciscoD) 2020-04-22 21:18:08 UTC
Hello, any updates here please? Has anyone had a chance to take a look at how much work this may be? Is this gradle based, or maven, for instance?

Comment 7 Ankur Sinha (FranciscoD) 2020-05-11 09:13:42 UTC
Hello, ping: any updates here please?

Comment 8 Alexander Ploumistos 2020-05-11 11:07:55 UTC
(In reply to Ankur Sinha (FranciscoD) from comment #7)
> Hello, ping: any updates here please?

I for one don't have any.

I've been using the Fiji package and it lists the current version of ImageJ as 1.52p - I think there was an update a few days ago.

Comment 9 Ankur Sinha (FranciscoD) 2020-05-11 12:19:22 UTC
Hrm, that's odd. There are no commits here:
https://src.fedoraproject.org/rpms/imagej/commits/master

Are you sure this is from the Fedora repositories? I still get 1.52h from the repositories:
imagej-1.50-9.h.fc32.noarch


And it doesn't seem to run here:

$ imagej 

Image display and analysis program. Opens formats including:
UNC, Analyze, Dicom, NIFTI, Tiff, Jpeg, Gif, PNG ...

imagej [options] image [ image2 ... image3 ]
    -h        print help and more options
    -o        open images in an open ImageJ panel
    -p <N>    open images in ImageJ panel number <N>
    -x <MB>   set available memory (default=768 max=15748)

Open other images in this ImageJ panel as follows:
  imagej -p 1 <image1> [<image2> ... <imageN>]

Unrecognized option: -d64
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.


Looks like the java command line arguments need to be updated.


Also, looks like 1.53a is now available:
https://imagej.nih.gov/ij/download/src/

I'll update the bug report.

Comment 10 Alexander Ploumistos 2020-05-11 12:29:36 UTC
(In reply to Ankur Sinha (FranciscoD) from comment #9)
> Hrm, that's odd. There are no commits here:
> https://src.fedoraproject.org/rpms/imagej/commits/master
> 
> Are you sure this is from the Fedora repositories? I still get 1.52h from
> the repositories:
> imagej-1.50-9.h.fc32.noarch

No, it's not, I was referring to the Fiji package from upstream:
https://imagej.net/Fiji

Comment 11 Ankur Sinha (FranciscoD) 2020-06-07 10:39:13 UTC
Adam, any updates here please? You've not responded to this since 2018, but I see from fedmsg that you are not inactive.

If you're not actively maintaining the package, could you please give the neuro-sig admin permissions on the repo so we can maintain it? The Java SIG has been reformed, so we may be able to do some work on java packages in the future.

Comment 12 Ben Cotton 2020-08-11 13:05:11 UTC
This bug appears to have been reported against 'rawhide' during the Fedora 33 development cycle.
Changing version to 33.

Comment 13 Ankur Sinha (FranciscoD) 2020-08-17 09:33:51 UTC
Bumping to rawhide. Adam, ping again---any comments here?

Comment 14 Adam Huffman 2020-08-19 10:13:27 UTC
Hi Ankur,

Yes, happy to give neuro-sig permissions here.

Comment 15 Adam Huffman 2020-08-20 08:22:24 UTC
Ankur,

Just checked and it looks like someone else has already given admin rights to neuro-sig?

Comment 16 Ankur Sinha (FranciscoD) 2020-08-20 08:57:48 UTC
Hi Adam,

Thanks for your replies. 

Not sure how the neuro-sig already has admin access now. I was waiting to confirm with you before making any changes.

Imagej, the current version, seems to be building fine for F33 at the moment, so there's nothing urgent that needs to be done here. I'll look at updating it to the new version and will open a PR when that's ready. I do hope the new version won't pull in new java deps. We're having a hard time with a lot of them.

Thanks again,
Ankur

Comment 17 Ben Cotton 2021-02-09 15:06:26 UTC
This bug appears to have been reported against 'rawhide' during the Fedora 34 development cycle.
Changing version to 34.

Comment 18 Ben Cotton 2022-02-08 20:24:30 UTC
This bug appears to have been reported against 'rawhide' during the Fedora 36 development cycle.
Changing version to 36.

Comment 20 Fedora Update System 2022-05-30 20:57:13 UTC
FEDORA-2022-055007802a has been submitted as an update to Fedora 37. https://bodhi.fedoraproject.org/updates/FEDORA-2022-055007802a

Comment 21 Ben Beasley 2022-05-30 20:59:03 UTC
(In reply to Fedora Update System from comment #20)
> FEDORA-2022-055007802a has been submitted as an update to Fedora 37.
> https://bodhi.fedoraproject.org/updates/FEDORA-2022-055007802a

Sorry, pasted the wrong RHBZ# into that python-hatchling update. The PR is still open.

Comment 22 Fedora Update System 2022-05-30 21:04:27 UTC
FEDORA-2022-055007802a has been pushed to the Fedora 37 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 23 Alexander Ploumistos 2022-05-30 23:07:19 UTC
Hi Ben,

I am reopening the bug because it was automatically closed by the wrong update.

I took a look at the PR and while Java is not my thing, everything looks good, you did quite some work there.

There's no point in waiting to merge, I think everyone will be happy to see ImageJ properly maintained again.

Comment 24 Ankur Sinha (FranciscoD) 2022-05-31 07:51:43 UTC
I also want to note it here in the bug:

We are looking for co-maintainers to maintain the ImageJ package in Fedora. Ben has updated it as part of the neuro-sig, but the neuro-sig maintains ~200 packages and will not always be able to prioritise package updates over FTBFS/FTI (fails to build from source/fails to install) bugs. So, the best way to keep ImageJ (and all packages really) up to date is to have move dedicated co-maintainers looking after it---ideally people who use the tool and so have a strong incentive to look after it.

If anyone would like to help here, please let us know. We're happy to sponsor you to the package maintainers group as a co-maintainer and neuro-sig member, and we will be very very happy to help you learn the packaging pipeline and so on.

Cheers,

Comment 25 Ankur Sinha (FranciscoD) 2022-05-31 08:46:04 UTC
(In reply to Alexander Ploumistos from comment #23)
> Hi Ben,
> 
> I am reopening the bug because it was automatically closed by the wrong
> update.
> 
> I took a look at the PR and while Java is not my thing, everything looks
> good, you did quite some work there.
> 
> There's no point in waiting to merge, I think everyone will be happy to see
> ImageJ properly maintained again.

Hi Alexander (and other ImageJ users),

If you use ImageJ, would you be able to please test the build to see if it works OK?

Here are test builds for:

F35: https://koji.fedoraproject.org/koji/taskinfo?taskID=87721441
F36: https://koji.fedoraproject.org/koji/taskinfo?taskID=87721442

Thanks,

Comment 26 Ben Beasley 2022-05-31 11:08:33 UTC
I’m going to go ahead and merge the PR. If there are any issues that I didn’t find, hopefully they can be detected while the updates are in updates-testing.

Comment 27 Fedora Update System 2022-05-31 11:14:49 UTC
FEDORA-2022-10f197db3e has been submitted as an update to Fedora 37. https://bodhi.fedoraproject.org/updates/FEDORA-2022-10f197db3e

Comment 28 Fedora Update System 2022-05-31 11:16:41 UTC
FEDORA-2022-10f197db3e has been pushed to the Fedora 37 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 29 Fedora Update System 2022-05-31 11:37:51 UTC
FEDORA-2022-afbc5a5a95 has been submitted as an update to Fedora 36. https://bodhi.fedoraproject.org/updates/FEDORA-2022-afbc5a5a95

Comment 30 Fedora Update System 2022-05-31 12:02:55 UTC
FEDORA-2022-29b591a5b9 has been submitted as an update to Fedora 35. https://bodhi.fedoraproject.org/updates/FEDORA-2022-29b591a5b9

Comment 31 Alexander Ploumistos 2022-05-31 13:20:25 UTC
I have all of my TEM images as Digital Micrograph files (.dm3) and neither this build or the current stable one can open them (I'm on F36). I get two error messages, the first one saying "Unsupported format or file not found:" along with the full path to the file and then a second message "Format not supported or reader plugin not found:" and the file name. 

The source package contains the DM3_Reader.class and DM3_Reader.java files, which are supposedly required in order to open dm3 files, but I tried copying them to ~/.imagej/plugins/ and /usr/share/imagej/plugins/ and I still wasn't able to open the files. Interestingly, the fiji distribution doesn't have these plugins (I searched with zipgrep in all the .jar files) but it does open them. I suspect the capability has been either integrated into ImageJ2 or into one of the other accompanying libraries.

It has been almost four years and I really do not remember how I got it working then, sorry…

All of the functions I tried seemed to work without any problems when editing regular images (tested with png, jpeg and tiff).

Comment 32 Ben Beasley 2022-05-31 13:51:26 UTC
(In reply to Alexander Ploumistos from comment #31)

> The source package contains the DM3_Reader.class and DM3_Reader.java files,
> which are supposedly required in order to open dm3 files, but I tried
> copying them to ~/.imagej/plugins/ and /usr/share/imagej/plugins/ and I
> still wasn't able to open the files.

Which source package are you looking at? There are no DM3_Reader.* files in the zip files at https://imagej.nih.gov/ij/download/src/, which the Fedora package uses.

It looks like all of the plugins (and there seem to be a ton of them! [1]) are distributed individually and separately from the main ImageJ program. I think the one you are using is the “Gatan DM3 Reader”[2].

[1] https://imagej.nih.gov/ij/plugins/index.html
[2] https://imagej.nih.gov/ij/plugins/DM3_Reader.html

I tried the following:

- Download DM3_Reader.java from https://imagej.nih.gov/ij/plugins/download/DM3_Reader.java
- Open ImageJ (here using the updated package)
- Select Plugins → Install… and pick the downloaded DM3_Reader.java file
- The next picker opens ~/.imagej/plugins; I click “Save”
- Now a “Load DM3 File…” dialog opens, provided by the plugin – I click Cancel, because I don’t have any DM3 files.
- Now “DM3 Reader” appears at the bottom of the “Plugins” menu.

I *think* this is all how it is supposed to work. Does the above process work for you?

Comment 33 Ben Beasley 2022-05-31 13:51:56 UTC
I did find that the patched launcher script is now accidentally creating broken symlinks called “*” in ~/.imagej/plugins and ~/.imagej/luts. That’s harmless, but a regression, and I’ll fix it shortly.

Comment 34 Alexander Ploumistos 2022-05-31 14:09:17 UTC
(In reply to Ben Beasley from comment #32)
> (In reply to Alexander Ploumistos from comment #31)
> 
> > The source package contains the DM3_Reader.class and DM3_Reader.java files,
> > which are supposedly required in order to open dm3 files, but I tried
> > copying them to ~/.imagej/plugins/ and /usr/share/imagej/plugins/ and I
> > still wasn't able to open the files.
> 
> Which source package are you looking at? There are no DM3_Reader.* files in
> the zip files at https://imagej.nih.gov/ij/download/src/, which the Fedora
> package uses.

My bad, I meant their binary package, ij153-linux64-java8.zip.


> I tried the following:
> 
> - Download DM3_Reader.java from
> https://imagej.nih.gov/ij/plugins/download/DM3_Reader.java
> - Open ImageJ (here using the updated package)
> - Select Plugins → Install… and pick the downloaded DM3_Reader.java file
> - The next picker opens ~/.imagej/plugins; I click “Save”
> - Now a “Load DM3 File…” dialog opens, provided by the plugin – I click
> Cancel, because I don’t have any DM3 files.
> - Now “DM3 Reader” appears at the bottom of the “Plugins” menu.
> 
> I *think* this is all how it is supposed to work. Does the above process
> work for you?

Yes, it does. Their instructions need some dusting off I guess. However, I am *almost* certain that's not what I used to do. Oh well.

If you need any sample files for testing, just let me know.


Thanks a lot!

Comment 35 Fedora Update System 2022-06-01 02:29:21 UTC
FEDORA-2022-afbc5a5a95 has been pushed to the Fedora 36 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2022-afbc5a5a95`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-afbc5a5a95

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 36 Fedora Update System 2022-06-01 02:42:45 UTC
FEDORA-2022-29b591a5b9 has been pushed to the Fedora 35 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2022-29b591a5b9`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-29b591a5b9

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 37 Ben Beasley 2022-06-01 22:11:39 UTC
Updated with new builds to fix the “*” symlink regression mentioned above, and to fix the self-reported version number[1].

[1] https://bodhi.fedoraproject.org/updates/FEDORA-2022-afbc5a5a95#comment-2551654

Comment 38 Fedora Update System 2022-06-09 01:05:00 UTC
FEDORA-2022-afbc5a5a95 has been pushed to the Fedora 36 stable repository.
If problem still persists, please make note of it in this bug report.

Comment 39 Fedora Update System 2022-06-09 12:24:19 UTC
FEDORA-2022-29b591a5b9 has been pushed to the Fedora 35 stable repository.
If problem still persists, please make note of it in this bug report.


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