Broken Fiji

[CARL Philippe (LBP)]

Dear (probably) Johannes,

Following a Fiji update I can’t anymore start Fiji with the fiji-win64.exe
(under Windows 7) and get the following error shown up in a window: Could
not find Fiji/Main.

I can of course still launch Fiji using the ImageJ-win64.exe.

Have I done something wrong? Is this an error within the update process or
something else?

I thank you very much in advance for your help.

My best regards,

Philippe

 

Philippe CARL

Laboratoire de Biophotonique et Pharmacologie

UMR 7213 CNRS - Université de Strasbourg

Faculté de Pharmacie

74 route du Rhin

67401 ILLKIRCH

Tel : [phone]

 


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[Richard Fetter]

I also experienced this after the last *update* by Fiji.  I essentially had
to delete the existing installation, download the Win64 version again and
install.

Richard Fetter


On Wed, May 21, 2014 at 8:10 AM, Philippe CARL <[hidden email]>wrote:

> Dear (probably) Johannes,
>
> Following a Fiji update I can’t anymore start Fiji with the fiji-win64.exe
> (under Windows 7) and get the following error shown up in a window: Could
> not find Fiji/Main.
>
> I can of course still launch Fiji using the ImageJ-win64.exe.
>
> Have I done something wrong? Is this an error within the update process or
> something else?
>
> I thank you very much in advance for your help.
>
> My best regards,
>
> Philippe
>
>
>
> Philippe CARL
>
> Laboratoire de Biophotonique et Pharmacologie
>
> UMR 7213 CNRS - Université de Strasbourg
>
> Faculté de Pharmacie
>
> 74 route du Rhin
>
> 67401 ILLKIRCH
>
> Tel : [phone]
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Volker Baecker]

Hello,
I seem to encounter the same problem on Ubuntu 14.04. After the last
update I get the error:

Exception in thread "main" java.lang.NoClassDefFoundError: fiji/Main
Caused by: java.lang.ClassNotFoundException: fiji.Main
...
Could not find fiji/Main

A newly downloaded FIJI works without problems.

Best regards,
Volker

Richard Fetter:

> I also experienced this after the last *update* by Fiji.  I
> essentially had to delete the existing installation, download the
> Win64 version again and install.
>
> Richard Fetter
>
>
> On Wed, May 21, 2014 at 8:10 AM, Philippe CARL
> <[hidden email]>wrote:
>
>> Dear (probably) Johannes,
>>
>> Following a Fiji update I can’t anymore start Fiji with the
>> fiji-win64.exe (under Windows 7) and get the following error
>> shown up in a window: Could not find Fiji/Main.
>>
>> I can of course still launch Fiji using the ImageJ-win64.exe.
>>
>> Have I done something wrong? Is this an error within the update
>> process or something else?
>>
>> I thank you very much in advance for your help.
>>
>> My best regards,
>>
>> Philippe
>>
>>
>>
>> Philippe CARL
>>
>> Laboratoire de Biophotonique et Pharmacologie
>>
>> UMR 7213 CNRS - Université de Strasbourg
>>
>> Faculté de Pharmacie
>>
>> 74 route du Rhin
>>
>> 67401 ILLKIRCH
>>
>> Tel : [phone]
>>
>>
>>
>>
>> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[dscho]

Hi,

On Wed, 21 May 2014, Volker Baecker wrote:

> I seem to encounter the same problem on Ubuntu 14.04. After the last
> update I get the error:
>
> Exception in thread "main" java.lang.NoClassDefFoundError: fiji/Main
> Caused by: java.lang.ClassNotFoundException: fiji.Main
> ...
> Could not find fiji/Main

To be sure, you are running via ImageJ-linux64?

If you are running via fiji-linx64, yes, I forgot to upload a new
ij-launcher.jar (the old one was removed and replaced by
imagej-launcher.jar). You can work around it locally either by using
ImageJ-linux64 instead.

Ciao,
Johannes

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[Volker Baecker]

Hi,
yes I'm running it via fiji-linx64. There is no ImageJ-linux64 in this
installation.
Volker

Johannes Schindelin:

> Hi,
>
> On Wed, 21 May 2014, Volker Baecker wrote:
>
>> I seem to encounter the same problem on Ubuntu 14.04. After the
>> last update I get the error:
>>
>> Exception in thread "main" java.lang.NoClassDefFoundError:
>> fiji/Main Caused by: java.lang.ClassNotFoundException: fiji.Main
>> ... Could not find fiji/Main
>
> To be sure, you are running via ImageJ-linux64?
>
> If you are running via fiji-linx64, yes, I forgot to upload a new
> ij-launcher.jar (the old one was removed and replaced by
> imagej-launcher.jar). You can work around it locally either by
> using ImageJ-linux64 instead.
>
> Ciao, Johannes
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[dscho]

Hi Volker,

On Thu, 22 May 2014, Volker Baecker wrote:

> yes I'm running it via fiji-linx64. There is no ImageJ-linux64 in this
> installation.

Then it is an incomplete installation :-)

Please keep in mind that maintaining two *different* launchers distracts
my time away from more valuable occupations, hence the fiji-* launchers
have been deprecated for over a year now (probably longer, I cannot
quickly look that up on my phone).

In case of a broken installation, you can always download individual files
from the very directory that is the source of the continuous Fiji release:

        http://jenkins.imagej.net/job/Stable-Fiji/ws/Fiji.app/

May I ask you to download ImageJ-linux64 (or ImageJ-linux32) from there,
put it into your Fiji.app/, mark it as executable and use it to start Fiji
from now on?

Ciao,
Johannes

P.S.: Please forgive me for not testing this upgrade with the fiji-*
launchers and making sure to upload a fix before replacing the
ij-launcher.jar with imagej-launcher.jar. As you know, we are really busy
preparing some rather big changes, and I am actually surprised that not
more things broke, as it were... :-)

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[dscho]

Hi Volker,

On Thu, 22 May 2014, Volker Baecker wrote:

> Just for information (ignore if not useful to you):
> When I download ImageJ-linux64 and use it with my older FIJI
> installation, FIJI starts and works, but the updater does not work.

If you find the time, could you please follow the steps described in
http://fiji.sc/Command-Line_Debugging and paste the console log? It should
at least fall back to running the remote updater (the same as if you
called File>Import>URL... and specified http://update.imagej.net/fix.js).

Ciao,
Johannes

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[Volker Baecker]

Hi Johannes,
here is the log.

I ran ./debug. FIJI opens and nothing more happens. I run the updater
from Help>Update Fiji. bootstrap.js is opened in the macro editor. I run
it. A log with the message

org.apache.xpath.XPathContext.<init>(Z)V

is shown.

Volker


Johannes Schindelin:

> Hi Volker,
>
> On Thu, 22 May 2014, Volker Baecker wrote:
>
>> Just for information (ignore if not useful to you):
>> When I download ImageJ-linux64 and use it with my older FIJI
>> installation, FIJI starts and works, but the updater does not work.
>
> If you find the time, could you please follow the steps described in
> http://fiji.sc/Command-Line_Debugging and paste the console log? It should
> at least fall back to running the remote updater (the same as if you
> called File>Import>URL... and specified http://update.imagej.net/fix.js).
>
> Ciao,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[dscho]

Hi Volker,

On Fri, 23 May 2014, Volker Baecker wrote:

> Hi Johannes,
> here is the log.
>
> I ran ./debug. FIJI opens and nothing more happens. I run the updater
> from Help>Update Fiji. bootstrap.js is opened in the macro editor. I run
> it. A log with the message
>
> org.apache.xpath.XPathContext.<init>(Z)V

This looks awfully like http://fiji.sc/bugzilla/show_bug.cgi?id=749. I
fixed it, but you'll need to run the updater to fix the updater ;-)

However, the idea is that you get -- as a last resort -- a window with a
Javascript that you can execute with Ctrl+J, which will load the updater
from a remote set of files (to be precise: it will load a known-good
updater from the files on the update site itself). Have you tried that?

Ciao,
Johannes

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[Volker Baecker]

Hi Johannes,

> This looks awfully like
> http://fiji.sc/bugzilla/show_bug.cgi?id=749. I fixed it, but you'll
> need to run the updater to fix the updater ;-)
>

Yes you're right. After I removed plugins/omero/libs/xalan.jar I could
run the updater. I could then put plugins/omero/libs/xalan.jar back
and everything works including the omero plugin.

> However, the idea is that you get -- as a last resort -- a window
> with a Javascript that you can execute with Ctrl+J, which will load
> the updater from a remote set of files (to be precise: it will load
> a known-good updater from the files on the update site itself).
> Have you tried that?

Yes, the script opened but running it just produced the
error

java.lang.NoSuchMethodError: org.apache.xpath.XPathContext.<init>(Z)V

which it reported in the log window.

Thank you,
Volker
> Ciao, Johannes
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[dscho]

Hi Volker,

On Fri, 23 May 2014, Volker Baecker wrote:

> > This looks awfully like
> > http://fiji.sc/bugzilla/show_bug.cgi?id=749. I fixed it, but you'll
> > need to run the updater to fix the updater ;-)
> >
>
> Yes you're right. After I removed plugins/omero/libs/xalan.jar I could
> run the updater. I could then put plugins/omero/libs/xalan.jar back
> and everything works including the omero plugin.

Good!

> > However, the idea is that you get -- as a last resort -- a window
> > with a Javascript that you can execute with Ctrl+J, which will load
> > the updater from a remote set of files (to be precise: it will load
> > a known-good updater from the files on the update site itself).
> > Have you tried that?
>
> Yes, the script opened but running it just produced the
> error
>
> java.lang.NoSuchMethodError: org.apache.xpath.XPathContext.<init>(Z)V
>
> which it reported in the log window.

Ah, my mistake. I had not yet updated the Javascript to the newest
versions! Will do so later today.

Thank you so much for your valuable feedback,
Johannes

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[Pulceblue]

Hi Johannes,
I just updated my FIJI bundle on my Win7 machine and got exactly the same described here i.e. I can run fiji from the ImageJ launcher but not from the fiji launcher. However, I do not have the omero plugin that you mentioned and that seems to generate the problem.
If I run the debugger I get the following log.Log.txt
I also re-downloaded the fiji-win64.exe file from the file repository you indicated in this thread but I still have the problem.
What happened? How can I get back back to be able to launch fiji using the fiji launcher?
Thanks
Claudio

[Pulceblue]

Hi Johannes,
I just updated my FIJI bundle on my Win7 machine and got exactly the same described here i.e. I can run fiji from the ImageJ launcher but not from the fiji launcher. However, I do not have the omero plugin that you mentioned and that seems to generate the problem.
I also re-downloaded the fiji-win64.exe file from the file repository you indicated in this thread but I still have the problem.
What happened? How can I get back back to be able to launch fiji using the fiji launcher?
Thanks
Claudio

[Pulceblue]

test

[Pulceblue]

Hi Johannes,
I just updated my FIJI bundle on my Win7 machine and got exactly the same described here i.e. I can run fiji from the ImageJ launcher but not from the fiji launcher. However, I do not have the omero plugin that you mentioned and that seems to generate the problem.
I also re-downloaded the fiji-win64.exe file from the file repository you indicated in this thread but I still have the problem.
What happened? How can I get back back to be able to launch fiji using the fiji launcher?
Thanks
Claudio

[dscho]

Hi Claudio,

On Thu, 5 Jun 2014, Pulceblue wrote:

> I just updated my FIJI bundle on my Win7 machine and got exactly the same
> described here i.e. I can run fiji from the ImageJ launcher but not from the
> fiji launcher. However, I do not have the omero plugin that you mentioned
> and that seems to generate the problem.

The Fiji launcher problem was actually not caused by the OMERO libraries
shadowing newer versions of XML libraries, but by the Fiji launcher not
being prepared to work with newer versions of ImageJ2.

I just fixed this, but there is a catch-22: unless you have a working
ImageJ-win64.exe, you will still have to download either ImageJ-win64.exe
or fiji-win64.exe from

        http://jenkins.imagej.net/job/Stable-Fiji/ws/Fiji.app/

> I also re-downloaded the fiji-win64.exe file from the file repository you
> indicated in this thread but I still have the problem.

Yep, I literally *just* got around to fix it.

> What happened? How can I get back back to be able to launch fiji using the
> fiji launcher?

Please keep in mind that the Fiji launcher and the ImageJ launcher are
actually the same. On Windows, there is a minor difference: the icon. But
that is really all: if you are interested in the details, the Jenkins job
http://jenkins.imagej.net/job/Windows-Fiji-launcher-with-icons/ is
responsible to take the latest ImageJ launcher and attach a Fiji icon to
it. It really does nothing else than that. On Linux, the Fiji and ImageJ
launchers are *really* identical. Byte for byte. MacOSX, due to its funny
way to launch applications, has no Fiji launcher at all anymore.

And since I deprecated the Fiji launcher more than two years ago, I really
was surprised to see that some people still use it (the downloadable
packages all ship without the Fiji launcher for quite some time now, but
they include the ImageJ launcher). If I had realized that there are still
some users of the Fiji launcher, I would have made certain to upload new
Fiji launcher versions (made exactly the way I indicated above, but of
course tested well before uploading, hence the delay).

In case you are *really* interested in the details of it all: in
preparation for the ImageJ 2.0.0 release, we renamed quite a bit of
components, cleaning up our software stack. In this process, we made it
not only much, much easier for developers to use only parts of ImageJ and
keep up-to-date with the individual parts' versions, but we also renamed
the image processing specific packages from ij-* to imagej-*. That
includes the support code for the launcher, which comes in the package
imagej-launcher (TAFKA ij-launcher). Now, the old Fiji launcher version
did not expect *not* to find ij-launcher, hence the breakage. The ImageJ
launcher was of course updated and has no such problem: it will work
whether there is an imagej-launcher.jar or an ij-launcher.jar.

Phew, quite a bit of information, right? Short version: your wish is
granted, there is a new, working version of the Fiji launcher.

Ciao,
Johannes

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[Pulceblue]

Hi Johannes,
thanks a lot for this. I downloaded the updated fiji-launcher that works perfectly.
One small thing is still that with the update I made yesterday I seem to have switched to ImageJ 2.0.0-rc-2, which in principle is a good thing since you guys are now moving everything in ImageJ2. However, since then my file open window has changed aspect, but more importantly it does not allow me anymore to navigate my shared folders on the institute servers. I had therefore to rollback to the bundle using "ImageJ 1", the Life-line version.
Do you have more clues about that? How can I provide you more details about the problem?
Thanks
Claudio
 href="Old_file_open_window.png">Old_file_open_window.png 
New_file_open_window.png

[Mark Hiner-2]

Hi Claudio,

 We actually put an option in so users that had problems with IJ2 handling
the image opening could disable the functionality if needed. The option
should have popped up the first time you ran Fiji after updating (along
with a "Welcome to ImageJ2" dialog).. so please let us know if it didn't!

 Anyway I think we didn't do a sufficient job of explaining when this
functionality should be disabled, so I filed a ticket
<https://github.com/imagej/imagej-legacy/issues/38>to re-evaluate how we're
presenting the toggle.

In the mean time, if you have an up-to-date Fiji, you can run "Edit >
Options > ImageJ2" and uncheck "Use SCIFIO when opening files". This will
cause Fiji to go back to ImageJ 1.x for File > Open, and  similar
operations.

Even with this option disabled, you can still use ImageJ2 to open files via
"File > Import > Image...".

Hope that helps!
- Mark

P.S. I just updated Fiji on a windows machine and noticed that the "Welcome
to ImageJ2" dialog didn't appear, although the "Use SCIFIO when opening
files" option did.. so there may be a problem with our welcome message on
Windows. So, an issue <https://github.com/imagej/imagej-legacy/issues/39>
for that as well.


On Fri, Jun 6, 2014 at 5:45 AM, Pulceblue <[hidden email]>
wrote:

> Hi Johannes,
> thanks a lot for this. I downloaded the updated fiji-launcher that works
> perfectly.
> One small thing is still that with the update I made yesterday I seem to
> have switched to ImageJ 2.0.0-rc-2, which in principle is a good thing
> since
> you guys are now moving everything in ImageJ2. However, since then my file
> open window has changed aspect, but more importantly it does not allow me
> anymore to navigate my shared folders on the institute servers. I had
> therefore to rollback to the bundle using "ImageJ 1", the Life-line
> version.
> Do you have more clues about that? How can I provide you more details about
> the problem?
> Thanks
> Claudio
>  href="Old_file_open_window.png">Old_file_open_window.png
> New_file_open_window.png
> <http://imagej.1557.x6.nabble.com/file/n5008067/New_file_open_window.png>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Broken-Fiji-tp5007825p5008067.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[dscho]

Hi Mark,

On Fri, 6 Jun 2014, Mark Hiner wrote:

>  We actually put an option in so users that had problems with IJ2 handling
> the image opening could disable the functionality if needed. The option
> should have popped up the first time you ran Fiji after updating (along
> with a "Welcome to ImageJ2" dialog).. so please let us know if it didn't!

I actually messed up: the welcome message was never picked up by the
updater and hence never transmitted to users.

Fixing this right now.

Ciao,
Dscho

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[Pulceblue]

Hi Mark and Johannes,
thanks a lot for your replies. I solved the issue with the file open window with the solution suggested by mark. I also re-updated FIJI hoping to see the welcome message (which has been downloaded as I saw it in the list of updated files) but when I launch FIJI it doesn't appear. Just to let you know.
Once again thanks for your valuable help!
Claudio