FIJI woes

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FIJI woes

Kenneth Sloan-3
First - this may be a FIJI question rather than an ImageJ question.  If so - I’m hoping someone will step up and re-direct me to a more appropriate forum.

I’m having continuous, long-standing problems with FIJI crashing (usually on opening an image - any image).
I have worked around this by doing development in a plain, vanilla ImageJ environment.  The .jar files I generate work fine for me in ImageJ, and work fine for my customers using FIJI.  But, FIJI on my machine is wedged.

In about 2 weeks, I will be at a point where I can completely uninstall FIJI and ImageJ, and re-install FIJI.  I may have to do the same thing with Java (I keep hearing about the need to be compatible - my build scripts specify a target of 1.6, but I’m ready to try anything).

This is all on a Mac Book Pro, with all updates to OS, etc. applied.
I use “ant” to compile and build .jar files, specifying Java 1.6 as the target.
“ant” is also used (on a virtual WinDoze machine) to build Windows .jar files, but
I don’t actually run ImageJ or FIJI on the WinDoze development machine.
I drag&drop .jar files into ImageJ and all is well.
My customers drag&drop .jar files into FIJI and all is well (for them).
For me…FIJI is wedged.  It seems to crash when loading any image file.

I would appreciate guidance on how to:

a) remove all traces of ImageJ and FIJI and Java from this machine
        (I’ll create backup copies, but I hope to *not* re-use anything
         that might be hanging around and can’t be re-generated from source)
b) re-install the appropriate level of Java
c) re-install the appropriate level of FIJI
d) perhaps re-install the appropriate level of a stand-alone ImageJ
         (but, I’d prefer to avoid this complication)

A generic answer to the list is appropriate, but I anticipate some off-list communication to deal with nitty-gritty details.

[note: “ant” might not be my first choice - but I’m supporting about 10 plugins that now work by simply editing the .java files and “pushing the button” - so I’m loathe to mess with that - especially since I don’t really understand all the “ant” incantations.  And, I doubt it’s the source of any of my problems.  So…please don’t suggest a better development environment.  I’m happy with emacs and ant, for now.]

Maybe I should just buy a new machine, and start over...

--
Kenneth Sloan
[hidden email] <mailto:[hidden email]>
Vision is the art of seeing what is invisible to others.





--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: FIJI woes

ctrueden
Hi Ken,

> First - this may be a FIJI question rather than an ImageJ question.
> If so - I’m hoping someone will step up and re-direct me to a more
> appropriate forum.

Questions about Fiji here are fine. But I would personally recommend using
the ImageJ Forum at http://forum.imagej.net/ since it is a better
communication medium with many active and helpful community members.

> I’m having continuous, long-standing problems with FIJI crashing
> (usually on opening an image - any image).

See this troubleshooting entry:

  https://imagej.net/Troubleshooting#If_ImageJ_crashes

> remove all traces of ImageJ and FIJI and Java from this machine

Here is a script which reports all the Java installations on your machine:

  https://github.com/ctrueden/ctr-scripts/blob/master/java-info

On macOS, you can rm -rf the installations if you really want to get rid of
them. But I don't think deleting everything is your best bet to
troubleshoot this.

Same for ImageJ and Fiji: you can directly delete the respective
application folders. Note that Fiji is not "installed" per se—there is just
a Fiji.app on your machine, typically (but not necessarily) in
/Applications. It is fine to have multiple copies of ImageJ and/or Fiji.

Try downloading a fresh Fiji from http://fiji.sc#download, double-click the
.dmg, drag the icon to your Desktop, and run from there via the CLI with
the invocation:

  ~/Desktop/Fiji.app/Contents/MacOS/ImageJ-macosx

You can override which version of Java is used via the --java-home option
as described here:

  https://imagej.net/Frequently_Asked_Questions#How_do_I_
launch_ImageJ_with_a_different_version_of_Java.3F

Note that the current download of Fiji requires Java 8. You can download an
old version of Fiji that still works with Java 6 from here:

  https://imagej.net/Fiji/Downloads#Java_6

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Mon, Oct 23, 2017 at 9:42 AM, Kenneth Sloan <[hidden email]>
wrote:

> First - this may be a FIJI question rather than an ImageJ question.  If so
> - I’m hoping someone will step up and re-direct me to a more appropriate
> forum.
>
> I’m having continuous, long-standing problems with FIJI crashing (usually
> on opening an image - any image).
> I have worked around this by doing development in a plain, vanilla ImageJ
> environment.  The .jar files I generate work fine for me in ImageJ, and
> work fine for my customers using FIJI.  But, FIJI on my machine is wedged.
>
> In about 2 weeks, I will be at a point where I can completely uninstall
> FIJI and ImageJ, and re-install FIJI.  I may have to do the same thing with
> Java (I keep hearing about the need to be compatible - my build scripts
> specify a target of 1.6, but I’m ready to try anything).
>
> This is all on a Mac Book Pro, with all updates to OS, etc. applied.
> I use “ant” to compile and build .jar files, specifying Java 1.6 as the
> target.
> “ant” is also used (on a virtual WinDoze machine) to build Windows .jar
> files, but
> I don’t actually run ImageJ or FIJI on the WinDoze development machine.
> I drag&drop .jar files into ImageJ and all is well.
> My customers drag&drop .jar files into FIJI and all is well (for them).
> For me…FIJI is wedged.  It seems to crash when loading any image file.
>
> I would appreciate guidance on how to:
>
> a) remove all traces of ImageJ and FIJI and Java from this machine
>         (I’ll create backup copies, but I hope to *not* re-use anything
>          that might be hanging around and can’t be re-generated from
> source)
> b) re-install the appropriate level of Java
> c) re-install the appropriate level of FIJI
> d) perhaps re-install the appropriate level of a stand-alone ImageJ
>          (but, I’d prefer to avoid this complication)
>
> A generic answer to the list is appropriate, but I anticipate some
> off-list communication to deal with nitty-gritty details.
>
> [note: “ant” might not be my first choice - but I’m supporting about 10
> plugins that now work by simply editing the .java files and “pushing the
> button” - so I’m loathe to mess with that - especially since I don’t really
> understand all the “ant” incantations.  And, I doubt it’s the source of any
> of my problems.  So…please don’t suggest a better development environment.
> I’m happy with emacs and ant, for now.]
>
> Maybe I should just buy a new machine, and start over...
>
> --
> Kenneth Sloan
> [hidden email] <mailto:[hidden email]>
> Vision is the art of seeing what is invisible to others.
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: FIJI woes

Kenneth Sloan-3
Success.  After a conversation with Wayne Rasband, I was convinced to try a simple “re-intall FIJI”.

While I *think* I tried this in the past, this time it worked.

But - you raise an issue - what’s the difference in coverage between this “ImageJ Interest Group” (which I’ve been on…forever) and the “ImageJ Forum”.  Is the Forum a replacement, or a supplement, to this group.

Please forgive my naive questions - I seem to only pay attention when I’m having problems.

Thank you for you prompt and very helpful reply.  It’s appreciated.

Details: I downloaded the latest and greatest FIJI *with* a Java JRE - so I’m guessing all is well.
The code I’m maintaining and extending specifies a target of 1.6 - should I be thinking about
changing this?  Or, do I only need to do this if/when I feel the urge to use 1.8 features?

I also need to worry about the Java level on my customer’s machines.  Some of them use *other* FIJI software
which is very finicky about the Java level, so I prefer to impose as few restrictions of my own as possible.

--
Kenneth Sloan
[hidden email] <mailto:[hidden email]>
Vision is the art of seeing what is invisible to others.




> On Oct 23, 2017, at 13:26 , Curtis Rueden <[hidden email]> wrote:
>
> Hi Ken,
>
>> First - this may be a FIJI question rather than an ImageJ question.
>> If so - I’m hoping someone will step up and re-direct me to a more
>> appropriate forum.
>
> Questions about Fiji here are fine. But I would personally recommend using
> the ImageJ Forum at http://forum.imagej.net/ <http://forum.imagej.net/> since it is a better
> communication medium with many active and helpful community members.
>
>> I’m having continuous, long-standing problems with FIJI crashing
>> (usually on opening an image - any image).
>
> See this troubleshooting entry:
>
>  https://imagej.net/Troubleshooting#If_ImageJ_crashes <https://imagej.net/Troubleshooting#If_ImageJ_crashes>
>
>> remove all traces of ImageJ and FIJI and Java from this machine
>
> Here is a script which reports all the Java installations on your machine:
>
>  https://github.com/ctrueden/ctr-scripts/blob/master/java-info <https://github.com/ctrueden/ctr-scripts/blob/master/java-info>
>
> On macOS, you can rm -rf the installations if you really want to get rid of
> them. But I don't think deleting everything is your best bet to
> troubleshoot this.
>
> Same for ImageJ and Fiji: you can directly delete the respective
> application folders. Note that Fiji is not "installed" per se—there is just
> a Fiji.app on your machine, typically (but not necessarily) in
> /Applications. It is fine to have multiple copies of ImageJ and/or Fiji.
>
> Try downloading a fresh Fiji from http://fiji.sc#download <http://fiji.sc/#download>, double-click the
> .dmg, drag the icon to your Desktop, and run from there via the CLI with
> the invocation:
>
>  ~/Desktop/Fiji.app/Contents/MacOS/ImageJ-macosx
>
> You can override which version of Java is used via the --java-home option
> as described here:
>
>  https://imagej.net/Frequently_Asked_Questions#How_do_I_ <https://imagej.net/Frequently_Asked_Questions#How_do_I_>
> launch_ImageJ_with_a_different_version_of_Java.3F
>
> Note that the current download of Fiji requires Java 8. You can download an
> old version of Fiji that still works with Java 6 from here:
>
>  https://imagej.net/Fiji/Downloads#Java_6 <https://imagej.net/Fiji/Downloads#Java_6>
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software <https://loci.wisc.edu/software>
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden <https://imagej.net/User:Rueden>
> Did you know ImageJ has a forum? http://forum.imagej.net/ <http://forum.imagej.net/>
>
>
> On Mon, Oct 23, 2017 at 9:42 AM, Kenneth Sloan <[hidden email] <mailto:[hidden email]>>
> wrote:
>
>> First - this may be a FIJI question rather than an ImageJ question.  If so
>> - I’m hoping someone will step up and re-direct me to a more appropriate
>> forum.
>>
>> I’m having continuous, long-standing problems with FIJI crashing (usually
>> on opening an image - any image).
>> I have worked around this by doing development in a plain, vanilla ImageJ
>> environment.  The .jar files I generate work fine for me in ImageJ, and
>> work fine for my customers using FIJI.  But, FIJI on my machine is wedged.
>>
>> In about 2 weeks, I will be at a point where I can completely uninstall
>> FIJI and ImageJ, and re-install FIJI.  I may have to do the same thing with
>> Java (I keep hearing about the need to be compatible - my build scripts
>> specify a target of 1.6, but I’m ready to try anything).
>>
>> This is all on a Mac Book Pro, with all updates to OS, etc. applied.
>> I use “ant” to compile and build .jar files, specifying Java 1.6 as the
>> target.
>> “ant” is also used (on a virtual WinDoze machine) to build Windows .jar
>> files, but
>> I don’t actually run ImageJ or FIJI on the WinDoze development machine.
>> I drag&drop .jar files into ImageJ and all is well.
>> My customers drag&drop .jar files into FIJI and all is well (for them).
>> For me…FIJI is wedged.  It seems to crash when loading any image file.
>>
>> I would appreciate guidance on how to:
>>
>> a) remove all traces of ImageJ and FIJI and Java from this machine
>>        (I’ll create backup copies, but I hope to *not* re-use anything
>>         that might be hanging around and can’t be re-generated from
>> source)
>> b) re-install the appropriate level of Java
>> c) re-install the appropriate level of FIJI
>> d) perhaps re-install the appropriate level of a stand-alone ImageJ
>>         (but, I’d prefer to avoid this complication)
>>
>> A generic answer to the list is appropriate, but I anticipate some
>> off-list communication to deal with nitty-gritty details.
>>
>> [note: “ant” might not be my first choice - but I’m supporting about 10
>> plugins that now work by simply editing the .java files and “pushing the
>> button” - so I’m loathe to mess with that - especially since I don’t really
>> understand all the “ant” incantations.  And, I doubt it’s the source of any
>> of my problems.  So…please don’t suggest a better development environment.
>> I’m happy with emacs and ant, for now.]
>>
>> Maybe I should just buy a new machine, and start over...
>>
>> --
>> Kenneth Sloan
>> [hidden email] <mailto:[hidden email]> <mailto:[hidden email] <mailto:[hidden email]>>
>> Vision is the art of seeing what is invisible to others.
>>
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: FIJI woes

ctrueden
Hi Ken,

> what’s the difference in coverage between this “ImageJ Interest Group”
> (which I’ve been on…forever) and the “ImageJ Forum”.  Is the Forum a
> replacement, or a supplement, to this group.

They both cover ImageJ and its ecosystem of plugins and extensions. The
ImageJ Forum is a bit broader in that it encourages discussion about other
related and complementary software, as well.

We started the forum because:
A) there were many requests from users and developers for a forum;
B) the Discourse software is excellent with many features useful for
facilitating community discussion;
C) there are technical issues with this ImageJ mailing list which the
developer community cannot realistically address: the need to manually
confirm every message sent, occasional dropping of messages, limitations
surrounding attachments, lack of easy/reliable/consistent rich formatting
capabilities such as math formulas and automatic syntax highlighting, no
fine-grained control over email notifications (e.g., receive mail only
about topics and/or tags of interest), lack of community moderation
capabilities, inability to delete spam after the fact, inability to edit
mistakes such as broken URLs...

From a user perspective, the ImageJ Forum has many active ImageJ users,
developers and image analysts, some of whom do not participate on this
mailing list. While the reverse is also true (i.e.: some people on this
list have not joined the forum), I think it is to a lesser extent.
Therefore, the ImageJ wiki recommends the forum as the best channel for
help (see https://imagej.net/Help).

> The code I’m maintaining and extending specifies a target of 1.6 -
> should I be thinking about changing this?  Or, do I only need to do
> this if/when I feel the urge to use 1.8 features?

From a developer standpoint, you can stick with 1.6, since Java 8 JVMs run
1.6 code just fine. (Java 9, with the introduction of Jigsaw, is a
different story—it will be some work to make ImageJ + all its update sites
work successfully with Java 9.) The bigger concern as a developer is
dependencies: if you use a library which requires Java 7 or 8, then in
practice so does your project. If you use Maven with the pom-scijava
parent, it makes the situation easier to manage, because the build will
fail if you try to construct an untenable organization of dependencies.

For users, it is increasingly difficult to install and use Java 6, and the
vast majority of users are now using at least Java 7. [1, 2]

> I also need to worry about the Java level on my customer’s machines.
> Some of them use *other* FIJI software which is very finicky about the
> Java level, so I prefer to impose as few restrictions of my own as
> possible.

Users can have a separate ImageJ installation for each analysis workflow,
especially if different workflows require different plugins with
incompatible restrictions (e.g. "only works with ImageJ 1.45 or earlier"
vs. "requires ImageJ 1.50 or newer").

To avoid the scenario where incompatible components need to function
together, it is highly desirable to keep components working with the
versions defined in the latest SciJava Bill of Materials [3]. This is one
big reason why it is so critical for plugins to be actively maintained.

If you have a specific issue where two components are incompatible somehow,
feel free to raise it in the Development category of the ImageJ Forum, and
people will try to help.

Regards,
Curtis

[1] https://plumbr.io/blog/java/java-version-and-vendor-data
-analyzed-2017-edition
[2] Related discussion: http://imagej.1557.x6.nabble.com/patch-Bugs-
with-Java-9-tt5019429.html
[3] https://imagej.net/BOM

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Mon, Oct 23, 2017 at 5:19 PM, Kenneth Sloan <[hidden email]>
wrote:

> Success.  After a conversation with Wayne Rasband, I was convinced to try
> a simple “re-intall FIJI”.
>
> While I *think* I tried this in the past, this time it worked.
>
> But - you raise an issue - what’s the difference in coverage between this
> “ImageJ Interest Group” (which I’ve been on…forever) and the “ImageJ
> Forum”.  Is the Forum a replacement, or a supplement, to this group.
>
> Please forgive my naive questions - I seem to only pay attention when I’m
> having problems.
>
> Thank you for you prompt and very helpful reply.  It’s appreciated.
>
> Details: I downloaded the latest and greatest FIJI *with* a Java JRE - so
> I’m guessing all is well.
> The code I’m maintaining and extending specifies a target of 1.6 - should
> I be thinking about
> changing this?  Or, do I only need to do this if/when I feel the urge to
> use 1.8 features?
>
> I also need to worry about the Java level on my customer’s machines.  Some
> of them use *other* FIJI software
> which is very finicky about the Java level, so I prefer to impose as few
> restrictions of my own as possible.
>
> --
> Kenneth Sloan
> [hidden email] <mailto:[hidden email]>
> Vision is the art of seeing what is invisible to others.
>
>
>
>
> > On Oct 23, 2017, at 13:26 , Curtis Rueden <[hidden email]> wrote:
> >
> > Hi Ken,
> >
> >> First - this may be a FIJI question rather than an ImageJ question.
> >> If so - I’m hoping someone will step up and re-direct me to a more
> >> appropriate forum.
> >
> > Questions about Fiji here are fine. But I would personally recommend
> using
> > the ImageJ Forum at http://forum.imagej.net/ <http://forum.imagej.net/>
> since it is a better
> > communication medium with many active and helpful community members.
> >
> >> I’m having continuous, long-standing problems with FIJI crashing
> >> (usually on opening an image - any image).
> >
> > See this troubleshooting entry:
> >
> >  https://imagej.net/Troubleshooting#If_ImageJ_crashes <
> https://imagej.net/Troubleshooting#If_ImageJ_crashes>
> >
> >> remove all traces of ImageJ and FIJI and Java from this machine
> >
> > Here is a script which reports all the Java installations on your
> machine:
> >
> >  https://github.com/ctrueden/ctr-scripts/blob/master/java-info <
> https://github.com/ctrueden/ctr-scripts/blob/master/java-info>
> >
> > On macOS, you can rm -rf the installations if you really want to get rid
> of
> > them. But I don't think deleting everything is your best bet to
> > troubleshoot this.
> >
> > Same for ImageJ and Fiji: you can directly delete the respective
> > application folders. Note that Fiji is not "installed" per se—there is
> just
> > a Fiji.app on your machine, typically (but not necessarily) in
> > /Applications. It is fine to have multiple copies of ImageJ and/or Fiji.
> >
> > Try downloading a fresh Fiji from http://fiji.sc#download <
> http://fiji.sc/#download>, double-click the
> > .dmg, drag the icon to your Desktop, and run from there via the CLI with
> > the invocation:
> >
> >  ~/Desktop/Fiji.app/Contents/MacOS/ImageJ-macosx
> >
> > You can override which version of Java is used via the --java-home option
> > as described here:
> >
> >  https://imagej.net/Frequently_Asked_Questions#How_do_I_ <
> https://imagej.net/Frequently_Asked_Questions#How_do_I_>
> > launch_ImageJ_with_a_different_version_of_Java.3F
> >
> > Note that the current download of Fiji requires Java 8. You can download
> an
> > old version of Fiji that still works with Java 6 from here:
> >
> >  https://imagej.net/Fiji/Downloads#Java_6 <https://imagej.net/Fiji/Downl
> oads#Java_6>
> >
> > Regards,
> > Curtis
> >
> > --
> > Curtis Rueden
> > LOCI software architect - https://loci.wisc.edu/software <
> https://loci.wisc.edu/software>
> > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden <
> https://imagej.net/User:Rueden>
> > Did you know ImageJ has a forum? http://forum.imagej.net/ <
> http://forum.imagej.net/>
> >
> >
> > On Mon, Oct 23, 2017 at 9:42 AM, Kenneth Sloan <[hidden email]
> <mailto:[hidden email]>>
> > wrote:
> >
> >> First - this may be a FIJI question rather than an ImageJ question.  If
> so
> >> - I’m hoping someone will step up and re-direct me to a more appropriate
> >> forum.
> >>
> >> I’m having continuous, long-standing problems with FIJI crashing
> (usually
> >> on opening an image - any image).
> >> I have worked around this by doing development in a plain, vanilla
> ImageJ
> >> environment.  The .jar files I generate work fine for me in ImageJ, and
> >> work fine for my customers using FIJI.  But, FIJI on my machine is
> wedged.
> >>
> >> In about 2 weeks, I will be at a point where I can completely uninstall
> >> FIJI and ImageJ, and re-install FIJI.  I may have to do the same thing
> with
> >> Java (I keep hearing about the need to be compatible - my build scripts
> >> specify a target of 1.6, but I’m ready to try anything).
> >>
> >> This is all on a Mac Book Pro, with all updates to OS, etc. applied.
> >> I use “ant” to compile and build .jar files, specifying Java 1.6 as the
> >> target.
> >> “ant” is also used (on a virtual WinDoze machine) to build Windows .jar
> >> files, but
> >> I don’t actually run ImageJ or FIJI on the WinDoze development machine.
> >> I drag&drop .jar files into ImageJ and all is well.
> >> My customers drag&drop .jar files into FIJI and all is well (for them).
> >> For me…FIJI is wedged.  It seems to crash when loading any image file.
> >>
> >> I would appreciate guidance on how to:
> >>
> >> a) remove all traces of ImageJ and FIJI and Java from this machine
> >>        (I’ll create backup copies, but I hope to *not* re-use anything
> >>         that might be hanging around and can’t be re-generated from
> >> source)
> >> b) re-install the appropriate level of Java
> >> c) re-install the appropriate level of FIJI
> >> d) perhaps re-install the appropriate level of a stand-alone ImageJ
> >>         (but, I’d prefer to avoid this complication)
> >>
> >> A generic answer to the list is appropriate, but I anticipate some
> >> off-list communication to deal with nitty-gritty details.
> >>
> >> [note: “ant” might not be my first choice - but I’m supporting about 10
> >> plugins that now work by simply editing the .java files and “pushing the
> >> button” - so I’m loathe to mess with that - especially since I don’t
> really
> >> understand all the “ant” incantations.  And, I doubt it’s the source of
> any
> >> of my problems.  So…please don’t suggest a better development
> environment.
> >> I’m happy with emacs and ant, for now.]
> >>
> >> Maybe I should just buy a new machine, and start over...
> >>
> >> --
> >> Kenneth Sloan
> >> [hidden email] <mailto:[hidden email]> <mailto:
> [hidden email] <mailto:[hidden email]>>
> >> Vision is the art of seeing what is invisible to others.
> >>
> >>
> >>
> >>
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <
> http://imagej.nih.gov/ij/list.html>
> >>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html <
> http://imagej.nih.gov/ij/list.html>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html