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reading in ...nii.gz image sequence

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Krieger, Donald N.
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reading in ...nii.gz image sequence

Krieger, Donald N.
Dear List,

I am running fiji, imageJ version 1.52b, with everything up to date as of this morning.
When I open a gzip'd nifty image sequence file.nii.gz, I get the Bio-Formats Import Options, click OK, and get an error with stack trace:
    Java.lang.NullPointerException
    at loci.formats.in.NiftiReader.initFile(NiftiReader.java:234)
     ...

If I gunzip the file first there is no error in reading or manipulating the images.
Can I get fiji/imageJ to do the gunzip for me?
I presume this is trivial for someone who knows what they're doing.

Thanks for your help.

Best - Don

[Signature0001]
Don Krieger, Ph.D.
Research Scientist
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


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

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David Gault (Staff)
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Re: reading in ...nii.gz image sequence

David Gault (Staff)
Hi Donald,

The Bio-Formats Importer should support “nii.gz” files but this looks like a bug in the reader. Which version of Bio-Formats do you currently have installed?
You can find out the version information from: Help -> About Plugins -> Bio-Formats Plugins

With Thanks,
David Gault

> On 8 May 2018, at 12:37, Krieger, Donald N. <[hidden email]> wrote:
>
> Dear List,
>
> I am running fiji, imageJ version 1.52b, with everything up to date as of this morning.
> When I open a gzip'd nifty image sequence file.nii.gz, I get the Bio-Formats Import Options, click OK, and get an error with stack trace:
>    Java.lang.NullPointerException
>    at loci.formats.in.NiftiReader.initFile(NiftiReader.java:234)
>     ...
>
> If I gunzip the file first there is no error in reading or manipulating the images.
> Can I get fiji/imageJ to do the gunzip for me?
> I presume this is trivial for someone who knows what they're doing.
>
> Thanks for your help.
>
> Best - Don
>
> [Signature0001]
> Don Krieger, Ph.D.
> Research Scientist
> Department of Neurological Surgery
> University of Pittsburgh
> (412)648-9654 Office
> (412)521-4431 Cell/Text
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> <image002.jpg>


The University of Dundee is a registered Scottish Charity, No: SC015096

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Krieger, Donald N.
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Re: reading in ...nii.gz image sequence

Krieger, Donald N.
Thanks for getting back, David.

The Bio-formats release is 5.1.0
with build date 6May2016

Yikes - that surely isn't up to date??
I just updated imageJ.
How do I update the plugin?

Thanks

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of David Gault (Staff)
Sent: Wednesday, May 9, 2018 9:39 AM
To: [hidden email]
Subject: Re: reading in ...nii.gz image sequence

Hi Donald,

The Bio-Formats Importer should support “nii.gz” files but this looks like a bug in the reader. Which version of Bio-Formats do you currently have installed?
You can find out the version information from: Help -> About Plugins -> Bio-Formats Plugins

With Thanks,
David Gault

> On 8 May 2018, at 12:37, Krieger, Donald N. <[hidden email]> wrote:
>
> Dear List,
>
> I am running fiji, imageJ version 1.52b, with everything up to date as of this morning.
> When I open a gzip'd nifty image sequence file.nii.gz, I get the Bio-Formats Import Options, click OK, and get an error with stack trace:
>    Java.lang.NullPointerException
>    at loci.formats.in.NiftiReader.initFile(NiftiReader.java:234)
>     ...
>
> If I gunzip the file first there is no error in reading or manipulating the images.
> Can I get fiji/imageJ to do the gunzip for me?
> I presume this is trivial for someone who knows what they're doing.
>
> Thanks for your help.
>
> Best - Don
>
> [Signature0001]
> Don Krieger, Ph.D.
> Research Scientist
> Department of Neurological Surgery
> University of Pittsburgh
> (412)648-9654 Office
> (412)521-4431 Cell/Text
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> <image002.jpg>


The University of Dundee is a registered Scottish Charity, No: SC015096

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

--
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David Gault (Staff)
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Re: reading in ...nii.gz image sequence

David Gault (Staff)
Hi Donald,

That would explain things, the support for nii.gz was added in 5.2.0.
To update the plugin you can follow the below instructions:

  *   Launch Update from the Help menu
  *   Click on 'Manage update sites’
  *   Ensure that the Java-8 update site is selected
  *   Run the updater and apply changes to any jars in the 'jars/bio-formats' folder

With Thanks,
David Gault

On 9 May 2018, at 14:51, Krieger, Donald N. <[hidden email]<mailto:[hidden email]>> wrote:

Thanks for getting back, David.

The Bio-formats release is 5.1.0
with build date 6May2016

Yikes - that surely isn't up to date??
I just updated imageJ.
How do I update the plugin?

Thanks

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of David Gault (Staff)
Sent: Wednesday, May 9, 2018 9:39 AM
To: [hidden email]<mailto:[hidden email]>
Subject: Re: reading in ...nii.gz image sequence

Hi Donald,

The Bio-Formats Importer should support “nii.gz” files but this looks like a bug in the reader. Which version of Bio-Formats do you currently have installed?
You can find out the version information from: Help -> About Plugins -> Bio-Formats Plugins

With Thanks,
David Gault

On 8 May 2018, at 12:37, Krieger, Donald N. <[hidden email]<mailto:[hidden email]>> wrote:

Dear List,

I am running fiji, imageJ version 1.52b, with everything up to date as of this morning.
When I open a gzip'd nifty image sequence file.nii.gz, I get the Bio-Formats Import Options, click OK, and get an error with stack trace:
  Java.lang.NullPointerException
  at loci.formats.in.NiftiReader.initFile(NiftiReader.java:234)
   ...

If I gunzip the file first there is no error in reading or manipulating the images.
Can I get fiji/imageJ to do the gunzip for me?
I presume this is trivial for someone who knows what they're doing.

Thanks for your help.

Best - Don

[Signature0001]
Don Krieger, Ph.D.
Research Scientist
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
<image002.jpg>


The University of Dundee is a registered Scottish Charity, No: SC015096

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

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


The University of Dundee is a registered Scottish Charity, No: SC015096

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Krieger, Donald N.
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Re: reading in ...nii.gz image sequence

Krieger, Donald N.
Thanks David,

Neither the Java-8 nor the BioFormats sites were selected.
I selected them both and did the update.

Now Fiji/imageJ is broken, maybe because I installed this quite a long time ago. I've put the stack trace below. What do you think?
Should I just uninstall it, however that's done, and reinstall from scratch?

Thanks - Don

/home/kriegerd/Contrib/Fiji.app/ImageJ-linux64

java.lang.UnsupportedClassVersionError: net/imagej/Main : Unsupported major.minor version 52.0
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
        at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:252)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
Falling back to remote updater at http://update.imagej.net/bootstrap.js
java.lang.UnsupportedClassVersionError: org/scijava/plugins/scripting/java/JavaScriptLanguage : Unsupported major.minor version 52.0
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
        at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:247)
        at sun.misc.Service$LazyIterator.next(Service.java:271)
        at javax.script.ScriptEngineManager.initEngines(ScriptEngineManager.java:109)
        at javax.script.ScriptEngineManager.access$000(ScriptEngineManager.java:37)
        at javax.script.ScriptEngineManager$1.run(ScriptEngineManager.java:80)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.script.ScriptEngineManager.init(ScriptEngineManager.java:78)
        at javax.script.ScriptEngineManager.<init>(ScriptEngineManager.java:51)
        at net.imagej.launcher.RemoteUpdater.runAsJavascript(RemoteUpdater.java:86)
        at net.imagej.launcher.RemoteUpdater.runRemote(RemoteUpdater.java:71)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:189)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)

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ctrueden
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Re: reading in ...nii.gz image sequence

ctrueden
In reply to this post by David Gault (Staff)
Hi Don,

Your easiest path forward is to download a fresh Fiji from
https://fiji.sc/#download

This will come with the latest Bio-Formats already installed.

If you _must_ upgrade your old installation for some reason, see here:
https://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D#Upgrading_an_old_installation

And note that you must be running ImageJ with Java 8. (Your error message
indicates you are still trying to run it with 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 Wed, May 9, 2018 at 11:33 AM, Krieger, Donald N. <[hidden email]>
wrote:

> Thanks David,
>
> Neither the Java-8 nor the BioFormats sites were selected.
> I selected them both and did the update.
>
> Now Fiji/imageJ is broken, maybe because I installed this quite a long
> time ago. I've put the stack trace below. What do you think?
> Should I just uninstall it, however that's done, and reinstall from
> scratch?
>
> Thanks - Don
>
> /home/kriegerd/Contrib/Fiji.app/ImageJ-linux64
>
> java.lang.UnsupportedClassVersionError: net/imagej/Main : Unsupported
> major.minor version 52.0
>         at java.lang.ClassLoader.defineClass1(Native Method)
>         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
>         at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
>         at java.security.SecureClassLoader.defineClass(
> SecureClassLoader.java:141)
>         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
>         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
>         at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>         at net.imagej.launcher.ClassLauncher.launch(
> ClassLauncher.java:252)
>         at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
>         at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
> Falling back to remote updater at http://update.imagej.net/bootstrap.js
> java.lang.UnsupportedClassVersionError: org/scijava/plugins/scripting/java/JavaScriptLanguage
> : Unsupported major.minor version 52.0
>         at java.lang.ClassLoader.defineClass1(Native Method)
>         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
>         at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
>         at java.security.SecureClassLoader.defineClass(
> SecureClassLoader.java:141)
>         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
>         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>         at java.lang.Class.forName0(Native Method)
>         at java.lang.Class.forName(Class.java:247)
>         at sun.misc.Service$LazyIterator.next(Service.java:271)
>         at javax.script.ScriptEngineManager.initEngines(
> ScriptEngineManager.java:109)
>         at javax.script.ScriptEngineManager.access$
> 000(ScriptEngineManager.java:37)
>         at javax.script.ScriptEngineManager$1.run(
> ScriptEngineManager.java:80)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at javax.script.ScriptEngineManager.init(
> ScriptEngineManager.java:78)
>         at javax.script.ScriptEngineManager.<init>(
> ScriptEngineManager.java:51)
>         at net.imagej.launcher.RemoteUpdater.runAsJavascript(
> RemoteUpdater.java:86)
>         at net.imagej.launcher.RemoteUpdater.runRemote(
> RemoteUpdater.java:71)
>         at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:189)
>         at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Krieger, Donald N.
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Re: reading in ...nii.gz image sequence

Krieger, Donald N.
Thanks, Curtis.
I think I'll reinstall ImageJ 1.
I'm concerned that if I update Java, it will break something else that I rely on more heavily.

When I upgrade my OS, I'll go to the latest version of ImageJ too.

If I have more trouble, I'll post back.

Best - Don

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: Wednesday, May 9, 2018 1:22 PM
To: [hidden email]
Subject: Re: reading in ...nii.gz image sequence

Hi Don,

Your easiest path forward is to download a fresh Fiji from https://fiji.sc/#download

This will come with the latest Bio-Formats already installed.

If you _must_ upgrade your old installation for some reason, see here:
https://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D#Upgrading_an_old_installation

And note that you must be running ImageJ with Java 8. (Your error message indicates you are still trying to run it with 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 Wed, May 9, 2018 at 11:33 AM, Krieger, Donald N. <[hidden email]>
wrote:

> Thanks David,
>
> Neither the Java-8 nor the BioFormats sites were selected.
> I selected them both and did the update.
>
> Now Fiji/imageJ is broken, maybe because I installed this quite a long
> time ago. I've put the stack trace below. What do you think?
> Should I just uninstall it, however that's done, and reinstall from
> scratch?
>
> Thanks - Don
>
> /home/kriegerd/Contrib/Fiji.app/ImageJ-linux64
>
> java.lang.UnsupportedClassVersionError: net/imagej/Main : Unsupported
> major.minor version 52.0
>         at java.lang.ClassLoader.defineClass1(Native Method)
>         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
>         at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
>         at java.security.SecureClassLoader.defineClass(
> SecureClassLoader.java:141)
>         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
>         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
>         at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>         at net.imagej.launcher.ClassLauncher.launch(
> ClassLauncher.java:252)
>         at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
>         at
> net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
> Falling back to remote updater at
> http://update.imagej.net/bootstrap.js
> java.lang.UnsupportedClassVersionError:
> org/scijava/plugins/scripting/java/JavaScriptLanguage
> : Unsupported major.minor version 52.0
>         at java.lang.ClassLoader.defineClass1(Native Method)
>         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
>         at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
>         at java.security.SecureClassLoader.defineClass(
> SecureClassLoader.java:141)
>         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
>         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>         at java.lang.Class.forName0(Native Method)
>         at java.lang.Class.forName(Class.java:247)
>         at sun.misc.Service$LazyIterator.next(Service.java:271)
>         at javax.script.ScriptEngineManager.initEngines(
> ScriptEngineManager.java:109)
>         at javax.script.ScriptEngineManager.access$
> 000(ScriptEngineManager.java:37)
>         at javax.script.ScriptEngineManager$1.run(
> ScriptEngineManager.java:80)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at javax.script.ScriptEngineManager.init(
> ScriptEngineManager.java:78)
>         at javax.script.ScriptEngineManager.<init>(
> ScriptEngineManager.java:51)
>         at net.imagej.launcher.RemoteUpdater.runAsJavascript(
> RemoteUpdater.java:86)
>         at net.imagej.launcher.RemoteUpdater.runRemote(
> RemoteUpdater.java:71)
>         at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:189)
>         at
> net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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--
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ctrueden
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Re: reading in ...nii.gz image sequence

ctrueden
In reply to this post by ctrueden
Hi Don,

> I'm concerned that if I update Java, it will break
> something else that I rely on more heavily.

The Fiji download comes bundled with a local copy of Java 8 in the
Fiji.app/java folder. So you should not need to upgrade your system Java.

Furthermore, Java supports having multiple versions installed
simultaneously. So in general, there is no need to worry about installing a
newer Java causing a breakage elsewhere.

Regards,
Curtis


On Thu, May 10, 2018, 05:35 Krieger, Donald N. <[hidden email]> wrote:

> Thanks, Curtis.
> I think I'll reinstall ImageJ 1.
> I'm concerned that if I update Java, it will break something else that I
> rely on more heavily.
>
> When I upgrade my OS, I'll go to the latest version of ImageJ too.
>
> If I have more trouble, I'll post back.
>
> Best - Don
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: Wednesday, May 9, 2018 1:22 PM
> To: [hidden email]
> Subject: Re: reading in ...nii.gz image sequence
>
> Hi Don,
>
> Your easiest path forward is to download a fresh Fiji from
> https://fiji.sc/#download
>
> This will come with the latest Bio-Formats already installed.
>
> If you _must_ upgrade your old installation for some reason, see here:
>
> https://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D#Upgrading_an_old_installation
>
> And note that you must be running ImageJ with Java 8. (Your error message
> indicates you are still trying to run it with 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 Wed, May 9, 2018 at 11:33 AM, Krieger, Donald N. <[hidden email]>
> wrote:
>
> > Thanks David,
> >
> > Neither the Java-8 nor the BioFormats sites were selected.
> > I selected them both and did the update.
> >
> > Now Fiji/imageJ is broken, maybe because I installed this quite a long
> > time ago. I've put the stack trace below. What do you think?
> > Should I just uninstall it, however that's done, and reinstall from
> > scratch?
> >
> > Thanks - Don
> >
> > /home/kriegerd/Contrib/Fiji.app/ImageJ-linux64
> >
> > java.lang.UnsupportedClassVersionError: net/imagej/Main : Unsupported
> > major.minor version 52.0
> >         at java.lang.ClassLoader.defineClass1(Native Method)
> >         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
> >         at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
> >         at java.security.SecureClassLoader.defineClass(
> > SecureClassLoader.java:141)
> >         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
> >         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
> >         at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
> >         at java.security.AccessController.doPrivileged(Native Method)
> >         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
> >         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
> >         at net.imagej.launcher.ClassLauncher.launch(
> > ClassLauncher.java:252)
> >         at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
> >         at
> > net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
> > Falling back to remote updater at
> > http://update.imagej.net/bootstrap.js
> > java.lang.UnsupportedClassVersionError:
> > org/scijava/plugins/scripting/java/JavaScriptLanguage
> > : Unsupported major.minor version 52.0
> >         at java.lang.ClassLoader.defineClass1(Native Method)
> >         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
> >         at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
> >         at java.security.SecureClassLoader.defineClass(
> > SecureClassLoader.java:141)
> >         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
> >         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
> > at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
> >         at java.security.AccessController.doPrivileged(Native Method)
> >         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
> >         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
> >         at java.lang.Class.forName0(Native Method)
> >         at java.lang.Class.forName(Class.java:247)
> >         at sun.misc.Service$LazyIterator.next(Service.java:271)
> >         at javax.script.ScriptEngineManager.initEngines(
> > ScriptEngineManager.java:109)
> >         at javax.script.ScriptEngineManager.access$
> > 000(ScriptEngineManager.java:37)
> >         at javax.script.ScriptEngineManager$1.run(
> > ScriptEngineManager.java:80)
> >         at java.security.AccessController.doPrivileged(Native Method)
> >         at javax.script.ScriptEngineManager.init(
> > ScriptEngineManager.java:78)
> >         at javax.script.ScriptEngineManager.<init>(
> > ScriptEngineManager.java:51)
> >         at net.imagej.launcher.RemoteUpdater.runAsJavascript(
> > RemoteUpdater.java:86)
> >         at net.imagej.launcher.RemoteUpdater.runRemote(
> > RemoteUpdater.java:71)
> >         at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:189)
> >         at
> > net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
> >
> > --
> > ImageJ mailing list: 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
>

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Krieger, Donald N.
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Re: reading in ...nii.gz image sequence

Krieger, Donald N.
Thanks, Curtis.

I discovered that after I posted.
I downloaded the latest and "voila" everything works including opening gzip'd nifty archives plus I can see that java 8 was included as you said.

When you're dealing with software packages,
it doesn't really matter how much you know -- there's always an infinite amount more to learn.
And if you're me, you expect the worst which in this case would be dependency nightmare.

That's addressed very well in this package which is a welcome surprise and commands my respect and appreciation.

Thanks again.

Best - Don

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: Thursday, May 10, 2018 7:13 AM
To: [hidden email]
Subject: Re: reading in ...nii.gz image sequence

Hi Don,

> I'm concerned that if I update Java, it will break something else that
> I rely on more heavily.

The Fiji download comes bundled with a local copy of Java 8 in the Fiji.app/java folder. So you should not need to upgrade your system Java.

Furthermore, Java supports having multiple versions installed simultaneously. So in general, there is no need to worry about installing a newer Java causing a breakage elsewhere.

Regards,
Curtis


On Thu, May 10, 2018, 05:35 Krieger, Donald N. <[hidden email]> wrote:

> Thanks, Curtis.
> I think I'll reinstall ImageJ 1.
> I'm concerned that if I update Java, it will break something else that
> I rely on more heavily.
>
> When I upgrade my OS, I'll go to the latest version of ImageJ too.
>
> If I have more trouble, I'll post back.
>
> Best - Don
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: Wednesday, May 9, 2018 1:22 PM
> To: [hidden email]
> Subject: Re: reading in ...nii.gz image sequence
>
> Hi Don,
>
> Your easiest path forward is to download a fresh Fiji from
> https://fiji.sc/#download
>
> This will come with the latest Bio-Formats already installed.
>
> If you _must_ upgrade your old installation for some reason, see here:
>
> https://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D
> #Upgrading_an_old_installation
>
> And note that you must be running ImageJ with Java 8. (Your error
> message indicates you are still trying to run it with 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 Wed, May 9, 2018 at 11:33 AM, Krieger, Donald N.
> <[hidden email]>
> wrote:
>
> > Thanks David,
> >
> > Neither the Java-8 nor the BioFormats sites were selected.
> > I selected them both and did the update.
> >
> > Now Fiji/imageJ is broken, maybe because I installed this quite a
> > long time ago. I've put the stack trace below. What do you think?
> > Should I just uninstall it, however that's done, and reinstall from
> > scratch?
> >
> > Thanks - Don
> >
> > /home/kriegerd/Contrib/Fiji.app/ImageJ-linux64
> >
> > java.lang.UnsupportedClassVersionError: net/imagej/Main :
> > Unsupported major.minor version 52.0
> >         at java.lang.ClassLoader.defineClass1(Native Method)
> >         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
> >         at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
> >         at java.security.SecureClassLoader.defineClass(
> > SecureClassLoader.java:141)
> >         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
> >         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
> >         at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
> >         at java.security.AccessController.doPrivileged(Native Method)
> >         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
> >         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
> >         at net.imagej.launcher.ClassLauncher.launch(
> > ClassLauncher.java:252)
> >         at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
> >         at
> > net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
> > Falling back to remote updater at
> > http://update.imagej.net/bootstrap.js
> > java.lang.UnsupportedClassVersionError:
> > org/scijava/plugins/scripting/java/JavaScriptLanguage
> > : Unsupported major.minor version 52.0
> >         at java.lang.ClassLoader.defineClass1(Native Method)
> >         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
> >         at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
> >         at java.security.SecureClassLoader.defineClass(
> > SecureClassLoader.java:141)
> >         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
> >         at
> > java.net.URLClassLoader.access$000(URLClassLoader.java:58)
> > at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
> >         at java.security.AccessController.doPrivileged(Native Method)
> >         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
> >         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
> >         at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
> >         at java.lang.Class.forName0(Native Method)
> >         at java.lang.Class.forName(Class.java:247)
> >         at sun.misc.Service$LazyIterator.next(Service.java:271)
> >         at javax.script.ScriptEngineManager.initEngines(
> > ScriptEngineManager.java:109)
> >         at javax.script.ScriptEngineManager.access$
> > 000(ScriptEngineManager.java:37)
> >         at javax.script.ScriptEngineManager$1.run(
> > ScriptEngineManager.java:80)
> >         at java.security.AccessController.doPrivileged(Native Method)
> >         at javax.script.ScriptEngineManager.init(
> > ScriptEngineManager.java:78)
> >         at javax.script.ScriptEngineManager.<init>(
> > ScriptEngineManager.java:51)
> >         at net.imagej.launcher.RemoteUpdater.runAsJavascript(
> > RemoteUpdater.java:86)
> >         at net.imagej.launcher.RemoteUpdater.runRemote(
> > RemoteUpdater.java:71)
> >         at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:189)
> >         at
> > net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
> >
> > --
> > ImageJ mailing list: 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
>

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