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adding a plugin to Fiji

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Rodrigo Gonçalves

adding a plugin to Fiji

Hi all,
I want to use the Cine File Importer (*) plugin in Fiji but can't figure out:
In ImageJ it works by downloading the jar file into the "Input-Output" directory in the plugins directory and then use it with
File>Import>Cine File

However in Fiji there is no "Input-Output" directory in the plugins, and creating it doesn't seem to work... how can I add this plugin and where to find it once installed?

Another thing: I tried to install it from Plugins-Install it says the plugin was installed, but I get also an error windows:
E:\RDE69~1.POR\Fiji.app\plugins\CINE_File.jar: java.util.zip.ZipException: error in opening zip file
E:\RDE69~1.POR\Fiji.app\plugins\CINE_File.jar: java.util.zip.ZipException: error in opening zip file
WARNING: The PluginClassLoader cannot be reset

Thanks a lot,Rodrigo

* http://rsb.info.nih.gov/ij/plugins/cine-reader/index.html

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

Mark Hiner

Re: adding a plugin to Fiji

Hi Rodrigo,

>how can I add this plugin and where to find it once installed?

Any plugin in the /plugins directory of Fiji, or subdirectory there of,
should be detected and loaded into Fiji *on launch*. The path to the plugin
on disk is actually independent of its menu path in ImageJ or Fiji - so
whether you put CINE_File.jar in /plugins or /plugins/Input-Output, it will
appear under "File>Import>Cine File" regardless.

>WARNING: The PluginClassLoader cannot be reset

This is, unfortunately, a known limitation of Fiji right now - that Refresh
Menus will not work like it does in ImageJ. Effectively, the plugins that
are present when you launch Fiji are fixed until you close and re-launch.

So you did the right thing by putting CINE_File.jar in Fiji.app/plugins;
you should just need to restart Fiji to see the new menu option.

Best,
Mark

On Thu, Nov 13, 2014 at 1:33 AM, Rodrigo Gonçalves <
[hidden email]> wrote:

> Hi all,
> I want to use the Cine File Importer (*) plugin in Fiji but can't figure
> out:
> In ImageJ it works by downloading the jar file into the "Input-Output"
> directory in the plugins directory and then use it with
> File>Import>Cine File
>
> However in Fiji there is no "Input-Output" directory in the plugins, and
> creating it doesn't seem to work... how can I add this plugin and where to
> find it once installed?
>
> Another thing: I tried to install it from Plugins-Install it says the
> plugin was installed, but I get also an error windows:
> E:\RDE69~1.POR\Fiji.app\plugins\CINE_File.jar: java.util.zip.ZipException:
> error in opening zip file
> E:\RDE69~1.POR\Fiji.app\plugins\CINE_File.jar: java.util.zip.ZipException:
> error in opening zip file
> WARNING: The PluginClassLoader cannot be reset
>
>
> Thanks a lot,Rodrigo
>
> * http://rsb.info.nih.gov/ij/plugins/cine-reader/index.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Rodrigo Gonçalves

Re: adding a plugin to Fiji

Hi Mark, thanks a lot for your answer.

I put the CINE_File.jar file into plugins directory, and then close Fiji. But after restarting, the option to import a CINE file is not there ... what am I doing wrong?
IJ.getVersion: 2.0.0-rc-15/1.49k
IJ.getFullVersion: 1.49k99Win 7 64 bits

Thanks!
Rodrigo

De: Mark Hiner <[hidden email]>
Para: [hidden email]
Enviado: Jueves, 13 de noviembre, 2014 11:04:54
Asunto: Re: adding a plugin to Fiji

Hi Rodrigo,

>how can I add this plugin and where to find it once installed?

Any plugin in the /plugins directory of Fiji, or subdirectory there of,
should be detected and loaded into Fiji *on launch*. The path to the plugin
on disk is actually independent of its menu path in ImageJ or Fiji - so
whether you put CINE_File.jar in /plugins or /plugins/Input-Output, it will
appear under "File>Import>Cine File" regardless.

>WARNING: The PluginClassLoader cannot be reset

This is, unfortunately, a known limitation of Fiji right now - that Refresh
Menus will not work like it does in ImageJ. Effectively, the plugins that
are present when you launch Fiji are fixed until you close and re-launch.

So you did the right thing by putting CINE_File.jar in Fiji.app/plugins;
you should just need to restart Fiji to see the new menu option.

Best,
Mark

On Thu, Nov 13, 2014 at 1:33 AM, Rodrigo Gonçalves <
[hidden email]> wrote:

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

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Mark Hiner

Re: adding a plugin to Fiji

Hi Rodrigo,

>E:\RDE69~1.POR\Fiji.app\plugins\CINE_File.jar: java.util.zip.ZipException:
error in opening zip file

Apologies for overlooking this in my original response. I don't think you
are doing anything wrong, but this error suggests your .jar is corrupted
<http://stackoverflow.com/questions/24799533/java-util-zip-zipexception-error-in-opening-zip-file-tomcat>
.

I would recommend re-downloading the CINE_File.jar and trying again. As
suggested on SO, you can also try unzipping the jar with your preferred zip
utility to verify its integrity.

Hope that works!

Best,
Mark

On Thu, Nov 13, 2014 at 10:27 AM, Rodrigo Gonçalves <
[hidden email]> wrote:

> Hi Mark, thanks a lot for your answer.
>
> I put the CINE_File.jar file into plugins directory, and then close Fiji.
> But after restarting, the option to import a CINE file is not there ...
> what am I doing wrong?
> IJ.getVersion: 2.0.0-rc-15/1.49k
> IJ.getFullVersion: 1.49k99Win 7 64 bits
>
>
> Thanks!
> Rodrigo
>
> De: Mark Hiner <[hidden email]>
> Para: [hidden email]
> Enviado: Jueves, 13 de noviembre, 2014 11:04:54
> Asunto: Re: adding a plugin to Fiji
>
> Hi Rodrigo,
>
> >how can I add this plugin and where to find it once installed?
>
> Any plugin in the /plugins directory of Fiji, or subdirectory there of,
> should be detected and loaded into Fiji *on launch*. The path to the plugin
> on disk is actually independent of its menu path in ImageJ or Fiji - so
> whether you put CINE_File.jar in /plugins or /plugins/Input-Output, it will
> appear under "File>Import>Cine File" regardless.
>
> >WARNING: The PluginClassLoader cannot be reset
>
> This is, unfortunately, a known limitation of Fiji right now - that Refresh
> Menus will not work like it does in ImageJ. Effectively, the plugins that
> are present when you launch Fiji are fixed until you close and re-launch.
>
> So you did the right thing by putting CINE_File.jar in Fiji.app/plugins;
> you should just need to restart Fiji to see the new menu option.
>
> Best,
> Mark
>
>
>
> On Thu, Nov 13, 2014 at 1:33 AM, Rodrigo Gonçalves <
> [hidden email]> wrote:
>
> > Hi all,
> > I want to use the Cine File Importer (*) plugin in Fiji but can't figure
> > out:
> > In ImageJ it works by downloading the jar file into the "Input-Output"
> > directory in the plugins directory and then use it with
> > File>Import>Cine File
> >
> > However in Fiji there is no "Input-Output" directory in the plugins, and
> > creating it doesn't seem to work... how can I add this plugin and where
> to
> > find it once installed?
> >
> > Another thing: I tried to install it from Plugins-Install it says the
> > plugin was installed, but I get also an error windows:
> > E:\RDE69~1.POR\Fiji.app\plugins\CINE_File.jar:
> java.util.zip.ZipException:
> > error in opening zip file
> > E:\RDE69~1.POR\Fiji.app\plugins\CINE_File.jar:
> java.util.zip.ZipException:
> > error in opening zip file
> > WARNING: The PluginClassLoader cannot be reset
> >
> >
> > Thanks a lot,Rodrigo
> >
> > * http://rsb.info.nih.gov/ij/plugins/cine-reader/index.html
> >
> >
> > --
> > 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
>
>

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

Rodrigo Gonçalves

Re: adding a plugin to Fiji

In reply to this post by Mark Hiner

Thanks a lot Mark! It was exactly that, I re-downloaded and it works like a charm!
And thanks to Terry Jordan for this wonderful, handy plugin!
Rodrigo________________________
De: Mark Hiner <[hidden email]>
Para: [hidden email]
Enviado: Jueves, 13 de noviembre, 2014 11:04:54
Asunto: Re: adding a plugin to Fiji

Hi Rodrigo,

>how can I add this plugin and where to find it once installed?

Any plugin in the /plugins directory of Fiji, or subdirectory there of,
should be detected and loaded into Fiji *on launch*. The path to the plugin
on disk is actually independent of its menu path in ImageJ or Fiji - so
whether you put CINE_File.jar in /plugins or /plugins/Input-Output, it will
appear under "File>Import>Cine File" regardless.

>WARNING: The PluginClassLoader cannot be reset

This is, unfortunately, a known limitation of Fiji right now - that Refresh
Menus will not work like it does in ImageJ. Effectively, the plugins that
are present when you launch Fiji are fixed until you close and re-launch.

So you did the right thing by putting CINE_File.jar in Fiji.app/plugins;
you should just need to restart Fiji to see the new menu option.

Best,
Mark

On Thu, Nov 13, 2014 at 1:33 AM, Rodrigo Gonçalves <
[hidden email]> wrote:

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

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