startup plugins from more than one folder on the menu

[robert atwood]

Hi, all
Is there an easy way (or even slightly not-so-easy way) to have the plugins from different folders installed in the menu when imagej starts up?
Looking here http://rsb.info.nih.gov/ij/docs/menus/plugins.html 


I tried to apply the plugins.dir property for  multiple plugin directorys, is there a certain way that Java likes path portions to be concatenated?
I tried

-Dplugins.dir="/first/folder;/second/folder"
-Dplugins.dir="/first/folder /second/folder"
-Dplugins.dir="/first/folder" -Dplugins.dir="/second/folder"

Where each of these folders contains a plugins/ folder with some .ijm files within. Each one can be included successfully on its own, but then the original defaults are not

Invariably I get one or neither of these folders included but not both, and if one is included.

Configurable site-wide plugins combined with  group- and/or personal-plugins would be handy but it seems not entirely obvious (to me) how to configure this.

Thanks
Robert
 


 
  Dr. Robert C. Atwood
  Senior Support Scientist
  Beamline I12-JEEP
  The Joint Engineering and Environmental Processing Beamline
  Diamond Light Source
  The Harwell Science and Innovation Campus
  Didcot,OXON
  OX11 0DE
  [phone]
 



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[ctrueden]

Hi Robert,

> Configurable site-wide plugins combined with  group- and/or
> personal-plugins would be handy but it seems not entirely obvious
> (to me) how to configure this.

ImageJ 1.x does not support this. It is something we are planning to
support in ImageJ2, however.

In the meantime, one thing you can do is symlink (on non-Windows platforms)
additional folders beneath your main plugins folder.

Regards,
Curtis


On Thu, Oct 17, 2013 at 6:41 AM, Robert Atwood
<[hidden email]>wrote:

> Hi, all
> Is there an easy way (or even slightly not-so-easy way) to have the
> plugins from different folders installed in the menu when imagej starts up?
> Looking here http://rsb.info.nih.gov/ij/docs/menus/plugins.html
>
>
> I tried to apply the plugins.dir property for  multiple plugin directorys,
> is there a certain way that Java likes path portions to be concatenated?
> I tried
>
> -Dplugins.dir="/first/folder;/second/folder"
> -Dplugins.dir="/first/folder /second/folder"
> -Dplugins.dir="/first/folder" -Dplugins.dir="/second/folder"
>
> Where each of these folders contains a plugins/ folder with some .ijm
> files within. Each one can be included successfully on its own, but then
> the original defaults are not
>
> Invariably I get one or neither of these folders included but not both,
> and if one is included.
>
> Configurable site-wide plugins combined with  group- and/or
> personal-plugins would be handy but it seems not entirely obvious (to me)
> how to configure this.
>
> Thanks
> Robert
>
>
>
>
>   Dr. Robert C. Atwood
>   Senior Support Scientist
>   Beamline I12-JEEP
>   The Joint Engineering and Environmental Processing Beamline
>   Diamond Light Source
>   The Harwell Science and Innovation Campus
>   Didcot,OXON
>   OX11 0DE
>   [phone]
>
>
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[dscho]

Hi,

On Thu, 17 Oct 2013, Curtis Rueden wrote:

> Hi Robert,
>
> > Configurable site-wide plugins combined with  group- and/or
> > personal-plugins would be handy but it seems not entirely obvious
> > (to me) how to configure this.
>
> ImageJ 1.x does not support this. It is something we are planning to
> support in ImageJ2, however.
>
> In the meantime, one thing you can do is symlink (on non-Windows platforms)
> additional folders beneath your main plugins folder.

In Fiji (actually, ImageJ2's legacy layer), we also added support for
$HOME/.plugins/:

https://github.com/imagej/imagej/blob/master/core/legacy/src/main/java/imagej/legacy/LegacyExtensions.java#L628

If you do not like that location, you can override it by setting the
system property ij1.plugin.dirs to a list of directories (on Windows, this
list is delimited by semicolons, everywhere else by colons) to search for
plugins:

https://github.com/imagej/imagej/blob/master/core/legacy/src/main/java/imagej/legacy/LegacyExtensions.java#L216

Ciao,
Johannes

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[ctrueden]

Hi Dscho,

> In Fiji (actually, ImageJ2's legacy layer), we also added support for
> $HOME/.plugins/
...
> If you do not like that location, you can override it by setting the
> system property ij1.plugin.dirs

Thanks for the reminder! To document all this, I created a new page on the
wiki:

    http://fiji.sc/Plugins

Unfortunately, I had some trouble getting the .plugins folder and the
ij1.plugins.dir system property override to work properly on my OS X system:

- When I put a plugin in $HOME/.plugins and launched Fiji, it was not
discovered.

- The following command run from $HOME still did not find the plugin:
    $FIJI/Contents/MacOS/ImageJ-macosx -Dij1.plugin.dirs=$HOME/.plugins

- The same command run from $HOME/.plugins *did* find it, but did not find
the system plugins anymore.

- So then I tried the following, also from $HOME/.plugins, and it worked:
    $FIJI/Contents/MacOS/ImageJ-macosx
-Dij1.plugin.dirs=$FIJI/jars:$FIJI/plugins:$HOME/.plugins

But the fact that the invocation is sensitive to your CWD seems like a bug
to me. Agreed?

Regards,
Curtis


On Thu, Oct 17, 2013 at 5:12 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Thu, 17 Oct 2013, Curtis Rueden wrote:
>
> > Hi Robert,
> >
> > > Configurable site-wide plugins combined with  group- and/or
> > > personal-plugins would be handy but it seems not entirely obvious
> > > (to me) how to configure this.
> >
> > ImageJ 1.x does not support this. It is something we are planning to
> > support in ImageJ2, however.
> >
> > In the meantime, one thing you can do is symlink (on non-Windows
> platforms)
> > additional folders beneath your main plugins folder.
>
> In Fiji (actually, ImageJ2's legacy layer), we also added support for
> $HOME/.plugins/:
>
>
> https://github.com/imagej/imagej/blob/master/core/legacy/src/main/java/imagej/legacy/LegacyExtensions.java#L628
>
> If you do not like that location, you can override it by setting the
> system property ij1.plugin.dirs to a list of directories (on Windows, this
> list is delimited by semicolons, everywhere else by colons) to search for
> plugins:
>
>
> https://github.com/imagej/imagej/blob/master/core/legacy/src/main/java/imagej/legacy/LegacyExtensions.java#L216
>
> Ciao,
> Johannes
>

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[dscho]

Hi Curtis,

On Fri, 18 Oct 2013, Curtis Rueden wrote:

> > In Fiji (actually, ImageJ2's legacy layer), we also added support for
> > $HOME/.plugins/
> ...
> > If you do not like that location, you can override it by setting the
> > system property ij1.plugin.dirs
>
> Thanks for the reminder! To document all this, I created a new page on the
> wiki:
>
>     http://fiji.sc/Plugins

Thanks!

> Unfortunately, I had some trouble getting the .plugins folder and the
> ij1.plugins.dir system property override to work properly on my OS X
> system:
>
> - When I put a plugin in $HOME/.plugins and launched Fiji, it was not
> discovered.
>
> - The following command run from $HOME still did not find the plugin:
>     $FIJI/Contents/MacOS/ImageJ-macosx -Dij1.plugin.dirs=$HOME/.plugins
>
> - The same command run from $HOME/.plugins *did* find it, but did not find
> the system plugins anymore.
>
> - So then I tried the following, also from $HOME/.plugins, and it worked:
>     $FIJI/Contents/MacOS/ImageJ-macosx
> -Dij1.plugin.dirs=$FIJI/jars:$FIJI/plugins:$HOME/.plugins
>
> But the fact that the invocation is sensitive to your CWD seems like a bug
> to me. Agreed?

Whoa. Yep, that is definitely at least one bug. Darn. I thought that the
unit test I wrote specifically to test this would make sure that it works.

I will spend some time on Monday to debug this.

Ciao,
Dscho

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[ctrueden]

Hi Dscho,

> Whoa. Yep, that is definitely at least one bug. Darn.

So that we do not forget (and hence to take away any immediate pressure), I
filed an issue:

    https://github.com/fiji/fiji/issues/48

Regards,
Curtis


On Fri, Oct 18, 2013 at 3:51 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Curtis,
>
> On Fri, 18 Oct 2013, Curtis Rueden wrote:
>
> > > In Fiji (actually, ImageJ2's legacy layer), we also added support for
> > > $HOME/.plugins/
> > ...
> > > If you do not like that location, you can override it by setting the
> > > system property ij1.plugin.dirs
> >
> > Thanks for the reminder! To document all this, I created a new page on
> the
> > wiki:
> >
> >     http://fiji.sc/Plugins
>
> Thanks!
>
> > Unfortunately, I had some trouble getting the .plugins folder and the
> > ij1.plugins.dir system property override to work properly on my OS X
> > system:
> >
> > - When I put a plugin in $HOME/.plugins and launched Fiji, it was not
> > discovered.
> >
> > - The following command run from $HOME still did not find the plugin:
> >     $FIJI/Contents/MacOS/ImageJ-macosx -Dij1.plugin.dirs=$HOME/.plugins
> >
> > - The same command run from $HOME/.plugins *did* find it, but did not
> find
> > the system plugins anymore.
> >
> > - So then I tried the following, also from $HOME/.plugins, and it worked:
> >     $FIJI/Contents/MacOS/ImageJ-macosx
> > -Dij1.plugin.dirs=$FIJI/jars:$FIJI/plugins:$HOME/.plugins
> >
> > But the fact that the invocation is sensitive to your CWD seems like a
> bug
> > to me. Agreed?
>
> Whoa. Yep, that is definitely at least one bug. Darn. I thought that the
> unit test I wrote specifically to test this would make sure that it works.
>
> I will spend some time on Monday to debug this.
>
> Ciao,
> Dscho
>

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[robert atwood]

Thanks , Curtis, Wayne for several replies confirming that it will not work as I would have liked in Imagej 1.x and look forward to ImageJ2 .

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: 17 October 2013 21:46
> To: [hidden email]
> Subject: Re: startup plugins from more than one folder on the menu
>
> Hi Robert,
>
> > Configurable site-wide plugins combined with  group- and/or
> > personal-plugins would be handy but it seems not entirely obvious (to
> > me) how to configure this.
>
> ImageJ 1.x does not support this. It is something we are planning to
> support in ImageJ2, however.
>
> In the meantime, one thing you can do is symlink (on non-Windows
> platforms) additional folders beneath your main plugins folder.
>
> Regards,
> Curtis
>
>
> On Thu, Oct 17, 2013 at 6:41 AM, Robert Atwood
> <[hidden email]>wrote:
>
> > Hi, all
> > Is there an easy way (or even slightly not-so-easy way) to have the
> > plugins from different folders installed in the menu when imagej
> starts up?
> > Looking here http://rsb.info.nih.gov/ij/docs/menus/plugins.html
> >
> >
> > I tried to apply the plugins.dir property for  multiple plugin
> > directorys, is there a certain way that Java likes path portions to
> be concatenated?
> > I tried
> >
> > -Dplugins.dir="/first/folder;/second/folder"
> > -Dplugins.dir="/first/folder /second/folder"
> > -Dplugins.dir="/first/folder" -Dplugins.dir="/second/folder"
> >
> > Where each of these folders contains a plugins/ folder with some .ijm
> > files within. Each one can be included successfully on its own, but
> > then the original defaults are not
> >
> > Invariably I get one or neither of these folders included but not
> > both, and if one is included.
> >
> > Configurable site-wide plugins combined with  group- and/or
> > personal-plugins would be handy but it seems not entirely obvious (to
> > me) how to configure this.
> >
> > Thanks
> > Robert
> >
> >
> >
> >
> >   Dr. Robert C. Atwood
> >   Senior Support Scientist
> >   Beamline I12-JEEP
> >   The Joint Engineering and Environmental Processing Beamline
> >   Diamond Light Source
> >   The Harwell Science and Innovation Campus
> >   Didcot,OXON
> >   OX11 0DE
> >   [phone]
> >
> >
> >
> >
> > --
> > This e-mail and any attachments may contain confidential, copyright
> > and or privileged material, and are for the use of the intended
> > addressee only. If you are not the intended addressee or an
> authorised
> > recipient of the addressee please notify us of receipt by returning
> > the e-mail and do not use, copy, retain, distribute or disclose the
> > information in or attached to the e-mail.
> > Any opinions expressed within this e-mail are those of the individual
> > and not necessarily of Diamond Light Source Ltd.
> > Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> > attachments are free from viruses and we cannot accept liability for
> > any damage which you may sustain as a result of software viruses
> which
> > may be transmitted in or with the message.
> > Diamond Light Source Limited (company no. 4375679). Registered in
> > England and Wales with its registered office at Diamond House,
> Harwell
> > Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United
> > Kingdom
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom


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