Export as .jar is gone

[Romwere]

Dear all,
I am writing Macros in ImageJ and I usually install them as plugins simply by using:
File > Export as .jar

But in the recent versions of ImageJ, the option has disappeared.
Why?
And how can I get this option back?

Thanks for your help.

Romain

[Rasband, Wayne (NIH/NIMH) [E]]

On Jul 15, 2014, at 5:21 AM, Romwere wrote:

> Dear all,
> I am writing Macros in ImageJ and I usually install them as plugins simply
> by using:
> File > Export as .jar
>
> But in the recent versions of ImageJ, the option has disappeared.
> Why?
> And how can I get this option back?

ImageJ has never had a File>Export As .jar command but the Script Editor in Fiji may have. If it did, use the Help>Report a Bug command to report that it is missing. In ImageJ, you can install a macro as a plugin by saving it in the plugins folder or in an immediate sub-folder. For this to work, the file name must have a .ijm extension or it must contain at least one underscore. You can also install a macro as a plugin by using the Plugins>Install command.

-wayne

> Thanks for your help.
>
> Romain
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Export-as-jar-is-gone-tp5008737.html
> Sent from the ImageJ mailing list archive at Nabble.com.

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

[ctrueden]

Hi Romain,

> ImageJ has never had a File>Export As .jar command but the Script
> Editor in Fiji may have.

Indeed, the Script Editor still has that command if your selected language
is "Java" but it is not present for "ImageJ1 Macro" as the language. If you
Report a Bug as Wayne suggests (so that we don't forget), we will look into
fixing it.

Regards,
Curtis


On Tue, Jul 15, 2014 at 8:03 AM, Rasband, Wayne (NIH/NIMH) [E] <
[hidden email]> wrote:

> On Jul 15, 2014, at 5:21 AM, Romwere wrote:
>
> > Dear all,
> > I am writing Macros in ImageJ and I usually install them as plugins
> simply
> > by using:
> > File > Export as .jar
> >
> > But in the recent versions of ImageJ, the option has disappeared.
> > Why?
> > And how can I get this option back?
>
> ImageJ has never had a File>Export As .jar command but the Script Editor
> in Fiji may have. If it did, use the Help>Report a Bug command to report
> that it is missing. In ImageJ, you can install a macro as a plugin by
> saving it in the plugins folder or in an immediate sub-folder. For this to
> work, the file name must have a .ijm extension or it must contain at least
> one underscore. You can also install a macro as a plugin by using the
> Plugins>Install command.
>
> -wayne
>
> > Thanks for your help.
> >
> > Romain
> >
> >
> > --
> > View this message in context:
> http://imagej.1557.x6.nabble.com/Export-as-jar-is-gone-tp5008737.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Romwere]

Hi Wayne, Curtis,
Yes, you're right. I have been using Fiji and not ImageJ.
I (wrongly) assumed it was a feature of ImageJ and not Fiji. Sorry about that.

As you both suggested, I will then report a bug.
Thanks a lot for your help.

Best regards,

Romain

[dscho]

Hi Romain,

On Tue, 15 Jul 2014, Romwere wrote:

> Hi Wayne, Curtis,
> Yes, you're right. I have been using Fiji and not ImageJ.
> I (wrongly) assumed it was a feature of ImageJ and not Fiji. Sorry about
> that.
>
> As you both suggested, I will then report a bug.
> Thanks a lot for your help.

Please note that the best way to ship macros and scripts to users is to
make a new update site.

To put macros or scripts into arbitrary menus, just place them inside the
plugins/Scripts/ menu structure. For example, Fiji's 'Spirals' example
(which is designed to demonstrate how little scientists *should* trust
their eyes when it comes to red-green merges) is stored in
plugins/Scripts/File/Open_Samples/Spirals_.ijm and consequently gets
installed into File>Open Samples>Spirals .

Ciao,
Johannes

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

[ctrueden]

Hi Romain,

> I (wrongly) assumed it was a feature of ImageJ and not Fiji. Sorry
> about that.

To be precise: you were not exactly wrong. The Script Editor is a feature
of ImageJ2, but not ImageJ1.

    http://imagej.net/Script_Editor

Regards,
Curtis


On Tue, Jul 15, 2014 at 10:34 AM, Romwere <[hidden email]> wrote:

> Hi Wayne, Curtis,
> Yes, you're right. I have been using Fiji and not ImageJ.
> I (wrongly) assumed it was a feature of ImageJ and not Fiji. Sorry about
> that.
>
> As you both suggested, I will then report a bug.
> Thanks a lot for your help.
>
> Best regards,
>
> Romain
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Export-as-jar-is-gone-tp5008737p5008748.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Romwere]

Hi Johannes,

> Please note that the best way to ship macros and scripts to users is to
> make a new update site.

Sorry. What is an update site?
Please bear in mind, I have only been using ImageJ macro language using
Fiji, not Java.
What is the advantage of it? And how to do it?

> To put macros or scripts into arbitrary menus, just place them inside
> the
> plugins/Scripts/ menu structure. For example, Fiji's 'Spirals' example
> (which is designed to demonstrate how little scientists *should* trust
> their eyes when it comes to red-green merges) is stored in
> plugins/Scripts/File/Open_Samples/Spirals_.ijm and consequently gets
> installed into File>Open Samples>Spirals .

Thanks for that !
That's very useful.

And thanks for your email.

Regards,

Romain


On 2014-07-15 20:12, Johannes Schindelin wrote:

> Hi Romain,
>
> On Tue, 15 Jul 2014, Romwere wrote:
>
>> Hi Wayne, Curtis,
>> Yes, you're right. I have been using Fiji and not ImageJ.
>> I (wrongly) assumed it was a feature of ImageJ and not Fiji. Sorry
>> about
>> that.
>>
>> As you both suggested, I will then report a bug.
>> Thanks a lot for your help.
>
> Please note that the best way to ship macros and scripts to users is to
> make a new update site.
>
> To put macros or scripts into arbitrary menus, just place them inside
> the
> plugins/Scripts/ menu structure. For example, Fiji's 'Spirals' example
> (which is designed to demonstrate how little scientists *should* trust
> their eyes when it comes to red-green merges) is stored in
> plugins/Scripts/File/Open_Samples/Spirals_.ijm and consequently gets
> installed into File>Open Samples>Spirals .
>
> Ciao,
> Johannes

--
Romain Laine, PhD in Biophotonics
Laser Analytics Group
Department of Chemical Engineering and Biotechnology
University of Cambridge
New Museums Site
Pembroke Street, Cambridge, CB2 3RA, UK
T: ([phone]

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

[Romwere]

Thanks Curtis as well !

[ctrueden]

Hi Romain,

> What is an update site?

An update site is a website that extends ImageJ's capabilities.

> What is the advantage of it? And how to do it?

With update sites, you do not need to manually download and install
anything; ImageJ takes care of it for you.

http://imagej.net/List_of_update_sites

Regards,
Curtis


On Wed, Jul 16, 2014 at 3:23 AM, R.F. Laine <[hidden email]> wrote:

> Hi Johannes,
>
>
>  Please note that the best way to ship macros and scripts to users is to
>> make a new update site.
>>
>
> Sorry. What is an update site?
> Please bear in mind, I have only been using ImageJ macro language using
> Fiji, not Java.
> What is the advantage of it? And how to do it?
>
>
>  To put macros or scripts into arbitrary menus, just place them inside the
>> plugins/Scripts/ menu structure. For example, Fiji's 'Spirals' example
>> (which is designed to demonstrate how little scientists *should* trust
>> their eyes when it comes to red-green merges) is stored in
>> plugins/Scripts/File/Open_Samples/Spirals_.ijm and consequently gets
>> installed into File>Open Samples>Spirals .
>>
>
> Thanks for that !
> That's very useful.
>
> And thanks for your email.
>
> Regards,
>
> Romain
>
>
>
> On 2014-07-15 20:12, Johannes Schindelin wrote:
>
>> Hi Romain,
>>
>> On Tue, 15 Jul 2014, Romwere wrote:
>>
>>  Hi Wayne, Curtis,
>>> Yes, you're right. I have been using Fiji and not ImageJ.
>>> I (wrongly) assumed it was a feature of ImageJ and not Fiji. Sorry about
>>> that.
>>>
>>> As you both suggested, I will then report a bug.
>>> Thanks a lot for your help.
>>>
>>
>> Please note that the best way to ship macros and scripts to users is to
>> make a new update site.
>>
>> To put macros or scripts into arbitrary menus, just place them inside the
>> plugins/Scripts/ menu structure. For example, Fiji's 'Spirals' example
>> (which is designed to demonstrate how little scientists *should* trust
>> their eyes when it comes to red-green merges) is stored in
>> plugins/Scripts/File/Open_Samples/Spirals_.ijm and consequently gets
>> installed into File>Open Samples>Spirals .
>>
>> Ciao,
>> Johannes
>>
>
> --
> Romain Laine, PhD in Biophotonics
> Laser Analytics Group
> Department of Chemical Engineering and Biotechnology
> University of Cambridge
> New Museums Site
> Pembroke Street, Cambridge, CB2 3RA, UK
> T: ([phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[dscho]

Hi,

On Wed, 16 Jul 2014, Curtis Rueden wrote:

> > What is an update site?
>
> An update site is a website that extends ImageJ's capabilities.

While it is true that update sites are hosted on web servers, that is more
out of convenience (so we did not have to invent another protocol nor
punch holes into firewalls).

It is better to think of update sites as web space used by the updater
enabling users to share their macros/scripts/plugins with other
researchers.

> > What is the advantage of it? And how to do it?
>
> With update sites, you do not need to manually download and install
> anything; ImageJ takes care of it for you.
>
> http://imagej.net/List_of_update_sites

While this page does not really point out the advantages of update sites,
it is actually not necessary to point them out, or is it? Is it really so
non-obvious that standing on each other's shoulders accelerates science
and brings you citations?

Ciao,
Johannes

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

[ctrueden]

Hi Dscho,

> > An update site is a website that extends ImageJ's capabilities.
>
> While it is true that update sites are hosted on web servers, that is
> more out of convenience (so we did not have to invent another protocol
> nor punch holes into firewalls).
>
> It is better to think of update sites as web space used by the updater
> enabling users to share their macros/scripts/plugins with other
> researchers.

The brief description I sent was copy/pasted from the ImageJ wiki, because
it was the only description of them anywhere, and I did not have time to
write a new description.

But since you do not like it, I have now improved the language and
consistency of the update-site-related pages on the ImageJ wiki:

* http://imagej.net/How_to_follow_a_3rd_party_update_site
* http://imagej.net/How_to_set_up_and_populate_an_update_site
* http://imagej.net/How_to_upload_to_core_update_sites
* http://imagej.net/List_of_update_sites

They now all share the same introductory paragraph explaining what update
sites are, as well as a floating right-hand menu with links to all four
pages.

The new language, adapted from what you wrote above, is:

"An update site is web space used by the Updater which enables users to
share their macros, scripts and plugins with other researchers. With update
sites, you do not need to manually download and install anything; ImageJ
takes care of it for you."

If you wish to improve it, you can edit
http://imagej.net/Template:UpdateSites to do so.

> While this page does not really point out the advantages of update
> sites, it is actually not necessary to point them out, or is it?

Personally, I think it would be useful if the ImageJ website outlined the
advantages more clearly and succinctly.

-Curtis



On Wed, Jul 16, 2014 at 9:30 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Wed, 16 Jul 2014, Curtis Rueden wrote:
>
> > > What is an update site?
> >
> > An update site is a website that extends ImageJ's capabilities.
>
> While it is true that update sites are hosted on web servers, that is more
> out of convenience (so we did not have to invent another protocol nor
> punch holes into firewalls).
>
> It is better to think of update sites as web space used by the updater
> enabling users to share their macros/scripts/plugins with other
> researchers.
>
> > > What is the advantage of it? And how to do it?
> >
> > With update sites, you do not need to manually download and install
> > anything; ImageJ takes care of it for you.
> >
> > http://imagej.net/List_of_update_sites
>
> While this page does not really point out the advantages of update sites,
> it is actually not necessary to point them out, or is it? Is it really so
> non-obvious that standing on each other's shoulders accelerates science
> and brings you citations?
>
> Ciao,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Romwere]

To all, thanks for your help.

I would like a quick clarification. Talking to Johannes, I am under the impression that the option of exporting a macro as .jar is gone on purpose and should only be available for java script.
What is the reason why that is the case, if it is, since this option was very useful and worked fine?