Re: [fiji-devel] Fiji vs ImageJ discrepancy.

[Johannes Schindelin]

Hi Jerome,

On Sat, 17 Nov 2012, jerome....@gmail.com wrote:

> The plugins.config file inside ImageJ plugins jar files allows adding menus
> entries like this:
> Menu>Submenu, "Command", Plugin
>
> In ImageJ you can use:
> Plugins>My Plugin, "My Command",
> ij.plugin.Macro_Runner("JAR:macros/my_macro.ijm")
>
> to install a 'Plugins>My Plugin>My Command' menu command that is provided
> by 'my_macro.ijm' macro in a 'macros' folder inside your jar file.
>
> For some reason, this does not work in Fiji.

Thanks for the Bug Report. However, I am missing information such as: what
ImageJ version are you using, what is the exact symptom of the problem?

I'd also like to suggest to use Fiji's Help-Report a Bug feature so that
useful information such as the ImageJ version is provided automatically.

Thanks!
Johannes
>
> see:
> http://fiji.sc/cgi-bin/gitweb.cgi?p=imagej.git;a=blob;f=ij/plugin/Macro_Runner.java#l36
>
> Sincerely,
> Jerome
>
> --
> Please avoid top-posting, and please make sure to reply-to-all!
>
> Mailing list web interface: http://groups.google.com/group/fiji-devel
>

[Jan Eglinger]

Hi Jerome,

just for follow-up on this mailing list:
I filed a bug report at
http://fiji.sc/bugzilla/show_bug.cgi?id=577
because Fiji still isn't showing the missing menu entries unless you run
'Help>Refresh Menus'.

Do you plan to setup an update site [1] for your FigureJ plugin? I know
a lot of users who would appreciate not having to check back at the
website if there are updates available every now and then.

Just out of interest: is the source code of FigureJ available for the
public? I would love to learn from it.

Jan

[1] see http://fiji.sc/List_of_update_sites

On 17.11.2012 9:32 PM, jerome....@gmail.com wrote:
> Hi Johannes.
>
> Sorry, I'll use Report a Bug next time.
>
> Blank Fiji fully updated today. ImageJ 1.47e
> vs ImageJ 1.47e
>
> Symptom:
> in Fiji, the commands added with the plugins.config file of a jarred
> plugin with ij.plugin.Macro_Runner("JAR:macros/my_macro.ijm") are
> missing from the plugin's menu.
>
> You can test this with the attached sample jar file. You get 2 menus
> entries in ImageJ, but only one in Fiji.
> Thanks a lot!
>
> Jerome

>
>
> On Saturday, 17 November 2012 20:43:48 UTC+1, Johannes Schindelin wrote:
>
> Hi Jerome,
>

> <http://groups.google.com/group/fiji-devel>

[Johannes Schindelin]

Re-adding the Fiji development mailing list as I do not see any benefit in
excluding the public from this discussion.

On Wed, 13 Mar 2013, Johannes Schindelin wrote:

> Hi Jerome,
>

> On Wed, 13 Mar 2013, Jerome Mutterer wrote:
>
> > I'm all ready for the update site, but it seems that FigureJ does not
> > work with the Fiji version of LSM Reader. It works with the attached
> > version, however, so maybe, you'll want to update LSM Reader in the main
> > Fiji updater before advertising the new update site.
>
> In light of the synchronization problems with LSM Reader upstream and Fiji
> lagging behind, I am in favor of removing LSM Reader altogether from
> Fiji's source code.
>
> Unless I hear strong objections, I will do that later.
>
> Ciao,
> Dscho
>

[Jan Eglinger]

Hi,

On 13.03.2013 9:13 PM, Johannes Schindelin wrote:
>> In light of the synchronization problems with LSM Reader upstream and Fiji
>> lagging behind, I am in favor of removing LSM Reader altogether from
>> Fiji's source code.
>>
>> Unless I hear strong objections, I will do that later.

Does that mean you'll also remove LSM_Reader.jar from the Fiji update
site? Jerome, what about creating an own update site for the LSM Reader
in that case?

What about keeping files up-to-date by mirroring the original repo (is
there any?)?

Jan

[Jan Eglinger]

Hi Jerome,

On 13.03.2013 4:21 PM, Jerome Mutterer wrote:
>
> Uploading the plugin to the update site worked OK, but I cannot seem to
> be able to follow it from another computer here. Could please check it
> from your place?
>
> site name: IBMP
> site address: http://www-ibmp.u-strasbg.fr/fijiupdates/
>
As it seems, the update site is still empty. Adding it in the Fiji
updater gives no errors, but no plugins are shown.
The db.xml.gz from your site contains (after unzipping) the tag
"<pluginRecords/>" indicating that the update site was initialized, but
no plugins were uploaded yet.

Jan

[Curtis Rueden]

Hi Jerome,

> As it seems, the update site is still empty.

FYI, a mistake I often make when uploading to an update site is to hit the "Update" button rather than "Upload" after flagging a file for upload. If uploaded successfully you will see some feedback confirming such in the UI.

-Curtis

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[Johannes Schindelin]

Hi Jerome,

On Thu, 14 Mar 2013, jerome....@gmail.com wrote:

> I checked the update sites from other labs that are listed under
> http://fiji.sc/List_of_update_sites and found that none of them has the
> *.lock file, so I suspect something is not fully functionnal with the
> uploading, even if I'm getting the success message from the updater.

A bummer that it does not work for you.

Maybe the Console log has more information.

Ciao,
Johannes

[Johannes Schindelin]

Hi Jerome,

On Wed, 27 Mar 2013, jerome....@gmail.com wrote:

> Hi, a little follow up about setting up our Fiji update site.
> It seems that the updater always leaves the db.xml.gz file with r-- r-- r--
> permissions. So the next time I upload or update a plugin it fails unless I
> manually set write permissions to the db.xml.gz file prior to uploading.
> Otherwise, I'm getting the db.xml.gz.lock file, and the following in the
> debug log:
>
> *err >override r--r--r-- mutterer/admin for
> /Library/WebServer/Documents/fijiupdates/db.xml.gz? (y/n [n]) not
> overwritten*

Oh. So your "mv" program is somehow configured to ask always whether to
overwrite files, *even if* started in non-interactive mode. Hmm. I thought
that was not possible on Unix, but I guess I stand corrected.

Can you try after overwriting jars/ij-updater-ssh-2.0.0-SNAPSHOT.jar with
the attached version?

The change I made can be seen here: http://git.io/tgfMjg

I would appreciate feedback on this issue so I can either try something
else or merge the fix into mainline.

Ciao,
Johannes

[Jan Eglinger]

Hi all,

thanks for setting up the update site for FigureJ and the LSM_Reader.
It's really great to have such a comfortable update mechanism. Many
thanks to Johannes in this regard for your work with the updater.

Since I'd like to use FigureJ for teaching a small practical course next
week, I was curious if we can get rid of that tiny little bug that
prevents the FigureJ menu entries from being displayed right away (and
not only after "Refresh Menus") by that time:
http://fiji.sc/bugzilla/show_bug.cgi?id=577

I would have liked to propose a fix myself, but have no clue about how
the ImageJ menu is being built on start-up and after 'Refresh Menus'.

Any suggestions?
Jan


On 27.03.2013 4:34 PM, jerome....@gmail.com wrote:
> Hi Johannes,
>
> Thanks for the updated version of the updater.
> The -f did the job: it works perfectly now.
> FYI, the system on this machine is MacOsX 10.5 server.
>
> Thanks a lot Johannes,
> sincerely,
>
> Jerome.

>
>
> On Wednesday, 27 March 2013 16:09:05 UTC+1, Johannes Schindelin wrote:
>
> Hi Jerome,
>