Broken Plugin w/ImageJ2

[Rebecca Keller]

Dear List,

does anyone know why upon changing over to IJ2 the Stower's plugins seem to
be broken? I get the following error message:

Plugin or class not found: "stack_temporal_fft_jru_v1"

(java.lang.ClassNotFoundException: stack_temporal_fft_jru_v1)


Does ij2 look somewhere else for the plugins? Any ideas?

JPK

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

[dscho]

Hi Rebecca,

On Tue, 1 Jul 2014, Rebecca Keller wrote:

> does anyone know why upon changing over to IJ2 the Stower's plugins seem to
> be broken? I get the following error message:
>
> Plugin or class not found: "stack_temporal_fft_jru_v1"
>
> (java.lang.ClassNotFoundException: stack_temporal_fft_jru_v1)
>
>
> Does ij2 look somewhere else for the plugins? Any ideas?

ImageJ2 tries to be as backwards-compatible as possible (believe me, this
has not always been easy). So it's a bummer for me that you see this
problem.

Could you please describe in detail how I can reproduce your problem on my
side? Or even better, call the "Make Fiji Package" command from the
command finder and upload the resulting .zip file via Help>Upload Sample
Image (and notifying me)?

Ciao,
Johannes

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

[Unruh, Jay-2]

Hi Johannes,

I am seeing the same issue.  My current version is 2.0.0-rc-8/1.49c.  That plugin doesn't have any gui elements other than the generic dialog.  In addition, my other plugins calling the same FFT routine don't have an issue.  I don't see the same problem with a version of Fiji that is ~1 month old.  I also don't see the problem if I compile a renamed version (stack_temporal_fft_jru_v2.java) from the script editor or run it as a stand-alone plugin compiled with the old ImageJ compiler.  On a related note, the stand alone plugin compiles and runs from my temp folder even if I have a precompiled class file in the plugins folder.  That's a bit problematic from plugin developer's standpoint.  I ran with the debug command switch and nothing showed up in the console.

Jay

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Johannes Schindelin
Sent: Wednesday, July 02, 2014 9:04 AM
To: [hidden email]
Subject: Re: Broken Plugin w/ImageJ2

Hi Rebecca,

On Tue, 1 Jul 2014, Rebecca Keller wrote:

> does anyone know why upon changing over to IJ2 the Stower's plugins
> seem to be broken? I get the following error message:
>
> Plugin or class not found: "stack_temporal_fft_jru_v1"
>
> (java.lang.ClassNotFoundException: stack_temporal_fft_jru_v1)
>
>
> Does ij2 look somewhere else for the plugins? Any ideas?

ImageJ2 tries to be as backwards-compatible as possible (believe me, this has not always been easy). So it's a bummer for me that you see this problem.

Could you please describe in detail how I can reproduce your problem on my side? Or even better, call the "Make Fiji Package" command from the command finder and upload the resulting .zip file via Help>Upload Sample Image (and notifying me)?

Ciao,
Johannes

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

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

[dscho]

Hi Jay,

On Wed, 2 Jul 2014, Unruh, Jay wrote:

> I am seeing the same issue.  My current version is 2.0.0-rc-8/1.49c.
> That plugin doesn't have any gui elements other than the generic dialog.
> In addition, my other plugins calling the same FFT routine don't have an
> issue.  I don't see the same problem with a version of Fiji that is ~1
> month old.  I also don't see the problem if I compile a renamed version
> (stack_temporal_fft_jru_v2.java) from the script editor or run it as a
> stand-alone plugin compiled with the old ImageJ compiler.  On a related
> note, the stand alone plugin compiles and runs from my temp folder even
> if I have a precompiled class file in the plugins folder.  That's a bit
> problematic from plugin developer's standpoint.  I ran with the debug
> command switch and nothing showed up in the console.

Please give me a clear recipe to reproduce the issue. It's not like I
planned to address this issue today, there is enough I have to do to fill
an entire month of 80-hour weeks. And then some.

So could you please make it a *little* easier for me to address your
problem? Something like: I made a Fiji package and uploaded it via
Help>Upload Sample Image and if you unpack it, click on Plugins>ABC. I see
Blub and I expect Blob instad.

Thank you,
Johannes

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

[ctrueden]

Hi Dscho,

> So could you please make it a *little* easier for me to address

* Enable the Stowers update site.
* Press L for Command Finder.
* Type "stack tem" into the Search box.
* Run the command "stack temporal fft jru v1" that matches.

Error message is:

Plugin or class not found: "stack_temporal_fft_jru_v1
(java.lang.ClassNotFoundException: stack_temporal_fft_jru_v1)

I'm debugging it now...

-Curtis


On Wed, Jul 2, 2014 at 10:50 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Jay,
>
> On Wed, 2 Jul 2014, Unruh, Jay wrote:
>
> > I am seeing the same issue.  My current version is 2.0.0-rc-8/1.49c.
> > That plugin doesn't have any gui elements other than the generic dialog.
> > In addition, my other plugins calling the same FFT routine don't have an
> > issue.  I don't see the same problem with a version of Fiji that is ~1
> > month old.  I also don't see the problem if I compile a renamed version
> > (stack_temporal_fft_jru_v2.java) from the script editor or run it as a
> > stand-alone plugin compiled with the old ImageJ compiler.  On a related
> > note, the stand alone plugin compiles and runs from my temp folder even
> > if I have a precompiled class file in the plugins folder.  That's a bit
> > problematic from plugin developer's standpoint.  I ran with the debug
> > command switch and nothing showed up in the console.
>
> Please give me a clear recipe to reproduce the issue. It's not like I
> planned to address this issue today, there is enough I have to do to fill
> an entire month of 80-hour weeks. And then some.
>
> So could you please make it a *little* easier for me to address your
> problem? Something like: I made a Fiji package and uploaded it via
> Help>Upload Sample Image and if you unpack it, click on Plugins>ABC. I see
> Blub and I expect Blob instad.
>
> Thank you,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[ctrueden]

Hi all,

> Plugin or class not found: "stack_temporal_fft_jru_v1
> (java.lang.ClassNotFoundException: stack_temporal_fft_jru_v1)
>
> I'm debugging it now...

The problem is that the class is actually called stack_temporal_FFT_jru_v1.
But the plugins.config of Jay_Plugins2.jar lists it as
stack_temporal_fft_jru_v1. The case matters.

Jay, I would suggest uploading a new version with the correct case.

Regards,
Curtis



On Wed, Jul 2, 2014 at 11:03 AM, Curtis Rueden <[hidden email]> wrote:

> Hi Dscho,
>
> > So could you please make it a *little* easier for me to address
>
> * Enable the Stowers update site.
> * Press L for Command Finder.
> * Type "stack tem" into the Search box.
> * Run the command "stack temporal fft jru v1" that matches.
>
> Error message is:
>
> Plugin or class not found: "stack_temporal_fft_jru_v1
> (java.lang.ClassNotFoundException: stack_temporal_fft_jru_v1)
>
> I'm debugging it now...
>
> -Curtis
>
>
> On Wed, Jul 2, 2014 at 10:50 AM, Johannes Schindelin <
> [hidden email]> wrote:
>
>> Hi Jay,
>>
>> On Wed, 2 Jul 2014, Unruh, Jay wrote:
>>
>> > I am seeing the same issue.  My current version is 2.0.0-rc-8/1.49c.
>> > That plugin doesn't have any gui elements other than the generic dialog.
>> > In addition, my other plugins calling the same FFT routine don't have an
>> > issue.  I don't see the same problem with a version of Fiji that is ~1
>> > month old.  I also don't see the problem if I compile a renamed version
>> > (stack_temporal_fft_jru_v2.java) from the script editor or run it as a
>> > stand-alone plugin compiled with the old ImageJ compiler.  On a related
>> > note, the stand alone plugin compiles and runs from my temp folder even
>> > if I have a precompiled class file in the plugins folder.  That's a bit
>> > problematic from plugin developer's standpoint.  I ran with the debug
>> > command switch and nothing showed up in the console.
>>
>> Please give me a clear recipe to reproduce the issue. It's not like I
>> planned to address this issue today, there is enough I have to do to fill
>> an entire month of 80-hour weeks. And then some.
>>
>> So could you please make it a *little* easier for me to address your
>> problem? Something like: I made a Fiji package and uploaded it via
>> Help>Upload Sample Image and if you unpack it, click on Plugins>ABC. I see
>> Blub and I expect Blob instad.
>>
>> Thank you,
>> Johannes
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>

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

[Rebecca Keller]

So the "case" is closed, I guess?

JPK


On Wed, Jul 2, 2014 at 12:07 PM, Curtis Rueden <[hidden email]> wrote:

> Hi all,
>
> > Plugin or class not found: "stack_temporal_fft_jru_v1
> > (java.lang.ClassNotFoundException: stack_temporal_fft_jru_v1)
> >
> > I'm debugging it now...
>
> The problem is that the class is actually called stack_temporal_FFT_jru_v1.
> But the plugins.config of Jay_Plugins2.jar lists it as
> stack_temporal_fft_jru_v1. The case matters.
>
> Jay, I would suggest uploading a new version with the correct case.
>
> Regards,
> Curtis
>
>
>
> On Wed, Jul 2, 2014 at 11:03 AM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Dscho,
> >
> > > So could you please make it a *little* easier for me to address
> >
> > * Enable the Stowers update site.
> > * Press L for Command Finder.
> > * Type "stack tem" into the Search box.
> > * Run the command "stack temporal fft jru v1" that matches.
> >
> > Error message is:
> >
> > Plugin or class not found: "stack_temporal_fft_jru_v1
> > (java.lang.ClassNotFoundException: stack_temporal_fft_jru_v1)
> >
> > I'm debugging it now...
> >
> > -Curtis
> >
> >
> > On Wed, Jul 2, 2014 at 10:50 AM, Johannes Schindelin <
> > [hidden email]> wrote:
> >
> >> Hi Jay,
> >>
> >> On Wed, 2 Jul 2014, Unruh, Jay wrote:
> >>
> >> > I am seeing the same issue.  My current version is 2.0.0-rc-8/1.49c.
> >> > That plugin doesn't have any gui elements other than the generic
> dialog.
> >> > In addition, my other plugins calling the same FFT routine don't have
> an
> >> > issue.  I don't see the same problem with a version of Fiji that is ~1
> >> > month old.  I also don't see the problem if I compile a renamed
> version
> >> > (stack_temporal_fft_jru_v2.java) from the script editor or run it as a
> >> > stand-alone plugin compiled with the old ImageJ compiler.  On a
> related
> >> > note, the stand alone plugin compiles and runs from my temp folder
> even
> >> > if I have a precompiled class file in the plugins folder.  That's a
> bit
> >> > problematic from plugin developer's standpoint.  I ran with the debug
> >> > command switch and nothing showed up in the console.
> >>
> >> Please give me a clear recipe to reproduce the issue. It's not like I
> >> planned to address this issue today, there is enough I have to do to
> fill
> >> an entire month of 80-hour weeks. And then some.
> >>
> >> So could you please make it a *little* easier for me to address your
> >> problem? Something like: I made a Fiji package and uploaded it via
> >> Help>Upload Sample Image and if you unpack it, click on Plugins>ABC. I
> see
> >> Blub and I expect Blob instad.
> >>
> >> Thank you,
> >> Johannes
> >>
> >> --
> >> 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

[Unruh, Jay-2]

I just realized it as Curtis's e-mail came.  I fixed it but with the newer version of FIJI, my "upload to server" button is gone despite the presence of the server address in the "manage update sites" window.  Any idea how to get that back?

Anyway, the new jar files are available here: http://research.stowers.org/imagejplugins/zipped_plugins.html

I will upload to the update site when I figure out the uploading settings.

Jay

 

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Rebecca Keller
Sent: Wednesday, July 02, 2014 11:28 AM
To: [hidden email]
Subject: Re: Broken Plugin w/ImageJ2

So the "case" is closed, I guess?

JPK


On Wed, Jul 2, 2014 at 12:07 PM, Curtis Rueden <[hidden email]> wrote:

> Hi all,
>
> > Plugin or class not found: "stack_temporal_fft_jru_v1
> > (java.lang.ClassNotFoundException: stack_temporal_fft_jru_v1)
> >
> > I'm debugging it now...
>
> The problem is that the class is actually called stack_temporal_FFT_jru_v1.
> But the plugins.config of Jay_Plugins2.jar lists it as
> stack_temporal_fft_jru_v1. The case matters.
>
> Jay, I would suggest uploading a new version with the correct case.
>
> Regards,
> Curtis
>
>
>
> On Wed, Jul 2, 2014 at 11:03 AM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Dscho,
> >
> > > So could you please make it a *little* easier for me to address
> >
> > * Enable the Stowers update site.
> > * Press L for Command Finder.
> > * Type "stack tem" into the Search box.
> > * Run the command "stack temporal fft jru v1" that matches.
> >
> > Error message is:
> >
> > Plugin or class not found: "stack_temporal_fft_jru_v1
> > (java.lang.ClassNotFoundException: stack_temporal_fft_jru_v1)
> >
> > I'm debugging it now...
> >
> > -Curtis
> >
> >
> > On Wed, Jul 2, 2014 at 10:50 AM, Johannes Schindelin <
> > [hidden email]> wrote:
> >
> >> Hi Jay,
> >>
> >> On Wed, 2 Jul 2014, Unruh, Jay wrote:
> >>
> >> > I am seeing the same issue.  My current version is 2.0.0-rc-8/1.49c.
> >> > That plugin doesn't have any gui elements other than the generic
> dialog.
> >> > In addition, my other plugins calling the same FFT routine don't
> >> > have
> an
> >> > issue.  I don't see the same problem with a version of Fiji that
> >> > is ~1 month old.  I also don't see the problem if I compile a
> >> > renamed
> version
> >> > (stack_temporal_fft_jru_v2.java) from the script editor or run it
> >> > as a stand-alone plugin compiled with the old ImageJ compiler.  
> >> > On a
> related
> >> > note, the stand alone plugin compiles and runs from my temp
> >> > folder
> even
> >> > if I have a precompiled class file in the plugins folder.  That's
> >> > a
> bit
> >> > problematic from plugin developer's standpoint.  I ran with the
> >> > debug command switch and nothing showed up in the console.
> >>
> >> Please give me a clear recipe to reproduce the issue. It's not like
> >> I planned to address this issue today, there is enough I have to do
> >> to
> fill
> >> an entire month of 80-hour weeks. And then some.
> >>
> >> So could you please make it a *little* easier for me to address
> >> your problem? Something like: I made a Fiji package and uploaded it
> >> via
> >> Help>Upload Sample Image and if you unpack it, click on
> >> Help>Plugins>ABC. I
> see
> >> Blub and I expect Blob instad.
> >>
> >> Thank you,
> >> Johannes
> >>
> >> --
> >> 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

[Robert Dougherty]

Johannes,

I tried ImageJ 2.0.0-rc-9-SNAPSHOT/1.49c on a handful of my legacy plugins to check compatibility.  The first observation is that the ImageJ2 UI is reassuringly familiar.  Some of the plugins do seem to run in compiled form without complaint.  The tiff reader seems to ignore slice labels in stacks.  This breaks my main commercial product, Beamform Interactive, which relies on the labels for the acoustic frequency. "Compile and Run…" does not work on any of my plugins, and probably most legacy plugins, because they all start with import ij.*; and this produces the error "package ij does not exist".  

Bob


Robert P. Dougherty
President
OptiNav, Inc.
1414 127th Pl NE #106
Bellevue, WA 98005
[phone]
FAX [phone]
[hidden email]
www.optinav. com

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

[dscho]

Hi Jay,

On Wed, 2 Jul 2014, Unruh, Jay wrote:

> my "upload to server" button is gone

Are you sure that your "Apply changes" button does *not* change into an
"Apply changes (upload)" button after you mark the file for upload?

Ciao,
Johannes

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

[Unruh, Jay-2]

I am certain.  I also don't have an "Upload it" option from the pull down menu.  I tried "Update it" but it simply replaced my files with the old ones from my update site.

Jay

-----Original Message-----
From: Johannes Schindelin [mailto:[hidden email]]
Sent: Wednesday, July 02, 2014 12:33 PM
To: Unruh, Jay
Cc: [hidden email]
Subject: Re: Broken Plugin w/ImageJ2

Hi Jay,

On Wed, 2 Jul 2014, Unruh, Jay wrote:

> my "upload to server" button is gone

Are you sure that your "Apply changes" button does *not* change into an "Apply changes (upload)" button after you mark the file for upload?

Ciao,
Johannes

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

[dscho]

Hi Bob,

On Wed, 2 Jul 2014, Robert Dougherty wrote:

> I tried ImageJ 2.0.0-rc-9-SNAPSHOT/1.49c on a handful of my legacy
> plugins to check compatibility.

Thank you!

I am just a little concerned: how did you get 2.0.0-rc-9-SNAPSHOT? When I
start my Fiji, it still shows 2.0.0-rc-8...

> The first observation is that the ImageJ2 UI is reassuringly familiar.

This is by design. We actually started to develop new UIs, but realized
that most ImageJ users will not want to learn a new UI. So the main
improvements of ImageJ 2.0.0 will be the flexibility in future plugins.

> Some of the plugins do seem to run in compiled form without complaint.
> The tiff reader seems to ignore slice labels in stacks.

I cannot find it right now, but this is definitely on our radar!

> This breaks my main commercial product, Beamform Interactive, which
> relies on the labels for the acoustic frequency.

Could you please upload a tiny sample image via Help>Upload Sample Image?
I will finagle it into my schedule then.

> "Compile and Run…" does not work on any of my plugins, and probably most
> legacy plugins, because they all start with import ij.*; and this
> produces the error "package ij does not exist".  

Hmm... Do they work in the Script Editor?

Ciao,
Dscho

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

[dscho]

Hi Bob,

On Wed, 2 Jul 2014, Johannes Schindelin wrote:

> On Wed, 2 Jul 2014, Robert Dougherty wrote:
>
> > "Compile and Run…" does not work on any of my plugins, and probably
> > most legacy plugins, because they all start with import ij.*; and this
> > produces the error "package ij does not exist".  
>
> Hmm... Do they work in the Script Editor?

For the record, I just ran the following example in a fully up-to-date
Fiji and it worked:

-- snipsnap --
import ij.*;
import ij.plugin.*;

/**
 * This is a template for a plugin that does not require one image
 * (be it that it does not require any, or that it lets the user
 * choose more than one image in a dialog).
 */
public class A_123 implements PlugIn {
        /**
         * This method gets called by ImageJ / Fiji.
         *
         * @param arg can be specified in plugins.config
         * @see ij.plugin.PlugIn#run(java.lang.String)
         */
        @Override
        public void run(String arg) {
                IJ.log("Hello 123");
        }
}

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

[dscho]

Hi Jay,

On Wed, 2 Jul 2014, Unruh, Jay wrote:

> I am certain.  I also don't have an "Upload it" option from the pull
> down menu.  I tried "Update it" but it simply replaced my files with the
> old ones from my update site.

I would like to request the same favor as I asked others who reported the
same problem (you probably missed my replies)? Call "Make Fiji Package"
and then upload the .zip via "Upload Sample Image".

After that, I will make a serious effort of finding some time to help you.

Ciao,
Johannes

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

[Robert Dougherty]

Dscho,

On Jul 2, 2014, at 12:20 PM, Johannes Schindelin <[hidden email]> wrote:

> Hi Bob,
>
> On Wed, 2 Jul 2014, Johannes Schindelin wrote:
>
>> On Wed, 2 Jul 2014, Robert Dougherty wrote:
>>
>>> "Compile and Run…" does not work on any of my plugins, and probably
>>> most legacy plugins, because they all start with import ij.*; and this
>>> produces the error "package ij does not exist".  
>>
>> Hmm... Do they work in the Script Editor?
>
> For the record, I just ran the following example in a fully up-to-date
> Fiji and it worked:
>
> -- snipsnap --
> import ij.*;
> import ij.plugin.*;
>
> /**
> * This is a template for a plugin that does not require one image
> * (be it that it does not require any, or that it lets the user
> * choose more than one image in a dialog).
> */
> public class A_123 implements PlugIn {
> /**
> * This method gets called by ImageJ / Fiji.
> *
> * @param arg can be specified in plugins.config
> * @see ij.plugin.PlugIn#run(java.lang.String)
> */
> @Override
> public void run(String arg) {
> IJ.log("Hello 123");
> }
> }

I'm not going through Fiji.  I got the latest ImageJ2 release from http://developer.imagej.net/downloads.
I'm repeating it now, choosing the latest stable release, v2.0.0-rc-2.  Click on the link, wait for it to download, expand, move the application ImageJ to Applications (on my Mac, 10.8.5). Control-click, show package contents.  Put A_123.java into the plugins folder.  Start ImageJ.  Click OK to "Use SCIFIO when opening files" (Humm…).
Do "Plugins/Compile and Run…" A_123.java  Error messages:
/Applications/ImageJ.app/plugins/A_123.java:1: package ij does not exist
import ij.*;
and then more related errors.

Bob



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

[Gabriel Landini]

On Wednesday 02 Jul 2014 18:31:28 you wrote:
> I am certain.  I also don't have an "Upload it" option from the pull down
> menu.  I tried "Update it" but it simply replaced my files with the old
> ones from my update site.

Sorry to barge in... isn't the same problem I am having now and reported to
the Fiji-devel list?

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

[Robert Dougherty]

Dscho,

>
> Could you please upload a tiny sample image via Help>Upload Sample Image?
> I will finagle it into my schedule then.

I uploaded tiny_IQ.tif.  (To the cloud?)  It represents the first two frequencies (out of 4094) of a cross spectral matrix for a 92 channel phased array.  The first slice is the real part of the CSM for the first frequency, and the second slice is the imaginary part.  The label of the first slice is supposed to be "I 23.44 0.00", but in ImageJ2 the slice labels  are blank. I am able to add slice labels using Stack Sorter.
>
>> "Compile and Run…" does not work on any of my plugins, and probably most
>> legacy plugins, because they all start with import ij.*; and this
>> produces the error "package ij does not exist".  
>
> Hmm... Do they work in the Script Editor?

Your sample A_123 does, and Script Editor is an interesting discovery!  I have not explored it for bigger things yet.

Bob

Robert P. Dougherty
President
OptiNav, Inc.
1414 127th Pl NE #106
Bellevue, WA 98005
[phone]
FAX [phone]
[hidden email]
www.optinav. com

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

[dscho]

Hi Jay,

On Wed, 2 Jul 2014, Unruh, Jay wrote:

> Done.  The file name is:
>
> fiji-win64-20140702023243.zip

I could reproduce and fix the problem (I believe). Version 0.4.3 of the
updater fixes the problem (it took a little bit longer because I added a
regression test that should prevent similar breakages in the future).

Ciao,
Johannes

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

[dscho]

Hi Bob,

On Wed, 2 Jul 2014, Robert Dougherty wrote:

> > Could you please upload a tiny sample image via Help>Upload Sample
> > Image?  I will finagle it into my schedule then.
>
> I uploaded tiny_IQ.tif.

Thank you!

> (To the cloud?)

Heh... not really. To a protected space on LOCI's servers that is
accessible via the Fiji/ImageJ wiki for trusted accounts (it is not enough
for random people to register an account, they have to be added to a
special user group by an administrator).

> It represents the first two frequencies (out of 4094) of a cross
> spectral matrix for a 92 channel phased array.  The first slice is the
> real part of the CSM for the first frequency, and the second slice is
> the imaginary part.  The label of the first slice is supposed to be "I
> 23.44 0.00", but in ImageJ2 the slice labels  are blank. I am able to
> add slice labels using Stack Sorter.

I *should* be able to figure out a way to resurrect those slice labels.
It might take until after Independence Day, though... sorry!

> >> "Compile and Run…" does not work on any of my plugins, and probably
> >> most legacy plugins, because they all start with import ij.*; and
> >> this produces the error "package ij does not exist".  
> >
> > Hmm... Do they work in the Script Editor?
>
> Your sample A_123 does, and Script Editor is an interesting discovery!
> I have not explored it for bigger things yet.

It is really one of the neatest things developed in the Fiji context, and
it has been "liberated" into the BSD-licensed ImageJ2 project. The best
thing about the move to ImageJ2 is that it integrates with the powerful
SciJava scripting framework, i.e. the languages themselves are decoupled
from how they are used, making it utterly easy to add a language without
touching the script editor source or the SciJava scripting source at all.

Ciao,
Dscho

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

[dscho]

Hi Bob,

On Wed, 2 Jul 2014, Robert Dougherty wrote:

> Dscho,
>
> On Jul 2, 2014, at 12:20 PM, Johannes Schindelin
> <[hidden email]> wrote:
>
> > For the record, I just ran the following example in a fully up-to-date
> > Fiji and it worked:
> >
> > -- snipsnap --
> > import ij.*;
> > import ij.plugin.*;
> >
> > /**
> > * This is a template for a plugin that does not require one image
> > * (be it that it does not require any, or that it lets the user
> > * choose more than one image in a dialog).
> > */
> > public class A_123 implements PlugIn {
> > /**
> > * This method gets called by ImageJ / Fiji.
> > *
> > * @param arg can be specified in plugins.config
> > * @see ij.plugin.PlugIn#run(java.lang.String)
> > */
> > @Override
> > public void run(String arg) {
> > IJ.log("Hello 123");
> > }
> > }
>
> I'm not going through Fiji.  I got the latest ImageJ2 release from
> http://developer.imagej.net/downloads.

Ah, there lies the rub. We have been so busy addressing bugs, updating the
issue tracker and BugZilla, deploying new releases for developers and
uploading new file versions for users, that I completely forgot to update
that page.

Thanks for pointing that out!

> I'm repeating it now, choosing the latest stable release, v2.0.0-rc-2.

That release is, like, from June! That is super old ;-)

Seriously again, we have tried very hard to strike a good balance between
stability (adding regression tests with fixes, for example, which arguably
takes more time in the short run, but saves *years* of bug hunting) and
usability.

Hopefully we found a good balance between diligent software development
and updates frequent enough to be useful. On average, we released a new
release candidate every four days, and that is only the top-level imagej
component.

So right now the release candidate I would recommend for testing is
v2.0.0-rc-3/1.49c.

But I am curious: the updater should have kicked in and suggested updating
to a newer release?

>  Click on the link, wait for it to download, expand, move the
>  application ImageJ to Applications (on my Mac, 10.8.5). Control-click,
>  show package contents.  Put A_123.java into the plugins folder.  Start
>  ImageJ.  Click OK to "Use SCIFIO when opening files" (Humm…).

If you are unsure whether you want SCIFIO, I encourage you to read the
introduction displayed when clicking on the "What is ImageJ2?" button.

I can summarize, of course: In short, SCIFIO is an application-independent
scientific image input/output library, intended to be flexible, extensible
and modular. For context: the same awesome Curtis Rueden who architected
Bio-Formats also served as architect for SCIFIO.

> Do "Plugins/Compile and Run…" A_123.java  Error messages:
> /Applications/ImageJ.app/plugins/A_123.java:1: package ij does not exist
> import ij.*;
> and then more related errors.

For what it's worth, I just tested it in 2.0.0-rc-8/1.49c and it works as
far as I can tell...

Ciao,
Dscho

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