Re: TANGO

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Re: TANGO

Curtis Rueden
Hi Alex,

> One of the developers of TANGO told me to use ImageJ1 because he
> wasn't sure how the switch between libraries is managed. Do I need to
> reinstall in this case?

When he says "use ImageJ1" he means:

But please, encourage the TANGO developer to contact the imagej-devel mailing list to discuss any roadblocks to TANGO working properly in ImageJ2. It would be best for TANGO to be distributed via an ImageJ update site, which are only supported in ImageJ2.

Regards,
Curtis

On Thu, May 28, 2015 at 3:48 PM, Alexandra Bortnick <[hidden email]> wrote:
Hi Curtis,

One of the developers of TANGO told me to use ImageJ1 because he wasn't sure how the switch between libraries is managed. Do I need to reinstall in this case?

-Alex



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Re: TANGO

Curtis Rueden
I take it there is no easy way to 'downgrade' from rc-30 back to rc-29?

No. But 2.0.0-rc-29 is still ImageJ2, not ImageJ1.

However, you can try downloading the Life-Line versions of Fiji from:

Maybe one of those will work better with the Tango update site.

Regards,
Curtis

On Thu, May 28, 2015 at 4:45 PM, Alexandra <[hidden email]> wrote:
I take it there is no easy way to 'downgrade' from rc-30 back to rc-29?

-Alex 

On May 28, 2015, at 2:25 PM, Curtis Rueden <[hidden email]> wrote:

Hi Alex,

> One of the developers of TANGO told me to use ImageJ1 because he
> wasn't sure how the switch between libraries is managed. Do I need to
> reinstall in this case?

When he says "use ImageJ1" he means:

But please, encourage the TANGO developer to contact the imagej-devel mailing list to discuss any roadblocks to TANGO working properly in ImageJ2. It would be best for TANGO to be distributed via an ImageJ update site, which are only supported in ImageJ2.

Regards,
Curtis

On Thu, May 28, 2015 at 3:48 PM, Alexandra Bortnick <[hidden email]> wrote:
Hi Curtis,

One of the developers of TANGO told me to use ImageJ1 because he wasn't sure how the switch between libraries is managed. Do I need to reinstall in this case?

-Alex




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Re: TANGO

Thomas Boudier
In reply to this post by Curtis Rueden
Dear Alex and IJ2 developers,

TANGO uses its own library for image processing and object analysis. We use ImageJ and IJ1 mainly for opening images and drawing Rois of our 3D objects as a overlay of the image. We would be happy to discuss more about integration of TANGO into IJ2 . For completeness if you want to add plugins into TANGO (filtering, segmentation, or measurements),you can use our own MCIB library. We however already provide basic functions to exchange image data between TANGO and IJ1, maybe we should write, using some help, basic data exchange between TANGO and IJ2.

Best,

Thomas

PS : in copy the main developer of TANGO, Jean

On 29/05/15 05:25, Curtis Rueden wrote:
Hi Alex,

> One of the developers of TANGO told me to use ImageJ1 because he
> wasn't sure how the switch between libraries is managed. Do I need to
> reinstall in this case?

When he says "use ImageJ1" he means:

But please, encourage the TANGO developer to contact the imagej-devel mailing list to discuss any roadblocks to TANGO working properly in ImageJ2. It would be best for TANGO to be distributed via an ImageJ update site, which are only supported in ImageJ2.

Regards,
Curtis

On Thu, May 28, 2015 at 3:48 PM, Alexandra Bortnick <[hidden email]> wrote:
Hi Curtis,

One of the developers of TANGO told me to use ImageJ1 because he wasn't sure how the switch between libraries is managed. Do I need to reinstall in this case?

-Alex




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http://imagej.net/mailman/listinfo/imagej-devel


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Re: TANGO

Jean Ollion

Hello To everyone,

There is no roadblock to tango working in ij2, the problem of Alexandra is only due to a problem with the fiji updater, for some reason in her system (macosx64) only tango is updated and not mcib (but it works properly in my system, linux64). Any clue about what the problem might be?

@Curtis, in your answer to Alexandra, what do you mean by "It would be best for TANGO to be distributed via an ImageJ update site, which are only supported in ImageJ2" ?
For the moment our pugin Tango is distributed under FIJI via an official update site, and works in legacy mode (uses the "old" plugin system, and doesn't use libraries of ImageJ2). Do you mean this type of distribution won't be supported anymore?

Best,
Jean

Dear Alex and IJ2 developers,

TANGO uses its own library for image processing and object analysis. We use ImageJ and IJ1 mainly for opening images and drawing Rois of our 3D objects as a overlay of the image. We would be happy to discuss more about integration of TANGO into IJ2 . For completeness if you want to add plugins into TANGO (filtering, segmentation, or measurements),you can use our own MCIB library. We however already provide basic functions to exchange image data between TANGO and IJ1, maybe we should write, using some help, basic data exchange between TANGO and IJ2.

Best,

Thomas

PS : in copy the main developer of TANGO, Jean

On 29/05/15 05:25, Curtis Rueden wrote:
Hi Alex,

> One of the developers of TANGO told me to use ImageJ1 because he
> wasn't sure how the switch between libraries is managed. Do I need to
> reinstall in this case?

When he says "use ImageJ1" he means:

But please, encourage the TANGO developer to contact the imagej-devel mailing list to discuss any roadblocks to TANGO working properly in ImageJ2. It would be best for TANGO to be distributed via an ImageJ update site, which are only supported in ImageJ2.

Regards,
Curtis

On Thu, May 28, 2015 at 3:48 PM, Alexandra Bortnick <[hidden email]> wrote:
Hi Curtis,

One of the developers of TANGO told me to use ImageJ1 because he wasn't sure how the switch between libraries is managed. Do I need to reinstall in this case?

-Alex




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[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel


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Re: TANGO

Curtis Rueden
Hi Jean,

> @Curtis, in your answer to Alexandra, what do you mean by "It would be
> best for TANGO to be distributed via an ImageJ update site, which are
> only supported in ImageJ2" ? 

I was responding to Alexandra's statement at the beginning of the thread:

> One of the developers of TANGO told me to use ImageJ1 because he
> wasn't sure how the switch between libraries is managed.

I understand that Tango has an official update site, which is great! What I meant is that I think update sites are the best way to distribute complex plugins like Tango—and update sites only work with ImageJ2, not ImageJ1.

Hence, the advice to "use ImageJ1" struck me as odd. Based on my conversation with Alex in another thread, I think there was some confusion about what constitutes "ImageJ1" vs. "ImageJ2", which has hopefully been cleared up.

> for some reason in her system (macosx64) only tango is updated and not
> mcib (but it works properly in my system, linux64). Any clue about
> what the problem might be?

I took a look at the Tango update site, and noticed a couple of problems:

1) TANGO's platform-specific libraries are not in the correct locations. TANGO ships its libraries in lib/Linux64, lib/Win64 and lib/Mac64, which will not be added to the java.library.path properly.

- 64-bit Linux libraries should go in lib/linux64
- 64-bit Windows libraries should go in lib/win64
- OS X libraries should go in lib/macosx

You can verify this for yourself on each platform by running "ImageJ-xyz --dry-run" and noting the value of the "-Djava.library.path" argument. E.g., on my OS X system, it is:

    -Djava.library.path=/Applications/Fiji.app/lib/macosx:/Applications/Fiji.app/mm/macosx

2) TANGO's lib/Mac64 directory does not have any OS X native libraries in it. I'm not sure whether this is intentional, though.

3) The TANGO update site does not ship any mcib libraries. You can verify this by running Help > Update..., changing the View Options to "View files of the 'Tango' update site" and typing "mcib" into the Search box.

I downloaded http://sites.imagej.net/Tango/db.xml.gz and searched it for "mcib" and the string does not appear. This means that in fact, no files with "mcib" in the name have ever been uploaded to the Tango update site.

Perhaps the reason TANGO works on your Linux system is that you have the mcib library present in a different directory of the java.library.path? Perhaps a system-wide installation? You may want to test on another fresh Linux system, rather than only your developer system.

HTH,
Curtis


On Sat, May 30, 2015 at 11:35 AM, Jean Ollion <[hidden email]> wrote:

Hello To everyone,

There is no roadblock to tango working in ij2, the problem of Alexandra is only due to a problem with the fiji updater, for some reason in her system (macosx64) only tango is updated and not mcib (but it works properly in my system, linux64). Any clue about what the problem might be?

@Curtis, in your answer to Alexandra, what do you mean by "It would be best for TANGO to be distributed via an ImageJ update site, which are only supported in ImageJ2" ?
For the moment our pugin Tango is distributed under FIJI via an official update site, and works in legacy mode (uses the "old" plugin system, and doesn't use libraries of ImageJ2). Do you mean this type of distribution won't be supported anymore?

Best,
Jean

Dear Alex and IJ2 developers,

TANGO uses its own library for image processing and object analysis. We use ImageJ and IJ1 mainly for opening images and drawing Rois of our 3D objects as a overlay of the image. We would be happy to discuss more about integration of TANGO into IJ2 . For completeness if you want to add plugins into TANGO (filtering, segmentation, or measurements),you can use our own MCIB library. We however already provide basic functions to exchange image data between TANGO and IJ1, maybe we should write, using some help, basic data exchange between TANGO and IJ2.

Best,

Thomas

PS : in copy the main developer of TANGO, Jean

On 29/05/15 05:25, Curtis Rueden wrote:
Hi Alex,

> One of the developers of TANGO told me to use ImageJ1 because he
> wasn't sure how the switch between libraries is managed. Do I need to
> reinstall in this case?

When he says "use ImageJ1" he means:

But please, encourage the TANGO developer to contact the imagej-devel mailing list to discuss any roadblocks to TANGO working properly in ImageJ2. It would be best for TANGO to be distributed via an ImageJ update site, which are only supported in ImageJ2.

Regards,
Curtis

On Thu, May 28, 2015 at 3:48 PM, Alexandra Bortnick <[hidden email]> wrote:
Hi Curtis,

One of the developers of TANGO told me to use ImageJ1 because he wasn't sure how the switch between libraries is managed. Do I need to reinstall in this case?

-Alex




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[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel



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Re: TANGO

Jean Ollion

Hello Curtis,
Thank you for your detailed answer.
Another developer took care of the distribution on the fiji update site so i'm not aware of these problems i will look at it. Though I think the system specific files are only installation scripts for the mongodb database, and do not need to be included in the java.library.path

About the confusion Ij1/Ij2 yes it has been cleared up, thank you. i wasn't aware that fiji was already ij2 so when i said "use imagej1" it actually meant "stay in legacy mode", but anyway it wasn'f the problem.

About mcib, it is an independent update site, and used as a dependency of tango (this is documented on tango's website but still not on the readme file of the update site, wich is bad!). We already tested this installation on fresh linux, windows and macosx systems, including Alexandra's system. The problem Alexandra is experimenting is recent, i am trying to solve it with her, if we don't manage, i will ask you for advice.
Best,
Jean

Le 31 mai 2015 10:06, "Curtis Rueden" <[hidden email]> a écrit :
Hi Jean,

> @Curtis, in your answer to Alexandra, what do you mean by "It would be
> best for TANGO to be distributed via an ImageJ update site, which are
> only supported in ImageJ2" ? 

I was responding to Alexandra's statement at the beginning of the thread:

> One of the developers of TANGO told me to use ImageJ1 because he
> wasn't sure how the switch between libraries is managed.

I understand that Tango has an official update site, which is great! What I meant is that I think update sites are the best way to distribute complex plugins like Tango—and update sites only work with ImageJ2, not ImageJ1.

Hence, the advice to "use ImageJ1" struck me as odd. Based on my conversation with Alex in another thread, I think there was some confusion about what constitutes "ImageJ1" vs. "ImageJ2", which has hopefully been cleared up.

> for some reason in her system (macosx64) only tango is updated and not
> mcib (but it works properly in my system, linux64). Any clue about
> what the problem might be?

I took a look at the Tango update site, and noticed a couple of problems:

1) TANGO's platform-specific libraries are not in the correct locations. TANGO ships its libraries in lib/Linux64, lib/Win64 and lib/Mac64, which will not be added to the java.library.path properly.

- 64-bit Linux libraries should go in lib/linux64
- 64-bit Windows libraries should go in lib/win64
- OS X libraries should go in lib/macosx

You can verify this for yourself on each platform by running "ImageJ-xyz --dry-run" and noting the value of the "-Djava.library.path" argument. E.g., on my OS X system, it is:

    -Djava.library.path=/Applications/Fiji.app/lib/macosx:/Applications/Fiji.app/mm/macosx

2) TANGO's lib/Mac64 directory does not have any OS X native libraries in it. I'm not sure whether this is intentional, though.

3) The TANGO update site does not ship any mcib libraries. You can verify this by running Help > Update..., changing the View Options to "View files of the 'Tango' update site" and typing "mcib" into the Search box.

I downloaded http://sites.imagej.net/Tango/db.xml.gz and searched it for "mcib" and the string does not appear. This means that in fact, no files with "mcib" in the name have ever been uploaded to the Tango update site.

Perhaps the reason TANGO works on your Linux system is that you have the mcib library present in a different directory of the java.library.path? Perhaps a system-wide installation? You may want to test on another fresh Linux system, rather than only your developer system.

HTH,
Curtis


On Sat, May 30, 2015 at 11:35 AM, Jean Ollion <[hidden email]> wrote:

Hello To everyone,

There is no roadblock to tango working in ij2, the problem of Alexandra is only due to a problem with the fiji updater, for some reason in her system (macosx64) only tango is updated and not mcib (but it works properly in my system, linux64). Any clue about what the problem might be?

@Curtis, in your answer to Alexandra, what do you mean by "It would be best for TANGO to be distributed via an ImageJ update site, which are only supported in ImageJ2" ?
For the moment our pugin Tango is distributed under FIJI via an official update site, and works in legacy mode (uses the "old" plugin system, and doesn't use libraries of ImageJ2). Do you mean this type of distribution won't be supported anymore?

Best,
Jean

Dear Alex and IJ2 developers,

TANGO uses its own library for image processing and object analysis. We use ImageJ and IJ1 mainly for opening images and drawing Rois of our 3D objects as a overlay of the image. We would be happy to discuss more about integration of TANGO into IJ2 . For completeness if you want to add plugins into TANGO (filtering, segmentation, or measurements),you can use our own MCIB library. We however already provide basic functions to exchange image data between TANGO and IJ1, maybe we should write, using some help, basic data exchange between TANGO and IJ2.

Best,

Thomas

PS : in copy the main developer of TANGO, Jean

On 29/05/15 05:25, Curtis Rueden wrote:
Hi Alex,

> One of the developers of TANGO told me to use ImageJ1 because he
> wasn't sure how the switch between libraries is managed. Do I need to
> reinstall in this case?

When he says "use ImageJ1" he means:

But please, encourage the TANGO developer to contact the imagej-devel mailing list to discuss any roadblocks to TANGO working properly in ImageJ2. It would be best for TANGO to be distributed via an ImageJ update site, which are only supported in ImageJ2.

Regards,
Curtis

On Thu, May 28, 2015 at 3:48 PM, Alexandra Bortnick <[hidden email]> wrote:
Hi Curtis,

One of the developers of TANGO told me to use ImageJ1 because he wasn't sure how the switch between libraries is managed. Do I need to reinstall in this case?

-Alex




_______________________________________________
ImageJ-devel mailing list
[hidden email]
http://imagej.net/mailman/listinfo/imagej-devel



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[hidden email]
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