Serious issues with the last ImageJ update

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Serious issues with the last ImageJ update

Philippe CARL
Dear all,

Since my last ImageJ update (going from the version 1.51n to 1.51o) I
experience (and this on several machines under window 7 or 10) that ImageJ
is getting completely frozen with no alternative option left then to kill
the process.

These freezings are highly non reproducible and thus sorry for not being
able to post a macro showing this issue for sure.

But I quite often experienced these issues by doing a
Image->Hyperstacks->Stack_to_hyperstack… transformation on a 1-channel,
14-z, 48-time stack image.

I also downgraded ImageJ back to the 1.50 version and there I found none of
these issues as well.

Did anybody of you experience the same problems?

Thanks a lot in advance for your hints and help.

"Make our planet great again!"

Philippe

 

Philippe CARL

Laboratoire de Biophotonique et Pharmacologie

UMR 7213 CNRS - Université de Strasbourg

Faculté de Pharmacie

74 route du Rhin

67401 ILLKIRCH

Tel : +33(0)3 68 85 41 84


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Re: Serious issues with the last ImageJ update

Cammer, Michael
I've noticed in the last few weeks that ImageJ has been freezing unpredictably.  Only way to stop it is from task manager (Win7).
I typically leave it running on my computer all day long and this new behavior is new after years of no problems with this.


_________________________________________
Michael Cammer, Optical Microscopy Specialist
http://ocs.med.nyu.edu/microscopy
http://microscopynotes.com/
Cell: (914) 309-3270

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Philippe CARL [[hidden email]]
Sent: Thursday, June 22, 2017 6:04 AM
To: [hidden email]
Subject: Serious issues with the last ImageJ update

Dear all,

Since my last ImageJ update (going from the version 1.51n to 1.51o) I
experience (and this on several machines under window 7 or 10) that ImageJ
is getting completely frozen with no alternative option left then to kill
the process.

These freezings are highly non reproducible and thus sorry for not being
able to post a macro showing this issue for sure.

But I quite often experienced these issues by doing a
Image->Hyperstacks->Stack_to_hyperstack… transformation on a 1-channel,
14-z, 48-time stack image.

I also downgraded ImageJ back to the 1.50 version and there I found none of
these issues as well.

Did anybody of you experience the same problems?

Thanks a lot in advance for your hints and help.

"Make our planet great again!"

Philippe



Philippe CARL

Laboratoire de Biophotonique et Pharmacologie

UMR 7213 CNRS - Université de Strasbourg

Faculté de Pharmacie

74 route du Rhin

67401 ILLKIRCH

Tel : +33(0)3 68 85 41 84


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Re: Serious issues with the last ImageJ update

ctrueden
Hi everyone,

It would be helpful if someone could generate and share a stack trace from
when a hang occurs. Please see:

https://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Jun 22, 2017 at 6:40 AM, Cammer, Michael <[hidden email]
> wrote:

> I've noticed in the last few weeks that ImageJ has been freezing
> unpredictably.  Only way to stop it is from task manager (Win7).
> I typically leave it running on my computer all day long and this new
> behavior is new after years of no problems with this.
>
>
> _________________________________________
> Michael Cammer, Optical Microscopy Specialist
> http://ocs.med.nyu.edu/microscopy
> http://microscopynotes.com/
> Cell: (914) 309-3270
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] on behalf of Philippe
> CARL [[hidden email]]
> Sent: Thursday, June 22, 2017 6:04 AM
> To: [hidden email]
> Subject: Serious issues with the last ImageJ update
>
> Dear all,
>
> Since my last ImageJ update (going from the version 1.51n to 1.51o) I
> experience (and this on several machines under window 7 or 10) that ImageJ
> is getting completely frozen with no alternative option left then to kill
> the process.
>
> These freezings are highly non reproducible and thus sorry for not being
> able to post a macro showing this issue for sure.
>
> But I quite often experienced these issues by doing a
> Image->Hyperstacks->Stack_to_hyperstack… transformation on a 1-channel,
> 14-z, 48-time stack image.
>
> I also downgraded ImageJ back to the 1.50 version and there I found none of
> these issues as well.
>
> Did anybody of you experience the same problems?
>
> Thanks a lot in advance for your hints and help.
>
> "Make our planet great again!"
>
> Philippe
>
>
>
> Philippe CARL
>
> Laboratoire de Biophotonique et Pharmacologie
>
> UMR 7213 CNRS - Université de Strasbourg
>
> Faculté de Pharmacie
>
> 74 route du Rhin
>
> 67401 ILLKIRCH
>
> Tel : +33(0)3 68 85 41 84
>
>
> --
> ImageJ mailing list: https://urldefense.proofpoint.
> com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DQIFAw&c=
> j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_
> vAdjXk3frDLx_CqKkuo&m=K7roKzgiQFyYbG-O0tiMzdSGU4Rev5GOQGroSXOVT-Y&s=N0bd_
> UzPI7VAIsGG5QQLKlOWPBScfiebzOKzkUceYqU&e=
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caused by any virus
> transmitted by this email.
> =================================
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Serious issues with the last ImageJ update

Philippe CARL
Dear Curtis,
You will be able to download such a stack (1-channel, 14-z, 48-t - 1.8GB) under the following link:
https://seafile.unistra.fr/f/43d6ae76e1/?raw=1
I tried to generate a stack trace from the link you indcated but wasn't able to go further than the step 2.
Thus is there a video which shows how to do this?
My best regards,
Philippe

Le Jeudi 22 Juin 2017 14:02 CEST, Curtis Rueden <[hidden email]> a écrit:

> Hi everyone,
>
> It would be helpful if someone could generate and share a stack trace from
> when a hang occurs. Please see:
>
> https://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Thu, Jun 22, 2017 at 6:40 AM, Cammer, Michael <[hidden email]
> > wrote:
>
> > I've noticed in the last few weeks that ImageJ has been freezing
> > unpredictably.  Only way to stop it is from task manager (Win7).
> > I typically leave it running on my computer all day long and this new
> > behavior is new after years of no problems with this.
> >
> >
> > _________________________________________
> > Michael Cammer, Optical Microscopy Specialist
> > http://ocs.med.nyu.edu/microscopy
> > http://microscopynotes.com/
> > Cell: (914) 309-3270
> >
> > ________________________________________
> > From: ImageJ Interest Group [[hidden email]] on behalf of Philippe
> > CARL [[hidden email]]
> > Sent: Thursday, June 22, 2017 6:04 AM
> > To: [hidden email]
> > Subject: Serious issues with the last ImageJ update
> >
> > Dear all,
> >
> > Since my last ImageJ update (going from the version 1.51n to 1.51o) I
> > experience (and this on several machines under window 7 or 10) that ImageJ
> > is getting completely frozen with no alternative option left then to kill
> > the process.
> >
> > These freezings are highly non reproducible and thus sorry for not being
> > able to post a macro showing this issue for sure.
> >
> > But I quite often experienced these issues by doing a
> > Image->Hyperstacks->Stack_to_hyperstack… transformation on a 1-channel,
> > 14-z, 48-time stack image.
> >
> > I also downgraded ImageJ back to the 1.50 version and there I found none of
> > these issues as well.
> >
> > Did anybody of you experience the same problems?
> >
> > Thanks a lot in advance for your hints and help.
> >
> > "Make our planet great again!"
> >
> > Philippe
> >
> >
> >
> > Philippe CARL
> >
> > Laboratoire de Biophotonique et Pharmacologie
> >
> > UMR 7213 CNRS - Université de Strasbourg
> >
> > Faculté de Pharmacie
> >
> > 74 route du Rhin
> >
> > 67401 ILLKIRCH
> >
> > Tel : +33(0)3 68 85 41 84
> >
> >
> > --
> > ImageJ mailing list: https://urldefense.proofpoint.
> > com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DQIFAw&c=
> > j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_
> > vAdjXk3frDLx_CqKkuo&m=K7roKzgiQFyYbG-O0tiMzdSGU4Rev5GOQGroSXOVT-Y&s=N0bd_
> > UzPI7VAIsGG5QQLKlOWPBScfiebzOKzkUceYqU&e=
> >
> > ------------------------------------------------------------
> > This email message, including any attachments, is for the sole use of the
> > intended recipient(s) and may contain information that is proprietary,
> > confidential, and exempt from disclosure under applicable law. Any

> > unauthorized review, use, disclosure, or distribution is prohibited. If you
> > have received this email in error please notify the sender by return email
> > and delete the original message. Please note, the recipient should check
> > this email and any attachments for the presence of viruses. The
> > organization accepts no liability for any damage caused by any virus
> > transmitted by this email.
> > =================================
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html





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Re: Serious issues with the last ImageJ update

Wayne Rasband-2
In reply to this post by Philippe CARL
> On Jun 22, 2017, at 6:04 AM, Philippe CARL <[hidden email]> wrote:
>
> Dear all,
>
> Since my last ImageJ update (going from the version 1.51n to 1.51o) I
> experience (and this on several machines under window 7 or 10) that ImageJ
> is getting completely frozen with no alternative option left then to kill
> the process.

This bug should be fixed in the latest ImageJ daily build (1.51p12). You can upgrade using the Help>Update ImageJ command and selecting “daily build” from the drop down menu.

-wayne

> These freezings are highly non reproducible and thus sorry for not being
> able to post a macro showing this issue for sure.
>
> But I quite often experienced these issues by doing a
> Image->Hyperstacks->Stack_to_hyperstack… transformation on a 1-channel,
> 14-z, 48-time stack image.
>
> I also downgraded ImageJ back to the 1.50 version and there I found none of
> these issues as well.
>
> Did anybody of you experience the same problems?
>
> Thanks a lot in advance for your hints and help.
>
> "Make our planet great again!"
>
> Philippe

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Re: Issue with recent ImageJ update

Michael Schmid-3
Hi Gilbert,

here I can't reproduce the problem (Ubuntu 16.04, java 1.8). I was using
various .png images (640 x 480, 893 x 678, 656 x 638, and 2400 x 1611
pixels), and I tried with and without 'setBatchMode(true)' in the
beginning of the macro.

It's the same for Oracle and OpenJDK, 1.51p and today's daily build,
neither freezes:
ImageJ 1.51p; Java 1.8.0_112 [64-bit]; Linux 4.4.0-81-generic
ImageJ 1.51p12; Java 1.8.0_112 [64-bit]; Linux 4.4.0-81-generic
ImageJ 1.51p; Java 1.8.0_131 [64-bit]; Linux 4.4.0-81-generic

Maybe it depends on the image; does it freeze with opening sample
images? With these, the test macro would be more easily reproducible.

Michael
________________________________________________________________
On 22/06/2017 22:38, Gilbert Bigras wrote:
 > I wonder if it is related to the recently posts reporting that ImageJ
randomly freezes but I noticed the following problem since imageJ > 1.50
 > The following macro code:
 >                   open(image1);
 >                   setBatchMode(false);
 >                   run("Set... ", "zoom=33");
 >                   setLocation(10,10);
 >                   call("ij.gui.ImageWindow.setNextLocation", 900, 10);
 >                   open(image2);
 >
 > ... after the first image is painted at the location 10,10, imageJ
freezes
 > If I add .... wait(100); just before calling
"ij.gui.ImageWindow.setNextLocation", then no freeze
 >
 >                   open(image1);
 >                   setBatchMode(false);
 >                   run("Set... ", "zoom=33");
 >                   setLocation(10,10);
 >                   wait(100);
 >
 >                   call("ij.gui.ImageWindow.setNextLocation", 900,
10);                 open(image2);
 >
 >
 > The freeze can be reproduced under Linux (Java 8) and Windows XP
(Java 6). But no freeze with ImageJ 1.50 and below
 > Thanks!
 > Gilbert

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