FIJI related memory issue

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

FIJI related memory issue

fabrice senger-2
Hi there,

I'm probably not the only one experiencing problems with memory wich
doesn't get released. Even no single image is open, and after hiting the
garbage collector.

Is there something new about that issue.

It seems it has been related at some point to the hyperstack opener of LOCI
...

In the meantime the only workarouns is to close FIJI and restart

Thank you all for your help,

Fabrice.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: FIJI related memory issue

ctrueden
Hi Fabrice,

> experiencing problems with memory wich doesn't get released. Even no
> single image is open, and after hiting the garbage collector.

I am unable to duplicate this problem. I tried opening the Mitosis sample,
repeatedly duplicating it, closing all images, and clicking the status bar.

Can you please describe a precise sequence of operations that, if executed
repeatedly on your system, results in memory consumption increasing?

> It seems it has been related at some point to the hyperstack opener of
> LOCI

Why do you think that? Do you mean the old Data Browser plugin [1]? Are you
using it? That plugin is not actively supported or maintained.

Thanks,
Curtis

[1] https://loci.wisc.edu/software/data-browser

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, Feb 8, 2018 at 11:18 AM, Fabrice Senger <[hidden email]>
wrote:

> Hi there,
>
> I'm probably not the only one experiencing problems with memory wich
> doesn't get released. Even no single image is open, and after hiting the
> garbage collector.
>
> Is there something new about that issue.
>
> It seems it has been related at some point to the hyperstack opener of LOCI
> ...
>
> In the meantime the only workarouns is to close FIJI and restart
>
> Thank you all for your help,
>
> Fabrice.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: FIJI related memory issue

fabrice senger-2
Hi there,

I'm using FIJI ImageJ 2.0.0-rc-64/1.51s;Java 1.8.0_66(64-bit) with 3 GB
allocated memory on a MacBookAir OS 10.10.4.

I really noticed the problem while opening Metamorph files. I usually open
them with BioFormats. All works fine but after a while I get a message
telling me that the selections I made would take too much memory. When I
check, by clicking on the status bar, while having no image open, it
happens that 30% of memory are used ...by what ?

Clicking on the garbage collector doesn't help, so I have to restart FIJI.

I think this thread is discussed for a while now on the forum but I have
the feeling there's no explanation on how and why this happens.

If you need further details or want me to perform some test ...

Best,

Fabrice.

2018-02-08 19:39 GMT+01:00 Curtis Rueden <[hidden email]>:

> Hi Fabrice,
>
> > experiencing problems with memory wich doesn't get released. Even no
> > single image is open, and after hiting the garbage collector.
>
> I am unable to duplicate this problem. I tried opening the Mitosis sample,
> repeatedly duplicating it, closing all images, and clicking the status bar.
>
> Can you please describe a precise sequence of operations that, if executed
> repeatedly on your system, results in memory consumption increasing?
>
> > It seems it has been related at some point to the hyperstack opener of
> > LOCI
>
> Why do you think that? Do you mean the old Data Browser plugin [1]? Are you
> using it? That plugin is not actively supported or maintained.
>
> Thanks,
> Curtis
>
> [1] https://loci.wisc.edu/software/data-browser
>
> 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, Feb 8, 2018 at 11:18 AM, Fabrice Senger <[hidden email]>
> wrote:
>
> > Hi there,
> >
> > I'm probably not the only one experiencing problems with memory wich
> > doesn't get released. Even no single image is open, and after hiting the
> > garbage collector.
> >
> > Is there something new about that issue.
> >
> > It seems it has been related at some point to the hyperstack opener of
> LOCI
> > ...
> >
> > In the meantime the only workarouns is to close FIJI and restart
> >
> > Thank you all for your help,
> >
> > Fabrice.
> >
> > --
> > 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
Reply | Threaded
Open this post in threaded view
|

Re: FIJI related memory issue

ctrueden
Hi Fabrice,

Would you be able to post a sample Metamorph file that suffers from this
issue? It may be a format-specific bug in Bio-Formats—these have arisen in
the past.

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 Fri, Feb 9, 2018 at 9:09 AM, Fabrice Senger <[hidden email]>
wrote:

> Hi there,
>
> I'm using FIJI ImageJ 2.0.0-rc-64/1.51s;Java 1.8.0_66(64-bit) with 3 GB
> allocated memory on a MacBookAir OS 10.10.4.
>
> I really noticed the problem while opening Metamorph files. I usually open
> them with BioFormats. All works fine but after a while I get a message
> telling me that the selections I made would take too much memory. When I
> check, by clicking on the status bar, while having no image open, it
> happens that 30% of memory are used ...by what ?
>
> Clicking on the garbage collector doesn't help, so I have to restart FIJI.
>
> I think this thread is discussed for a while now on the forum but I have
> the feeling there's no explanation on how and why this happens.
>
> If you need further details or want me to perform some test ...
>
> Best,
>
> Fabrice.
>
> 2018-02-08 19:39 GMT+01:00 Curtis Rueden <[hidden email]>:
>
> > Hi Fabrice,
> >
> > > experiencing problems with memory wich doesn't get released. Even no
> > > single image is open, and after hiting the garbage collector.
> >
> > I am unable to duplicate this problem. I tried opening the Mitosis
> sample,
> > repeatedly duplicating it, closing all images, and clicking the status
> bar.
> >
> > Can you please describe a precise sequence of operations that, if
> executed
> > repeatedly on your system, results in memory consumption increasing?
> >
> > > It seems it has been related at some point to the hyperstack opener of
> > > LOCI
> >
> > Why do you think that? Do you mean the old Data Browser plugin [1]? Are
> you
> > using it? That plugin is not actively supported or maintained.
> >
> > Thanks,
> > Curtis
> >
> > [1] https://loci.wisc.edu/software/data-browser
> >
> > 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, Feb 8, 2018 at 11:18 AM, Fabrice Senger <
> [hidden email]>
> > wrote:
> >
> > > Hi there,
> > >
> > > I'm probably not the only one experiencing problems with memory wich
> > > doesn't get released. Even no single image is open, and after hiting
> the
> > > garbage collector.
> > >
> > > Is there something new about that issue.
> > >
> > > It seems it has been related at some point to the hyperstack opener of
> > LOCI
> > > ...
> > >
> > > In the meantime the only workarouns is to close FIJI and restart
> > >
> > > Thank you all for your help,
> > >
> > > Fabrice.
> > >
> > > --
> > > 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