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Recent Fiji gets slow in constructing an image

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Yuekan Jiao-2

Recent Fiji gets slow in constructing an image

Hi,

I have a plugin which constructs a mosaic image imp (ImageProcessor ip)
simply based on the tiles' coordinates. Each tile (ipTile) is read into the
mosaic image being shown, and the mosaic image is updated. the workflow is:

loop through each tile{
for (int j = 0; j < heightTile; j++) {
for (int i = 0; i < widthTile; i++) {
ip.set(xCoor + i, yCoor + j, ipTile.get(i, j));
}
}
imp.updateAndDraw();
}

This process gets much slower with recently released Fiji, and hangs. I
tracked the Fiji versions on all my computers:

1. Jave 8 ImageJ-win64.exe dated 12/14/2016 works fine but May 30 2017
version and a bit earlier ones do not.

2. Java 6 life-line versions earlier than May 30, 2017 work fine, but May
30 2017 version does not.

All my systems are windows 7 with Java 8 installed.

Thank you.

Yuekan

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

ctrueden

Re: Recent Fiji gets slow in constructing an image

Hi Yuekan,

Which version of ImageJ 1.x is being used in each case?

Have you tried the Help > Update ImageJ... command to up/downgrade ImageJ
1.x, to see whether that makes a difference?

Have you tried generating a stack trace after the hang, to shed some light
on the culprit?
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 Tue, May 30, 2017 at 6:36 PM, Yuekan Jiao <[hidden email]> wrote:

> Hi,
>
> I have a plugin which constructs a mosaic image imp (ImageProcessor ip)
> simply based on the tiles' coordinates. Each tile (ipTile) is read into the
> mosaic image being shown, and the mosaic image is updated. the workflow is:
>
> loop through each tile{
> for (int j = 0; j < heightTile; j++) {
> for (int i = 0; i < widthTile; i++) {
> ip.set(xCoor + i, yCoor + j, ipTile.get(i, j));
> }
> }
> imp.updateAndDraw();
> }
>
> This process gets much slower with recently released Fiji, and hangs. I
> tracked the Fiji versions on all my computers:
>
> 1. Jave 8 ImageJ-win64.exe dated 12/14/2016 works fine but May 30 2017
> version and a bit earlier ones do not.
>
> 2. Java 6 life-line versions earlier than May 30, 2017 work fine, but May
> 30 2017 version does not.
>
> All my systems are windows 7 with Java 8 installed.
>
> Thank you.
>
>
> Yuekan
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Wayne Rasband-2

Re: Recent Fiji gets slow in constructing an image

In reply to this post by Yuekan Jiao-2

> On May 30, 2017, at 7:36 PM, Yuekan Jiao <[hidden email]> wrote:
>
> Hi,
>
> I have a plugin which constructs a mosaic image imp (ImageProcessor ip)
> simply based on the tiles' coordinates. Each tile (ipTile) is read into the
> mosaic image being shown, and the mosaic image is updated. the workflow is:

Please provide a minimal, complete and runnable script or plugin that reproduces this problem. The ImageJ developers cannot fix this problem without a way to reproduce it.

-wayne

> loop through each tile{
> for (int j = 0; j < heightTile; j++) {
> for (int i = 0; i < widthTile; i++) {
> ip.set(xCoor + i, yCoor + j, ipTile.get(i, j));
> }
> }
> imp.updateAndDraw();
> }
>
> This process gets much slower with recently released Fiji, and hangs. I
> tracked the Fiji versions on all my computers:
>
> 1. Jave 8 ImageJ-win64.exe dated 12/14/2016 works fine but May 30 2017
> version and a bit earlier ones do not.
>
> 2. Java 6 life-line versions earlier than May 30, 2017 work fine, but May
> 30 2017 version does not.
>
> All my systems are windows 7 with Java 8 installed.
>
> Thank you.
>
>
> Yuekan

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

Yuekan Jiao-2

Re: Recent Fiji gets slow in constructing an image

In reply to this post by ctrueden

Additional information: with Java 6 May 30, 2017 version, ImageJ-win64.exe
has the problem, but fiji-win64.exe does not.

Yuekan

On Tue, May 30, 2017 at 5:05 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Yuekan,
>
> Which version of ImageJ 1.x is being used in each case?
>
> Have you tried the Help > Update ImageJ... command to up/downgrade ImageJ
> 1.x, to see whether that makes a difference?
>
> Have you tried generating a stack trace after the hang, to shed some light
> on the culprit?
> 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 Tue, May 30, 2017 at 6:36 PM, Yuekan Jiao <[hidden email]>
> wrote:
>
> > Hi,
> >
> > I have a plugin which constructs a mosaic image imp (ImageProcessor ip)
> > simply based on the tiles' coordinates. Each tile (ipTile) is read into
> the
> > mosaic image being shown, and the mosaic image is updated. the workflow
> is:
> >
> > loop through each tile{
> > for (int j = 0; j < heightTile; j++) {
> > for (int i = 0; i < widthTile; i++) {
> > ip.set(xCoor + i, yCoor + j, ipTile.get(i, j));
> > }
> > }
> > imp.updateAndDraw();
> > }
> >
> > This process gets much slower with recently released Fiji, and hangs. I
> > tracked the Fiji versions on all my computers:
> >
> > 1. Jave 8 ImageJ-win64.exe dated 12/14/2016 works fine but May 30 2017
> > version and a bit earlier ones do not.
> >
> > 2. Java 6 life-line versions earlier than May 30, 2017 work fine, but May
> > 30 2017 version does not.
> >
> > All my systems are windows 7 with Java 8 installed.
> >
> > Thank you.
> >
> >
> > Yuekan
> >
> > --
> > 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

ctrueden

Re: Recent Fiji gets slow in constructing an image

Hi Yuekan,

> Additional information: with Java 6 May 30, 2017 version,
> ImageJ-win64.exe has the problem, but fiji-win64.exe does not.

That makes me wonder whether the condition is intermittent on your system
-- i.e., sometimes it works, and sometimes it doesn't, apparently randomly.

I say that because fiji-win64.exe is AFAIK just a thin wrapper which
invokes ImageJ-win64.exe. You could verify that for yourself by running the
"System information" command (use Ctrl+L to find it via the Command Finder)
in both cases, save the output (Ctrl+A Ctrl+C to copy it, then paste into a
text editor), and diff the two against each other. I would be surprised if
the environments are meaningfully different.

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 1, 2017 at 3:59 PM, Yuekan Jiao <[hidden email]> wrote:

> Additional information: with Java 6 May 30, 2017 version, ImageJ-win64.exe
> has the problem, but fiji-win64.exe does not.
>
> Yuekan
>
> On Tue, May 30, 2017 at 5:05 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Yuekan,
> >
> > Which version of ImageJ 1.x is being used in each case?
> >
> > Have you tried the Help > Update ImageJ... command to up/downgrade ImageJ
> > 1.x, to see whether that makes a difference?
> >
> > Have you tried generating a stack trace after the hang, to shed some
> light
> > on the culprit?
> > 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 Tue, May 30, 2017 at 6:36 PM, Yuekan Jiao <[hidden email]>
> > wrote:
> >
> > > Hi,
> > >
> > > I have a plugin which constructs a mosaic image imp (ImageProcessor ip)
> > > simply based on the tiles' coordinates. Each tile (ipTile) is read into
> > the
> > > mosaic image being shown, and the mosaic image is updated. the workflow
> > is:
> > >
> > > loop through each tile{
> > > for (int j = 0; j < heightTile; j++) {
> > > for (int i = 0; i < widthTile; i++) {
> > > ip.set(xCoor + i, yCoor + j, ipTile.get(i, j));
> > > }
> > > }
> > > imp.updateAndDraw();
> > > }
> > >
> > > This process gets much slower with recently released Fiji, and hangs. I
> > > tracked the Fiji versions on all my computers:
> > >
> > > 1. Jave 8 ImageJ-win64.exe dated 12/14/2016 works fine but May 30 2017
> > > version and a bit earlier ones do not.
> > >
> > > 2. Java 6 life-line versions earlier than May 30, 2017 work fine, but
> May
> > > 30 2017 version does not.
> > >
> > > All my systems are windows 7 with Java 8 installed.
> > >
> > > Thank you.
> > >
> > >
> > > Yuekan
> > >
> > > --
> > > 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

Yuekan Jiao-2

Re: Recent Fiji gets slow in constructing an image

Hi Curtis,

On all my three computers, fiji-win64.exe and ImageJ-win64.exe function the
same in constructing an image, i.e. fiji-win64.exe works fine but
ImageJ-win64.exe does not.

I did system information comparison of fiji-win64.exe and ImageJ-win64.exe
on two of my computers, the comparison results are the same. I have
attached the system information here. The difference is following:

System information for fiji-win64.exe:

fiji.executable = C:\fiji-java6-20170530\Fiji.app\fiji-win64.exe
ij.executable = C:\fiji-java6-20170530\Fiji.app\fiji-win64.exe
sun.java2d.noddraw = true

System information for ImageJ-win64.exe:

fiji.executable = C:\fiji-java6-20170530\Fiji.app\ImageJ-win64.exe
ij.executable = C:\fiji-java6-20170530\Fiji.app\ImageJ-win64.exe
scijava.context.strict = false

Will this explain the functional difference between fiji-win64.exe and
ImageJ-win64win.exe?

Thank you.

Yuekan

On Thu, Jun 1, 2017 at 2:57 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Yuekan,
>
> > Additional information: with Java 6 May 30, 2017 version,
> > ImageJ-win64.exe has the problem, but fiji-win64.exe does not.
>
> That makes me wonder whether the condition is intermittent on your system
> -- i.e., sometimes it works, and sometimes it doesn't, apparently randomly.
>
> I say that because fiji-win64.exe is AFAIK just a thin wrapper which
> invokes ImageJ-win64.exe. You could verify that for yourself by running the
> "System information" command (use Ctrl+L to find it via the Command Finder)
> in both cases, save the output (Ctrl+A Ctrl+C to copy it, then paste into a
> text editor), and diff the two against each other. I would be surprised if
> the environments are meaningfully different.
>
> 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 1, 2017 at 3:59 PM, Yuekan Jiao <[hidden email]> wrote:
>
> > Additional information: with Java 6 May 30, 2017 version,
> ImageJ-win64.exe
> > has the problem, but fiji-win64.exe does not.
> >
> > Yuekan
> >
> > On Tue, May 30, 2017 at 5:05 PM, Curtis Rueden <[hidden email]>
> wrote:
> >
> > > Hi Yuekan,
> > >
> > > Which version of ImageJ 1.x is being used in each case?
> > >
> > > Have you tried the Help > Update ImageJ... command to up/downgrade
> ImageJ
> > > 1.x, to see whether that makes a difference?
> > >
> > > Have you tried generating a stack trace after the hang, to shed some
> > light
> > > on the culprit?
> > > 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 Tue, May 30, 2017 at 6:36 PM, Yuekan Jiao <[hidden email]>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I have a plugin which constructs a mosaic image imp (ImageProcessor
> ip)
> > > > simply based on the tiles' coordinates. Each tile (ipTile) is read
> into
> > > the
> > > > mosaic image being shown, and the mosaic image is updated. the
> workflow
> > > is:
> > > >
> > > > loop through each tile{
> > > > for (int j = 0; j < heightTile; j++) {
> > > > for (int i = 0; i < widthTile; i++) {
> > > > ip.set(xCoor + i, yCoor + j, ipTile.get(i, j));
> > > > }
> > > > }
> > > > imp.updateAndDraw();
> > > > }
> > > >
> > > > This process gets much slower with recently released Fiji, and
> hangs. I
> > > > tracked the Fiji versions on all my computers:
> > > >
> > > > 1. Jave 8 ImageJ-win64.exe dated 12/14/2016 works fine but May 30
> 2017
> > > > version and a bit earlier ones do not.
> > > >
> > > > 2. Java 6 life-line versions earlier than May 30, 2017 work fine, but
> > May
> > > > 30 2017 version does not.
> > > >
> > > > All my systems are windows 7 with Java 8 installed.
> > > >
> > > > Thank you.
> > > >
> > > >
> > > > Yuekan
> > > >
> > > > --
> > > > 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
>

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

fiji-win64-system-info.txt (337K) Download Attachment

ImageJ-win64-system-info.txt (337K) Download Attachment

ctrueden

Re: Recent Fiji gets slow in constructing an image

Hi Yuekan,

> Will this explain the functional difference between fiji-win64.exe and
> ImageJ-win64win.exe?

Perhaps. There is one line that might be relevant:

> sun.java2d.noddraw = true

We used to pass that flag:

https://github.com/imagej/imagej-launcher/commit/6202e847b4b896e08c74966db4b7471a824d1f5b

So I guess it makes sense that fiji-win64.exe still does so. (And it thus
stands to reason that my assumption that fiji-win64.exe does nothing else
but delegate to ImageJ-win64.exe is incorrect.)

How new are your graphics drivers? Perhaps there is a problem relating to
DirectDraw?

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 1, 2017 at 6:32 PM, Yuekan Jiao <[hidden email]> wrote:

> Hi Curtis,
>
> On all my three computers, fiji-win64.exe and ImageJ-win64.exe function the
> same in constructing an image, i.e. fiji-win64.exe works fine but
> ImageJ-win64.exe does not.
>
> I did system information comparison of fiji-win64.exe and ImageJ-win64.exe
> on two of my computers, the comparison results are the same. I have
> attached the system information here. The difference is following:
>
> System information for fiji-win64.exe:
>
> fiji.executable = C:\fiji-java6-20170530\Fiji.app\fiji-win64.exe
> ij.executable = C:\fiji-java6-20170530\Fiji.app\fiji-win64.exe
> sun.java2d.noddraw = true
>
> System information for ImageJ-win64.exe:
>
> fiji.executable = C:\fiji-java6-20170530\Fiji.app\ImageJ-win64.exe
> ij.executable = C:\fiji-java6-20170530\Fiji.app\ImageJ-win64.exe
> scijava.context.strict = false
>
> Will this explain the functional difference between fiji-win64.exe and
> ImageJ-win64win.exe?
>
> Thank you.
>
>
> Yuekan
>
>
>
>
>
> On Thu, Jun 1, 2017 at 2:57 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Yuekan,
> >
> > > Additional information: with Java 6 May 30, 2017 version,
> > > ImageJ-win64.exe has the problem, but fiji-win64.exe does not.
> >
> > That makes me wonder whether the condition is intermittent on your system
> > -- i.e., sometimes it works, and sometimes it doesn't, apparently
> randomly.
> >
> > I say that because fiji-win64.exe is AFAIK just a thin wrapper which
> > invokes ImageJ-win64.exe. You could verify that for yourself by running
> the
> > "System information" command (use Ctrl+L to find it via the Command
> Finder)
> > in both cases, save the output (Ctrl+A Ctrl+C to copy it, then paste
> into a
> > text editor), and diff the two against each other. I would be surprised
> if
> > the environments are meaningfully different.
> >
> > 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 1, 2017 at 3:59 PM, Yuekan Jiao <[hidden email]>
> wrote:
> >
> > > Additional information: with Java 6 May 30, 2017 version,
> > ImageJ-win64.exe
> > > has the problem, but fiji-win64.exe does not.
> > >
> > > Yuekan
> > >
> > > On Tue, May 30, 2017 at 5:05 PM, Curtis Rueden <[hidden email]>
> > wrote:
> > >
> > > > Hi Yuekan,
> > > >
> > > > Which version of ImageJ 1.x is being used in each case?
> > > >
> > > > Have you tried the Help > Update ImageJ... command to up/downgrade
> > ImageJ
> > > > 1.x, to see whether that makes a difference?
> > > >
> > > > Have you tried generating a stack trace after the hang, to shed some
> > > light
> > > > on the culprit?
> > > > 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 Tue, May 30, 2017 at 6:36 PM, Yuekan Jiao <[hidden email]>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I have a plugin which constructs a mosaic image imp (ImageProcessor
> > ip)
> > > > > simply based on the tiles' coordinates. Each tile (ipTile) is read
> > into
> > > > the
> > > > > mosaic image being shown, and the mosaic image is updated. the
> > workflow
> > > > is:
> > > > >
> > > > > loop through each tile{
> > > > > for (int j = 0; j < heightTile; j++) {
> > > > > for (int i = 0; i < widthTile; i++) {
> > > > > ip.set(xCoor + i, yCoor + j, ipTile.get(i, j));
> > > > > }
> > > > > }
> > > > > imp.updateAndDraw();
> > > > > }
> > > > >
> > > > > This process gets much slower with recently released Fiji, and
> > hangs. I
> > > > > tracked the Fiji versions on all my computers:
> > > > >
> > > > > 1. Jave 8 ImageJ-win64.exe dated 12/14/2016 works fine but May 30
> > 2017
> > > > > version and a bit earlier ones do not.
> > > > >
> > > > > 2. Java 6 life-line versions earlier than May 30, 2017 work fine,
> but
> > > May
> > > > > 30 2017 version does not.
> > > > >
> > > > > All my systems are windows 7 with Java 8 installed.
> > > > >
> > > > > Thank you.
> > > > >
> > > > >
> > > > > Yuekan
> > > > >
> > > > > --
> > > > > 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
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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