<div dir="ltr">Hi Niko,<div><br></div><div>You're probably right that the File.isHidden() in BioFormats isn't called in the OMERO importer at the client side. However, from quickly grepping through the source of openmicroscopy/components/insight I found several calls to File.isHidden(). I was wondering if these are also meant to be optimized as part of this issue.</div><div><br></div><div>What we experience in the OMERO importer is for very low latency network drives that the import is relatively slow (compared to file copy). For higher latency network drives the import is slow and the importer UI becomes unresponsive (although the import continues). If you want me to quantify these experiences, I could do that.</div><div><br></div><div>Thanks,</div><div><br></div><div>Paul</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Dec 11, 2014 at 8:22 PM, Niko Ehrenfeuchter <span dir="ltr"><<a href="mailto:nikolaus.ehrenfeuchter@unibas.ch" target="_blank">nikolaus.ehrenfeuchter@unibas.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Paul,<br>
<br>
I doubt this is related - as I understand it, the (current) import process using OMERO.insight just copies the image file(s) onto the server before it is processing them. So the first time the BioFormats kicks in there is *after* the actual transfer and therefore the network drive issue should not apply here.<br>
<br>
I might be wrong, though...<br>
<br>
Cheers<br>
Niko<span class=""><br>
<br>
On 11.12.2014 17:29, Paul van Schayck wrote:<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
Hi Melissa,<br>
<br>
Would this bug also explain slowness in the OMERO importer while<br>
importing files which are located on a network drive (in Windows)?<br>
<br>
Thanks,<br>
<br>
Paul<br>
<br>
On Thu, Dec 11, 2014 at 3:26 PM, Niko Ehrenfeuchter<br>
<<a href="mailto:nikolaus.ehrenfeuchter@unibas.ch" target="_blank">nikolaus.ehrenfeuchter@<u></u>unibas.ch</a><br></span><span class="">
<mailto:<a href="mailto:nikolaus.ehrenfeuchter@unibas.ch" target="_blank">nikolaus.<u></u>ehrenfeuchter@unibas.ch</a>>> wrote:<br>
<br>
Hi Melissa,<br>
<br>
could you please add me to the CC list on that ticket as well? We're<br>
also suffering from the performance issue when opening files from<br>
network shares, especially on Windows.<br>
<br>
Cheers<br>
Niko<br>
<br>
<br>
On 11.12.2014 03:34, Melissa Linkert wrote:<br>
<br>
Hi Rafael and Lorenz,<br>
<br>
You are both now CC'd on ticket 6586, and will receive an automated<br>
email with "[OME] #6586" in the subject line each time the<br>
ticket is updated.<br>
<br>
Regards,<br>
-Melissa<br>
<br>
On Thu, Dec 11, 2014 at 12:55:24PM +0100, Maier, Lorenz wrote:<br>
<br>
Hi Rafael,<br>
<br>
probably Zen Blue reads only the planes and zoom levels that<br>
it actually displays.<br>
<br>
Best,<br>
Lorenz<br>
<br>
PS: please CC me on that ticket!<br>
<br>
-----Ursprüngliche Nachricht-----<br>
Von: ome-users<br></span>
[mailto:<a href="mailto:ome-users-bounces@" target="_blank">ome-users-bounces@</a>__<a href="http://lists.openmicroscopy.org.uk" target="_blank">li<u></u>sts.openmicroscopy.org.uk</a><span class=""><br>
<mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@<u></u>lists.openmicroscopy.org.uk</a>>] Im<br>
Auftrag von r b<br>
Gesendet: Donnerstag, 11. Dezember 2014 01:20<br>
An: Melissa Linkert<br></span>
Cc: ome-users@lists.__<a href="http://openmicroscopy.org.uk" target="_blank">openmicrosco<u></u>py.org.uk</a><br>
<mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.<u></u>openmicroscopy.org.uk</a>><span class=""><br>
Betreff: Re: [ome-users] Network drive slowness<br>
<br>
Hi Melissa and list,<br>
<br>
I would like to be automatically notified of updates about<br>
that ticket.<br>
<br>
Is there an obvious reason why the same file opens so much<br>
faster in Zen Blue 2012?<br>
<br>
Thank you,<br>
<br>
Rafael Buono<br>
<br>
On Wed, Dec 10, 2014 at 5:45 PM, Melissa Linkert<br>
<<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a><br></span><div><div class="h5">
<mailto:<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@<u></u>glencoesoftware.com</a>>> wrote:<br>
<br>
Hi Rafael,<br>
<br>
I did the test with a 460MB czi file.<br>
<br>
If I copy it to the desktop and then open it, it<br>
takes ~20 seconds in Fiji.<br>
If I open it from the network drive:<br>
1st time: 10 minutes<br>
2nd time: 2 minutes<br>
3rd time: ~20 seconds<br>
4th time: ~20 seconds<br>
<br>
Opening the same file from the network storage or<br>
directly from the<br>
desktop takes less than 4 seconds with Zen Blue 2012.<br>
<br>
<br>
Thank you for the additional information.<br>
<br>
20 seconds to open a 460MB file is within the range of<br>
what I would<br>
expect - even more so if the images are compressed<br>
within the file.<br>
The fact that only the first opening from the network<br>
drive takes 10<br>
minutes suggests that this is not related to file format<br>
itself. I<br>
strongly suspect that this ticket on our issue tracking<br>
system is the<br>
problem that you are experiencing:<br>
<br></div></div>
<a href="http://trac.openmicroscopy." target="_blank">http://trac.openmicroscopy.</a>__<u></u>org/ome/ticket/6586<div><div class="h5"><br>
<<a href="http://trac.openmicroscopy.org/ome/ticket/6586" target="_blank">http://trac.openmicroscopy.<u></u>org/ome/ticket/6586</a>><br>
<br>
If you would like to be automatically notified of<br>
updates to that<br>
ticket, please let me know.<br>
<br>
Regards,<br>
-Melissa<br>
<br>
On Mon, Dec 08, 2014 at 06:33:51PM -0600, r b wrote:<br>
<br>
Hi Melissa and list,<br>
<br>
I did the test with a 460MB czi file.<br>
<br>
If I copy it to the desktop and then open it, it<br>
takes ~20 seconds in Fiji.<br>
If I open it from the network drive:<br>
1st time: 10 minutes<br>
2nd time: 2 minutes<br>
3rd time: ~20 seconds<br>
4th time: ~20 seconds<br>
<br>
Opening the same file from the network storage or<br>
directly from the<br>
desktop takes less than 4 seconds with Zen Blue 2012.<br>
<br>
<br>
About the "Bio-Formats Import Options" window. I<br>
don't go through it. I go:<br>
File>Open...> then I double click the file and it<br>
opens it without<br>
asking anything else..<br>
If I use the Bio-Formats Importer route to open the<br>
file from the<br>
desktop, selecting:<br>
-View stack with: Hyperstack<br>
-Stack order: XYCZT<br>
-Display metadata<br>
-Display OME-XML metadata<br>
-Display ROIs<br>
<br>
I still get ~20 seconds for it to open.<br>
<br>
<br>
Thank you<br>
<br>
Rafael Buono<br>
<br>
On Mon, Dec 8, 2014 at 12:27 PM, Melissa Linkert<br>
<<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a><br></div></div><div><div class="h5">
<mailto:<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@<u></u>glencoesoftware.com</a>>> wrote:<br>
<br>
Hi Rafael,<br>
<br>
First, as an example, I have a .czi of<br>
~210MB that opens:<br>
- ZEN Blue Lite 2012 loading from network<br>
drive: about 2 seconds<br>
- Copying from network drive and pasting to<br>
the Desktop: about 4<br>
seconds<br>
- Fiji loading from network drive: 30 seconds<br>
<br>
In the ImageJ list I was informed that<br>
taking longer to load czi<br>
files might be a widespread issue with czi<br>
files.<br>
<br>
<br>
How long does it take to read the file using<br>
Fiji, after it has<br>
been copied to the Desktop? That would help us<br>
to know if this is<br>
strictly due to the network file system, or if<br>
the procedure for<br>
reading the file is too slow.<br>
<br>
It would also be useful to know which options<br>
you have selected in<br>
the "Bio-Formats Import Options" window.<br>
<br>
The second problem was found while testing<br>
the speeds above. If I<br>
put the same file one folder deeper and try<br>
to open it in Fiji,<br>
the time grows from 30 seconds to 12 minutes.<br>
<br>
I am one of those people who organizes<br>
things by creating folder,<br>
inside folder, inside folder.<br>
In the following structure:<br></div></div>
O:\Folder1\Folder2\Folder3\__<u></u>Folder4\Folder5\Folder6\__<u></u>Folder7<div><div class="h5"><br>
If I have the czi file in Folder6, it takes<br>
30 seconds to open. If<br>
I move it to Folder7, it takes 12 minutes to<br>
open.<br>
<br>
Is there an obvious reason for this increase<br>
in time?<br>
<br>
<br>
Having more folders can cause subtle performance<br>
degradation, but<br>
typically not as much as you describe. If you<br>
open the file in<br>
Folder7 twice in a row, does it take 12 minutes<br>
both times?<br>
<br>
Regards,<br>
-Melissa<br>
<br>
On Fri, Dec 05, 2014 at 11:05:21AM -0600, r b wrote:<br>
<br>
Hi all,<br>
<br>
I recently got our lab workstation connected<br>
through the 1Gbps<br>
network to the building's server. Among<br>
other reasons, I was<br>
hoping to process images directly from the<br>
network drive. However,<br>
even with the upgrade to 1Gbps, loading<br>
images in Fiji is still<br>
slow. I have encountered two problems and I<br>
am not sure they are related.<br>
<br>
First, as an example, I have a .czi of<br>
~210MB that opens:<br>
- ZEN Blue Lite 2012 loading from network<br>
drive: about 2 seconds<br>
- Copying from network drive and pasting to<br>
the Desktop: about 4<br>
seconds<br>
- Fiji loading from network drive: 30 seconds<br>
<br>
In the ImageJ list I was informed that<br>
taking longer to load czi<br>
files might be a widespread issue with czi<br>
files.<br>
<br>
The second problem was found while testing<br>
the speeds above. If I<br>
put the same file one folder deeper and try<br>
to open it in Fiji,<br>
the time grows from 30 seconds to 12 minutes.<br>
<br>
I am one of those people who organizes<br>
things by creating folder,<br>
inside folder, inside folder.<br>
In the following structure:<br></div></div>
O:\Folder1\Folder2\Folder3\__<u></u>Folder4\Folder5\Folder6\__<u></u>Folder7<span class=""><br>
If I have the czi file in Folder6, it takes<br>
30 seconds to open. If<br>
I move it to Folder7, it takes 12 minutes to<br>
open.<br>
<br>
Is there an obvious reason for this increase<br>
in time?<br>
<br>
Thank you<br>
<br>
Rafael Buono<br>
<br>
PS:<br>
Some info about my system below:<br>
Java information:<br>
os.arch => amd64<br></span>
<a href="http://os.name" target="_blank">os.name</a> <<a href="http://os.name" target="_blank">http://os.name</a>> => Windows 7<span class=""><br>
os.version => 6.1<br>
java.version => 1.6.0_24<br>
java.vendor => Sun Microsystems Inc.<br></span>
<a href="http://java.runtime.name" target="_blank">java.runtime.name</a> <<a href="http://java.runtime.name" target="_blank">http://java.runtime.name</a>><span class=""><br>
=> Java(TM) SE Runtime Environment<br>
java.runtime.version => 1.6.0_24-b07<br></span>
<a href="http://java.vm.name" target="_blank">java.vm.name</a> <<a href="http://java.vm.name" target="_blank">http://java.vm.name</a>> => Java<span class=""><br>
HotSpot(TM) 64-Bit Server VM<br>
java.vm.version => 19.1-b02<br>
java.vm.vendor => Sun Microsystems Inc.<br></span>
<a href="http://java.vm.info" target="_blank">java.vm.info</a> <<a href="http://java.vm.info" target="_blank">http://java.vm.info</a>> => mixed mode<br>
java.awt.graphicsenv =><br>
sun.awt.__<u></u>Win32GraphicsEnvironment<br>
<a href="http://java.specification.name" target="_blank">java.specification.name</a><br>
<<a href="http://java.specification.name" target="_blank">http://java.specification.<u></u>name</a>> => Java<span class=""><br>
Platform API Specification<br>
java.specification.version => 1.6<br>
sun.cpu.endian => little<br>
sun.desktop => windows<br>
file.separator => \<br>
<br>
The up-to-date check says: UP_TO_DATE<br>
<br>
Information relevant to JAVA_HOME related<br>
problems:<br>
<br>
JAVA_HOME is set to:<br></span>
C:\Users\ADMINI~1\Desktop\__<u></u>Fiji.app/java/win64/jdk1.6.0__<u></u>_24//jre<br>
imagej.dir =><br>
C:\Users\ADMINI~1\Desktop\__<u></u>Fiji.app<span class=""><br>
<br>
Information about the version of each plugin:<br>
<br>
Activated update sites:<br>
ImageJ: <a href="http://update.imagej.net/" target="_blank">http://update.imagej.net/</a> (last<br>
check:20141126151327)<br>
Fiji: <a href="http://fiji.sc/update/" target="_blank">http://fiji.sc/update/</a> (last<br>
check:20141125101145) MOSAIC<br>
ToolSuite:<br></span>
<a href="http://mosaic.mpi-cbg.de/__Downloads/update/Fiji/__MosaicToolsuite/" target="_blank">http://mosaic.mpi-cbg.de/__<u></u>Downloads/update/Fiji/__<u></u>MosaicToolsuite/</a><span class=""><br>
<<a href="http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/" target="_blank">http://mosaic.mpi-cbg.de/<u></u>Downloads/update/Fiji/<u></u>MosaicToolsuite/</a>><br>
(last<br>
check:20141105181755)<br>
<br>
<br>
<br>
Bio-Formats information:<br>
Release 5.0.6, revision 33b1150, built 10<br>
November 2014.<br></span>
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<br>
<br>
--<br>
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum,<br>
University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel<br></span>
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter@unibas.<u></u>__ch<br>
<mailto:<a href="mailto:nikolaus.ehrenfeuchter@unibas.ch" target="_blank">nikolaus.<u></u>ehrenfeuchter@unibas.ch</a>> | <a href="http://www.biozentrum.unibas.ch" target="_blank">www.biozentrum.unibas.ch</a><br>
<<a href="http://www.biozentrum.unibas.ch" target="_blank">http://www.biozentrum.unibas.<u></u>ch</a>> |<br>
www.microscopynetwork.unibas._<u></u>_ch<br>
<<a href="http://www.microscopynetwork.unibas.ch" target="_blank">http://www.microscopynetwork.<u></u>unibas.ch</a>><br>
<br>
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<br>
<br>
<br>
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<br>
</span></blockquote><div class="HOEnZb"><div class="h5">
<br>
-- <br>
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel<br>
Phone: +41 (61) 26 72673 | <a href="mailto:nikolaus.ehrenfeuchter@unibas.ch" target="_blank">nikolaus.ehrenfeuchter@unibas.<u></u>ch</a> | <a href="http://www.biozentrum.unibas.ch" target="_blank">www.biozentrum.unibas.ch</a> | <a href="http://www.microscopynetwork.unibas.ch" target="_blank">www.microscopynetwork.unibas.<u></u>ch</a><br>
</div></div></blockquote></div><br></div>