<div dir="ltr"><div>Hi Melissa,<br><br>Would this bug also explain slowness in the OMERO importer while importing files which are located on a network drive (in Windows)?<br><br></div>Thanks,<br><br>Paul<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Dec 11, 2014 at 3:26 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 Melissa,<br>
<br>
could you please add me to the CC list on that ticket as well? We're also suffering from the performance issue when opening files from network shares, especially on Windows.<br>
<br>
Cheers<br>
Niko<div class="HOEnZb"><div class="h5"><br>
<br>
On 11.12.2014 03:34, Melissa Linkert wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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 ticket is updated.<br>
<br>
Regards,<br>
-Melissa<br>
<br>
On Thu, Dec 11, 2014 at 12:55:24PM +0100, Maier, Lorenz wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Rafael,<br>
<br>
probably Zen Blue reads only the planes and zoom levels that 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 [mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@<u></u>lists.openmicroscopy.org.uk</a>] Im Auftrag von r b<br>
Gesendet: Donnerstag, 11. Dezember 2014 01:20<br>
An: Melissa Linkert<br>
Cc: <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.<u></u>openmicroscopy.org.uk</a><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 that ticket.<br>
<br>
Is there an obvious reason why the same file opens so much 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 <<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Rafael,<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I did the test with a 460MB czi file.<br>
<br>
If I copy it to the desktop and then open it, it 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 directly from the<br>
desktop takes less than 4 seconds with Zen Blue 2012.<br>
</blockquote>
<br>
Thank you for the additional information.<br>
<br>
20 seconds to open a 460MB file is within the range of what I would<br>
expect - even more so if the images are compressed within the file.<br>
The fact that only the first opening from the network drive takes 10<br>
minutes suggests that this is not related to file format itself. I<br>
strongly suspect that this ticket on our issue tracking system is the<br>
problem that you are experiencing:<br>
<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 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>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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 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 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 don't go through it. I go:<br>
File>Open...> then I double click the file and it opens it without<br>
asking anything else..<br>
If I use the Bio-Formats Importer route to open the 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>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Rafael,<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
First, as an example, I have a .czi of ~210MB that opens:<br>
- ZEN Blue Lite 2012 loading from network drive: about 2 seconds<br>
- Copying from network drive and pasting to the Desktop: about 4<br>
seconds<br>
- Fiji loading from network drive: 30 seconds<br>
<br>
In the ImageJ list I was informed that taking longer to load czi<br>
files might be a widespread issue with czi files.<br>
</blockquote>
<br>
How long does it take to read the file using Fiji, after it has<br>
been copied to the Desktop? That would help us to know if this is<br>
strictly due to the network file system, or if the procedure for<br>
reading the file is too slow.<br>
<br>
It would also be useful to know which options you have selected in<br>
the "Bio-Formats Import Options" window.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
The second problem was found while testing the speeds above. If I<br>
put the same file one folder deeper and try 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 things by creating folder,<br>
inside folder, inside folder.<br>
In the following structure:<br>
O:\Folder1\Folder2\Folder3\<u></u>Folder4\Folder5\Folder6\<u></u>Folder7<br>
If I have the czi file in Folder6, it takes 30 seconds to open. If<br>
I move it to Folder7, it takes 12 minutes to open.<br>
<br>
Is there an obvious reason for this increase in time?<br>
</blockquote>
<br>
Having more folders can cause subtle performance degradation, but<br>
typically not as much as you describe. If you open the file in<br>
Folder7 twice in a row, does it take 12 minutes both times?<br>
<br>
Regards,<br>
-Melissa<br>
<br>
On Fri, Dec 05, 2014 at 11:05:21AM -0600, r b wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
I recently got our lab workstation connected through the 1Gbps<br>
network to the building's server. Among other reasons, I was<br>
hoping to process images directly from the network drive. However,<br>
even with the upgrade to 1Gbps, loading images in Fiji is still<br>
slow. I have encountered two problems and I am not sure they are related.<br>
<br>
First, as an example, I have a .czi of ~210MB that opens:<br>
- ZEN Blue Lite 2012 loading from network drive: about 2 seconds<br>
- Copying from network drive and pasting to the Desktop: about 4<br>
seconds<br>
- Fiji loading from network drive: 30 seconds<br>
<br>
In the ImageJ list I was informed that taking longer to load czi<br>
files might be a widespread issue with czi files.<br>
<br>
The second problem was found while testing the speeds above. If I<br>
put the same file one folder deeper and try 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 things by creating folder,<br>
inside folder, inside folder.<br>
In the following structure:<br>
O:\Folder1\Folder2\Folder3\<u></u>Folder4\Folder5\Folder6\<u></u>Folder7<br>
If I have the czi file in Folder6, it takes 30 seconds to open. If<br>
I move it to Folder7, it takes 12 minutes to open.<br>
<br>
Is there an obvious reason for this increase 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>
<a href="http://os.name" target="_blank">os.name</a> => Windows 7<br>
os.version => 6.1<br>
java.version => 1.6.0_24<br>
java.vendor => Sun Microsystems Inc.<br>
<a href="http://java.runtime.name" target="_blank">java.runtime.name</a> => Java(TM) SE Runtime Environment<br>
java.runtime.version => 1.6.0_24-b07<br>
<a href="http://java.vm.name" target="_blank">java.vm.name</a> => Java HotSpot(TM) 64-Bit Server VM<br>
java.vm.version => 19.1-b02<br>
java.vm.vendor => Sun Microsystems Inc.<br>
<a href="http://java.vm.info" target="_blank">java.vm.info</a> => mixed mode<br>
java.awt.graphicsenv => sun.awt.<u></u>Win32GraphicsEnvironment<br>
<a href="http://java.specification.name" target="_blank">java.specification.name</a> => Java 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 problems:<br>
<br>
JAVA_HOME is set to:<br>
C:\Users\ADMINI~1\Desktop\<u></u>Fiji.app/java/win64/jdk1.6.0_<u></u>24//jre<br>
imagej.dir => C:\Users\ADMINI~1\Desktop\<u></u>Fiji.app<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 check:20141126151327)<br>
Fiji: <a href="http://fiji.sc/update/" target="_blank">http://fiji.sc/update/</a> (last check:20141125101145) MOSAIC<br>
ToolSuite:<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 November 2014.<br>
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<br></div></div><span class="HOEnZb"><font color="#888888">
-- <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></font></span><div class="HOEnZb"><div class="h5"><br>
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