Open Microscopy Environment

Hi,

I am on the way for tiffinfo and tiffutil.
I can upload the file to a (s)ftp server if you wish...

Best

Jacques

Hi,

here are the results of
tiffinfo 20110629-Spat-1_1.tif 1> tiffinfo.out 2>tiffinfo.err
and
tiffutil -info 20110629-Spat-1_1.tif 1> tiffutil.out 2>tiffutil.err

Thank you for your help

Jacques

Hi,

the file was transfered yesterday evening with its original name. Let me know if you need more info.

Thanks for your help

Jacques

Hello,

I saw that you closed the bug on the tracker. Is there a patch that I can load ? Do I have to fully update omero server to a "night-build" version containing the fix or can I surgically replace only a part if it promises a better stability.
Thank you very much for your help
and of course to the team for offering omero open source and for the great support!

Jacques

Did you miss this comment at the bottom of the page:
http://qa.openmicroscopy.org.uk/qa/feedback/3905 (is this the right feedback)?

2011 07 29 00:01:40 by melissa@...
This should be fixed now; you can try the fix using the latest trunk build of OMERO.importer:
http://hudson.openmicroscopy.org.uk/job ... k-clients/

Hope that helps?

Will.

Hello,
we have observed the same issue with images imported using version 4.3.0. After downloading the latest client version 4.3.2 (build 1835), the problem seems to be solved for TIFF images, i.e. now we get a thumbnail and can render them.
However, the problem persists for imported JPEG and PNG files, meaning those still cannot be rendered! I can supply example images if desired. Here is the excerpt of the INSIGHT log file for the import process:

2011-08-09 16:00:27,113 INFO [ ome.formats.importer.ImportConfig] ( Thread-54) OMERO Version: 4.3.2-DEV-b00b38af-b2629
2011-08-09 16:00:27,113 INFO [ ome.formats.importer.ImportConfig] ( Thread-54) Bioformats version: 4.3.2-DEV revision: d1242b7 date: 19 July 2011
2011-08-09 16:00:27,149 WARN [ ome.formats.importer.ImportLibrary] ( Thread-54) Pre 4.3.2 server or empty omero.pixeldata.fs_lite_readers, using hard coded readers!
2011-08-09 16:00:27,177 WARN [ ome.formats.importer.ImportLibrary] ( Thread-54) Pre 4.3.2 server or empty missing omero.pixeldata.max_plane_width, using hard coded maximum plane width!
2011-08-09 16:00:27,204 WARN [ ome.formats.importer.ImportLibrary] ( Thread-54) Pre 4.3.2 server or empty missing omero.pixeldata.max_plane_height, using hard coded maximum plane height!
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Big image, enabling metadata only and archiving.
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) File format: Animated PNG
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Base reader: loci.formats.in.APNGReader
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Metadata only import? false
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Archiving enabled? true
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Container metadata only import? true
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Reader is not of HCS domain, use metafile: true
2011-08-09 16:00:28,093 WARN [ ome.formats.model.ReferenceProcessor] ( Thread-54) Unknown target class for LSID: Image:0

Let me know if you need any further information regarding this bug.
Cheers,
Joern

Hi,
I tried Melissa suggestion about the importer. I thus used this new importer without modifying anything on server side (was that the idea you suggested?) and it somewhat fixed the issue. Indeed, images are uploaded, preview generated, etc... but it takes a dreadfully long time. About 4 hours for a 2 GB tiff containing about 4000 frames. This is typically 10 times longer than what I experienced with 4.2.2. The importer and the server runs on the same computer. Did I missed something?

By the way, the bug into link (http://qa.openmicroscopy.org.uk/qa/feedback/3905) is different from the one in this topic and was triggered using small tiff file by an other user of my server. However, that's great that you could fix it. Thanks a lot!

Any suggestion about the importer of large tiff file would be welcome

Thank you very much for your help

Best

JAcques

toedling wrote:Hello,
we have observed the same issue with images imported using version 4.3.0. After downloading the latest client version 4.3.2 (build 1835), the problem seems to be solved for TIFF images, i.e. now we get a thumbnail and can render them.
However, the problem persists for imported JPEG and PNG files, meaning those still cannot be rendered! I can supply example images if desired. Here is the excerpt of the INSIGHT log file for the import process:

2011-08-09 16:00:27,113 INFO [ ome.formats.importer.ImportConfig] ( Thread-54) OMERO Version: 4.3.2-DEV-b00b38af-b2629
2011-08-09 16:00:27,113 INFO [ ome.formats.importer.ImportConfig] ( Thread-54) Bioformats version: 4.3.2-DEV revision: d1242b7 date: 19 July 2011
2011-08-09 16:00:27,149 WARN [ ome.formats.importer.ImportLibrary] ( Thread-54) Pre 4.3.2 server or empty omero.pixeldata.fs_lite_readers, using hard coded readers!
2011-08-09 16:00:27,177 WARN [ ome.formats.importer.ImportLibrary] ( Thread-54) Pre 4.3.2 server or empty missing omero.pixeldata.max_plane_width, using hard coded maximum plane width!
2011-08-09 16:00:27,204 WARN [ ome.formats.importer.ImportLibrary] ( Thread-54) Pre 4.3.2 server or empty missing omero.pixeldata.max_plane_height, using hard coded maximum plane height!
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Big image, enabling metadata only and archiving.
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) File format: Animated PNG
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Base reader: loci.formats.in.APNGReader
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Metadata only import? false
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Archiving enabled? true
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Container metadata only import? true
2011-08-09 16:00:28,084 INFO [ ome.formats.importer.ImportLibrary] ( Thread-54) Reader is not of HCS domain, use metafile: true
2011-08-09 16:00:28,093 WARN [ ome.formats.model.ReferenceProcessor] ( Thread-54) Unknown target class for LSID: Image:0

Let me know if you need any further information regarding this bug.
Cheers,
Joern

How large are these images in X and Y? You may need to increase the memory available to the PixelData process that is creating image pyramids for your images.

jacques2020 wrote:Hi,
I tried Melissa suggestion about the importer. I thus used this new importer without modifying anything on server side (was that the idea you suggested?) and it somewhat fixed the issue. Indeed, images are uploaded, preview generated, etc... but it takes a dreadfully long time. About 4 hours for a 2 GB tiff containing about 4000 frames. This is typically 10 times longer than what I experienced with 4.2.2. The importer and the server runs on the same computer. Did I missed something?

By the way, the bug into link (http://qa.openmicroscopy.org.uk/qa/feedback/3905) is different from the one in this topic and was triggered using small tiff file by an other user of my server. However, that's great that you could fix it. Thanks a lot!

Any suggestion about the importer of large tiff file would be welcome

Thank you very much for your help

Best

JAcques

Can I have your importer log please Jacques?

Hello,

thanks for the quick reply. However, it's certainly not a problem of the dimension. Rendering and thumbnail generation simply do not work for PNG (and JPEG) files! That is true even for trivial images such as the attached logo, which is of size 260x116, while it works for TIFF files of size 3264x2448. So there seems to be a general problem with importing PNG and JPEG images.
The error message in the INSIGHT log file is the same as the one I posted above. Could it be an issue because the server is version 4.3.0 while the client is version 4.3.2?

Cheers,
Joern

Hi Chris,

images are 512x512 (I attach output and errors of a tiffinfo).
I also attach the importer.log (the import I mention here started on 10th of August morning).

PixelData has 6 GB RAM (over 24 GB on the server)

/usr/local/OMERO.server-Current/etc/grid$ cat templates.xml | grep -A 10 -B 1 -e "<server-template id=\"PixelDataTemplate\">"

<server-template id="PixelDataTemplate">
<parameter name="index"/>
<parameter name="dir"/>
<parameter name="config" default="default"/>
<server id="PixelData-${index}" exe="${JAVA}" activation="always" pwd="${OMERO_HOME}">
<option>-Xmx6144M</option>
<option>-Djava.awt.headless=true</option>
<option>-Dlog4j.configuration=${OMERO_ETC}log4j-indexing.xml</option>
<option>-Domero.logfile=${OMERO_LOGFILE}</option>
<option>-Domero.name=PixelData-${index}</option>
<option>-jar</option>

Do you have an idea of the issue?

Thanks for our help

Jacques