[ome-devel] Housekeeping..

Claude Bonnard cbonnard at isrec-sg1.unil.ch
Wed Jul 21 17:58:11 BST 2004


Dear Tom,

I tried with success the suggested file and I can import images from the
defined data directory. This is perfect, Thanks!

This raise the question of ease of import: users want to have a simple and
successful operation, regardless of the format. Should i remind that  we don't
have much power on the image format, especially for equipment we have already
in the lab and we plan to keep for their life. "Next generation" will hopefully
support OME!

I also tried a STK file which was also imported without problem and I can view
and export it (as far as your file.. The other -rather large stack- did not).

Apropos OME format, I tried an ome file as generated by Imaris (4.0.5) and this
was a failure. Later in this message, the extract of error_log, regarding this
import operation.

Any idea?  Bitplane? OME Team?

Regards, Claude


04/07/21 15:54:10 serve.pl[3987]: OME::Tasks::OMEImport->importFile: imported
bla77_MLE.ome
04/07/21 15:54:10 serve.pl[3987]: OME::ImportExport::HierarchyImport->new
called with parameters:
        session=>OME::Session=HASH(0x94f664c)
        semanticTypes=>
        semanticColumns=>
        _parser=>XML::LibXML=HASH(0x918ef8c)
04/07/21 15:54:10 serve.pl[3987]: OME::ImportExport::HierarchyImport->new
returning successfully
04/07/21 15:54:10 serve.pl[3987]:
OME::ImportExport::HierarchyImport->processDOM: Processing Projects
04/07/21 15:54:10 serve.pl[3987]:
OME::ImportExport::HierarchyImport->processDOM: Processing Datasets
04/07/21 15:54:10 serve.pl[3987]:
OME::ImportExport::HierarchyImport->processDOM: Processing Images
04/07/21 15:54:10 serve.pl[3987]:
OME::ImportExport::HierarchyImport->importObject: Importing node Image type 1
[Wed Jul 21 15:54:10 2004] -e: DBD::Pg::st execute failed: ERROR:  ExecInsert:
Fail to add null value in not null attribute experimenter_id at /usr
/lib/perl5/site_perl/5.8.0/OME/DBObject.pm line 2329.
04/07/21 15:54:10 serve.pl[3987]: Error DBD::Pg::st execute failed: ERROR:
 ExecInsert: Fail to add null value in not null attribute experimenter_i
d at /usr/lib/perl5/site_perl/5.8.0/OME/DBObject.pm line 2329.
        OME::Factory::newObject('OME::Factory=HASH(0x90f2c2c)','OME::Image','HASH(0x8a29c24)')
called at /usr/lib/perl5/site_perl/5.8.0/OME/ImportE
xport/HierarchyImport.pm line 442
        OME::ImportExport::HierarchyImport::importObject('OME::ImportExport::HierarchyImport=HASH(0x8a299f0)','XML::LibXML::Element=SCALAR(0x8a29ab
c)','undef','undef','undef') called at
/usr/lib/perl5/site_perl/5.8.0/OME/ImportExport/HierarchyImport.pm line 245
        OME::ImportExport::HierarchyImport::processDOM('OME::ImportExport::HierarchyImport=HASH(0x8a299f0)','XML::LibXML::Element=SCALAR(0x8a296c0)
') called at /usr/lib/perl5/site_perl/5.8.0/OME/Tasks/OMEImport.pm line 256
        OME::Tasks::OMEImport::processDOM('OME::Tasks::OMEImport=HASH(0x961769c)','XML::LibXML::Element=SCALAR(0x8a296c0)','IgnoreAlterTableErrors'
,1,'NoDuplicates',0) called at
/usr/lib/perl5/site_perl/5.8.0/OME/Tasks/OMEImport.pm line 172
        OME::Tasks::OMEImport::importFile('OME::Tasks::OMEImport=HASH(0x961769c)','OME::Image::Server::File=ARRAY(0x959e8a8)','NoDuplicates',0,'Ign
oreAlterTableErrors',1) called at
/usr/lib/perl5/site_perl/5.8.0/OME/ImportEngine/XMLreader.pm line 85
        OME::ImportEngine::XMLreader::importGroup('OME::ImportEngine::XMLreader=HASH(0x964108c)','OME::Image::Server::File=ARRAY(0x959e8a8)','CODE(
0x8eaa24c)') called at
/usr/lib/perl5/site_perl/5.8.0/OME/ImportEngine/ImportEngine.pm line 333
        eval {...} called at
/usr/lib/perl5/site_perl/5.8.0/OME/ImportEngine/ImportEngine.pm line 332
        OME::ImportEngine::ImportEngine::importFiles('OME::ImportEngine::ImportEngine=HASH(0x94bb1bc)','ARRAY(0x8f798c4)')
called at /usr/lib/perl5
/site_perl/5.8.0/OME/Tasks/ImageTasks.pm line 212
        OME::Tasks::ImageTasks::forkedImportFiles('OME::Dataset=HASH(0x94bb06c)','ARRAY(0x8f96f04)')
called at /usr/lib/perl5/site_perl/5.8.0/OME/W
eb/ImportFiles.pm line 546
        OME::Web::ImportFiles::__getImportBody('OME::Web::ImportFiles=HASH(0x94ec124)')
called at /usr/lib/perl5/site_perl/5.8.0/OME/Web/ImportFile
s.pm line 592
        OME::Web::ImportFiles::getPageBody('OME::Web::ImportFiles=HASH(0x94ec124)')
called at /usr/lib/perl5/site_perl/5.8.0/OME/Web.pm line 404
        OME::Web::createOMEPage('OME::Web::ImportFiles=HASH(0x94ec124)') called
at /usr/lib/perl5/site_perl/5.8.0/OME/Web.pm line 270
        OME::Web::serve('OME::Web::ImportFiles=HASH(0x94ec124)') called at
/OME/perl2/serve.pl line 98
        eval {...} called at /OME/perl2/serve.pl line 86
        ModPerl::ROOT::ModPerl::Registry::OME_perl2_serve_2epl::handler('Apache::RequestRec=SCALAR(0x9633068)')
called at /usr/lib/perl5/vendor_per
l/5.8.0/i386-linux-thread-multi/ModPerl/RegistryCooker.pm line 184
        eval {...} called at
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/ModPerl/RegistryCooker.pm
line 184
        ModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0x96330ec)')
called at /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/ModPer
l/RegistryCooker.pm line 154
        ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0x96330ec)')
called at /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-
multi/ModPerl/Registry.pm line 16
        ModPerl::Registry::handler('ModPerl::Registry','Apache::RequestRec=SCALAR(0x9633068)')
called at -e line 0
        eval {...} called at -e line 0
 importing image: OME::ImportEngine::XMLreader bla77_MLE.ome
04/07/21 15:54:11 serve.pl[3799]: Serving package - OME::Web::TaskProgress.
04/07/21 15:54:11 serve.pl[3799]: getApacheSession:
sessionKey=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:11 serve.pl[3799]: getApacheSession: timestamp = 1090418050.
 Session is 0.0166666666666667 minutes old
04/07/21 15:54:11 serve.pl[3799]: getApacheSession: username=cbonnard
04/07/21 15:54:11 serve.pl[3799]: getApacheSession:
key=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:11 serve.pl[3799]: createWithKey: username=cbonnard
04/07/21 15:54:11 serve.pl[3799]: createWithKey:
key=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:12 serve.pl[3987]: Loading attribute type package
OME::SemanticType::__Pixels
04/07/21 15:54:12 serve.pl[3987]: Loading data table package
OME::DataTable::__IMAGE_PIXELS
04/07/21 15:54:12 serve.pl[3799]: getOMESession: looking for userState,
experimenter_id=1
04/07/21 15:54:12 serve.pl[3799]: getOMESession: found existing userState(s)
04/07/21 15:54:13 serve.pl[3799]: getOMESession: updating userState
04/07/21 15:54:13 serve.pl[3799]: getOMESession: returning session
04/07/21 15:54:13 serve.pl[3799]: createWithKey:
{SessionKey}=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:13 serve.pl[3799]: createWithKey:
SessionKey()=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:13 serve.pl[3799]: storeApacheSession:
sessionKey=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:15 serve.pl[3801]: Serving package - OME::Web::TaskProgress.
04/07/21 15:54:15 serve.pl[3801]: getApacheSession:
sessionKey=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:15 serve.pl[3801]: getApacheSession: timestamp = 1090418051.
 Session is 0.0666666666666667 minutes old
04/07/21 15:54:15 serve.pl[3801]: getApacheSession: username=cbonnard
04/07/21 15:54:15 serve.pl[3801]: getApacheSession:
key=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:15 serve.pl[3801]: createWithKey: username=cbonnard
04/07/21 15:54:15 serve.pl[3801]: createWithKey:
key=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:15 serve.pl[3801]: getOMESession: looking for userState,
experimenter_id=1
04/07/21 15:54:15 serve.pl[3801]: getOMESession: found existing userState(s)
04/07/21 15:54:15 serve.pl[3801]: getOMESession: updating userState
04/07/21 15:54:16 serve.pl[3801]: getOMESession: returning session
04/07/21 15:54:16 serve.pl[3801]: createWithKey:
{SessionKey}=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:16 serve.pl[3801]: createWithKey:
SessionKey()=0d8d085025a445b41d53bd015343a9ff
04/07/21 15:54:16 serve.pl[3801]: storeApacheSession:
sessionKey=0d8d085025a445b41d53bd015343a9ff
------------------------------------------------------------------------


On Jul 20,  9:01am, Tomasz Macura wrote:
> Subject: Re: [ome-devel] Housekeeping..
> Dear Claude,
>
> I think I might be able to help you with your OME problems.
>
> > As far as import, I have tested again with a jpg, although my tiff
> > were very
> > standard single image tiff
> You received an email from Jason, I believe, that explains jpegs are
> not supported.
>
> "Standard single image tiffs" are often RGB tiffs. Those are not
> supported by OME 2.2 and probably its forthcoming patch.
> To verify this run tiffinfo against the tiff image you are trying to
> import. Please include this info with your reply.
>
> If the "Photometric Interpretation" is RGB then the import is known not
> to work.
>
> To test whether OME is properly installed, and the image importer is
> functioning correctly for tiff images, please download
> http://www.openmicroscopy.org/TestImages/n2_plate18_P24_w1.tif and try
> to import it.
> This import is expected to succeed.
>
> Hope this helps,
>
> Tom
>
>
>
>
>
> On Jul 20, 2004, at 6:13 AM, Claude Bonnard wrote:
>
> > Thanks for your reply, Ilya.
> >
> > The "zealous spam filter" has been submitted to the  IT people , and I
> > want to
> > present my appologies for this possible problem which made some of
> > Chris'reply
> >  lost who knows where. I now carefully watch in
> > http://lists.openmicroscopy.org.uk/pipermail/ome-devel/
> >
> > and .. let's try all to do our best :-)
> >
> >
> >
> >
> > I have the same "Successfully imported 0 images" as result, but I
> > found a line
> > in the error log... Is this a clue for you?
> >
> > ....
> >
> > *DEBUG* PARAM[import_queue]: /DATA_OME/cbonnard/zoom.jpg
> > *DEBUG* PARAM[Path]: /DATA_OME/cbonnard
> > *DEBUG* PARAM[action]: import
> > *DEBUG* PARAM[new_or_existing]: existing
> > *DEBUG* PARAM[existing_dataset]: new_dataset
> > *DEBUG* PARAM[name]:
> > *DEBUG* PARAM[description]: Une image jpg (nom de l'image= zoom,
> > taille 171KB)
> > *DEBUG* PARAM[q_selected]: /DATA_OME/cbonnard/zoom.jpg
> > [Tue Jul 20 09:47:39 2004] -e: Use of uninitialized value in -d at
> > /usr/lib/perl5/site_perl/5.8.0/OME/Web/ImportFiles.pm line 94.
> > ....
> >
> > Thanks for your help!
> >
> > Claude
> >
> >
> > On Jul 19,  6:26pm, Ilya Goldberg wrote:
> >> Subject: Re: [ome-devel] Housekeeping..
> >>
> >> On Jul 16, 2004, at 6:15 AM, Claude Bonnard wrote:
> >>
> >>> When images import terminates without the "two active imports"
> >>> message
> >>> above,
> >>> the success message is: "Successfully imported 0 images". The images
> >>> are tif.
> >>
> >> Ahh.  But what kind of tiff?  The release unfortunately has this
> >> 'hanging' bug which is fixed in the release we're currently packing
> >> up.
> >> You can release all the hung database handles by restarting apache
> >> (sudo apachectl restart).
> >> Sorry about this, but we'll have a release candidate up in a few days
> >> (not to be used in production environments).
> >>
> >> Also, it appears that email sent to you from ome-devel is rejected at
> >> your end.  Probably an over-zealous spam filter.
> >> -Ilya
> >> -- End of excerpt from Ilya Goldberg
> >
> >
> >
> > --
> > Claude Bonnard Ph.D.
> > ISREC (Swiss Institute for Experimental Cancer Research)
> > Microscopy, Imaging and Morphology Core Facility [MIM]
> > Lab F216
> > Ch des Boveresses 155
> > CH-1066 Epalinges
> > Switzerland
> > phone: [41-21]-692-5891
> >   fax: [41-21]-652-6933
> > _______________________________________________
> > ome-devel mailing list
> > ome-devel at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> >
>-- End of excerpt from Tomasz Macura



-- 
Claude Bonnard Ph.D.
ISREC (Swiss Institute for Experimental Cancer Research)
Microscopy, Imaging and Morphology Core Facility [MIM] 
Lab F216
Ch des Boveresses 155
CH-1066 Epalinges
Switzerland
phone: [41-21]-692-5891
  fax: [41-21]-652-6933


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