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<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Ilya,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Thanks for the response. The thumbnails have a red X. Lower right click
gives a white image with the RGB values set correctly. I loaded the sample
files (see images below: *Morph*.TIF) from a completely new install (dropdb
ome, and rm –rf /OME)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I can try it again from a completely new directory structure to get rid
of the changes I made (I only added INCellRunXM.pm and changed
CoreDatabaseTablesTask.pm), but would like to hear from you first.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Is there a way to test OMEIS, since you mentioned that this might be
the problem?<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><img width=1053 height=590 id="_x0000_i1025"
src="cid:image001.jpg@01C6D7F5.093363C0" border=0><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><img width=612 height=533 id="_x0000_i1026"
src="cid:image002.jpg@01C6D7F5.093363C0" border=0><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Thanks again,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Bernd<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|-----Original Message-----</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|From: Ilya Goldberg [mailto:igg@nih.gov]</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Sent: Tuesday, September 12, 2006 12:34 PM</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|To: Bernd Jagla</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Cc: 'Curtis Rueden'; ome-devel@lists.openmicroscopy.org.uk</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Subject: Re: [ome-devel] image display problem</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Hi Guys</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|All of the errors in the log that you sent are in fact normal. More</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|comments inline.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|You also said:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|"The problem I have is that the images are not displayed on the
screen"</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Do you get the thumbnails? What do they look like - an icon with
a</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|question mark inside? A black square? What happens if you
click the</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|lower-right corner of the square/icon/thumbnail - does it launch the</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|SVG image viewer?</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Click on the upper-left corner of the square/icon/thumbnail, and you</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|should get the image detail view.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|In the lower-right corner of this page (you may need to scroll down)</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|it says "View with template:" followed by a drop-down menu,
which</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|says "detail". Select "large" and click the
Go button. Still</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|nothing? Black square, or icon with question mark?</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|If instead of images, you get an icon with a question mark, then</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|something may be wrong with the image server (OMEIS).</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|If you get a black square, it means that the default rendering</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|settings were no good for your images. You can fix this yourself</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|temporarily by launching the SVG viewer, adjusting the color mapping</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|and clicking "Save settings".</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|You can adjust these settings specifically in the InCell importer,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|which is probably a better idea.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Launching VisBio from the image view should work, but I'm not the</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|best source if this is a problem. It uses Java Web-Start to do
its</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|magic.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Shoola does not detect that its session expired, and gives a non-</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|informative error. You really have to not do anything with your</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|logged in session from any client for over a half hour for the</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|session to expire. Every request refreshes the session, so it</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|shouldn't expire in normal use.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Give a little more info about images not displaying, and we should be</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|able to resolve that.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|The InCell importer should have set the display options. You can</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|check this from the image detail view (select "detail" from
the "View</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|with template" menu when looking at an image). On the
upper-right</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|click on "Image import" in the "Module Executions"
table. The</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Outputs table should have DisplayChannel and DisplayOptions listed in</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|the "Untyped Outputs" column. Click on
DisplayOptions. These two</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|outputs specify how planes in your image are mapped to RGB channels</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|for display. Each plane in your image that's used for display is</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|listed in "DisplayChannel" with its white level and black
level. The</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|DisplayOptions table sets how each DisplayChannel is mapped to RGB.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|These two STs control how the image is displayed by the web UI and</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|any other client that reads these settings.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Try importing one or more of the test images here:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|http://openmicrosocpy.org/TestImages/</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|(maybe try the whole 011B1_Morph* set, which is a partial screening</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|set from MetaMorph). Are these displayed properly?</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|-Ilya</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|On Sep 8, 2006, at 10:43 AM, Bernd Jagla wrote:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Curtis,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> I can see the image even though I have to adjust the
intensities...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> I see this LDAP message in the error_log of httpd:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Can anyone make sense of this?</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Here is the error log from the following steps:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Remove /OME (rm -rf)</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Dropdb ome</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Sudo perl install -y</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> ome import ~/allOMEs/inca/Screening.ome</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> (=> no problems)</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> ome import ~/test/Ai_compound_import.ome</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> => problems with</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> OME::Tasks::LSIDManager::getRemoteObject() is not implemented. at</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> /usr/lib/perl5/site_perl/5.8.6/OME/ImportExport/ModuleImport.pm</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> line 183</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|This is a warning (not an error), and is normal and expected.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Could it be that this error comes up when doing the second import</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> within a</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> certain timeframe? There is no error log entry when this error
occurs.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Thanks,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Bernd</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Ok here is finally the snippet from the error_log:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:21 2006] [notice] Digest: generating secret for</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> digest</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> authentication ...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:21 2006] [notice] Digest: done</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:21 2006] [notice] LDAP: Built with OpenLDAP
LDAP SDK</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:21 2006] [notice] LDAP: SSL support unavailable</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|This is probably from mod_auth_ldap (not a part of OME). Anyway,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|this doesn't look like an error.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:22 2006] [notice] mod_python: Creating 4
session</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> mutexes</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> based on 150 max processes and 0 max threads.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:22 2006] [notice] Apache/2.0.54 (Fedora)</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> configured --</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> resuming normal operations</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Use of uninitialized value in print at</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/mod_perl_test.pl line
6.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Use of uninitialized value in print at</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/mod_perl_test.pl line
6.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|These appear sporadically and are generally harmless. We try to
get</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|rid of them as we see them, but these apparently we missed.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:22 2006] [error] [client 127.0.0.1] In PID
10585,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Error</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> calling OMEIS: Method parameter missing</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:26 2006] [error] [client 127.0.0.1] In PID
10601,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Error</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> calling OMEIS: Method parameter missing</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|These are the expected responses from OMEIS if the test is</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|successful. So when installing, this is a good thing.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:44 2006] [notice] SIGHUP received.
Attempting to</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> restart</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:44 2006] [warn] The ScriptAlias directive in</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> /OME/conf/httpd2.omeis-dev.conf at line 2 will probably never
match</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> because</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> it overlaps an</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> earlier ScriptAlias.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|This one always comes up, and we haven't figured out what to do about</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|it. Anyway, its harmless because the installer copied the omeis</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|binary to whatever ScriptAlias was set to (otherwise the above</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|expected "Missing parameter" error would not have been
generated by</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|OMEIS).</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Use of uninitialized value in concatenation (.) or string at</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Install/</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> ApacheConfigTask.pm</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> line 75.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Again, one of the ones we missed. Harmless.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Processing OME-startup.pl</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> DBD::Pg::st execute failed: ERROR: permission denied for
relation</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> experimenters</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|During the server startup, it tries to get an OME session as the user</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|who launched apache. Usually this is root, and usually this
fails,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|so it tries to get a session as the Apache user:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Tring to get a session as the Apache user...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|And it succeeds as the Apache user, so all is well because it goes on</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|to pre-load the STs:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Pre-loading SemanticTypes...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> WARNING: Explicit deletion of OME::Session at /OME/conf/OME-</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> startup.pl line</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> 76</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> OME::Session __destroySession: $self->__destroySession();</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> at /OME/conf/OME-startup.pl line 76</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|This is also normal because we explicitly shut down the temporary DB</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|handle we allocated to pre-load the STs.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Pre-loading classes for OME::Web...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|This is the last thing the pre-load script does, so all is well.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:47 2006] [notice] Digest: generating secret for</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> digest</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> authentication ...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:47 2006] [notice] Digest: done</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:47 2006] [notice] LDAP: Built with OpenLDAP
LDAP SDK</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:47 2006] [notice] LDAP: SSL support unavailable</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|These are probably from mod_auth_ldap - has nothing to do with OME.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:48 2006] [notice] mod_python: Creating 4
session</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> mutexes</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> based on 150 max processes and 0 max threads.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|These are probably from mod_python - also has nothing to do with OME.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> [Fri Sep 08 09:31:48 2006] [notice] Apache/2.0.54 (Fedora)</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> configured --</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> resuming normal operations</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|And this means we're good to go.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |-----Original Message-----</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |From: ctrueden.wisc@gmail.com [mailto:ctrueden.wisc@gmail.com]
On</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> Behalf Of</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |Curtis Rueden</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |Sent: Friday, September 08, 2006 9:40 AM</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |To: Bernd Jagla</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |Cc: ome-devel@lists.openmicroscopy.org.uk</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |Subject: Re: [ome-devel] image display problem</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |Hi Bernd,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |You could try reading the binary .ome files with VisBio from
disk,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> to see</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |how things look.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |-Curtis</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |On 9/7/06, Bernd Jagla < baj2107@columbia.edu</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> <mailto:baj2107@columbia.edu></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |> wrote:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> | Hi there,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> | I managed to get the images from the INCell imported
again with the</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |new version of OME. The images are in OMEIS (verified). They 16</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> bit Tiffs.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> | The problem I have is that the images are not displayed
on the</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> screen.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |They cannot be exported to VisBio. I get an XML from the
download</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> with some</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |binary data but can't confirm that this is what I want since I</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> don't know</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |how to read them. I believe that the attached error log has</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> something to do</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |with this. I couldn't see anything interesting in the http error</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> logs.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> | Please advise where look for possible solutions.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> | Thanks,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> | Bernd</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> | _______________________________________________</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> | ome-devel mailing list</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> | ome-devel@lists.openmicroscopy.org.uk</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> | http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> |</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> _______________________________________________</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> ome-devel mailing list</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> ome-devel@lists.openmicroscopy.org.uk</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|></span></font></p>
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