<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On 21 May 2013, at 16:02, Roger Leigh <<a href="mailto:r.leigh@dundee.ac.uk">r.leigh@dundee.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">On 21/05/2013 10:37, Colin Rickman wrote:<br><br><blockquote type="cite">On 15 May 2013, at 11:13, Roger Leigh <<a href="mailto:r.leigh@DUNDEE.AC.UK">r.leigh@DUNDEE.AC.UK</a><br><<a href="mailto:r.leigh@DUNDEE.AC.UK">mailto:r.leigh@DUNDEE.AC.UK</a>>> wrote:<br></blockquote><br><blockquote type="cite"><blockquote type="cite">Can you reproduce the failure with a smaller series?<br></blockquote><br>I've tested this and I can with what seems to be any number of<br>individual files. In all cases the importer states "imported 0 of 1" and<br>sits scanning indefinitely. However, I did try entering the directory in<br>the import window and selecting all of the individual tiff files (a<br>10,000 file subset) and after a long wait to start the importer stated<br>"imported 0 of 10,000" and slowly started working through the files - it<br>is currently just over half way through.<br></blockquote><br>This sounds like progress, albeit slow. If you have any sample plain<br>TIFF files like this you'd like us to look at WRT import speed, then you<br>can also upload these as a zip as for the other data, below.<br></blockquote><div><br></div><div>I'l upload a small subset shortly. The upload of 10,000 files failed after just over 5000 files. All remaining files failed to upload. I hit submit failures (unticking file and selecting log) so you can see what happened - it looks like it may have generated a single log for every file rather than one log file for all files. </div><div><br></div><br><blockquote type="cite"><blockquote type="cite">I've uploaded a test data set to the link above. I also tested uploading<br>the same dataset to our OMERO server. The dataset consists of *.apl,<br>*.mtb and *.tnb files which contain all of the metadata etc. In a<br>separate subdirectory are the multidimensional tiff files. Importing the<br>whole dataset sort of worked. In the example I sent you the resulting<br>upload contained 16 image stacks (the correct number). However, one of<br>the .tif files was now given the *.apl file name and the metadata was<br>not imported fully. All of the remaining .tif files had their cryptic<br>name used by the database rather than their human understandable name<br>given in the metadata. There were a couple of errors reported trying to<br>access this dataset on the OMERO server and these have been reported<br>under my email address.<br><br>Hope that helps. Let me know what else you need to know.<br></blockquote><br>Thanks for uploading the data, I've tested it with the current dev_4_4<br>development code, and I think I have reproduced what you've described.<br>I've opened ticket #10942<br>(<a href="http://trac.openmicroscopy.org.uk/ome/ticket/10942">http://trac.openmicroscopy.org.uk/ome/ticket/10942</a>) for this issue.<br></blockquote><div><br></div><div>Thanks. Hopefully this can be rectified in the next release. If you require any other sample datasets for testing just let me know.</div><div><br></div><div>Colin</div><br></div><div><br></div><div><div><div style="line-height: 16px; margin: 6px 0px; padding: 8px; border-top-width: 1px; border-top-color: rgb(174, 177, 166); border-top-style: dotted; border-bottom-width: 1px; border-bottom-color: rgb(174, 177, 166); border-bottom-style: dotted; font-family: Calibri, Verdana, Arial, sans-serif; font-size: 13px; color: rgb(85, 85, 85); "><p>Dr Colin Rickman<br>Institute of Biological Chemistry, Biophysics and Bioengineering<br>School of Engineering and Physical Sciences<br>Heriot-Watt University<br>Edinburgh<br>EH14 4AS</p><p>Tel: +44 131 4514193 (Office)</p><p><a href="http://www.ib3.eps.hw.ac.uk" style="text-decoration: none !important; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: rgb(170, 170, 170); color: rgb(0, 136, 204); ">http://www.ib3.eps.hw.ac.uk</a><br><a href="http://www.esric.org" style="text-decoration: none !important; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: rgb(170, 170, 170); color: rgb(0, 136, 204); ">http://www.esric.org</a><br></p></div><br class="Apple-interchange-newline"></div></div><div><br></div><br><br>
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