Hi James,<div><br class="webkit-block-placeholder"></div><div>The ZVI timestamp bug should be fixed in the latest trunk build of Bio-Formats. Also, please note that there is a typo in the code snippet that I originally sent you - getPlaneTimingDeltaT returns the number of seconds since acquisition began, not the number of milliseconds.</div>
<div><br class="webkit-block-placeholder"></div><div>Please let us know if you continue to experience problems with OME software.</div><div><br class="webkit-block-placeholder"></div><div>Regards,</div><div>-Melissa</div>
<br><div class="gmail_quote">On Tue, May 27, 2008 at 12:10 PM, Melissa Linkert <<a href="mailto:linkert@wisc.edu">linkert@wisc.edu</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi James,<div><br></div><div>It looks like you are doing everything correctly - there is probably still a bug in Bio-Formats.</div><div><br></div><div>If you could send one or more ZVI files that exhibit this problem, that would be extremely helpful in debugging. Files smaller than 15 MB can be sent as an email attachment; otherwise, you can send them by FTP (I will provide server details off-list).</div>
<div><br></div><div>Regards,</div><div>-Melissa<div><div></div><div class="Wj3C7c"><br><br><div class="gmail_quote">On Tue, May 27, 2008 at 11:51 AM, James Chen <<a href="mailto:james.chenn@gmail.com" target="_blank">james.chenn@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Melissa,<br>Thanks for your input. I'm using the matlab version of bio-formats and I tried running a matlab version of the code you posted below. However, the results are still the same: the retrieve structure basically has no data in it. Here is what I ran:<br>
<br>javaaddpath('loci_tools.jar');<br>store = loci.formats.MetadataTools.createOMEXMLMetadata();<br>reader = loci.formats.ImageReader();<br>reader.setMetadataStore(store);<br><br>reader.setId(zvi_file);<br><br>retrieve = reader.getMetadataStore();<br>
<br>creationDate = retrieve.getImageCreationDate(0);<br> <br>for plane = 0:reader.getImageCount()<div><br> timestamp = retrieve.getPlaneTimingDeltaT(0,0,plane)<br></div>end<br><br>When I run a get(retrieve), all the fields in the structure are either 0 or empty. I made sure I was running the latest daily build of bio-formats and I double checked to make sure the zvi file had time stamps, but I am still getting nothing. Am I doing something wrong?<br>
<br>Thanks,<br><font color="#888888">-James</font><div><div></div><div><br><br><br><div class="gmail_quote">On Mon, May 26, 2008 at 12:33 PM, Melissa Linkert <<a href="mailto:linkert@wisc.edu" target="_blank">linkert@wisc.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
Hi James,<div><br></div><div>The latest daily build of Bio-Formats (available at <a href="http://loci.wisc.edu/ome/formats.html" target="_blank">http://loci.wisc.edu/ome/formats.html</a>) should fix this problem. If timestamps are present in the file, they will be in the hashtable under the key "Timestamp <n>", where <n> is the timepoint number indexed from 0. Note that this will only work for ZVI files - other formats store their timestamps using different keys.</div>
<div><br></div><div>I don't how you are using Bio-Formats; if you are using it as a library within your own application, then you should consider using the MetadataStore API to retrieve timestamps. Following is some example code:</div>
<div><br></div><div>MetadataStore store = MetadataTools.createOMEXMLMetadata();</div><div>ImageReader reader = new ImageReader();</div><div>reader.setMetadataStore(store);</div><div><br>
</div><div>reader.setId("/path/to/file");</div><div>MetadataRetrieve retrieve = (MetadataRetrieve) reader.getMetadataStore();</div><div><br></div><div> // get the time when acquisition began, in "yyyy-MM-dd'T'HH:mm:ss" format<br>
</div><div>String creationDate = retrieve.getImageCreationDate(0);</div><div> </div><div>for (int plane=0; plane<reader.getImageCount(); plane++) {</div><div> // get the timestamp for this plane</div><div> // this is the time in milliseconds since acquisition began</div>
<div> Float timestamp = retrieve.getPlaneTimingDeltaT(0, 0, plane);</div><div>}</div><div><br></div><div>Please let us know if you have any other questions, or if the latest daily build does not work for you.</div><div>
<br>
</div><div>Regards,</div><div>-Melissa<br><br><div class="gmail_quote"><div><div></div><div>On Thu, May 22, 2008 at 12:22 PM, James Chen <<a href="mailto:james.chenn@gmail.com" target="_blank">james.chenn@gmail.com</a>> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex"><div><div></div><div>Hello everyone,<br>I'm having trouble pulling out time stamp information from a time lapsed series in the ZVI file from bio-formats. I've gone over the entire metadata hashtable but can't seem to find any link to it. Does anyone have any suggestions?<br>
<br>Thanks,<br><font color="#888888">-James<br>
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