<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Nuno,<div><br></div><div> Now that this issue is fixed, and 5.0.2 will be released soon, you wanted to know how to access the "Original Metadata" via code?</div><div><br></div><div>Do you want Python? Java?</div><div><br></div><div>You can find a Python example of reading the Original Metadata key-value pairs at</div><div><a href="https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/python/Metadata.py#L111">https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/python/Metadata.py#L111</a></div><div><br></div><div>Cheers,</div><div><br></div><div> Will.</div><div><br></div><div><br><div><div>On 8 Apr 2014, at 00:46, Melissa Linkert <<a href="mailto:melissa@glencoesoftware.com">melissa@glencoesoftware.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Nuno,<br><br><blockquote type="cite">I submitted a Gatan file<br><a href="http://qa.openmicroscopy.org.uk/qa/feedback/8024/">http://qa.openmicroscopy.org.uk/qa/feedback/8024/</a><br></blockquote><br>Thank you for the report.<br><br><blockquote type="cite">acquired in montage mode using a TEM. This file has metadata<br>information about the montage size and overlap, as read in FIJI:<br><br>root.ImageList.1.ImageTags.Montage.Acquisition.Number of X Steps = 7<br>root.ImageList.1.ImageTags.Montage.Acquisition.Number of Y Steps = 8<br>root.ImageList.1.ImageTags.Montage.Acquisition.Overlap between<br>images (%) = 14.999999<br><br>And this is what I get from OME now:<br><br>Number of X Steps<span class="Apple-tab-span" style="white-space:pre"> </span>8.388608E7<br>Number of Y Steps<span class="Apple-tab-span" style="white-space:pre"> </span>1.34217728E8<br>Overlap between images (%)<span class="Apple-tab-span" style="white-space:pre"> </span>14.999999046325684<br><br>The number of X and Y steps is clearly wrong; the overlap is 15% and<br>there really is no need/point in having that many decimal places.<br></blockquote><br>The step count issue is now ticketed here:<br><br><a href="http://trac.openmicroscopy.org.uk/ome/ticket/12182">http://trac.openmicroscopy.org.uk/ome/ticket/12182</a><br><br>The overlap value is what is stored in the file; Bio-Formats does not<br>perform rounding or truncation of decimal values.<br><br><blockquote type="cite">There might be other information in this file that is not included<br>in your current data model, but these 3 items are all I need at the<br>moment. You're welcome to go through the rest of the metadata and<br>add more fields to the model, of course.<br></blockquote><br>Adding the tiling fields to the OME-XML model is ticketed here:<br><br>http://trac.openmicroscopy.org.uk/ome/ticket/6250<br><br><blockquote type="cite">I'd like to receive updates on this issue, particularly when a fix<br>becomes implemented. At that time, it would be nice to see a code<br>example for reading these values.<br></blockquote><br>You have been CC'd on all of the above-mentioned tickets, and so you<br>will receive an automated email each time one of the tickets changes.<br><br>Regards,<br>-Melissa<br><br>On Thu, Apr 03, 2014 at 07:01:48PM +0100, Nuno Goncalo Dias wrote:<br><blockquote type="cite">Hi,<br><br>I submitted a Gatan file<br>http://qa.openmicroscopy.org.uk/qa/feedback/8024/<br><br>acquired in montage mode using a TEM. This file has metadata<br>information about the montage size and overlap, as read in FIJI:<br><br>root.ImageList.1.ImageTags.Montage.Acquisition.Number of X Steps = 7<br>root.ImageList.1.ImageTags.Montage.Acquisition.Number of Y Steps = 8<br>root.ImageList.1.ImageTags.Montage.Acquisition.Overlap between<br>images (%) = 14.999999<br><br>And this is what I get from OME now:<br><br>Number of X Steps<span class="Apple-tab-span" style="white-space:pre"> </span>8.388608E7<br>Number of Y Steps<span class="Apple-tab-span" style="white-space:pre"> </span>1.34217728E8<br>Overlap between images (%)<span class="Apple-tab-span" style="white-space:pre"> </span>14.999999046325684<br><br>The number of X and Y steps is clearly wrong; the overlap is 15% and<br>there really is no need/point in having that many decimal places.<br><br>There might be other information in this file that is not included<br>in your current data model, but these 3 items are all I need at the<br>moment. You're welcome to go through the rest of the metadata and<br>add more fields to the model, of course.<br><br>I'd like to receive updates on this issue, particularly when a fix<br>becomes implemented. At that time, it would be nice to see a code<br>example for reading these values.<br><br>Thank you,<br>Nuno.<br><br><br>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></blockquote>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></blockquote></div><br></div></body></html>