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<div>Hi Martin</div>
<div>I forgot to mention in my previous e-mail.</div>
<div>Could you submit one of the files that currently failed to import?</div>
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<div>Thanks</div>
<div>Jmarie</div>
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<span style="font-weight:bold">From: </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf of Martin Jones <<a href="mailto:Martin.Jones@crick.ac.uk">Martin.Jones@crick.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Monday, 14 September 2015 14:42<br>
<span style="font-weight:bold">To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ome-users] GatanReader bug<br>
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<div>Thanks, I’ve downloaded the latest versions of bioformats (via Fiji updater) and bftools.zip (from <a href="http://www.openmicroscopy.org/site/support/bio-formats5.1/users/comlinetools/">http://www.openmicroscopy.org/site/support/bio-formats5.1/users/comlinetools/</a> today)
but I’m still unable to open my .dm4 files.</div>
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<div>Importing with Fiji results in a popup message that I don’t think I got before saying “Sorry, there was a problem during import."</div>
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<div>Here are the results of ./showinf:</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">G12-Laptop02:bftools jones58$ ./showinf ~/Desktop/Example_Gatan_File.dm4 </div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Checking file format [Gatan Digital Micrograph]</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Initializing reader</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">GatanReader initializing /Users/jones58/Desktop/Example_Gatan_File.dm4</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Verifying Gatan format</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Reading tags</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Exception in thread "main" loci.formats.FormatException: Unable to parse metadata tag</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.GatanReader.initFile(GatanReader.java:202)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1426)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ImageReader.setId(ImageReader.java:835)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1028)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.tools.ImageInfo.main(ImageInfo.java:1117)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Caused by: java.lang.NumberFormatException: For input string: "50"</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Double.parseDouble(Double.java:538)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Double.<init>(Double.java:608)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.GatanReader.parseTags(GatanReader.java:487)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.GatanReader.parseTags(GatanReader.java:474)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.GatanReader.initFile(GatanReader.java:200)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;"><span class="Apple-tab-span" style="white-space:pre"></span>... 5 more</div>
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<div>Any help or advice is much appreciated!</div>
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<div>Cheers,</div>
<div>Martin</div>
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<div>On 4 Sep 2015, at 11:17, Jean-Marie Burel (Staff) <<a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>> wrote:</div>
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<div>Hi Martin</div>
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<div>Thanks for reporting the issue. The problem has already been solved see <a href="https://github.com/openmicroscopy/bioformats/pull/1928">https://github.com/openmicroscopy/bioformats/pull/1928</a></div>
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<div>The fix will be included in the 5.1.4 version of Bio-Formats, version that we are planning to release early next week.</div>
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<div>Cheers</div>
<div><br>
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<div>Jmarie</div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span></div>
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<font color="#919191" face="Trebuchet MS" size="1"><br>
Dr. Martin Jones<br>
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Electron Microscopy STP<br>
The Francis Crick Institute<br>
Lincoln's Inn Fields Laboratory</font></div>
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<div><font color="#919191" face="Trebuchet MS" size="1">T: +44 (0)20 7269 3346 (Room 1B16)</font></div>
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<font color="#919191" face="Trebuchet MS" size="1">E: <a href="mailto:Martin.Jones@crick.ac.uk">Martin.Jones@crick.ac.uk</a></font></div>
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