<div dir="ltr">Hi Guilhem,<div><br></div><div>Thank you again for offering to send a file - FTP details have now been sent to you via private email. We will continue to investigate once a file is uploaded.</div><div><br></div><div>Regards,</div><div>-Melissa</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Mon, Nov 26, 2018 at 6:11 AM David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk">d.gault@dundee.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hi,
<div><br>
</div>
<div>Thank you for raising this bug. If you have any smaller files (< 2GB) that reproduce the same behaviour you can upload them to
<a href="https://www.openmicroscopy.org/qa2/qa/upload/" target="_blank">https://www.openmicroscopy.org/qa2/qa/upload/</a>, otherwise we will arrange FTP details for you to transfer the larger original file for testing.</div>
<div>I have opened a Bio-Formats Trello card to track this issue: <a href="https://trello.com/c/dDcSZtur/296-indexoutofboundsexception" target="_blank">https://trello.com/c/dDcSZtur/296-indexoutofboundsexception</a></div>
<div><br>
</div>
<div>With Thanks,</div>
<div>David Gault</div>
<div><br>
<div>
<blockquote type="cite">
<div>On 23 Nov 2018, at 18:05, Guilhem Chenon <<a href="mailto:guilhem.chenon@espci.fr" target="_blank">guilhem.chenon@espci.fr</a>> wrote:</div>
<br class="m_6064013233316681339Apple-interchange-newline">
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<div text="#000000" bgcolor="#FFFFFF">
<p><font face="Karla">Hello,</font></p>
<p><font face="Karla">I am having trouble with several random .nd2 files which will not open with Bio-Formats plugin either in ImageJ or Matlab. When I call bfGetReader on the file, I get this error message:</font></p>
<p><font face="Karla">Error using bfGetReader (line 85)<br>
Java exception occurred:<br>
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<br>
<br>
at java.util.ArrayList.rangeCheck(ArrayList.java:653)<br>
<br>
at java.util.ArrayList.get(ArrayList.java:429)<br>
<br>
at loci.formats.FormatReader.getSizeC(FormatReader.java:689)<br>
<br>
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1348)<br>
<br>
at loci.formats.FormatReader.setId(FormatReader.java:1401)<br>
<br>
at loci.formats.DelegateReader.setId(DelegateReader.java:291)<br>
<br>
at loci.formats.ImageReader.setId(ImageReader.java:835)<br>
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)<br>
<br>
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)<br>
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)<br>
<br>
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)<br>
</font></p>
<p><font face="Karla">The original file is quite big (10Gb), so I can only upload it through FTP. When I crop the file in NIS, interestingly, it works, so for now my workaround is to crop the image itself because apparently NIS re-encodes
channels and timepoints during cropping so I can open it with Bio-Formats. <br>
</font></p>
<p><font face="Karla">Moreover, these problematic files open fine with the ImageJ ND2 Reader plugin (<a class="m_6064013233316681339moz-txt-link-freetext" href="https://imagej.nih.gov/ij/plugins/nd2-reader.html" target="_blank">https://imagej.nih.gov/ij/plugins/nd2-reader.html</a>).
<br>
</font></p>
<p><font face="Karla">Thank you for your time.</font></p>
<p><font face="Karla">Best regards,</font><br>
</p>
<div class="m_6064013233316681339moz-signature">-- <br>
Guilhem CHENON <br>
LCMD - ESPCI Paris</div>
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