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Hi,
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<div class="">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/" class="">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 class="">I have opened a Bio-Formats Trello card to track this issue: <a href="https://trello.com/c/dDcSZtur/296-indexoutofboundsexception" class="">https://trello.com/c/dDcSZtur/296-indexoutofboundsexception</a></div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 23 Nov 2018, at 18:05, Guilhem Chenon <<a href="mailto:guilhem.chenon@espci.fr" class="">guilhem.chenon@espci.fr</a>> wrote:</div>
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<p class=""><font face="Karla" class="">Hello,</font></p>
<p class=""><font face="Karla" class="">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 class=""><font face="Karla" class="">Error using bfGetReader (line 85)<br class="">
Java exception occurred:<br class="">
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<br class="">
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at java.util.ArrayList.rangeCheck(ArrayList.java:653)<br class="">
<br class="">
at java.util.ArrayList.get(ArrayList.java:429)<br class="">
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at loci.formats.FormatReader.getSizeC(FormatReader.java:689)<br class="">
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at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1348)<br class="">
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at loci.formats.FormatReader.setId(FormatReader.java:1401)<br class="">
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at loci.formats.DelegateReader.setId(DelegateReader.java:291)<br class="">
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at loci.formats.ImageReader.setId(ImageReader.java:835)<br class="">
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at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)<br class="">
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at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)<br class="">
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at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)<br class="">
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at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)<br class="">
</font></p>
<p class=""><font face="Karla" class="">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 class="">
</font></p>
<p class=""><font face="Karla" class="">Moreover, these problematic files open fine with the ImageJ ND2 Reader plugin (<a class="moz-txt-link-freetext" href="https://imagej.nih.gov/ij/plugins/nd2-reader.html">https://imagej.nih.gov/ij/plugins/nd2-reader.html</a>).
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<p class=""><font face="Karla" class="">Thank you for your time.</font></p>
<p class=""><font face="Karla" class="">Best regards,</font><br class="">
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<div class="moz-signature">-- <br class="">
Guilhem CHENON <br class="">
LCMD - ESPCI Paris</div>
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