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Hi Johan,
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<div class="">sorry for the late reply. We have received your sample file and will be adding it to our</div>
<div class="">testing data repository.</div>
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<div class="">Thanks,</div>
<div class="">Sebastien</div>
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<blockquote type="cite" class="">
<div class="">On 21 Apr 2016, at 07:40, Johan Herz <<a href="mailto:johan@lambertinstruments.com" class="">johan@lambertinstruments.com</a>> wrote:</div>
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<div dir="ltr" class="">Dear Sebastien,
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<div class="">Thank you for your quick followup.</div>
<div class="">I have uploaded the following file: ExampleFile - LiFlimReader fix ExposureTime.fli</div>
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<div class="">Looking forward to see it being fixed.</div>
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<div dir="ltr" class=""><span style="font-size:12.8px" class="">With best regards,</span><br style="font-size:12.8px" class="">
<br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Johan Herz, Sales Engineer </span><br style="font-size:12.8px" class="">
<br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Tel: +31-50-501-8461 | Skype: lambert-johan</span><br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Lambert Instruments BV|Leonard Springerlaan 19 (5th floor)|9727 KB Groningen|The Netherlands</span><br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Dutch Chamber of Commerce nr.: 52396940 | </span><a href="http://www.lambertinstruments.com/" style="font-size:12.8px" target="_blank" class="">www.lambertinstruments.com</a><br class="">
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<br class="">
<div class="gmail_quote">2016-04-20 23:19 GMT+02:00 Sebastien Besson (Staff) <span dir="ltr" class="">
<<a href="mailto:s.besson@dundee.ac.uk" target="_blank" class="">s.besson@dundee.ac.uk</a>></span>:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Dear Johan,
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</div>
<div class="">many thanks for your bug report. It looks like your assumption is correct and that</div>
<div class="">the metadata check for ExposureTime key is not stringent enough. I have</div>
<div class="">opened a Pull Request <a href="https://github.com/openmicroscopy/bioformats/pull/2364" target="_blank" class="">https://github.com/openmicroscopy/bioformats/pull/2364</a></div>
<div class="">with a proposed fix which I would expect to be available with Bio-Formats 5.2.0.</div>
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</div>
<div class="">In order to facilitate our testing and to prevent future regressions, would it be</div>
<div class="">possible for you to upload a sample .fli file at <a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank" class="">http://qa.openmicroscopy.org.uk/qa/upload/</a></div>
<div class="">reproducing the problem?</div>
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<div class="">Best regards,</div>
<div class="">Sebastien</div>
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<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">
<div class="h5">
<div class="">On 20 Apr 2016, at 11:35, Johan Herz <<a href="mailto:johan@lambertinstruments.com" target="_blank" class="">johan@lambertinstruments.com</a>> wrote:</div>
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<div dir="ltr" class=""><font face="monospace, monospace" class="">Dear All,</font>
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</font></div>
<div class=""><font face="monospace, monospace" class="">To whom it may concern, I would like to report a Bug I encounter in Bioformats.</font></div>
<div class=""><font face="monospace, monospace" class="">The following exception is thrown by Fiji:</font></div>
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</font></div>
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<div class=""><font face="monospace, monospace" class="">java.lang.StringIndexOutOfBoundsException: String index out of range: -1</font></div>
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<div class=""><font face="monospace, monospace" class=""><span style="white-space:pre-wrap" class=""></span>at java.lang.String.substring(String.java:1937)</font></div>
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<div class=""><font face="monospace, monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.in.LiFlimReader.initOriginalMetadata(LiFlimReader.java:334)</font></div>
</div>
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</font></div>
<div class=""><font face="monospace, monospace" class="">I have a .fli file with the following header entry:</font></div>
<div class=""><font face="monospace, monospace" class=""><span style="white-space:pre-wrap" class="">
</span>'LockExposureTime = 0'<br class="">
</font></div>
<div class=""><font face="monospace, monospace" class="">and while looking at the code in LiFlimReader.java I think that this conflicts with to following:</font></div>
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</font></div>
<div class=""><font face="monospace, monospace" class="">315<span style="white-space:pre-wrap" class="">
</span>else if (metaKey.endsWith("ExposureTime")) {</font></div>
<div class=""><font face="monospace, monospace" class="">316<span style="white-space:pre-wrap" class=""> </span><span style="white-space:pre-wrap" class="">
</span>int space = value.indexOf(" ");</font></div>
<div class=""><font face="monospace, monospace" class="">317<span style="white-space:pre-wrap" class=""> </span><span style="white-space:pre-wrap" class="">
</span><span style="white-space:pre-wrap" class=""></span>double expTime = Double.parseDouble(value.substring(0, space));</font></div>
<div class=""><font face="monospace, monospace" class="">318<span style="white-space:pre-wrap" class=""> </span><span style="white-space:pre-wrap" class="">
</span>String units = value.substring(space + 1).toLowerCase();</font></div>
<div class=""><font face="monospace, monospace" class="">319<span style="white-space:pre-wrap" class=""> </span><span style="white-space:pre-wrap" class="">
</span>if (units.equals("ms")) {</font></div>
<div class=""><font face="monospace, monospace" class="">320<span style="white-space:pre-wrap" class=""> </span><span style="white-space:pre-wrap" class=""> </span><span style="white-space:pre-wrap" class="">
</span><span style="white-space:pre-wrap" class=""></span>expTime /= 1000;</font></div>
<div class=""><font face="monospace, monospace" class="">321<span style="white-space:pre-wrap" class=""> </span><span style="white-space:pre-wrap" class="">
</span>}</font></div>
<div class=""><font face="monospace, monospace" class=""><br class="">
</font></div>
<div class=""><font face="monospace, monospace" class="">I think for future releases of Bioformats this still can cause a conflict in case a different Header entry ends with "ExposureTime"</font></div>
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</font></div>
<div class=""><font face="monospace, monospace" class="">Please contact me for further questions and I will be looking forward to receiving a reply.</font></div>
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</font>
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<div dir="ltr" class=""><font face="monospace, monospace" class=""><span style="font-size:12.8px" class="">With best regards,</span><br style="font-size:12.8px" class="">
<br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Johan Herz, Sales Engineer </span><br style="font-size:12.8px" class="">
<br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Tel: <a href="tel:%2B31-50-501-8461" value="+31505018461" target="_blank" class="">
+31-50-501-8461</a> | Skype: lambert-johan</span><br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Lambert Instruments BV|Leonard Springerlaan 19 (5th floor)|9727 KB Groningen|The Netherlands</span><br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Dutch Chamber of Commerce nr.: 52396940 | </span><a href="http://www.lambertinstruments.com/" style="font-size:12.8px" target="_blank" class="">www.lambertinstruments.com</a></font><br class="">
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<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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