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<p>Thanks for looking at the issue.</p>
<p>I can confirm that the crash no longer occurs if I nest the files
2 folders up from root. However, FIJI has been trying to read a
3.5GB test file for now over 40 MINUTES and is now only at
"reading plane 3/3". Ifranview64 AND windows picture viewer app
both can open the same file in about 15 SECONDS. Something is
still wrong....</p>
<p>best regards,</p>
<p>Vytas<br>
</p>
<br>
<div class="moz-cite-prefix">On 7/18/2017 5:51 AM, David Gault
(Staff) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:29DC9CBB-3938-4E19-A7F8-E5F11AA800BE@dundee.ac.uk">
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charset=windows-1252">
Hi Curtis and Vytas,
<div class=""><br class="">
</div>
<div class="">This error is seen when attempting to open a file
from the root directory. While Bio-Formats attempts to identify
the format type some of the readers will search for associated
files in parent folders. This error is then seen if those
locations do not exist. Moving the files up from the root
directory (at least 2 levels) should provide a work around to
enable you to open the files normally.</div>
<div class=""><br class="">
</div>
<div class="">This is a scenario which should be handled better
without an exception being thrown. I have created a card on the
Bio-Formats Trello inbox to further investigate a long term fix.</div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 17 Jul 2017, at 21:05, Curtis Rueden <<a
href="mailto:ctrueden@WISC.EDU" class=""
moz-do-not-send="true">ctrueden@WISC.EDU</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class="">Hi,</div>
<div class=""><br class="">
</div>
<div class="">Below is a Bio-Formats bug report from
Vytas Bindokas (CCed).</div>
<div class=""><br class="">
</div>
<div class="">I also uploaded the sample image ('AbI
1-200 1to4_Caption.tif') to the OME QA system on his
behalf.</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Curtis</div>
<div class=""><br class="">
</div>
<div class="">
<div
class="gmail-m_5713317768945510061gmail_signature">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class=""><span
style="font-size:12.8px" class="">--</span></div>
<div class=""><span
style="font-size:12.8px" class="">Curtis
Rueden</span><br class="">
</div>
<div class=""><span
style="font-size:12.8px" class="">LOCI
software architect - <a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__loci.wisc.edu_software&d=DwMFAg&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=7ukIxNxspqJuFY_Dl5sx9ganU_k-_lqSbbNrEu8Y3es&s=Oq_3SA9xhnjYUkrQMeN09J0NZ-iZDvAgGe0MgkNYK7Y&e="
target="_blank" class=""
moz-do-not-send="true">
https://loci.wisc.edu/software</a></span></div>
<div class="">ImageJ2 lead, Fiji
maintainer - <span
style="font-size:12.8px" class=""><a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__imagej.net_User-3ARueden&d=DwMFAg&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=7ukIxNxspqJuFY_Dl5sx9ganU_k-_lqSbbNrEu8Y3es&s=tVkA4OcKqF_EmMYkanSV7srrKtDxjYlGGhwG14neeIA&e="
target="_blank" class=""
moz-do-not-send="true">https://imagej.net/User:<wbr
class="">Rueden</a></span></div>
<div class="">Did you know ImageJ has
a forum? <a
href="https://urldefense.proofpoint.com/v2/url?u=http-3A__forum.imagej.net_&d=DwMFAg&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=7ukIxNxspqJuFY_Dl5sx9ganU_k-_lqSbbNrEu8Y3es&s=DVXZdDIESTW8arorbMOrlCLaoCGs4DGSnJl-jmfoeGI&e="
target="_blank" class=""
moz-do-not-send="true">
http://forum.imagej.net/</a></div>
<div class=""><br class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
<div class="gmail_quote">---------- Forwarded message
----------<br class="">
From: <b class="gmail_sendername">vbindokas</b> <span
dir="ltr" class=""><<a
href="mailto:vbindoka@bsd.uchicago.edu"
target="_blank" class="" moz-do-not-send="true">vbindoka@bsd.uchicago.edu</a>></span><br
class="">
Date: Mon, Jul 17, 2017 at 2:30 PM<br class="">
Subject: bio-formats importer bug<br class="">
To: Curtis Rueden <<a
href="mailto:ctrueden@wisc.edu" target="_blank"
class="" moz-do-not-send="true">ctrueden@wisc.edu</a>><br
class="">
<br class="">
<br class="">
<div bgcolor="#FFFFFF" class="">
<p class="">Hello Curtis,</p>
<p class="">I'm sure you're busy, so can you please
forward to LOCI dev team? [GUI reporter tool still
not working]<br class="">
</p>
<p class="">Back in March we were able to open
automated scanner TIF exports using bio-formats,
however recent attempts result in red ink:</p>
<p class="">(Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n;
Java 1.8.0_66 [64-bit]; Windows 7 6.1; 1130MB of
15000MB (7%)<br class="">
java.lang.NullPointerException<br class="">
at loci.common.Location.<init>(Lo<wbr
class="">cation.java:104)<br class="">
at loci.common.Location.getParent<wbr class="">File(Location.java:623)<br
class="">
at <a
href="https://urldefense.proofpoint.com/v2/url?u=http-3A__loci.formats.in_&d=DwMFAg&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=7ukIxNxspqJuFY_Dl5sx9ganU_k-_lqSbbNrEu8Y3es&s=fzRZjgHCLt5i4SWaooY1yOLpTb_pebsVBTzRhfCbRlo&e="
target="_blank" class="" moz-do-not-send="true">loci.formats.in</a>.CellVoyagerRea<wbr
class="">der.isThisType(CellVoyagerRead<wbr
class="">er.java:256)<br class="">
at loci.formats.ImageReader.getRe<wbr class="">ader(ImageReader.java:185)<br
class="">
at loci.plugins.in.ImportProcess.<wbr class="">createBaseReader(ImportProcess<wbr
class="">.java:618)<br class="">
at loci.plugins.in.ImportProcess.<wbr class="">initializeReader(ImportProcess<wbr
class="">.java:484)<br class="">
at loci.plugins.in.ImportProcess.<wbr class="">execute(ImportProcess.java:137<wbr
class="">)<br class="">
at loci.plugins.in.Importer.showD<wbr class="">ialogs(Importer.java:140)<br
class="">
at loci.plugins.in.Importer.run(I<wbr class="">mporter.java:76)<br
class="">
at loci.plugins.LociImporter.run(<wbr class="">LociImporter.java:78)<br
class="">
at ij.IJ.runUserPlugIn(IJ.java:21<wbr class="">7)<br
class="">
at ij.IJ.runPlugIn(IJ.java:181)<br class="">
at ij.Executer.runCommand(Execute<wbr class="">r.java:137)<br
class="">
at ij.Executer.run(Executer.java:<wbr class="">66)<br
class="">
at java.lang.Thread.run(Thread.ja<wbr class="">va:745)<br
class="">
</p>
<p class="">I've uploaded a sample via the Help UI;
<br class="">
</p>
<p class=""><!DOCTYPE HTML PUBLIC "-//IETF//DTD
HTML 2.0//EN"><br class="">
<html><head><br class="">
<title>201 Created</title><br class="">
</head><body><br class="">
<h1>Created</h1><br class="">
<p>Resource /<b class="">AbI%201-200%201to4_Caption.ti<wbr
class="">f </b>has been created.</p><br
class="">
<hr /><br class="">
<address>Apache/2.4.18 (Ubuntu) Server at <a
href="https://urldefense.proofpoint.com/v2/url?u=http-3A__upload.imagej.net_&d=DwMFAg&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=7ukIxNxspqJuFY_Dl5sx9ganU_k-_lqSbbNrEu8Y3es&s=Z-p6JYY2UNRli6My0Ud_u2n5kWhdfoynPG-80b96TVc&e="
target="_blank" class="" moz-do-not-send="true">
upload.imagej.net</a> Port 80</address><br
class="">
</body></html><br class="">
</p>
<p class="">I can open this file in IrafanView and
resave it there-- that resave opens normally in
fiji. It's a work-around, but time and space
consuming.</p>
<p class="">BEST REGARDS!~</p>
<p class="">Vytas<br class="">
</p>
<pre class="gmail-m_5713317768945510061gmail-m_-4617302372585742484moz-signature" cols="72">--
__
Vytas Bindokas, Ph.D.
Research Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
phone: <a href="tel:%28773%29%20702-4875" value="+17737024875" target="_blank" class="" moz-do-not-send="true">773-702-4875</a> [alt's: <a href="tel:%28773%29%20834-9040" value="+17738349040" target="_blank" class="" moz-do-not-send="true">773-834-9040</a> or <a href="tel:%28773%29%20834-2639" value="+17738342639" target="_blank" class="" moz-do-not-send="true">773-834-2639</a>]
[address for letters ONLY (see shipping addr below):]
Dept Pharmacol Physiol Sci MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room Abbott 129
shipping address (main KCBD site):
V. Bindokas
900 E 57th Street
KCBD room 1250, Microscopy Core
The University of Chicago
Chicago IL 60637
email <a class="gmail-m_5713317768945510061gmail-m_-4617302372585742484moz-txt-link-abbreviated" href="mailto:vbindoka@bsd.uchicago.edu" target="_blank" moz-do-not-send="true">vbindoka@bsd.uchicago.edu</a>
web site for LMCF:
<a class="gmail-m_5713317768945510061gmail-m_-4617302372585742484moz-txt-link-freetext" href="http://digital.uchicago.edu/" target="_blank" moz-do-not-send="true">http://digital.uchicago.edu</a></pre>
</div>
</div>
<br class="">
</div>
_______________________________________________<br
class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk"
class="" moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a><br
class="">
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br
class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a
registered Scottish Charity, No: SC015096</span>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
__
Vytas Bindokas, Ph.D.
Research Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
phone: 773-702-4875 [alt's: 773-834-9040 or 773-834-2639]
[address for letters ONLY (see shipping addr below):]
Dept Pharmacol Physiol Sci MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room Abbott 129
shipping address (main KCBD site):
V. Bindokas
900 E 57th Street
KCBD room 1250, Microscopy Core
The University of Chicago
Chicago IL 60637
email <a class="moz-txt-link-abbreviated" href="mailto:vbindoka@bsd.uchicago.edu">vbindoka@bsd.uchicago.edu</a>
web site for LMCF:
<a class="moz-txt-link-freetext" href="http://digital.uchicago.edu">http://digital.uchicago.edu</a></pre>
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