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<p>Hi David,</p>
<p><br>
</p>
<p>thank you very much for your quick help.</p>
<p><br>
</p>
<p>The problem seems to arise when we abort the acquisition.</p>
<p>µManager failed to cleanup files due to some issue</p>
<p>with the camera shutter, thus the last frame in the</p>
<p>metadata text file stops at the shutter line.</p>
<p><br>
</p>
<p>I haven't managed to correct the metadata properly so that</p>
<p>matlab can load the data, but I found a much simpler solution: just remove the metadata file.</p>
<p><br>
</p>
<p>Cheers,</p>
<p>pablo<br>
</p>
<p><br>
</p>
<p><br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Von:</b> ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> im Auftrag von David Gault (Staff) <d.gault@dundee.ac.uk><br>
<b>Gesendet:</b> Donnerstag, 19. April 2018 14:11:00<br>
<b>An:</b> OME User Support List<br>
<b>Betreff:</b> Re: [ome-users] problem loading multiple ome.tiff files in Matlab</font>
<div> </div>
</div>
<div>Hi Pablo,
<div class=""><br class="">
</div>
<div class="">I was able to test the uploaded file you submitted and reproduced the second issue you were seeing, NoSuchElementException.</div>
<div class=""><br class="">
</div>
<div class="">From looking at the metadata text file it appears that the the last FrameKey at the end of the file is missing its losing bracket “}”, adding this back into the file should resolve the NoSuchElementException and allow the file to be read. It does
look as though that last frame also has less metadata than previous entries so it may be worth checking that the data at the end of the file is correct and all present.</div>
<div class=""><br class="">
</div>
<div class="">Also as a side note there is a bug fix for the MicroManagerReader included in the upcoming Bio-Formats 5.8.2 release which may help with some of these issues.</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 18 Apr 2018, at 15:29, Fernandez, Pablo <<a href="mailto:pablo.fernandez@tum.de" class="">pablo.fernandez@tum.de</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi David,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I just uploaded it. Thank you very much<span class="Apple-converted-space"> </span><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">for looking at this.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Incidentally, depending on the particular set of files</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I sometimes get a different error message, namely:</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div class="">Error using bfGetReader (line 85)<br class="">
Java exception occurred:<br class="">
java.util.NoSuchElementException<br class="">
<br class="">
at java.util.StringTokenizer.nextToken(Unknown Source)<br class="">
<br class="">
at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:870)<br class="">
<br class="">
at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:429)<br class="">
<br class="">
at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:297)<br class="">
<br class="">
at loci.formats.FormatReader.setId(FormatReader.java:1397)<br class="">
<br class="">
at loci.formats.ImageReader.setId(ImageReader.java:839)<br class="">
<br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<br class="">
<br class="">
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)<br class="">
<br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<br class="">
<br class="">
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)</div>
<br class="">
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
</div>
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">Von:</b><span class="Apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
im Auftrag von David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" class="">d.gault@dundee.ac.uk</a>><br class="">
<b class="">Gesendet:</b><span class="Apple-converted-space"> </span>Mittwoch, 18. April 2018 11:36:25<br class="">
<b class="">An:</b><span class="Apple-converted-space"> </span>OME User Support List<br class="">
<b class="">Betreff:</b><span class="Apple-converted-space"> </span>Re: [ome-users] problem loading multiple ome.tiff files in Matlab</font>
<div class=""> </div>
</div>
<div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
Hi Pablo,
<div class=""><br class="">
</div>
<div class="">Have your files have been saved with a companion metadata file? </div>
<div class="">If so then uploading it to the link below should provide us with the information required to debug this problem further:</div>
<div class=""><a href="https://www.openmicroscopy.org/qa2/qa/upload/" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a></div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 17 Apr 2018, at 15:45, Fernandez, Pablo <<a href="mailto:pablo.fernandez@tum.de" class="">pablo.fernandez@tum.de</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div id="divtagdefaultwrapper" dir="ltr" class="" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;">
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Hi ome-users,</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">I am having an issue loading a set of multiple<span class="Apple-converted-space"> </span><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">ome.tiff files in Matlab. The files were created</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">by<span class="Apple-converted-space"> </span><span class="">micro-manager</span><span class="Apple-converted-space"> </span>running a long multidimensional<span class="Apple-converted-space"> </span><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">acquisition, saving the data as a series of 4 GB ome.tiff files,</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">appending to the filename "_1", "_2" and so on.<br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Now, I intend to analyze the data in Matlab, so I have</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">installed bfmatlab.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">To my surprise I am able to open all files - except for the first one.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">With bfGetReader I get the following error:</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<p class="" style="margin-top: 0px; margin-bottom: 0px;"></p>
<div class="">Error using bfGetReader (line 85)<br class="">
Java exception occurred:<br class="">
java.lang.StringIndexOutOfBoundsException: String index out of range: -2<br class="">
<br class="">
at java.lang.String.substring(Unknown Source)<br class="">
<br class="">
at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:810)<br class="">
<br class="">
at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:429)<br class="">
<br class="">
at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:297)<br class="">
<br class="">
at loci.formats.FormatReader.setId(FormatReader.java:1397)<br class="">
<br class="">
at loci.formats.ImageReader.setId(ImageReader.java:839)<br class="">
<br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<br class="">
<br class="">
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)<br class="">
<br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<br class="">
<br class="">
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)</div>
<br class="">
<p class="" style="margin-top: 0px; margin-bottom: 0px;"></p>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">I am using Windows 10, Java 8u40, Bioformats 5.8.1.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Incidentally, although the images correspond to stacks at different positions and timepoints µManager stores all frames along the</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">time direction, as a stack with many timepoints and only one Z</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">value.<br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">The file is 4 GB large; I will be glad to upload it if that<br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">helps solve the issue.<br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">I would greatly appreciate any help...We are generating</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">tons of data and really need to analyze it as soon</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">as possible, before our servers explode<span class="Apple-converted-space"> </span><span class="">😊</span></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class=""><br class="">
</span></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class="">Keep up the great work!</span></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class="">Cheers,</span></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class="">Pablo<br class="">
</span></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
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