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<p>Dear OME - team,</p>
<p>I wish to use the Bio-formats importer GUI to group single .tif
images (<a moz-do-not-send="true"
href="https://filesender.switch.ch/filesender/?vid=05a3b989-3c7a-76a9-f342-000049dc76a6">download,
20 MB</a>).<br>
</p>
<p>My files consits of tiles, physical sections (physec), optical
sections (osec) and channels expressed in the file name,e.g.:<br>
</p>
<p>tile0001-physec0001-osec0001-ch01.tif</p>
<p>I would like to group all channels and optical sections of
tile0001, but ignore the pattern for the physical section.</p>
<p>From the java regex Class Pattern [1] I understood that the
placeholder for any character is ".", and hence I have tried the
following pattern: <br>
</p>
<p>tile0001-physec....-osec<0001-0004>-ch<01-04>.tif</p>
<p>Which raised the exception quoted below.</p>
<p>Could you point me to the right solution?</p>
<p>Thank you and cheers,<br>
Kai</p>
<p>[1]
<a class="moz-txt-link-freetext" href="https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html">https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html</a></p>
<p>
<blockquote type="cite">java.io.FileNotFoundException:
/home/kai/Pictures/Small_Fluorescent_Test_Dataset/image-tiles2/tile0001-physec....-osec0001-ch01.tif
(No such file or directory)<br>
at java.io.RandomAccessFile.open0(Native Method)<br>
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)<br>
at
java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)<br>
at
loci.common.NIOFileHandle.<init>(NIOFileHandle.java:123)<br>
at
loci.common.NIOFileHandle.<init>(NIOFileHandle.java:139)<br>
at
loci.common.NIOFileHandle.<init>(NIOFileHandle.java:148)<br>
at loci.common.Location.getHandle(Location.java:324)<br>
at loci.common.Location.getHandle(Location.java:294)<br>
at loci.common.Location.getHandle(Location.java:284)<br>
at loci.common.Location.getHandle(Location.java:274)<br>
at loci.common.Location.checkValidId(Location.java:349)<br>
at loci.formats.ImageReader.getReader(ImageReader.java:177)<br>
at
loci.formats.ImageReader.fileGroupOption(ImageReader.java:609)<br>
at
loci.formats.ReaderWrapper.fileGroupOption(ReaderWrapper.java:395)<br>
at loci.formats.FileStitcher.initFile(FileStitcher.java:947)<br>
at loci.formats.FileStitcher.setId(FileStitcher.java:926)<br>
at
loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:515)<br>
at
loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)<br>
at loci.plugins.in.Importer.showDialogs(Importer.java:140)<br>
at loci.plugins.in.Importer.run(Importer.java:76)<br>
at loci.plugins.LociImporter.run(LociImporter.java:78)<br>
at ij.IJ.runUserPlugIn(IJ.java:222)<br>
at ij.IJ.runPlugIn(IJ.java:186)<br>
at ij.Executer.runCommand(Executer.java:137)<br>
at ij.Executer.run(Executer.java:66)<br>
at ij.IJ.run(IJ.java:302)<br>
at ij.IJ.run(IJ.java:277)<br>
at ij.macro.Functions.doRun(Functions.java:615)<br>
at ij.macro.Functions.doFunction(Functions.java:96)<br>
at ij.macro.Interpreter.doStatement(Interpreter.java:249)<br>
at ij.macro.Interpreter.doStatements(Interpreter.java:235)<br>
at ij.macro.Interpreter.run(Interpreter.java:118)<br>
at ij.macro.Interpreter.run(Interpreter.java:89)<br>
at ij.macro.MacroRunner.run(MacroRunner.java:139)<br>
at java.lang.Thread.run(Thread.java:748)<br>
</blockquote>
<br>
</p>
<pre class="moz-signature" cols="72">--
>> Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | <a class="moz-txt-link-abbreviated" href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch">www.biozentrum.unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.microscopynetwork.unibas.ch">www.microscopynetwork.unibas.ch</a></pre>
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