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<p>Hi David,</p>
<p>Thanks for your feedback! sorry for not coming back to this
earlier.</p>
<p>
<blockquote type="cite">This is the same result as if you simply
use the option for filename contains tile0001. Is that suitable
for what you are trying to do?</blockquote>
</p>
<p>Yes, that was actually perfectly fine. In the end I simply
imported all tile0001, sorted the stack into a hyperstack and
repeated this for all tiles separately.</p>
<p>Cheers,<br>
Kai<br>
</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 06/18/2018 02:07 PM, David Gault
(Staff) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:0486CB94-177D-4568-BF3B-BA951B94E234@dundee.ac.uk">
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charset=windows-1252">
Hi Kai,
<div class=""><br class="">
</div>
<div class="">If you wish to use a Java regular expression in the
pattern then the whole pattern should be in the Java regex
notation, so<b class=""> tile0001-physec....-osec000[1-4]-ch0[1-4].tif</b>
will open 8 images. However using the regex it is not smart
enough to identify which are channels etc and has grouped them
all as a time series so you may need to reorder the dimensions
if using this method. This is the same result as if you simply
use the option for filename contains tile0001. Is that suitable
for what you are trying to do?</div>
<div class=""><br class="">
</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 Jun 2018, at 14:25, Kai Schleicher <<a
href="mailto:kai.schleicher@unibas.ch" class=""
moz-do-not-send="true">kai.schleicher@unibas.ch</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class="">
<p class="">Dear OME - team,</p>
<p class="">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"
class="">download, 20 MB</a>).<br class="">
</p>
<p class="">My files consits of tiles, physical sections
(physec), optical sections (osec) and channels
expressed in the file name,e.g.:<br class="">
</p>
<p class="">tile0001-physec0001-osec0001-ch01.tif</p>
<p class="">I would like to group all channels and
optical sections of tile0001, but ignore the pattern
for the physical section.</p>
<p class="">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 class="">
</p>
<p class="">tile0001-physec....-osec<0001-0004>-ch<01-04>.tif</p>
<p class="">Which raised the exception quoted below.</p>
<p class="">Could you point me to the right solution?</p>
<p class="">Thank you and cheers,<br class="">
Kai</p>
<p class="">[1] <a class="moz-txt-link-freetext"
href="https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html"
moz-do-not-send="true">
https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html</a></p>
<div class=""><br class="webkit-block-placeholder">
</div>
<blockquote type="cite" class="">java.io.FileNotFoundException:
/home/kai/Pictures/Small_Fluorescent_Test_Dataset/image-tiles2/tile0001-physec....-osec0001-ch01.tif
(No such file or directory)<br class="">
at java.io.RandomAccessFile.open0(Native Method)<br
class="">
at
java.io.RandomAccessFile.open(RandomAccessFile.java:316)<br
class="">
at
java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)<br
class="">
at
loci.common.NIOFileHandle.<init>(NIOFileHandle.java:123)<br
class="">
at
loci.common.NIOFileHandle.<init>(NIOFileHandle.java:139)<br
class="">
at
loci.common.NIOFileHandle.<init>(NIOFileHandle.java:148)<br
class="">
at
loci.common.Location.getHandle(Location.java:324)<br
class="">
at
loci.common.Location.getHandle(Location.java:294)<br
class="">
at
loci.common.Location.getHandle(Location.java:284)<br
class="">
at
loci.common.Location.getHandle(Location.java:274)<br
class="">
at
loci.common.Location.checkValidId(Location.java:349)<br
class="">
at
loci.formats.ImageReader.getReader(ImageReader.java:177)<br
class="">
at
loci.formats.ImageReader.fileGroupOption(ImageReader.java:609)<br
class="">
at
loci.formats.ReaderWrapper.fileGroupOption(ReaderWrapper.java:395)<br
class="">
at
loci.formats.FileStitcher.initFile(FileStitcher.java:947)<br
class="">
at
loci.formats.FileStitcher.setId(FileStitcher.java:926)<br
class="">
at
loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:515)<br
class="">
at
loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)<br
class="">
at
loci.plugins.in.Importer.showDialogs(Importer.java:140)<br
class="">
at loci.plugins.in.Importer.run(Importer.java:76)<br
class="">
at
loci.plugins.LociImporter.run(LociImporter.java:78)<br
class="">
at ij.IJ.runUserPlugIn(IJ.java:222)<br class="">
at ij.IJ.runPlugIn(IJ.java:186)<br class="">
at ij.Executer.runCommand(Executer.java:137)<br
class="">
at ij.Executer.run(Executer.java:66)<br class="">
at ij.IJ.run(IJ.java:302)<br class="">
at ij.IJ.run(IJ.java:277)<br class="">
at ij.macro.Functions.doRun(Functions.java:615)<br
class="">
at
ij.macro.Functions.doFunction(Functions.java:96)<br
class="">
at
ij.macro.Interpreter.doStatement(Interpreter.java:249)<br
class="">
at
ij.macro.Interpreter.doStatements(Interpreter.java:235)<br
class="">
at ij.macro.Interpreter.run(Interpreter.java:118)<br
class="">
at ij.macro.Interpreter.run(Interpreter.java:89)<br
class="">
at ij.macro.MacroRunner.run(MacroRunner.java:139)<br
class="">
at java.lang.Thread.run(Thread.java:748)<br
class="">
</blockquote>
<br class="">
<div class=""><br class="webkit-block-placeholder">
</div>
<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" moz-do-not-send="true">kai.schleicher@unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch/" moz-do-not-send="true">www.biozentrum.unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.microscopynetwork.unibas.ch/" moz-do-not-send="true">www.microscopynetwork.unibas.ch</a></pre>
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</blockquote>
<br>
<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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