[ome-users] Grouping files

[David Gault (Staff)]

Hi Kai,

If you wish to use a Java regular expression in the pattern then the whole pattern should be in the Java regex notation, so tile0001-physec....-osec000[1-4]-ch0[1-4].tif 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?


With Thanks,
David Gault

On 17 Jun 2018, at 14:25, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:


Dear OME - team,

I wish to use the Bio-formats importer GUI to group single .tif images (download, 20 MB<https://filesender.switch.ch/filesender/?vid=05a3b989-3c7a-76a9-f342-000049dc76a6>).

My files consits of tiles, physical sections (physec), optical sections (osec) and channels expressed in the file name,e.g.:

tile0001-physec0001-osec0001-ch01.tif

I would like to group all channels and optical sections of tile0001, but ignore the pattern for the physical section.

>From the java regex Class Pattern [1] I understood that the placeholder for any character is ".", and hence I have tried the following pattern:

tile0001-physec....-osec<0001-0004>-ch<01-04>.tif

Which raised the exception quoted below.

Could you point me to the right solution?

Thank you and cheers,
Kai

[1] https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html

java.io.FileNotFoundException: /home/kai/Pictures/Small_Fluorescent_Test_Dataset/image-tiles2/tile0001-physec....-osec0001-ch01.tif (No such file or directory)
    at java.io.RandomAccessFile.open0(Native Method)
    at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
    at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
    at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:123)
    at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:139)
    at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:148)
    at loci.common.Location.getHandle(Location.java:324)
    at loci.common.Location.getHandle(Location.java:294)
    at loci.common.Location.getHandle(Location.java:284)
    at loci.common.Location.getHandle(Location.java:274)
    at loci.common.Location.checkValidId(Location.java:349)
    at loci.formats.ImageReader.getReader(ImageReader.java:177)
    at loci.formats.ImageReader.fileGroupOption(ImageReader.java:609)
    at loci.formats.ReaderWrapper.fileGroupOption(ReaderWrapper.java:395)
    at loci.formats.FileStitcher.initFile(FileStitcher.java:947)
    at loci.formats.FileStitcher.setId(FileStitcher.java:926)
    at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:515)
    at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
    at loci.plugins.in.Importer.showDialogs(Importer.java:140)
    at loci.plugins.in.Importer.run(Importer.java:76)
    at loci.plugins.LociImporter.run(LociImporter.java:78)
    at ij.IJ.runUserPlugIn(IJ.java:222)
    at ij.IJ.runPlugIn(IJ.java:186)
    at ij.Executer.runCommand(Executer.java:137)
    at ij.Executer.run(Executer.java:66)
    at ij.IJ.run(IJ.java:302)
    at ij.IJ.run(IJ.java:277)
    at ij.macro.Functions.doRun(Functions.java:615)
    at ij.macro.Functions.doFunction(Functions.java:96)
    at ij.macro.Interpreter.doStatement(Interpreter.java:249)
    at ij.macro.Interpreter.doStatements(Interpreter.java:235)
    at ij.macro.Interpreter.run(Interpreter.java:118)
    at ij.macro.Interpreter.run(Interpreter.java:89)
    at ij.macro.MacroRunner.run(MacroRunner.java:139)
    at java.lang.Thread.run(Thread.java:748)



--
>> 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) | kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch/>

_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20180618/c35436d4/attachment.html>