[ome-users] Grouping files

[Kai Schleicher]

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 | www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

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