[ome-users] Grouping files

Tue Jun 26 21:58:40 BST 2018

Hi David,

Thanks for your feedback! sorry for not coming back to this earlier.

> 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?

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.

Cheers,
Kai

On 06/18/2018 02:07 PM, David Gault (Staff) wrote:
> 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  |www.biozentrum.unibas.ch  |www.microscopynetwork.unibas.ch
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-- 
>> 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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