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PreibischLab / BigStitcher

ImgLib2/BDV implementation of Stitching for large datasets
GNU General Public License v2.0
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Spaces in file names #86

Open saskra opened 3 years ago

saskra commented 3 years ago

Unfortunately, the recognition of the numbering of channels, tiles and z-levels in the file names fails as soon as a space appears in the name. I would also like to avoid spaces, but the files are not mine, and their names are noted in all metadata etc., so a simple renaming is not necessarily enough. Is it possible to make the programme tolerant of spaces?

Screenshot with spaces in file names: Bildschirmfoto zu 2020-12-03 11-23-50

Screenshot without spaces: Bildschirmfoto zu 2020-12-03 13-40-36

StephanPreibisch commented 3 years ago

@hoerldavid maybe you know how to simply do that? :)

hoerldavid commented 3 years ago

I did a quick test and could not reproduce the problem with files that have a space in them - this should not affect the pattern detection.

What I think is going on is that BioFormats (which we use to load the files) recognizes that the individual files belong to a stack and automatically groups them - for our pattern detector, the Z pattern is therefore ignored because we assume BioFormats takes care of that. By renaming the files, you break the metadata somehow and the files can no longer be grouped by BioFormats, this is why the pattern shows up then.

The most important question here is: If you continue with the un-renamed files, does it actually result in an error? Because ideally, BioFormats would combine the files into stacks that we can use in BigStitcher without problems..