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BDV: store relative path instead of absolute#4440

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melissalinkert:gh-3957
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BDV: store relative path instead of absolute#4440
melissalinkert wants to merge 1 commit into
ome:developfrom
melissalinkert:gh-3957

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Fixes #3957.

I could easily reproduce the original issue in #3957 with curated/bdv/public/samples/:

$ showinf -no-upgrade -cache HisYFP-SPIM.xml
$ mkdir tmp
$ mv HisYFP* tmp
$ mv .*.bfmemo tmp
$ cd tmp
$ $ showinf -no-upgrade -cache HisYFP-SPIM.xml 
Checking file format [BDV]
Initializing reader
Exception in thread "main" ch.systemsx.cisd.hdf5.exceptions.HDF5FileNotFoundException: Path does not exit. (/home/melissa/data/bf-data-repo/automated-tests/curated/bdv/public/samples/HisYFP-SPIM.h5)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.openFile(HDF5BaseReader.java:221)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:177)
	at ch.systemsx.cisd.hdf5.HDF5BaseReader.<init>(HDF5BaseReader.java:155)
	at ch.systemsx.cisd.hdf5.HDF5ReaderConfigurator.reader(HDF5ReaderConfigurator.java:81)
	at ch.systemsx.cisd.hdf5.HDF5FactoryProvider$HDF5Factory.openForReading(HDF5FactoryProvider.java:55)
	at ch.systemsx.cisd.hdf5.HDF5Factory.openForReading(HDF5Factory.java:62)
	at loci.formats.services.JHDFServiceImpl.setFile(JHDFServiceImpl.java:92)
	at loci.formats.in.BDVReader.initializeJHDFService(BDVReader.java:378)
	at loci.formats.in.BDVReader.reopenFile(BDVReader.java:365)
	at loci.formats.ImageReader.reopenFile(ImageReader.java:870)
	at loci.formats.Memoizer.setId(Memoizer.java:712)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1054)
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:1165)

This fix does not make it so that a pre-existing memo file will work, but does make it so that newly generated memo files no longer exhibit this problem.

I have not tried to address any more structural concerns about relative vs absolute paths in memo files that were mentioned in #3957. We likely need to discuss that internally first, given the potential impact on OMERO.

@melissalinkert melissalinkert added this to the 9.0.0 milestone Jun 11, 2026
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BDV: Remove absolute file paths

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