Open Microscopy Environment

Hi All -

If I inplace import a czi file that does not have the 'czi' extension, the importer throws an error.

Code: Select all

java.lang.StringIndexOutOfBoundsException: String index out of range: -1
   at java.lang.String.substring(String.java:1967) ~[na:1.8.0_121]
   at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:578) ~[formats-gpl.jar:5.5.2]
   at loci.formats.FormatReader.setId(FormatReader.java:1397) ~[formats-api.jar:5.5.2]
   at loci.formats.ImageReader.setId(ImageReader.java:839) ~[formats-api.jar:5.5.2]
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) ~[formats-api.jar:5.5.2]
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:223) ~[formats-bsd.jar:5.5.2]
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) ~[formats-api.jar:5.5.2]
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291) ~[formats-bsd.jar:5.5.2]
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) ~[formats-api.jar:5.5.2]
   at loci.formats.Memoizer.setId(Memoizer.java:649) ~[formats-bsd.jar:5.5.2]
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650) ~[formats-api.jar:5.5.2]
   at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427) [blitz.jar:na]
   at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576) [blitz.jar:na]
   at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384) [blitz.jar:na]
   at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222) [blitz.jar:na]
   at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174) [blitz.jar:na]
   at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:147) [blitz.jar:na]
   at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:955) [blitz.jar:na]


Is there a way to tell the importer that this is a czi file? Renaming the file is sadly not an option due to some complexities of the system we have...

Hi,

Thank you submitting you issue.

This looks like a Bio-Formats issue and I have filed a ticket for the same,
https://trello.com/c/m7LqcpdM/167-czi-r ... is-missing

We look forward to pushing a fix at the earliest, and hopefully the same should be available via OMERO in the next stable release.

Hope that helps.

Best,
Balaji