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fmi-basel / faim-imagej-stitching

BSD 2-Clause "Simplified" License
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Be more tolerant with missing/wrong metadata #9

Closed imagejan closed 3 years ago

imagejan commented 3 years ago

It can happen that when opening a 3D dataset, bio-formats reads the metadata from a 2D file in the same folder (see also https://github.com/ome/bioformats/issues/2613). In that case, omeMeta.getPixelsPhysicalSizeZ(0) is null, so we should handle it more gently here:

https://github.com/fmi-basel/faim-imagej-stitching/blob/36be9c86b8db2b0a175d685d162f5ab6de4d025e/src/main/java/ch/fmi/stitching/visiview/StitchVisiviewDatasetCommand.java#L408

imagejan commented 3 years ago

Fixed in https://github.com/fmi-basel/faim-imagej-stitching/commit/e69151fe62789b079762b607f56e28d8a78a3c69.