search

ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
371 stars 241 forks source link

Olympus OIR: MetadataTools.populatePixelsOnly: 0 must be non-null and strictly positive. #4132

Open dominikl opened 6 months ago

dominikl commented 6 months ago

See QA 40683 

java.lang.IllegalArgumentException: 0 must be non-null and strictly positive.
    at ome.xml.model.primitives.PositiveInteger.(PositiveInteger.java:48)
    at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:310)
    at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:262)
...

Note: QA used older Insight/Bioformats. But I can replicate the issue with the latest build too:

(bf) ➜  bftools ./showinf -version
Version: 7.1.0
Build date: 11 December 2023
VCS revision: 05c7b2413cfad19a73b619c61ddf77ca2d038ce7
(bf) ➜  bftools ./showinf -nopix ~/40683/Image_10.oir
Checking file format [Olympus OIR]
Initializing reader
OIRReader initializing /Users/dom/40683/Image_10.oir
Reading pixel blocks from /Users/dom/40683/Image_10.oir
Exception in thread "main" java.lang.IllegalArgumentException: 0 must be non-null and strictly positive.
    at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:48)
    at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:310)
    at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:262)