Fixed SPIDER images for use with Bio-formats library #5956
Merged
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Resolves #2518
The issue reports that Spider images saved with Pillow have a black line at the end when opened with Fiji.
Fiji uses bioformats as a dependency. So https://github.com/ome/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/SpiderReader.java would be the reader that Fiji is using.
Testing, I find that doubling the length of the header fixes the display of the image in Fiji. There is code in bioformats that looks like it could double the header length. This code is apparently searching for a local header for each frame, not just the global header.
That code is triggered based on the
irec
value. According to a specification,irec
is theSo Bio-Formats is using the number of records to determine if we have included local headers.
We don't currently write an irec value - possibly because one specification denotes it as unused.
This PR adds the number of records in an image as an
irec
value. I have tested this in Fiji and found it to work.