Zeiss CZI: add support for slides #2481
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Pyramid detection is not enabled (yet), so mosaics are always stitched for now. Conflicts: components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
Conflicts: components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
Multiple resolutions are now required for a pyramid to be detected.
This prevents OME-XML validation errors when an ImageInstrumentRef is present without the corresponding Instrument.
Some non-slide large images will have resolutions which are a power of 3 smaller. As we only support power-of-2, these resolutions must be ignored.
This should speed up repeated calls to getOptimalTile*(), as iterating over potentially all SubBlocks for each call is no longer necessary.
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Additional commits have been added to reduce the number of existing files affected by this PR to just three. A configuration PR is now open (https://github.com/openmicroscopy/data_repo_config/pull/117), so removing the exclude label. The list of files to test and corresponding screenshots in Zen are in the config PR - double-checking the configuration changes and comparing ImageJ vs. Zen should be sufficient. |
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The code changes here make sense and look good. The slide data now appears to be handled and stored correctly. Additionally this also allows enables us to fix other issues such as #2467 by enabling use of coreIndex as opposed to seriesIndex. Ive tested comparisons with affected files between the Zen screenshots provided and importing through Bio-Formats via Fiji. The results of the testing can be found on the associated configuration PR. With all tests passing both this and the configuration PR look good to merge. |
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Thanks, merging this and the configuration PR. In terms of documentation, we should be able to add |
See https://trello.com/c/OHKk0BiI/161-jpeg-xr.
This adds more polished support for slide data from Axio Scan.Z1 systems. Slides should now be detected as a complete full-resolution image (instead of each tile being a separate series), pyramid sub-resolutions are detected, and label/overview images are detected.
This is excluded for now, pending conclusion of m5 and a configuration PR. Further testing instructions will be added once the configuration PR is set - I'm just in the process of importing the 13 files for which configurations have changed, verifying that the new behavior is correct, and assembling supporting screenshots.