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Olympus .vsi: only read pixels from frame_*.ets files #3925

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merged 2 commits into from
Jan 27, 2023

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@melissalinkert melissalinkert commented Dec 21, 2022

Backported from a private PR. This is expected to fix #3859.

inbox/gh-3859curated/cellsens/gh-3859 can be used to test. I may have additional test datasets, but am waiting for confirmation that they can be shared.

Without this change, showinf -nopix -noflat on the .vsi file should throw an exception. With this change, usual showinf commands, opening in ImageJ, etc. should display images and metadata without error. The blob*.ets and blob*.meta files should be included at the end of the used files list.

I would expect this to impact memo files, so requires a minor release.

This ignores any blobs* files, which are not pixel data.
Any files other than frame_*.ets that are in the data directory will be added
to the used files list as non-pixels files. This means they will be preserved
on import to OMERO.
@melissalinkert melissalinkert added this to the 6.12.0 milestone Dec 21, 2022
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This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/vsi-format-update-unable-to-open-new-files/70366/11

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All builds and tests have been green with this PR and the config PR's included. PR does not show any regressions or behaviour changes in existing datasets.

Tested using the newly provided sample files. Without this PR and testing curated/cellsens/gh-3859 results in an exception as below:

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 3, Size: 3
	at java.util.ArrayList.rangeCheck(ArrayList.java:653)
	at java.util.ArrayList.get(ArrayList.java:429)

With the PR included there is no exception and the file can be opened and displayed without issue. The list of included files also looks to be correct.

Testing the additional new samples from curated/cellsens/public/evident and each opens and displays without issue, matching the screenshots provided from OlyVIA.

@dgault dgault merged commit 3493350 into ome:develop Jan 27, 2023
@sbesson sbesson mentioned this pull request Feb 13, 2023
@melissalinkert melissalinkert deleted the vsi-blob-files-develop branch September 6, 2024 19:02
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VSI: Exception loading files from VS200 scanner with software version 3.4.1
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