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ZarrReader performance improvements#64

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dgault merged 37 commits intoome:mainome/ZarrReader:mainfrom dgault:zarr-performancedgault/ZarrReader:zarr-performanceCopy head branch name to clipboardDec 8, 2023

+405-77

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Commits on Sep 7, 2023

• ZarrReader performance improvements

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  a90a305

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• Add new setResolution if option to open-air

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• ZarrReader: Remove incorrect override

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Commits on Sep 10, 2023

• Merge list pixels option for getUsedFiles

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Commits on Sep 11, 2023

• Add quick read option if shape and pixel type remains consistent

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Commits on Sep 12, 2023

• Generate groupKeys and arrayPaths from top level attributes

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Commits on Sep 13, 2023

• Update arrayKey generation to revert if resolution counts differ

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Commits on Sep 14, 2023

• update setResolution to call openZarr

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• Avoid duplicate calls in openZarr

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Commits on Sep 15, 2023

• Store resolution shapes after converting to 5D

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Commits on Sep 18, 2023

• Update close to clear existing variables

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• Add additional initFile logging

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• Update getRequiredDirectories

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• Update close to reset variables

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• Merge reorder group keys changes from ZarrReader/pull/53

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Commits on Sep 20, 2023

• Temporarily use error level logging

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• Add logging for getUsedFiles

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• Check directory when generating group keys and array paths

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• Add additional logging to getUsedFiles

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Commits on Sep 21, 2023

• revert getUsedFiles behaviour to remove skipPixels

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Commits on Sep 26, 2023

• Remove unused listPixels option

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• Update logging statements

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Commits on Oct 4, 2023

• Revert "Remove unused listPixels option"

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• Revert "revert getUsedFiles behaviour to remove skipPixels"

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Commits on Oct 23, 2023

• Do not assume label images have same resolution levels

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Commits on Oct 24, 2023

• Add new option for handling images in labels folder

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Commits on Oct 26, 2023

• Add support for environment variable OME_ZARR_LIST_PIXELS

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• Change default value of list pixels to true

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• Add new method to reload options file

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Commits on Oct 30, 2023

• Force ZarrReader to read bfoptions file

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Commits on Oct 31, 2023

• Remove unnecessary bfoptions extension

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Commits on Nov 3, 2023

• Ensure WellSampleIndex is used when comparing to OME-XML

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Commits on Nov 13, 2023

• Remove unnecessary logging statements

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Commits on Nov 15, 2023

• Update getRequiredDirectories

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Commits on Dec 5, 2023

• Unify options prefixes to omezarr

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• Change default behaviour to not include performance changes

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• Add some Javadoc for options

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