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ZarrReader performance improvements #64

Merged
merged 37 commits into from
Dec 8, 2023
Merged

ZarrReader performance improvements #64

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37 commits
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a90a305
ZarrReader performance improvements
dgault Sep 7, 2023
d30c0f0
Add new setResolution if option to open-air
dgault Sep 7, 2023
434cf20
ZarrReader: Remove incorrect override
dgault Sep 7, 2023
a1d4bea
Merge list pixels option for getUsedFiles
dgault Sep 10, 2023
3f09254
Add quick read option if shape and pixel type remains consistent
dgault Sep 11, 2023
a1af893
Generate groupKeys and arrayPaths from top level attributes
dgault Sep 12, 2023
f14c44b
Update arrayKey generation to revert if resolution counts differ
dgault Sep 13, 2023
3246a71
update setResolution to call openZarr
dgault Sep 14, 2023
f32b8bc
Avoid duplicate calls in openZarr
dgault Sep 14, 2023
3e7dfaa
Store resolution shapes after converting to 5D
dgault Sep 15, 2023
66d1559
Update close to clear existing variables
dgault Sep 18, 2023
a96f0ad
Add additional initFile logging
dgault Sep 18, 2023
d4d77dc
Update getRequiredDirectories
dgault Sep 18, 2023
2a7bd44
Update close to reset variables
dgault Sep 18, 2023
6371c79
Merge reorder group keys changes from ZarrReader/pull/53
dgault Sep 18, 2023
38d5fa8
Temporarily use error level logging
dgault Sep 20, 2023
bff43c9
Add logging for getUsedFiles
dgault Sep 20, 2023
ff7b031
Check directory when generating group keys and array paths
dgault Sep 20, 2023
aeadb2d
Add additional logging to getUsedFiles
dgault Sep 20, 2023
8aee5d8
revert getUsedFiles behaviour to remove skipPixels
dgault Sep 21, 2023
0f3fcdd
Remove unused listPixels option
dgault Sep 26, 2023
f2a2fb3
Update logging statements
dgault Sep 26, 2023
82ac198
Revert "Remove unused listPixels option"
dgault Oct 4, 2023
b20ef9c
Revert "revert getUsedFiles behaviour to remove skipPixels"
dgault Oct 4, 2023
e3b1d23
Do not assume label images have same resolution levels
dgault Oct 23, 2023
7bba003
Add new option for handling images in labels folder
dgault Oct 24, 2023
290d767
Add support for environment variable OME_ZARR_LIST_PIXELS
dgault Oct 26, 2023
12617b8
Change default value of list pixels to true
dgault Oct 26, 2023
f51ae44
Add new method to reload options file
dgault Oct 26, 2023
a7ec0c4
Force ZarrReader to read bfoptions file
dgault Oct 30, 2023
4357f54
Remove unnecessary bfoptions extension
dgault Oct 31, 2023
6b1da51
Ensure WellSampleIndex is used when comparing to OME-XML
dgault Nov 3, 2023
ae65321
Remove unnecessary logging statements
dgault Nov 13, 2023
30f87f7
Update getRequiredDirectories
dgault Nov 15, 2023
e50eb50
Unify options prefixes to omezarr
dgault Dec 5, 2023
94f707f
Change default behaviour to not include performance changes
dgault Dec 5, 2023
d4b1130
Add some Javadoc for options
dgault Dec 5, 2023
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