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set-scale
utility
#228
Merged
talonchandler
merged 40 commits into
czbiohub-sf:main
from
aaronalvarezcz:update-scale-metadata-util
Sep 26, 2024
Merged
set-scale
utility
#228
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9e0bc16
add update_scale_metadata.py
aaronalvarezcz 59ab2ac
add update-scale-metadata command to cli
aaronalvarezcz 6217bad
add zyx flags for update-scale-metadata utility
aaronalvarezcz 7bda4b3
add handling of missing zyx cli flags for update-scale-metadata
aaronalvarezcz 953b4b9
update order of params in update_scale_metadata to be passed as z, y, x
aaronalvarezcz 4e158d6
Merge branch 'main' into update-scale-metadata-util
talonchandler ea4dd73
black
talonchandler fdfca08
isort
talonchandler a5ec62f
flake8
talonchandler 826b250
Merge branch 'main' into update-scale-metadata-util
talonchandler e660042
update to `iohub.ngff.models`
talonchandler fcc408d
move parsing utilities to iohub
talonchandler c8816e5
move update_scale_metadata inside cli folder
talonchandler 2642a51
typo
talonchandler e0ff8e2
update import for refactor
talonchandler 7fac9f8
require -z, -y, -x flags
talonchandler de5c883
simplify interface and print statements
talonchandler 9d6492e
clean up print statement
talonchandler 387ac59
update the last three dimensions for OME compatibility
talonchandler 461dc65
fix tests
talonchandler dcb00a1
fix test
talonchandler 37add16
helper functions for axis names
talonchandler 6b4461d
set_scale API
talonchandler 353ab65
consolidate and clean CLI
talonchandler a900763
test get_axis_index
talonchandler b98381f
test_set_scale
talonchandler 74bdb7b
case insensitive axis name
talonchandler 6b857a9
tests don't overwrite data
talonchandler 9e6d676
save old metadata in a namespace
talonchandler 9df8007
test multiple inputs to cli
talonchandler e858dc6
handle empty current_transforms
talonchandler 75d2525
improved empty handling
talonchandler b46c5f3
unit test CLI plate expansion into positions
talonchandler d657c88
cleanup test
talonchandler 0e3ac36
test OptionEatAll
talonchandler e1a04cc
stronger plate-expansion test
talonchandler f678f44
fix bug when scale transform does not exist
ieivanov a551257
create "iohub" dict if it doesn't exist, and update it
talonchandler b49980e
test old_* metadata
talonchandler bb419b2
rename old_x to prior_x_scale
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@ziw-liu our original line didn't update the metadata in the way we intended. My fault for not testing this.
@ziw-liu this is the simplest solution I could get to work, but it's a bit ugly. Should
.zattrs["iohub"]
be part of the pydantic models so that we can usedump_meta
?