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ComputationalCryoEM / ASPIRE-Python Public

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ImageSource.save Optics Block#1337

Merged

j-c-c merged 31 commits intodevelopComputationalCryoEM/ASPIRE-Python:developfrom

save_optics_groupComputationalCryoEM/ASPIRE-Python:save_optics_groupCopy head branch name to clipboard

Dec 12, 2025

Conversation Commits31 (31)Checks Files changed

Merged

ImageSource.save Optics Block#1337
j-c-c merged 31 commits intodevelopfrom
save_optics_group

Commits

Commits on Dec 12, 2025

initial ImageSource.save with optics block
j-c-c
committed
add _rlnImageSize column to metadata when saving.
j-c-c
committed
Add _rlnImageSize to coordinate source test.
j-c-c
committed
use rlnImageName to get n_rows
j-c-c
committed
test for sim save with optics block
j-c-c
committed
add _rlnImageDimensionality
j-c-c
committed
test save/load roundtrip w/ phase_flip.
j-c-c
committed
update coord source test
j-c-c
committed
cleanup
j-c-c
committed
remove unused var
j-c-c
committed
missing optics fields warning. warning test. code comments.
j-c-c
committed
removed unused import.
j-c-c
committed
deprecate _rlnAmplitude in favor of private __amplitude field.
j-c-c
committed
use _aspireAmplitude to retain ampitudes for saved files
j-c-c
committed
ensure pixel size is added to mrc header
j-c-c
committed
test mrc pixel_size in header
j-c-c
committed
Use defaultdict
j-c-c
committed
Remove old file compatibility
j-c-c
committed
Remove _aspireAmplitude from relion_metadata_fields dict.
j-c-c
committed
Test save on source slices
j-c-c
committed
Always write an optics block
j-c-c
committed
Gallery example simulation -> relion
j-c-c
committed
clean up gallery
j-c-c
committed
_aspireMetadata 'no_ctf' tag for missing optics fields. Detect ASPIRE-generated dummy values when loading. Unit test.
j-c-c
committed
test cleanup
j-c-c
committed
optics group level not_ctf flag
j-c-c
committed
clean up gallery
j-c-c
committed
tox
j-c-c
committed
typo
j-c-c
committed
gallery comment update
j-c-c
committed
float64 amplitude code comment
j-c-c
committed

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