ImageSource.save Optics Block - #1337

Merged

j-c-c merged 31 commits into

save_optics_group

Dec 12, 2025

Commits on Dec 12, 2025

initial ImageSource.save with optics block
j-c-c
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ca93e2b
add _rlnImageSize column to metadata when saving.
j-c-c
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7f47993
Add _rlnImageSize to coordinate source test.
j-c-c
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a2e7aa8
use rlnImageName to get n_rows
j-c-c
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8a6bf92
test for sim save with optics block
j-c-c
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0ea7134
add _rlnImageDimensionality
j-c-c
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909fcd5
test save/load roundtrip w/ phase_flip.
j-c-c
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2481513
update coord source test
j-c-c
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65dba23
cleanup
j-c-c
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c429f24
remove unused var
j-c-c
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98cf5e1
missing optics fields warning. warning test. code comments.
j-c-c
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c386447
removed unused import.
j-c-c
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cfa30a8
deprecate _rlnAmplitude in favor of private __amplitude field.
j-c-c
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06d7b45
use _aspireAmplitude to retain ampitudes for saved files
j-c-c
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fe65e40
ensure pixel size is added to mrc header
j-c-c
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56e600b
test mrc pixel_size in header
j-c-c
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b92c305
Use defaultdict
j-c-c
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118482a
Remove old file compatibility
j-c-c
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c56aba5
Remove _aspireAmplitude from relion_metadata_fields dict.
j-c-c
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a0b0a20
Test save on source slices
j-c-c
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362c1bd
Always write an optics block
j-c-c
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57c6853
Gallery example simulation -> relion
j-c-c
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e4dc91c
clean up gallery
j-c-c
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fff6b7e
_aspireMetadata 'no_ctf' tag for missing optics fields. Detect ASPIRE-generated dummy values when loading. Unit test.
j-c-c
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58394be
test cleanup
j-c-c
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873d3ce
optics group level not_ctf flag
j-c-c
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f13e024
clean up gallery
j-c-c
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f5c334a
tox
j-c-c
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6acb49d
typo
j-c-c
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0e8dda6
gallery comment update
j-c-c
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63e6983
float64 amplitude code comment
j-c-c
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41adb21