copick export alignment

core

Export alignments to AreTomo3, Warp, RELION, IMOD or the CryoET Data Portal format.

Usage

copick export alignment [OPTIONS]

Description

Converts each run's selected alignment from copick's CETS frame to the tool's frame and row order: AreTomo3 '.aln' with '_TLT.txt', Warp '.xml', RELION 'tomograms.star' with 'tilt_series/.star' for all runs, IMOD '/.xf/.tlt/.xtilt' with tilt.com and newst.com, or '_alignment.json'. RELION's rlnTomoNominalStageTiltAngle holds the nominal tilt angles, and its pre-exposure the accumulated dose.

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--run-names, -r`	text · multiple	—	Specific run names to process (default: all runs). Repeatable; pass -r once per run.
`--alignment-uri`	text	required	Alignments to export, one per run (e.g. 'aretomo3' or '*@raw?default=true').
`--output-dir`	directory	required	Output directory for exported files.
`--output-format`	choice (aretomo3 \| warp \| relion \| imod \| cdp)	required	Format to write.
`--reference-tomogram`	text	—	Each run's tomogram ('tomo_type@voxel_size') the tool should reconstruct. Default: the alignment's reference volume.
`--include-ctf`	boolean flag	`False`	Also write the CTF fits of the tilt series.
`--drop-x-tilt`	boolean flag	`False`	AreTomo3: drop the tilt about x, which .aln files cannot represent.
`--hand`	float	`-1.0`	RELION: rlnTomoHand.
`--relion-tomo-name`	text	—	RELION: rlnTomoName of a single exported run. Default: the run name.
`--assume-frame`	choice (half \| floor)	—	IMOD only: centre convention for odd image or volume sizes.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Examples

# The default alignment of every run's raw tilt series, for RELION 5 with CTF
copick export alignment -c config.json --alignment-uri "*@raw?default=true" --output-dir relion \
    --output-format relion --include-ctf