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copick export cets

core

Export a project's tilt series, alignments and tomograms as a CETS dataset.

Usage

copick export cets [OPTIONS]

Description

Writes one CETS (https://github.com/TomoBabel/cets-data-models) Dataset document: a Region per run with its tilt series (per-image stage angle, acquisition order, dose and CTF), alignments (one ProjectionAlignment per aligned image) and tomograms (with the tilt series they were reconstructed from), and the instruments and acquisition sessions. Identifiers are prefixed with the run name. What CETS has no field for (copick's extensions, alignment names and reference volumes, tomogram links) goes to a companion file next to it.

Options

Option Type Default Description
-c, --config path — Path to the configuration file.
--output, -o file required Path of the CETS JSON document to write.
--run-names text "" Comma-separated run names to export. Omit to export all runs.
--tomograms / --no-tomograms boolean flag True Export the runs' tomograms (with their frames and the tilt series they were reconstructed from).
--paths / --no-paths boolean flag True Record the URL of each tilt series and tomogram store.
--validate / --no-validate boolean flag True Validate the document against the targeted CETS schema (needs jsonschema: pip install 'copick[cets]').
--companion / --no-companion boolean flag True Write .copick-companion.json with the data CETS has no field for.
--name text — Name of the dataset. Default: the project's name.
--debug / --no-debug boolean flag False Enable debug logging.

Examples

# Export all runs
copick export cets -c config.json -o dataset.cets.json

# Export two runs without their tomograms
copick export cets -c config.json -o dataset.cets.json --run-names TS_001,TS_002 --no-tomograms

See also