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copick sync alignments

core

Synchronize alignments between two Copick projects.

Usage

copick sync alignments [OPTIONS]

Description

Copies alignments from a source Copick project to a target project; the target runs must hold the tilt series they align (see copick sync tiltseries).

Options

Option Type Default Description
-c, --config path — Path to the configuration file.
--source-dataset-ids text "" Comma-separated list of dataset IDs to use as source from CryoET Data Portal. If provided, --config will be ignored and a temporary dataportal configuration will be created.
--target-config path required Path to the target configuration file.
--source-runs text "" Comma-separated list of source run names to synchronize. If not specified, all runs will be synced.
--target-runs text "" Comma-separated mapping of source run names to target run names (e.g. 'run1:target1,run2:target2'). If not specified, source run names will be used.
--names text "" Comma-separated list of alignment names to synchronize. If not specified, all alignments will be synced.
--target-ts-types text "" Comma-separated mapping of source tilt series types to the target types the copies align (e.g. 'raw:original').
--valid-only / --no-valid-only boolean flag False Leave out alignments that do not come from their author (e.g. CryoET Data Portal placeholders).
--exist-ok / --no-exist-ok boolean flag False Allow overwriting existing objects in the target project.
--max-workers integer 4 Maximum number of worker threads to use for synchronization.
--log / --no-log boolean flag False Enable verbose logging of the synchronization process.
--debug / --no-debug boolean flag False Enable debug logging.

Examples

# Copy the alignments from their authors of a portal dataset
copick sync alignments --source-dataset-ids 10445 --target-config local.json --valid-only

See also