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copick sync tiltseries

core

Synchronize tilt series between two Copick projects.

Usage

copick sync tiltseries [OPTIONS]

Description

Copies tilt series, images and metadata, from a source Copick project to a target project. The metadata is stored with each copy, so tilt series of the CryoET Data Portal (--source-dataset-ids) carry their per-image angles, dose and CTF in the target. --with-alignments copies their alignments too.

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.
--source-ts-types text "" Comma-separated list of source tilt series types to synchronize. If not specified, all tilt series will be synced.
--target-ts-types text "" Comma-separated mapping of source tilt series types to target types (e.g. 'raw:original'). If not specified, source types will be used.
--with-alignments / --no-with-alignments boolean flag False Also synchronize the alignments of each tilt series.
--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 tilt series and alignments of two portal datasets into a local project
copick sync tiltseries --source-dataset-ids 10445,10446 --target-config local.json --with-alignments

# Copy raw tilt series under another type
copick sync tiltseries -c source.json --target-config target.json --source-ts-types raw \
    --target-ts-types raw:original

See also