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copick sync tomograms

core

Synchronize tomograms between two Copick projects.

Usage

copick sync tomograms [OPTIONS]

Description

Copies tomogram data from a source Copick project to a target project. You can restrict the sync to specific runs, voxel spacings, and tomogram types, and optionally remap source tomogram types to different target types. The source may instead be one or more CryoET Data Portal datasets via --source-dataset-ids, in which case --config is ignored and a temporary dataportal configuration is created.

Use --exist-ok to overwrite tomograms that already exist in the target.

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.
--voxel-spacings text "" Comma-separated list of voxel spacings to consider for synchronization. If not specified, all voxel spacings will be synced.
--source-tomo-types text "" Comma-separated list of source tomogram types to synchronize. If not specified, all tomogram types will be synced.
--target-tomo-types text "" Comma-separated mapping of source tomogram types to target types (e.g. 'wbp:filtered,raw:original'). If not specified, source tomogram types will be used.
--exist-ok / --no-exist-ok boolean flag False Allow overwriting existing tomograms 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

# Sync all tomograms from all runs
copick sync tomograms -c source_config.json --target-config target_config.json

# Sync specific runs and voxel spacings
copick sync tomograms -c source_config.json --target-config target_config.json \
    --source-runs "run1,run2" --voxel-spacings "10.0,20.0"

# Sync specific tomogram types with name mapping
copick sync tomograms -c source_config.json --target-config target_config.json \
    --source-tomo-types "wbp,raw" --target-tomo-types "wbp:filtered,raw:original"

See also