copick logical clippicks

utils

Limit picks to those within distance of a reference surface.

Plugin command — copick-utils

This command is provided by the copick-utils plugin, not copick core. Install it to make this command available:

pip install copick-utils

See the plugin system guide for details.

DefaultInvert (beyond)

copick logical clippicks Default input — Input

copick logical clippicks Default output — Output

Limit picks to those within distance of a reference surface.

copick logical clippicks Invert (beyond) input — Input

copick logical clippicks Invert (beyond) output — Output

Limit picks to those within distance of a reference surface.

Usage

copick logical clippicks [OPTIONS]

Description

The reference surface can be a mesh, segmentation, or tomogram boundary. Each input pick is kept or dropped based on its distance to the nearest point on that surface. By default, picks within the specified --max-distance are kept; use --invert to keep only the picks that lie beyond that distance instead.

Exactly one reference must be supplied via --ref-mesh, --ref-seg, or --ref-tomogram. Distances are measured in angstroms.

URI Format

Picks: object_name:user_id/session_id
Meshes: object_name:user_id/session_id
Segmentations: name:user_id/session_id@voxel_spacing
Tomograms: tomo_type@voxel_spacing

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Input Options

Option	Type	Default	Description
`--run-names, -r`	text · multiple	—	Specific run names to process (default: all runs).
`--input, -i`	COPICK_URI	required	Input picks URI (format: object_name:user_id/session_id). Supports glob patterns.

Reference Options

Option	Type	Default	Description
`--ref-mesh, -rm`	COPICK_URI	—	Reference mesh URI (format: object_name:user_id/session_id). Supports glob patterns.
`--ref-seg, -rs`	COPICK_URI	—	Reference segmentation URI (format: name:user_id/session_id@voxel_spacing). Supports glob patterns.
`--ref-tomogram, -rt`	COPICK_URI	—	Reference tomogram boundary URI (format: tomo_type@voxel_spacing). Uses tomogram volume boundaries as reference surface. Example: 'wbp@10.0'

Tool Options

Option	Type	Default	Description
`--max-distance, -d`	float	`100.0`	Maximum distance from reference surface (in angstroms).
`--mesh-voxel-spacing, -mvs`	float	—	Voxel spacing for mesh voxelization when using mesh reference (defaults to target voxel spacing).
`--invert / --no-invert`	boolean flag	`False`	Invert filtering: keep data BEYOND max_distance instead of WITHIN (default: keep within).
`--workers, -w`	integer	`8`	Number of worker processes.

Output Options

Option	Type	Default	Description
`--output, -o`	COPICK_URI	required	Output picks URI. Supports smart defaults (e.g., "ribosome", "ribosome/my-session", or "/my-session"). Full format: object_name:user_id/session_id.

Examples

# Keep picks within 50A of a mesh reference
copick logical clippicks -i "ribosome:user1/all-001" -rm "boundary:user1/boundary-001" \
    -o "ribosome:clippicks/near-001" --max-distance 50.0

# Remove picks within 50A of a tomogram boundary (keep interior picks)
copick logical clippicks -i "ribosome:user1/all-001" -rt "wbp@10.0" \
    -o "ribosome:clippicks/interior-001" --max-distance 50.0 --invert

# Keep picks beyond 100A from a segmentation reference
copick logical clippicks -i "ribosome:user1/all-001" -rs "mask:user1/mask-001@10.0" \
    -o "ribosome:clippicks/far-001" --max-distance 100.0 --invert