copick process hull

utils

Compute hull operations on meshes.

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.

Compute hull operations on meshes.

Usage

copick process hull [OPTIONS]

Description

Currently supports convex hull computation, where the convex hull is the smallest convex shape that contains all vertices of the original mesh. Each input mesh is replaced by its hull; with --individual-meshes a separate hull is written per instance using the {instance_id} placeholder in the output URI.

URI Format

Meshes: object_name:user_id/session_id

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 mesh URI (format: object_name:user_id/session_id). Supports glob patterns.

Tool Options

Option	Type	Default	Description
`--hull-type`	choice (convex)	`convex`	Type of hull to compute.
`--workers, -w`	integer	`8`	Number of worker processes.

Output Options

Option	Type	Default	Description
`--output, -o`	COPICK_URI	required	Output mesh URI. Supports smart defaults (e.g., "membrane", "membrane/my-session", or "/my-session"). Full format: object_name:user_id/session_id.
`--individual-meshes, -im / --no-individual-meshes`	boolean flag	`False`	Create individual meshes for each instance (enables {instance_id} placeholder).

Examples

# Compute convex hull for meshes
copick process hull -i "membrane:user1/session1" -o "membrane:hull/hull-session"

# Process specific runs with an explicit hull type
copick process hull -r run1 -r run2 --hull-type convex \
    -i "membrane:user1/session1" -o "membrane:hull/convex-001"

# Emit one hull mesh per instance using the {instance_id} placeholder
copick process hull --individual-meshes \
    -i "membrane:user1/session1" -o "membrane:hull/inst-{instance_id}"