Skip to content

copick convert mesh2caps

utils

Extract the top/bottom surfaces (caps) of a slab box mesh.

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.

copick convert mesh2caps Default input
Input

copick convert mesh2caps Default output
Output

Extract the top/bottom surfaces (caps) of a slab box mesh.

copick convert mesh2caps Top input
Input

copick convert mesh2caps Top output
Output

Extract the top/bottom surfaces (caps) of a slab box mesh.

copick convert mesh2caps Bottom input
Input

copick convert mesh2caps Bottom output
Output

Extract the top/bottom surfaces (caps) of a slab box mesh.

Usage

copick convert mesh2caps [OPTIONS]

Description

Extract the top/bottom surfaces ("caps") of a closed slab box mesh as an open mesh.

A boundary slab (e.g. the valid-sample mesh) is a closed box: a top surface, a parallel bottom surface, and 4 side walls. This command keeps only the near-horizontal cap faces and drops the near-vertical side walls, classifying faces geometrically by their normal orientation relative to the slab axis (so it works even on a re-triangulated boolean result).

The resulting open mesh feeds copick logical clippicks to select particles within a distance of the top/bottom of the specimen WITHOUT the side walls contaminating the distance field.

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
--axis choice (x | y | z) z Slab-normal axis in physical mesh coordinates (z = beam direction).
--angle-threshold float 45.0 Max angle (degrees) between a face normal and the axis for a face to count as a cap (rather than a side wall).
--surface choice (both | top | bottom) both Which cap surfaces to extract.
--auto-axis / --no-auto-axis boolean flag False Infer the slab normal from the mesh's thinnest bounding-box extent instead of --axis (useful for strongly tilted slabs).
--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.

Examples

# Extract both caps of the valid-sample slab
copick convert mesh2caps -i "valid-sample:meshop/0" -o "valid-sample-caps:mesh2caps/0"

# Extract only the top cap, with a tighter cap angle
copick convert mesh2caps --surface top --angle-threshold 30 \
    -i "valid-sample:meshop/0" -o "valid-sample-caps:mesh2caps/top-0"

# Strongly tilted slab: infer the slab normal automatically
copick convert mesh2caps --auto-axis -i "valid-sample:meshop/0" -o "valid-sample-caps:mesh2caps/0"

See also