copick add picks-em

core

Add picks from EM motivelist files containing multiple tomograms.

Usage

copick add picks-em [OPTIONS] PATH

Description

Imports particle picks from one or more TOM toolbox EM motivelists, where a single file can hold picks from many tomograms. Each particle's tomogram is identified by an index stored in a configurable motivelist row (--tomo-index-row, default 4 for the Artiatomi convention), and --index-map provides a 2-column CSV/TSV that maps those indices to copick run names (e.g. 1,TS_001). A voxel size is required to convert coordinates.

Arguments

Argument	Description
`PATH`	Path to the EM motivelist file (.em) or a glob pattern.

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--object-name`	text	required	Name of the pickable object (must exist in config).
`--session-id`	text	`1`	Session ID for the annotation.
`--user-id`	text	`copick`	User ID for the annotation.
`--voxel-size`	float	required	Voxel size in Angstrom (required for coordinate conversion).
`--index-map`	path	required	Path to a CSV/TSV file mapping tomogram index to run name (2 columns: index, run_name).
`--tomo-index-row`	integer	`4`	Row index (0-based) for tomogram index in EM motivelists. Default is row 4 (Artiatomi convention).
`--max-workers`	integer	`4`	Maximum number of worker threads.
`--overwrite / --no-overwrite`	boolean flag	`False`	Overwrite the object if it exists.
`--create / --no-create`	boolean flag	`True`	Create the object if it does not exist.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Examples

# Import an EM motivelist with an index map
copick add picks-em motivelist.em -c config.json --object-name ribosome \
    --voxel-size 10.0 --index-map tomo_mapping.csv

# Import with a custom tomogram-index row
copick add picks-em motivelist.em -c config.json --object-name ribosome \
    --voxel-size 10.0 --index-map tomo_mapping.csv --tomo-index-row 5

# Import multiple files via a glob pattern
copick add picks-em "*.em" -c config.json --object-name ribosome \
    --voxel-size 10.0 --index-map tomo_mapping.csv