copick process downsample

torch

Downsample tomograms via Fourier rescaling.

Plugin command — copick-torch

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

pip install copick-torch

See the plugin system guide for details.

Usage

copick process downsample [OPTIONS]

Description

Downsample tomograms on the GPU with Fourier rescaling.

For every run in the project (or only the runs given by --run-names/-r), queries the input tomogram, Fourier-rescales it to the output voxel spacing on the GPU, and writes the downsampled tomogram back into the project. The output voxel spacing (and optional rename) is taken from -o/--output. Runs are processed in parallel on a GPU pool.

URI Format

Tomograms: tomo_type@voxel_spacing

Options

Option	Type	Default	Description
`-c, --config`	path	—	Path to the configuration file.
`--run-names, -r`	text · multiple	—	Specific run names to process (default: all runs). Repeatable; pass -r once per run.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Input Options

Option	Type	Default	Description
`--input, -i`	COPICK_URI	—	Input tomogram URI (format: tomo_type@voxel_spacing). Supports glob patterns.

Output Options

Option	Type	Default	Description
`--output, -o`	COPICK_URI	—	Output tomogram URI (format: tomo_type@voxel_spacing). Example: 'wbp@20.0'.

Tool Options

Option	Type	Default	Description
`--delete-source / --keep-source`	boolean flag	`False`	Delete the source tomograms after downsampling.

Examples

# Downsample wbp tomograms from 10 A to 20 A
copick process downsample -c config.json -i wbp@10.0 -o wbp@20.0

# Downsample and rename the output, then delete the source tomograms
copick process downsample -c config.json -i wbp@10.0 -o wbp-bin2@20.0 --delete-source