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, queries the tomogram of the given algorithm at the source voxel spacing, Fourier-rescales it to the target voxel spacing on the GPU, and writes the downsampled tomogram back into the project. 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.
`--debug / --no-debug`	boolean flag	`False`	Enable debug logging.

Input Options

Option	Type	Default	Description
`--tomo-alg, -ta`	text	required	Tomogram algorithm/type to query and downsample (e.g. 'wbp').
`--voxel-size, -vs`	float	`10.0`	Source voxel spacing to query, in angstroms.

Tool Options

Option	Type	Default	Description
`--target-resolution, -tr`	float	`10.0`	Target voxel spacing to downsample to, in angstroms.
`--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 --tomo-alg wbp \
    --voxel-size 10.0 --target-resolution 20.0

# Downsample, then delete the source tomograms
copick process downsample -c config.json --tomo-alg wbp \
    --voxel-size 10.0 --target-resolution 20.0 --delete-source