copick process bandpass

torch

Band-pass filter tomograms in 3D.

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 bandpass [OPTIONS]

Description

For every run in the project (or only the runs given by --run-ids), queries the tomogram of the given algorithm at the requested voxel spacing, applies a Gaussian band-pass filter on the GPU, and writes the filtered tomogram back into the project under a new algorithm name (the source name with -lpA and/or -hpA suffixes). Runs are processed in parallel on a GPU pool.

Low-pass and high-pass cutoffs are given as resolutions in angstroms; a value of 0 disables that side of the filter, but both cannot be 0. Cutoffs finer than Nyquist (2 * voxel_size) are rejected, and for a true band-pass the high-pass resolution must be coarser than the low-pass resolution. Optionally writes a PNG preview of the filter profile (filter3d.png).

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
`--run-ids`	text	—	Run ID to process (No Input would process the entire dataset.)
`--tomo-alg`	text	required	Tomogram Algorithm to use
`--voxel-size`	float	`10`	Voxel Size to Query the Data

Tool Options

Option	Type	Default	Description
`--lp-freq`	float	`0`	Low-pass cutoff frequency (in Angstroms)
`--lp-decay`	float	`50`	Low-pass decay width (in pixels)
`--hp-freq`	float	`0`	High-pass cutoff frequency (in Angstroms)
`--hp-decay`	float	`50`	High-pass decay width (in pixels)
`--show-filter`	boolean	`True`	Save the filter as a PNG (filter3d.png)

Examples

# Low-pass filter wbp tomograms at 10 A voxel spacing to 30 A resolution
copick process bandpass -c config.json --tomo-alg wbp \
    --voxel-size 10.0 --lp-freq 30.0

# Band-pass a single run between 100 A (high-pass) and 30 A (low-pass)
copick process bandpass -c config.json --tomo-alg wbp \
    --voxel-size 10.0 --run-ids TS_001 --lp-freq 30.0 --hp-freq 100.0

# High-pass the whole dataset and skip the filter preview PNG
copick process bandpass -c config.json --tomo-alg wbp \
    --voxel-size 10.0 --hp-freq 150.0 --show-filter false