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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-names/-r), queries the input tomogram, applies a Gaussian band-pass filter on the GPU, and writes the filtered tomogram back into the project. The output is named by -o/--output, or (when omitted) the source name with -lpA and/or -hpA suffixes. Band-pass does not resample, so the output voxel spacing matches the input. 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.
--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
--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 -i wbp@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 -i wbp@10.0 -r TS_001 \
    --lp-freq 30.0 --hp-freq 100.0

# High-pass the whole dataset into a named output, skipping the preview PNG
copick process bandpass -c config.json -i wbp@10.0 -o wbp-hp150A@10.0 \
    --hp-freq 150.0 --show-filter false

See also