brkraw-sordino

SORDINO reconstruction hook for BrkRaw.

Install

pip install -e .

Hook install

brkraw hook install brkraw-sordino

This installs the hook rule from the package manifest (brkraw_hook.yaml).

Usage

Once installed, brkraw applies the hook automatically when a dataset matches the rule.

Basic conversion:

brkraw convert /path/to/study --scan-id 3 --reco-id 1

The hook behaves the same whether invoked via the CLI or via the Python API (the same hook entrypoint and arguments are used).

To explicitly pass hook options (or override defaults), use --hook-arg / --hook-args-yaml below.

Hook options

Hook arguments can be passed via brkraw convert using --hook-arg with the entrypoint name (sordino):

brkraw convert /path/to/study -s 3 -r 1 \
  --hook-arg sordino:ext_factors=1.2 \
  --hook-arg sordino:offset=2 \
  --hook-arg sordino:split_ch=false

Pass hook options via YAML (--hook-args-yaml)

BrkRaw can also load hook arguments from YAML. Generate a template like this:

brkraw hook preset sordino -o hook_args.yaml

Edit the generated YAML, then pass it to brkraw convert (repeatable):

brkraw convert /path/to/study -s 3 -r 1 --hook-args-yaml hook_args.yaml

Example:

hooks:
  sordino:
    ext_factors: 1.2
    offset: 2
    split_ch: false
    # as_complex: true  # optional, return (real, imag)
    # cache_dir: ~/.brkraw/cache/sordino  # optional (add manually if needed)

Notes:

• CLI --hook-arg values override YAML.
• YAML supports both {hooks: {sordino: {...}}} and {sordino: {...}} shapes.
• You can also set BRKRAW_CONVERT_HOOK_ARGS_YAML (comma-separated paths).

Supported keys:

• ext_factors: scalar or 3-item sequence (default: 1.0)
• ignore_samples: int (default: 1)
• offset: int (default: 0)
• num_frames: int or null (default: None)
• correct_spoketiming: bool (default: false)
• correct_ramptime: bool (default: true)
• offreso_ch: int or null (default: None)
• offreso_freq: float (default: 0.0)
• mem_limit: float (default: 0.5)
• clear_cache: bool (default: true)
• split_ch: bool (default: false, merge channels)
• as_complex: bool (default: false, return complex as (real, imag))
• cache_dir: string path (default: ~/.brkraw/cache/sordino)

Notes

• The hook reconstructs data using an adjoint NUFFT and returns magnitude images by default.
• Converted NIfTI outputs apply slope/intercept scaling for uint16 storage.
• ext_factors scales the affine around the FOV center during conversion.
• Multi-channel data defaults to merged channels; set split_ch=true to keep channels split.
• When split_ch=false, magnitude uses RSS while complex uses coherent sum.
• Orientation is normalized when the first 3D axes are spatial; see notebooks/orientation.ipynb.
• Cache files live under ~/.brkraw/cache/sordino (or BRKRAW_CONFIG_HOME) and are cleared when clear_cache=true.