odx 0.1.3

Python bindings for the ODX format — TRX-style mmap container for ODFs, peaks, and SH coefficients

odx — Python bindings for the ODX format

Python bindings for odx-rs, a TRX-style mmap-friendly container for orientation density functions (ODFs), peaks, and spherical-harmonic coefficients from diffusion MRI.

Install

pip install odx           # core package (numpy only)
pip install odx[dipy]     # with the dipy adapter for PeaksAndMetrics interop

Quickstart

Compute CSD in dipy, dump to a peaked ODX in one call:

import odx
from dipy.reconst.csdeconv import ConstrainedSphericalDeconvModel
from dipy.direction.peaks import peaks_from_model

# ... fit a model, get csd_fit.shm_coeff (X, Y, Z, K)

peaked = odx.from_sh_coefficients(
    csd_fit.shm_coeff, mask=mask, affine=affine,
    basis="descoteaux07", sh_order=8, legacy=True,
)
peaked.save("csd.odx")              # native, mmap-friendly
peaked.save_fz("autotrack.fz")      # → DSI Studio fz
peaked.save_mrtrix("mrtrix_out/")   # → MRtrix mif (auto-converts basis)

# Round-trip back to dipy if you want
pam = odx.to_peaks_and_metrics(peaked)

Features

• Native ODX I/O — read/write .odx archives or directories, mmap-backed for zero-copy NumPy views.
• Peak finder — sphere-mesh local-maxima detection with MRtrix-style Gauss-Newton sub-vertex refinement on the SH series itself.
• Foreign format converters — load and save DSI Studio (.fz, .fib.gz), MRtrix (fixel directories + .mif), Tortoise MAP-MRI, pyAFQ asymmetric ODFs.
• dipy adapter (optional) — bidirectional conversion between odx.Odx and dipy's PeaksAndMetrics. Lazy-imported so dipy isn't required for the core package.
• SH basis conversion — descoteaux07 ↔ tournier07 round-trips via amplitudes, including legacy/modern variants.

License

The bulk of odx-rs (and the Python bindings) is dual-licensed under the MIT and Apache 2.0 licenses, the typical Rust ecosystem dual-license. Pick whichever you prefer.

Two source files in the underlying Rust crate (src/peak_finder.rs and src/mrtrix_sh.rs) port code from MRtrix3 and remain governed by the Mozilla Public License v. 2.0. That's a file-scoped (weak) copyleft — modifications to those specific files must remain MPL and source-available, but the license has no effect on projects that simply use odx as a dependency.

SPDX summary: (MIT OR Apache-2.0) AND MPL-2.0.