bifti (Rust) 0.3.0

Published to crates.io: https://crates.io/crates/bifti/0.3.0

bifti (Rust) 0.2.0

Changed

• Breaking: Phantom::load(path, max_substeps) and
  Phantom::load_from_config(config, base_dir, max_substeps) take the cap on quadrature
  samples per axis used when an oblique reslice_to is resampled, previously fixed at 8.
  Pass bifti::DEFAULT_MAX_SUBSTEPS for the old behaviour.
• Resampling onto an oblique reslice_to now warns (through tracing with the tracing
  feature, on stderr otherwise): the result is averaged by approximate midpoint quadrature
  instead of the exact box average used for axis-aligned grids. The warning says when
  max_substeps leaves the quadrature under-sampled, so the result may alias
  (#23).

Added

• DEFAULT_MAX_SUBSTEPS (8).

bifti (Python) 0.3.0

Published to PyPI: https://pypi.org/project/bifti/0.3.0/

bifti (Python) 0.2.1

Published to PyPI: https://pypi.org/project/bifti/0.2.1/

bifti (Python) 0.2.0

Added

• max_substeps keyword on NumpyPhantom.load, NumpyPhantom.load_from_config and
  load_tissue (default 8): the cap on quadrature samples per axis used when an oblique
  reslice_to is resampled, previously only settable through Resampler.build.
• Resampler.weight_sum / resample_weighted accept a (C, X, Y, Z) weight, one per
  channel, so a 4-D phantom NIfTI (one density per tissue) goes through a single call
  (#23).
• ObliqueResampleWarning and Resampler.capped.

Changed

• Resampling onto an oblique grid now emits an ObliqueResampleWarning: the result is
  averaged by approximate midpoint quadrature instead of the exact box average used for
  axis-aligned grids. The warning says when max_substeps leaves the quadrature
  under-sampled, so the result may alias
  (#23).
• A weight whose shape matches neither the source grid nor (C, *source grid) now raises
  ValueError instead of failing inside the contraction.

BiftiPhantoms-v0.3.0

BiftiPhantoms BiftiPhantoms-v0.3.0

Diff since BiftiPhantoms-v0.2.1

Added

• save_bifti(...; constant_threshold=...): store a map as a constant when its RMS
  deviation from the real part of its mean (its standard deviation, for a real map) is at
  most the threshold. nothing (the default) or a negative value disables it; density
  always stays a map.

Changed

• Breaking: save_bifti prefixes every NIfTI with the name of the JSON file
  (phantom_density.nii.gz, phantom_B1plus_0.nii.gz, ... for phantom.json), so several
  phantoms can be saved into one directory without overwriting each other's maps.

Merged pull requests:

• Prefix saved NIfTIs, constant threshold on save, complex maps in Python (0.3.0) (#34) (@J-Endres)

BiftiPhantoms-v0.2.1

BiftiPhantoms BiftiPhantoms-v0.2.1

Diff since BiftiPhantoms-v0.2.0

Added

• load_bifti(...; max_substeps=8): the cap on quadrature samples per axis used when an
  oblique reslice_to is resampled, previously fixed at 8.

Changed

• Reslicing onto an oblique reslice_to now logs a warning: the result is averaged by
  approximate midpoint quadrature instead of the exact box average used for axis-aligned
  grids. The warning says when max_substeps leaves the quadrature under-sampled, so the
  result may alias (#23).

Merged pull requests:

• setup publishing workflow (#31) (@J-Endres)
• Warn on oblique resampling, per-channel weights; bump all packages to 0.2 (fixes #23) (#32) (@J-Endres)
• python: parse func expressions instead of eval (0.2.1) (#33) (@J-Endres)

Closed issues:

• resample: the oblique path is silently approximate, and a per-tissue weight can't be batched (#23)

bifti (Python) 0.1.0

First release of bifti on PyPI: a Python package for loading, saving and resampling
BIfTI MRI simulation phantoms (one JSON file
plus NIfTI files).

pip install bifti          # or: uv add bifti
pip install "bifti[torch]" # optional: torch-accelerated resampling (CPU or CUDA)

Requires Python 3.12 or newer.

Features

• Load phantoms into NumPy: NumpyPhantom.load(path) reads the phantom JSON and every
  NIfTI it references into one NumpyTissue per tissue (density, T1, T2, T2', ADC,
  dB0, multi-channel B1+/B1-), with property defaults and func value mappings applied.
• Reslicing (reslice_to): density-weighted footprint averaging, so downsampling really
  averages instead of dropping data and edges are not pulled towards zero. Uses torch when it is
  installed, NumPy otherwise (override with BIFTI_RESAMPLE_BACKEND=numpy|torch).
• Saving: NumpyPhantom.save(dir) writes a self-contained, deterministic folder (float64
  NIfTIs + JSON, func baked in, no reslice_to), so you can reslice a phantom on disk or
  export one you built in memory.
• JSON data model: BiftiPhantom.load / .save parse and write just the JSON, for
  generating or editing phantoms without touching voxel data.
• Patient position: patient_to_scanner / to_scanner_affine map phantom coordinates to
  scanner coordinates.
• Public registry: load_catalog(), load_registry() and
  load_registry_phantom(collection, name) download phantoms from Zenodo into a local cache.
  Browse them at https://mrx-org.github.io/bifti-phantoms/.

Known limitations

• func mappings are evaluated with Python's eval: only load phantoms you trust.
• Complex-valued NIfTI data is not supported yet: the imaginary part of a complex B1+/B1-
  map is dropped.
• Only the default units are accepted.

This package was built with LLM assistance and has not been reviewed thoroughly yet. Expect
rough edges while the version is 0.x. Please report problems at
https://github.com/mrx-org/bifti-phantoms/issues.

Full documentation: https://github.com/mrx-org/bifti-phantoms/blob/main/python/bifti/README.md

BiftiPhantoms-v0.2.0

BiftiPhantoms BiftiPhantoms-v0.2.0

Diff since BiftiPhantoms-v0.1.0

Breaking changes

None. 0.2.0 only adds functionality; existing code keeps working.
The minor version was bumped because the package is still pre-1.0.

Added

• save_bifti / save_nifti: save a loaded VoxelPhantom as a deterministic, self-contained
  folder (stacked NIfTI-1 files plus JSON; func mappings baked in, no reslice_to).

Merged pull requests:

• feat: add option to save phantoms to disk for all impls (#29) (@J-Endres)
• feat: PR template; docs for easier phantom contribution (#30) (@J-Endres)

BiftiPhantoms-v0.1.0

BiftiPhantoms BiftiPhantoms-v0.1.0

Initial release. Reads, writes and loads BIfTI phantoms, with density-weighted resampling, patient positions and registry downloads.

Closed issues:

• Proposal: bifti_registry_v3 — phantom groups (shared NIfTIs + multiple JSON configs) (#10)
• please add semantic versioning to readme or release notes etc. (#18)