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Changelog

Source: NEWS.md

riot 2.0.0

API rename: read_bundle() and write_bundle()

  • Breaking change: read_tractogram() and write_tractogram() are renamed to read_bundle() and write_bundle() for consistency with the bundle data model.

DIPY dependency declaration modernised

  • The optional DIPY Python dependency is now declared via reticulate::py_require("dipy") (reticulate ≥ 1.41) instead of the previous manual py_module_available() check. Reticulate will automatically provision DIPY in an ephemeral virtual environment when one of the DIPY-backed formats (.trx, .fib, .dpy) is first used.

S7 data model: streamline and bundle classes moved to {fiber}

  • Breaking change: the maf_df tibble (with columns X, Y, Z, PointId, StreamlineId) is replaced by two S7 classes now defined in the fiber package:
    • streamline — stores three typed slots accessed with @:
      • @points: an n×3n \times 3 numeric matrix with columns "X", "Y", "Z" for the ordered coordinates of the nn points along the tract. PointId is implicit in row order and is no longer stored.
      • @point_data: a named list of numeric vectors of length nn, holding per-point scalar attributes (e.g. fractional anisotropy at each point).
      • @streamline_data: a named list of numeric scalars (length-1 vectors) holding per-streamline attributes (e.g. a tract-level weight or mean FA).
    • bundle — stores two typed slots:
      • @streamlines: a list of streamline objects. StreamlineId is implicit in list position and is no longer stored.
      • @bundle_data: a named list of bundle-level metadata (e.g. the affine transform used during tracking).
  • riot no longer depends on S7 directly; the S7 classes, constructors, predicates, and methods (new_streamline(), is_streamline(), new_bundle(), is_bundle(), format(), print(), length(), [[, [, …) are all provided by fiber and re-exported from there.
  • riot now imports fiber instead of S7.
  • read_bundle() returns a streamline when the file contains exactly one tract, and a bundle otherwise.
  • write_bundle() accepts both streamline and bundle objects.
  • The readr package is no longer a dependency.

C++ layer: elimination of intermediate CSV files

  • Breaking change (internal): the C++ reader functions (ReadVTK, ReadVTP, ReadFDS) no longer write a temporary CSV file. They now return a cpp11::writable::list directly to R, eliminating all temporary file I/O and the associated string-reference issues.
  • The C++ writer functions (WriteVTK, WriteVTP, WriteFDS) no longer read from a temporary CSV. They now accept a cpp11::list directly from R.
  • The helper WriteCSV (vtkPolyData → CSV) and ReadCSV (CSV → vtkPolyData) are replaced by PolyDataToList and ListToPolyData respectively, operating entirely in memory.

VTK bindings delegated to rvtk

  • VTK discovery, compilation flags, and pre-built static library distribution are now handled entirely by the rvtk package (pending CRAN submission). rvtk supplies pre-compiled VTK headers and libraries so that no manual VTK installation is required on most platforms: it honours a user-supplied VTK_DIR environment variable first, then tries Homebrew (macOS), pkg-config (macOS/Linux), and well-known system prefixes; on Windows it checks VTK_DIR, Rtools45 pacman, and common MSYS2 prefixes; if no suitable system VTK is found it downloads pre-built static libraries automatically from the rvtk GitHub releases.
  • rvtk is listed as an Imports dependency; downstream packages no longer need to locate VTK themselves.
  • The Remotes: astamm/rvtk field will be removed from DESCRIPTION once rvtk is available on CRAN.

riot 1.2.0

  • Breaking change in system requirements: riot no longer bundles VTK source files. Instead, it links against an externally installed VTK (>= 9.1.0) at compile time. VTK must be present on the host before installing the package. Both shared and static VTK builds are supported; static builds on macOS and Linux must have been compiled with -fPIC.
  • VTK is discovered at install time via configure / configure.win using, in order of preference:
    1. A user-supplied VTK_DIR environment variable.
    2. Homebrew (macOS).
    3. pkg-config (macOS and Linux).
    4. Well-known system include paths (/usr, /usr/local) (Linux).
    5. The Rtools42+ pacman package for the active MSYS2 environment (e.g. mingw-w64-ucrt-x86_64-vtk for UCRT64) (Windows).
  • On Windows, VTK is loaded dynamically at run time via addDLLDirectory() to avoid having to bundle VTK runtime DLLs inside the package.
  • Removed all bundled VTK source files, reducing the installed package size considerably.
  • Updated SystemRequirements in DESCRIPTION to document the external VTK dependency.

riot 1.1.1

  • Modified VTK source files to avoid compilation warnings arising when using LLVM or Apple clang or GNU gcc compilers.
  • Now ships a shrunk version of VTK source files to avoid unsuccessful downloads from VTK website.
  • Fix compilation errors in vtkzlib raised by clang16.

riot 1.1.0

CRAN release: 2023-01-06

  • Update VTK to v9.2.4;
  • Avoid some prototype checks for vtkzlib when using LLVM Clang compiler.

riot 1.0.0

CRAN release: 2022-05-10

In this first major release, we:

  • Added support to read MRtrix .tck/.tsf file formats (#5).
  • Added support to read TrackVis .trk file formats (#5).
  • Use only one core to compile VTK for compliance with CRAN policy (thanks to Prof. B. Ripley).
  • Added tilde expansion on file paths.

We make it the first major release as we consider that the most popular tractography formats are now supported by riot. We chose by design to support only VTK and medInria file formats for writing.

riot 0.0.1

CRAN release: 2022-05-05

  • Added a NEWS.md file to track changes to the package.
  • Supports for reading from and writing to .vtk, .vtp and .fds file formats.