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Changelog

Source: NEWS.md

neuroim2 0.11.0

Bug Fixes

  • Fixed NeuroSpace() to derive spacing() and origin() from the affine matrix when constructed with trans=. Previously, spacing() returned (1,1,1) for spaces created from an explicit affine.
  • Fixed drop_dim() for 3D-to-2D NeuroSpace objects to properly subset the affine matrix, preserving spatial transforms instead of lossy reconstruction from spacing/origin.

Dependency Changes

  • Replaced crayon with cli for all user-facing output. The cli package provides structured error messages, progress bars, and consistent ANSI formatting.
  • Replaced assertthat with cli::cli_abort() across all 253 assertion sites, providing richer error messages with argument and class markup.
  • Added vdiffr to Suggests for visual regression testing.

Improvements

  • All 28 show() methods now use a unified formatting style via internal show_header()/show_rule()/show_field() helpers.
  • New show() methods for DenseNeuroVol and NeuroSpace (previously had no informative display).
  • random_searchlight() and searchlight(eager=TRUE) now display a cli progress bar in interactive sessions.
  • New normalize_mask() internal helper consolidates duplicated mask-coercion logic.

Testing

  • New NeuroSpace test suite (26 tests) covering construction, coordinate transforms, affine operations, and dimension manipulation.
  • New NIfTI I/O round-trip tests (9 tests) verifying data/affine preservation across read-write cycles.
  • New oblique affine regression tests (6 tests) for downsample, resample, and deoblique.
  • New vdiffr plot snapshot tests (7 tests) for plot(), plot_ortho(), plot_montage(), and plot_overlay().
  • New shared test helper module with factory functions (make_vol(), make_vec(), make_mask(), etc.).

Documentation

  • New “Coordinate Systems and Spatial Transforms” vignette explaining affine transforms, voxel/world coordinate conversion, orientation codes, and common gotchas.
  • Consolidated @rdname method families, reducing man pages from 276 to 265.

neuroim2 0.10.0

  • Fixed downsample() for DenseNeuroVol and DenseNeuroVec so output NeuroSpace objects now carry a correctly rescaled affine transform. Previously, voxel dimensions could change while trans() still reflected the pre-downsample grid.

neuroim2 0.9.1

  • plot_overlay() gains an ov_alpha_mode argument: "binary" (default, existing behaviour) applies a uniform alpha to thresholded pixels, while "proportional" scales per-pixel alpha by the absolute overlay value for smoother blending. Internal helpers matrix_to_colors(), matrix_to_rgba(), and matrix_to_raster_grob() now accept an alpha_map argument to support this.
  • Refactored orientation internals in R/axis.R: new helpers .default_axcode_labels(), .validate_ornt(), ornt_transform(), inv_ornt_aff(), apply_orientation(), flip_axis(), io_orientation(), axcodes2ornt(), and ornt2axcodes() provide a comprehensive NiBabel-compatible orientation API.
  • Plot colorbar guides improved with better default labelling.
  • Fixed dimension comments in the ClusteredNeuroVec vignette: searchlight values() dimensions were documented as N x T but are actually T x N (time points x neighbors).
  • Removed stale albersdown dependency from vignette setup chunks; all vignettes now use neuroim2::theme_neuro() exclusively.
  • Added .ecosystem.yml to .Rbuildignore to silence hidden-file NOTE.
  • Added AFNI-style deoblique() for NeuroSpace/NeuroVol, with gridset/newgrid controls and default isotropic grid spacing equal to the minimum input voxel size. NeuroVol inputs are resampled to an axis-aligned deobliqued target space.
  • Fixed plot(NeuroVol) and plot(NeuroSlice) memory blowups for oblique/sheared affines by rasterizing on pixel-grid coordinates instead of world-coordinate grids; added regression tests for oblique affine plotting.

neuroim2 0.9.0

  • Added 5D NIfTI support for hyper-vectors: new read_hyper_vec() reader returns NeuroHyperVec; read_image(type = "auto") now dispatches to NeuroHyperVec for 5D inputs (with optional spatial masking); and write_vec() now supports NeuroHyperVec so 5D NIfTI read/write round-trips are supported.
  • Fixed write_vec() affine round-trip regression: NIfTI sform (direct affine) is now preferred over qform (quaternion-derived) on read, matching the convention used by FSL, FreeSurfer, and ANTs. Previously, the sform was silently replaced by the qform, causing world-coordinate drift for vector fields and warp images.
  • Fixed as_nifti_header() to derive qoffset from the transform matrix translation column, ensuring internal header consistency between quaternion parameters and the sform.
  • Relaxed NeuroSpace affine precision from 6 to 7 significant digits, matching NIfTI float32 precision and reducing cumulative round-trip truncation.

neuroim2 0.8.7

neuroim2 0.8.5

CRAN release: 2026-01-14

  • Windows build fix: added Makevars.win to correctly link TBB libraries from RcppParallel without the non-existent -lRcppParallel flag.
  • PDF manual fix: replaced Unicode characters (Greek letters, special symbols) in roxygen documentation with ASCII equivalents to resolve LaTeX errors during PDF generation.

neuroim2 0.8.4

  • I/O reliability: enforce full-length binary reads (detects truncated images) and ensure gz connections are cleaned up on error.
  • Data correctness: apply per-volume slope+intercept scaling consistently across NeuroVol/NeuroVec/SparseNeuroVec loaders (treat NIfTI slope==0 as identity).
  • Performance: SparseNeuroVecSource no longer materializes full 4D arrays; reads masked voxels via mmap for uncompressed files or streams volumes sequentially for gz files.
  • Docs: fix missing Rd entries/aliases for several exported functions and S4 methods; remove vignette dependency on albersdown.

neuroim2 0.8.3

  • Arithmetic/comparison fixes: SparseNeuroVec now unions masks and keeps outputs sparse; sparse–sparse NeuroVol arithmetic returns SparseNeuroVol; numeric vs SparseNeuroVol comparison no longer errors.
  • 4D bilateral filter now measures intensity variance across all timepoints in the mask and skips non-finite neighbours, eliminating spurious NaNs on constant or noisy inputs.
  • Added regression tests covering the zero-window identity and constant-volume stability for the parallel 4D bilateral filter backend.
  • New meta_info() helper returns a normalized list of basic header metadata from a filename or FileMetaInfo (dim, spacing, origin, trans, path, etc.), making 3D/4D image introspection simpler for new users.

neuroim2 0.8.2

  • README refreshed: CRAN/R-universe install, CI/coverage badges, website & cheatsheet links.
  • Docs: spherical_roi() now cross-links to spherical_roi_set(); ROI vignette shows multi-ROI creation.
  • SparseNeuroVec:
    • New validity checks to catch data/mask/space shape mismatches (#5).
    • Robust as.matrix.SparseNeuroVec() implementation (#2).
  • New resample_to() wrapper for readable interpolation names; delegates to existing resample() methods.

neuroim2 0.8.1

CRAN release: 2025-04-10

  • Initial CRAN submission.