neuroim2 0.13.0

New Features

• NeuroVecSeq now supports matrix conversion and dense coercion helpers for easier interoperability with standard matrix workflows.
• NeuroVec now supports optional per-volume volume_labels() metadata across dense, sparse, mapped, file-backed, bigvec, and NeuroVecSeq backends.
• Named volume access is now supported via vec[["label"]], with strict unique-match semantics, and sub_vector() now accepts character label vectors.
• write_vec() now round-trips per-volume labels through a custom NIfTI extension; read_vec() and low-footprint readers restore labels on load.

Documentation

• Added new introductory workflow and container vignettes and refocused the advanced volume and ROI vignettes around current package workflows.
• Standardized vignette theme/setup chunks, fixed vignette metadata and dependency declarations, and clarified return types in the read_vec(), read_vol(), and read_image() documentation.

Improvements

• Fixed NeuroVec label inference for lists of NeuroVol inputs and refreshed the generated documentation for volume_labels() and related extractors.

neuroim2 0.12.0

New Features

• NeuroVec now supports optional per-volume volume_labels() metadata across dense, sparse, mapped, file-backed, bigvec, and NeuroVecSeq backends.
• Named volume access is now supported via vec[["label"]], with strict unique-match semantics, and sub_vector() now accepts character label vectors.
• write_vec() now round-trips per-volume labels through a custom NIfTI extension; read_vec() and low-footprint readers restore labels on load.

Testing

• Added focused tests for per-volume label access, concatenation semantics, NeuroVecSeq, and NIfTI label round-tripping.

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

• New public orientation utility API: affine_to_orientation(), orientation_transform(), apply_orientation(), orientation_inverse_affine(), orientation_to_axcodes(), axcodes_to_orientation(), and affine_to_axcodes().
• New public space utility API: output_aligned_space() (with NiBabel-compatible alias vox2out_vox()) and slice_to_volume_affine() (alias slice2volume()), including support for NeuroSpace/NeuroVol inputs, >3D spatial handling via first 3 axes, and optional zero-based indexing compatibility.
• New public affine utility API: apply_affine(), to_matvec(), from_matvec(), append_diag(), dot_reduce(), voxel_sizes(), obliquity(), and rescale_affine(), with stricter validation and center-preserving affine rescaling semantics.
• Fixed reorient(NeuroSpace, orient) so returned spaces now carry the requested orientation axes (instead of preserving original axes).
• New sub_clusters() generic: subset a ClusteredNeuroVol or ClusteredNeuroVec by integer cluster ID, numeric, or character name (looked up in the label map). Returns a new object of the same class containing only the selected clusters.
• scale_series() for DenseNeuroVec is now ~10x faster by operating row-wise on the voxels-by-time matrix instead of double-transposing through base::scale.
• New dedicated scale_series() method for SparseNeuroVec: scales only masked voxels in-place on the T×K @data matrix, returns 0 (not NaN) for zero-variance voxels, and stays sparse.
• as.dense() is now an identity (no-copy) for DenseNeuroVol.
• Arithmetic ops (+, -, *, /, ^) now work for ClusteredNeuroVol (with a warning that cluster structure is not preserved) and scalar ops for DenseNeuroVol and SparseNeuroVol.
• Logic ops (&, |) and negation (!) now work across DenseNeuroVol, SparseNeuroVol, and LogicalNeuroVol, returning LogicalNeuroVol.
• Compare ops (>, <, ==, etc.) for SparseNeuroVol and DenseNeuroVol now correctly return LogicalNeuroVol instead of raw sparse vectors or mistyped volumes.
• Added NIfTI extension classes (NiftiExtension, NiftiExtensionList) and read_image() convenience wrapper.

neuroim2 0.8.5

• 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

• Initial CRAN submission.