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Changelog

Source: NEWS.md

ravetools 0.2.7

  • Added color_ramp_continuous helper to create a vectorized color-mapping function from a palette and a numeric domain
  • Fixed make_error to properly protect the error class string from garbage collection, preventing class names from being silently lost in nested error calls
  • Guarded design_filter against bandstop configurations where automatically derived transition bandwidths overlap each other, producing unordered frequency breakpoints
  • Added mris_curvature to estimate per-vertex mean, Gaussian, and principal curvatures by fitting an osculating quadratic surface to each vertex’s two-ring neighborhood
  • Added mris_smooth to smooth a triangular surface mesh via iterative Laplacian or Taubin smoothing
  • Added mris_inflate to inflate a cortical surface mesh by iteratively smoothing and expanding toward a sphere while preserving total surface area
  • Added mris_sphere to project an inflated cortical surface onto a sphere and relax metric distortion via area-preserving gradient descent
  • Added mris_remesh to re-mesh a triangular surface to uniform edge length using the Botsch and Kobbelt (2004) isotropic re-meshing algorithm
  • Added mris_make_surfaces to localize white-matter and pial surfaces from an intensity volume
  • Added vcg_average_edge_length and vcg_max_edge_length to query edge-length statistics of a mesh
  • Added vcg_count_edge_defects to count non-manifold edge defects in a mesh
  • Added vcg_fix_defects to repair mesh topology defects via VCG
  • Added vcg_subdivide_max_edge_length to subdivide only edges that exceed a specified length, avoiding global super-sampling and improving Dijkstra path quality
  • Added vcg_mesh_patch to extract a geodesic patch of a mesh bounded by a closed curve of user-supplied waypoint vertices
  • All mesh3d objects returned by ravetools now carry the ravetools_mesh3d class, enabling a plot() generic that dispatches automatically to plot_mesh_polygon or plot_mesh_dotcloud
  • register_volume3d (SyN mode) re-implemented from the ANTs paper in pure Rcpp/RcppEigen; no longer depends on RNiftyReg or any external registration library
  • register_volume3d gains a points argument to additionally warp a matrix of anatomical coordinates (e.g. cortical surface vertices) through the estimated transform, enabling direct cortical mapping without a separate resampling step
  • Exported apply_transform3d to apply a previously estimated rigid, affine, or SyN transform to a new 3D volume
  • register_volume3d now returns an object of class ravetools_register_volume3d (carrying the grid geometry and a vox2ras attribute on each deformation field) with a print method
  • Added write_ants_transform/read_ants_transform to read and write the linear transform as an ITK affine .mat file (a MATLAB level-4 binary in LPS convention) compatible with antsApplyTransforms; implemented in base R with no new dependency
  • Added write_ants_warp/read_ants_warp to read and write the deformation field as an ANTs 5-D warp NIfTI (LPS displacement vectors, vector intent code) via the suggested freesurferformats package; the RAS affine can optionally be hidden in the header text fields for single-file recovery
  • Added ras_lps_conjugate to convert a 4x4 transform between the RAS and LPS conventions
  • Added save_registration/load_registration to write a registration result to (or read it from) ANTs-style files plus a dependency-free manifest

ravetools 0.2.6

CRAN release: 2026-05-31

  • Added plot_mesh_dotcloud for rendering one or more mesh3d objects as an orthographic rim-lit dot cloud in base R (no rgl dependency); supports per-vertex colors, depth-gradient palettes, per-mesh alpha, side filtering, and painter’s-algorithm depth sorting across multiple meshes
  • Added plot_mesh_polygon for rendering one or more mesh3d objects as flat-shaded Lambert-lit triangles in base R; point-cloud meshes (no face matrix) are automatically substituted by small sphere instances; supports camera-facing clipping (mesh_clipping), side filtering, per-mesh alpha blending, and configurable shadow_color, light_intensity, and ambient_intensity
  • plot_mesh_dotcloud and plot_mesh_polygon gain a clipping_plane argument (a 4-element numeric normal-and-offset vector, or a list of such vectors) to discard geometry on one side of arbitrary planes before rendering, and a per-mesh clipping_plane_enabled logical toggle to opt individual meshes in or out of clipping
  • Exported ensure_mesh3d for coercing various surface formats (mesh3d, ieegio_surface, fs.surface, surf.asc) to a canonical mesh3d object; previously internal-only
  • Fixed freqz2 plot legend: the cutoff legend used the raw cutoffs argument (and could index past the color palette, yielding NA colors) when a requested cutoff did not actually intersect the magnitude curve; the legend now only lists cutoffs that are drawn, and labels the unit as dB instead of the filter’s frequency unit

ravetools 0.2.5

CRAN release: 2026-05-23

  • morlet_wavelet gains a segment_length argument (default NULL) that processes long signals (e.g. multi-hour recordings) in overlapping segments using batched mvfftw_c2c convolutions, dramatically reducing peak memory and FFT cost while preserving the legacy result on the signal interior
  • baseline_array now supports seven baseline methods: "percentage", "sqrt_percentage", "decibel", "zscore", "sqrt_zscore", "db_zscore", and "subtract_mean"; newly added methods include decibel z-score normalization
  • Added spike sorting helpers for normality test, spike detection, per-channel waveform extraction, and Haar wavelet feature extraction
  • Replaced wavelets package dependency with waveslim for discrete wavelet transform used in spike sorting utilities
  • project_plane gains an n_iters argument to control the number of projection iterations (default is 5)
  • Applied lint fixes and improved code style consistency across all source files
  • Added carla implementing the Common Average Re-referencing by Least Anti-Correlation (CARLA) algorithm (see CITATION) for selecting an optimal subset of channels as the common average reference in CCEP data
  • Added crp implementing the Canonical Response Parameterization (CRP) method for characterizing single-trial evoked responses (e.g. CCEPs): estimates response duration, extracts the canonical response shape, and reports per-trial weights, SNR, and explained variance; additionally reports a canonical shape (C_full) spanning the entire loaded time range (including the baseline period), and gains an optional reverse-scan response-onset estimator (detect_onset, with an onset_search_start floor) that locates the response start time for delayed responses - even before the analysis window - while keeping the per-trial weights unchanged; non-finite time points are dropped automatically and the analysis window is clamped into the available time range
  • Exposed low-level FFTW3 wrappers (fftw_r2c, fftw_c2r, fftw_c2c, mvfftw_r2c, mvfftw_c2c, mvfftw_c2r, and their 2D/3D variants) with memory bugs fixed; these are thin bindings for advanced users requiring maximum throughput
  • Fixed design_filter_fir band-pass scaling reference frequency to use the average of the transition-band midpoints (matching MATLAB fir1/scale_filter), and fixed band-stop scaling to always normalize at DC; previously both could produce incorrect gain for asymmetric transition bands
  • filtfilt now accepts a Sos (second-order sections) object from gsignal and delegates to gsignal::filtfilt in that case
  • Added catmull_rom_3d for smooth Catmull-Rom spline interpolation through 3D point sequences, including closest-point projection from an arbitrary 3D point onto the curve
  • Fixed qfac handling in the matrix to quaternion conversion so that right-handed transforms (negative determinant) are correctly represented
  • fir1 filter computation is significantly faster via an optimized internal implementation

ravetools 0.2.4

CRAN release: 2025-09-10

  • Added a naive implementation of non-negative matrix factorization in pure R
  • Added finding and aligning stimulation pulses (for continuous stimulation)
  • Added find_peaks to provide finding peaks along a trace of signal

ravetools 0.2.3

CRAN release: 2025-07-22

  • Added gammatone_fast filters to obtain the audio envelope at different frequencies
  • Added vcg_subset_certex to subset mesh
  • Added vcg_subdivision to up-sample mesh
  • Added plane-generating function to create mesh for plane

ravetools 0.2.2

CRAN release: 2025-03-05

  • Fixed clang20 warning and removed problematic vcglib code that use pointers after free.

ravetools 0.2.1

CRAN release: 2025-01-24

  • Using std::nearbyint instead std::round to round numbers to comply to IEC-60559 standard that half numbers round to nearest even integers
  • Implemented low-level 3D volume sampling in C++: resample_3d_volume
  • Exported gsignal::resample (however, some edits might be needed in the future to produce the same results as Matlab)
  • Supported converting ieegio surface geometries to mesh3d to be used in VCG related functions
  • Added K-D tree search to find closest points among two point clouds

ravetools 0.2.0

CRAN release: 2024-12-16

  • Added vcg_raycaster to find intersection of rays and given mesh object.

ravetools 0.1.9

CRAN release: 2024-11-08

  • Hot fix by adding vctrs to Suggests to fix the issue that fails the unit test due to an update in testthat package.

ravetools 0.1.8

CRAN release: 2024-09-03

  • design_filter ensures frequency window cuts off within 0 to Nyquist
  • fftfilt allows matrix input
  • filtfilt with a=1 (FIR filter) calls fftfilt to speed up
  • Fixed pwelch incorrect power calculation. The results agrees mostly with Matlab function
  • Using hamming window as the default in pwelch; exported additional window options such as blackman families, bohmanwin, flattopwin, and hanning

ravetools 0.1.7

CRAN release: 2024-07-17

  • Fixed a c++ template issue caused by vcglib, which fails to compile under clang19
  • decimate agrees with Matlab now (both fir and iir filters)
  • Implemented freqz2 to obtain the frequency response of a digital filter (similar to gsignal::freqz but with more accurate cutoff frequency calculation and more customize plots)
  • Added filter diagnostic plot diagnose_filter
  • Added check_filter to obtain expected magnitude at given frequency and reciprocal condition number
  • Removed dependency signal and use gsignal instead
  • Added design_filter for both fir and iir filters, allowing both entry and intermediate users to design band-pass/stop, low/high pass filters easily.
  • The iir filter order generated from design_filter will be checked against rcond_filter_ar (reciprocal condition number) to make improve the numeric stability
  • Fixed (hopefully) memory issues caused by dijkstra; the package passed asan, valgrind test provided by rhub2

ravetools 0.1.6

CRAN release: 2024-06-02

  • Fixed dijkstra method occasionally causing memory error. New method is much faster now.
  • Fixed plot.pwelch not displaying the signal names correctly.
  • Removed c++17 requirement and supports 11, 14, and 17 standards

ravetools 0.1.5

CRAN release: 2024-05-19

  • Fixed FIR1 filter
  • Fixed pwelch throwing warnings when signal is zero (or zero power)
  • Updated authorship

ravetools 0.1.4

  • Implemented dijkstra to find shortest paths in mesh
  • Migrated and incorporated vcglib
  • Fixed a C++ template issue via type explicit calls
  • Fixed fir1 filter when band-passing signals with incorrect n
  • pwelch plot works with zero power now; mv_pwelch plot error fixed

ravetools 0.1.3

CRAN release: 2023-12-04

  • Rewrote band_pass2 to avoid NA generated when upper band frequency is Nyquist
  • Added Vector3, Matrix4, Quaternion for in-place calculation
  • Added support for WASM
  • Fixed issues reported by CRAN: “format string is not a string literal (potentially insecure)”

ravetools 0.1.2

CRAN release: 2023-07-16

  • Compatible with the latest filearray
  • Exported grow_volume
  • mesh_from_volume no longer throw errors if the mesh does not form a manifold

ravetools 0.1.1

CRAN release: 2023-04-19

  • Fixed a precision issue that caused test failure on some machine

ravetools 0.1.0

CRAN release: 2023-02-18

  • Added fill_surface to fill in volume based on given surface mesh
  • Added mesh_from_volume to generate mesh from volume. This function can be used together with fill_surface to generate surface envelope
  • Added register_volume to align two imaging data using linear or non-linear registration
  • Added fftw on 2D image and 3D volume data
  • Added convolution for 1D, 2D, 3D data using FFT

ravetools 0.0.9

CRAN release: 2023-01-20

  • Fixed pwelch frequency not starting from zero issue
  • Upgraded TinyThread using the latest pull-request to RcppParallel

ravetools 0.0.8

CRAN release: 2022-10-14

  • Added interpolate_stimulation to detect stimulation signals within the response and interpolate with smooth signals
  • The package now imports splines
  • Added fast_quantile and fast_mvquantile to improve the quantile/median calculation speed
  • Fixed the plot_signals plotting range too large when signals have large values (such as stimulation)
  • Fixed TinyThreads library memory leak issues
  • Simplified diagnose_channel, avoid duplicated pwelch calculation

ravetools 0.0.7

CRAN release: 2022-09-19

  • Added signal filter, filtfilt that produce the same results as Matlab (with precision error)
  • Added two ways to perform band-pass filters
  • Allows multiple channels through pwelch as a row-major matrix to speed up calculation
  • Added wavelet_cycles_suggest to provide default calculation of wavelet cycles
  • Added internal argument signature to wavelet to resolve potential cache conflicts when running in multiple processes. (This allows RAVE to run wavelet on multiple subjects at the same time)

ravetools 0.0.6

CRAN release: 2022-08-25

  • Added decibel average in pwelch
  • Allowed pwelch sampling frequency to be greater than the signal length
  • Adjusted parameters diagnostic plot and pwelch plot to properly handle graph text, margin, axis
  • Added plot_signals to plot multiple functional data within the same canvas

ravetools 0.0.5

CRAN release: 2022-08-06

  • Exposed C++ code to inst/includes so other users can dynamically link to the functions (https://github.com/dipterix/ravetools/issues/5)
  • Removed confusing in-place arguments in the fftw related code
  • Corrected fftw plans to respect the flags
  • Added C++ to convert raw binary bytes to uint, int, float, and string

ravetools 0.0.4

CRAN release: 2022-05-29

Parallel processes might use different temporary directory paths. To improve the performance, it is recommended to set a shared temporary directory, hence this version

  • Allows temporary directories to be set via environment variable RAVETOOLS_TEMPDIR or option ravetools.tempdir.

ravetools 0.0.3

CRAN release: 2022-02-16

This version fixes a memory issue reported by CRAN check (gcc-UBSAN).

  • There is a potential integer overflow where NA_INTEGER is subtracted by one before being converted to R_xlen_t type. This update fixes this issue
  • Removed RcppParallel and copied part of it into inst/include folder, with TBB removed under the GPL-3 license framework.

ravetools 0.0.2

CRAN release: 2022-02-14

This is an initial version of ravetools. Although a bare minimal set of signal processing functions are provided, it is sufficient to perform preprocess pipelines on most iEEG signals. Some functions are added from the dipsaus package, with considerable performance improvement. The C++ functions have been tested on all major platforms, with different architectures (ARM, i386, x64).

Documentation

  • Added README file to demonstrate basic usage
  • Added a NEWS.md file to track changes to the package.

Signal processing functions

  • Re-implemented decimate with FIR filters creating the same results as in Matlab
  • Added detrend function to
  • Added diagnose_channel to visually inspect channel signals
  • Added morlet_wavelet to enable fast and memory efficient wavelet decomposition; the result agrees with existing Matlab code with floating errors (10^-7)
  • Added multitaper
  • Added pwelch (Welch periodogram)
  • Added notch_filter to remove line noise

High-performance functions

The following functions are implemented in C++ parallel. They tend to be faster than normal base-R implementations, depending on the number of CPU cores used.

  • Added collapse to collapse arrays
  • Added shift_array to shift array along certain indices
  • Added fast_cov to calculate pearson covariance matrix in parallel
  • Added baseline_array to calculate baseline arrays with multiple margins