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Changelog

Source: NEWS.md

ravetools 0.2.4

  • 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