Package: ravetools 0.2.6.10

Zhengjia Wang

ravetools: Signal and Image Processing Toolbox for Analyzing Intracranial Electroencephalography Data

Implemented fast and memory-efficient Notch-filter, Welch-periodogram, discrete wavelet spectrogram for minutes of high-resolution signals, fast 3D convolution, image registration, 3D mesh manipulation; providing fundamental toolbox for intracranial Electroencephalography (iEEG) pipelines. Documentation and examples about 'RAVE' project are provided at <https://rave.wiki>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for details.

Authors:Zhengjia Wang [aut, cre], John Magnotti [aut], Michael Beauchamp [aut], Trustees of the University of Pennsylvania [cph], Karim Rahim [cph, ctb], Thomas Possidente [cph, ctb], Michael Prerau [cph, ctb], Marcus Geelnard [ctb, cph], Stefan Schlager [ctb, cph], Visual Computing Lab, ISTI [ctb, cph]

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manual.pdf |manual.html✨
card.svg |card.png
ravetools/json (API)
NEWS

# Install 'ravetools' in R:
install.packages('ravetools', repos = c('https://rave-ieeg.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dipterix/ravetools/issues

Pkgdown/docs site:https://dipterix.org

Uses libs:
  • fftw3– Library for computing Fast Fourier Transforms
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

fftw3cpp

5.43 score 3 stars 2 packages 25 scripts 894 downloads 145 exports 14 dependencies

Last updated from:8a53896ec6. Checks:13 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK261
linux-devel-x86_64OK271
source / vignettesOK280
linux-release-arm64OK263
linux-release-x86_64OK263
macos-release-arm64OK168
macos-release-x86_64OK339
macos-oldrel-arm64OK181
macos-oldrel-x86_64OK440
windows-develOK343
windows-releaseOK347
windows-oldrelOK317
wasm-releaseOK180

Exports:apply_transform3das_matrix4as_quaternionas_vector3band_pass1band_pass2baseline_arrayblackmanblackmanharrisblackmannuttallbohmanwinbuttapbutterbutter_max_orderbuttordcarlacatmull_rom_3dcheb1apcheb1ordcheb2apcheb2ordcheby1cheby2check_filtercollapsecolor_ramp_continuousconvolve_imageconvolve_signalconvolve_volumecrpdecimatedesign_filterdesign_filter_firdesign_filter_iirdetect_threadsdetrenddiagnose_channeldiagnose_filterdijkstras_surface_distanceellipellipapellipordensure_mesh3dfast_covfast_medianfast_mvmedianfast_mvquantilefast_quantilefftw_c2cfftw_c2c_2dfftw_c2c_3dfftw_c2rfftw_r2cfftw_r2c_2dfftw_r2c_3dfill_surfacefilter_signalfiltfiltfind_peaksfir1firlsflattopwinfreqz2gammatone_fastgrow_volumehamminghanninghilbertinternal_rave_functionis_not_cranload_registrationmatlab_palettemesh_from_volumemorlet_waveletmris_curvaturemris_inflatemris_make_surfacesmris_remeshmris_smoothmris_spheremultitapermultitaper_configmv_pwelchmvfftw_c2cmvfftw_c2rmvfftw_r2cnaive_nmfnew_matrix4new_quaternionnew_vector3notch_filterplane_geometryplot_mesh_dotcloudplot_mesh_polygonplot_signalsproject_planepwelchravetools_threadsraw_to_floatraw_to_int16raw_to_int32raw_to_int64raw_to_int8raw_to_stringraw_to_uint16raw_to_uint32raw_to_uint8rcond_filter_arread_ants_transformread_ants_warpregister_volumeregister_volume3dresampleresample_3d_volumergl_callrgl_plot_normalsrgl_viewsave_registrationshift_arraystimpulse_alignstimpulse_extractstimpulse_findstimpulse_interpolatesurface_pathvcg_average_edge_lengthvcg_count_edge_defectsvcg_fix_defectsvcg_isosurfacevcg_kdtree_nearestvcg_max_edge_lengthvcg_mesh_patchvcg_mesh_volumevcg_raycastervcg_smooth_explicitvcg_smooth_implicitvcg_spherevcg_subdivide_max_edge_lengthvcg_subdivisionvcg_subset_vertexvcg_uniform_remeshvcg_update_normalswavelet_cycles_suggestwavelet_kernelswrite_ants_transformwrite_ants_warp

Dependencies:BHdigestfastmapfilearraygsignalmultitaperpracmaR6RcppRcppEigenRNiftiRNiftyReguuidwaveslim

Readme and manuals

Help Manual

Help pageTopics
Apply a linear RAS transform to resample a 3D volumeapply_transform3d
Band-pass signalsband_pass band_pass1 band_pass2
Calculate Contrasts of Arrays in Different Methodsbaseline_array baseline_array.array
'Butterworth' filter with maximum orderbutter_max_order
Common Average Re-referencing by Least Anti-Correlation (CARLA)carla
Catmull-Rom 3D Spline Curvecatmull_rom_3d
Check 'Arma' filtercheck_filter
Collapse arraycollapse collapse.array
Map continuous values to colorscolor_ramp_continuous
Convolution of '1D', '2D', '3D' data via 'FFT'convolve convolve_image convolve_signal convolve_volume
Canonical Response Parameterization (CRP)crp
Decimate with 'FIR' or 'IIR' filterdecimate
Design a digital filterdesign_filter
Design ''FIR'' filter using 'firls'design_filter_fir
Design an 'IIR' filterdesign_filter_iir
Remove the trend for one or more signalsdetrend
Show channel signals with diagnostic plotsdiagnose_channel
Diagnose digital filterdiagnose_filter
Calculate distances along a surfacedijkstras-path dijkstras_surface_distance surface_path
Coerce a surface object to a ''mesh3d'' meshensure_mesh3d
Calculate massive covariance matrix in parallelfast_cov
Compute quantilesfast_median fast_mvmedian fast_mvquantile fast_quantile
Low-level 'FFTW3' wrappersfftw-internal fftw_c2c fftw_c2c_2d fftw_c2c_3d fftw_c2r fftw_r2c fftw_r2c_2d fftw_r2c_3d mvfftw_c2c mvfftw_c2r mvfftw_r2c
Fill a volume cube based on water-tight surfacefill_surface
Filter one-dimensional signalfilter_signal
Filter window functionsblackman blackmanharris blackmannuttall bohmanwin filter-window flattopwin hamming hanning
Forward and reverse filter a one-dimensional signalfiltfilt
Find peaks of a signalfind_peaks
Window-based 'FIR' filter designfir1
Least-squares linear-phase 'FIR' filter designfirls
Frequency response of digital filterfreqz2
Apply gamma-tone filters to obtain auditory envelopesgammatone_fast
Grow volume maskgrow_volume
Get external function from 'RAVE'internal_rave_function
Left 'Hippocampus' of 'N27-Collin' brainleft_hippocampus_mask
'Matlab' heat-map plot palettematlab_palette
Generate 3D mesh surface from volume datamesh_from_volume
Estimate per-node curvature of a surface meshmris_curvature
Inflate a cortical surface meshmris_inflate
Localize white-matter and pial surfaces from an intensity volumemris_make_surfaces
Isotropic re-triangulation of a surface meshmris_remesh
Smooth a surface meshmris_smooth
Project a surface onto a sphere and relax metric distortionmris_sphere
Compute 'multitaper' spectral densities of time-series datamultitaper multitaper_config
A naive implementation of non-negative matrix factorizationnaive_nmf
Create a 'Matrix4' instance for ''Affine'' transformas_matrix4 new_matrix4
Create a 'Quaternion' instance to store '3D' rotationas_quaternion new_quaternion
Create a 'Vector3' instance to store '3D' pointsas_vector3 new_vector3
Apply 'Notch' filternotch_filter
Set or get thread optionsdetect_threads parallel-options ravetools_threads
Create a two-dimensional plane in three dimensional spaceplane_geometry
Render one or more meshes as an orthographic dot cloud in base Rplot_mesh_dotcloud
Render one or more meshes as flat-shaded triangles in base Rplot_mesh_polygon
Plot one or more signal traces in the same figureplot_signals
Plot CRP resultsplot.ravetools_crp
Plot method for 'ravetools_curve'plot.ravetools_curve
Print method for 'ravetools_curve'print.ravetools_curve
Project plane to a surfaceproject_plane
Calculate 'Welch Periodogram'mv_pwelch plot.ravetools-pwelch print.ravetools-pwelch pwelch
Convert raw vectors to R vectorsraw-to-sexp raw_to_float raw_to_int16 raw_to_int32 raw_to_int64 raw_to_int8 raw_to_string raw_to_uint16 raw_to_uint32 raw_to_uint8
Computer reciprocal condition number of an 'Arma' filterrcond_filter_ar
Imaging registration using ''NiftyReg''register_volume
Native 3D volume registration (''rigid'', ''affine'', or ''SyN'')register_volume3d
Sample '3D' volume in the world (anatomical ''RAS'') spaceresample_3d_volume
Safe ways to call package ''rgl'' without requiring ''x11''rgl-call rgl_call rgl_plot_normals rgl_view
Save or load a registration result in 'ANTs'-compatible filesload_registration save_registration save_registration.default save_registration.ravetools_register_volume3d
Shift array by indexshift_array
Find and interpolate stimulation pulsesstimpulse_align stimpulse_extract stimpulse_find stimpulse_interpolate
Sample stimulation recordingstimulation_signal
Compute the average edge length of a triangular meshvcg_average_edge_length
Count boundary and non-manifold edges of a triangular meshvcg_count_edge_defects
Detect and repair defects in a triangular surface meshvcg_fix_defects
Create surface mesh from 3D-arrayvcg_isosurface
Find nearest 'k' pointsvcg_kdtree_nearest
Maximum edge length of a triangular meshvcg_max_edge_length
Split a mesh into two patches along a geodesic boundaryvcg_mesh_patch
Compute volume for manifold meshesvcg_mesh_volume
Cast rays to intersect with meshvcg_raycaster
Implicitly smooth a triangular meshvcg_smooth vcg_smooth_explicit vcg_smooth_implicit
Simple 3-dimensional sphere meshvcg_sphere
Selectively subdivide mesh edges that exceed a length thresholdvcg_subdivide_max_edge_length
Sub-divide (up-sample) a triangular meshvcg_subdivision
Subset mesh by vertexvcg_subset_vertex
Sample a surface mesh uniformlyvcg_uniform_remesh
Update vertex normalvcg_update_normals
'Morlet' wavelet transform (Discrete)morlet_wavelet wavelet wavelet_cycles_suggest wavelet_kernels
Read and write an 'ITK'/'ANTs' affine transformread_ants_transform write_ants_transform
Read and write an 'ANTs' deformation (warp) fieldread_ants_warp write_ants_warp