jCell: Tools for operating on cell arrays of column vectors
Basic mathematical operations
cellabs - Absolute value of each element in a cell array.
cellmax - Maximum of each element in a cell array.
cellmin - Minimum of each element in a cell array.
cellsum - Sum of each element a cell array, possibly weighted.
cellmean - Mean value of each element a cell array, possibly weighted.
cellstd - Standard deviation of each element a cell array, possibly weighted.
cellmed - Median value of each element a cell array.
cellreal - Real part of each element in a cell array.
cellimag - Imaginary part of each element in a cell array.
cellpair - Complex pairing for elements in a cell array.
celllog10 - Base ten logarithm of each element in a cell array.
celladd - Addition acting on each element in a cell array.
cellmult - Multiplication acting on each element in a cell array.
celldiv - Division acting on each element in a cell array.
celldot - Dot product for arrays of column vectors.
Reshaping, indexing, and sizes
cell2col - Converts cell arrays of numeric arrays into 'column-appended' form.
col2cell - Converts 'column-appended' data into cell arrays of numeric arrays.
cellindex - Applies a cell array of indices to a cell array of column vectors.
cellchunk - Converts cell array data into uniform length 'chunks'.
cellength - Length of each element in a cell array.
cellsize - Size of each element in a cell array along specified dimension.
cellget - Indexes a cell array of numerical arrays by ID number.
cellimit - Limits the ranges of times in a cell array of numerical arrays.
Data processing
cellstrip - Strips INF values from the beginnings or ends of cell arrays.
cellsplit - Splits cell arrays of numeric arrays at data gaps.
cellprune - Removes all empty cells, or cells less than a specified length.
cellpack - Removes all INF values from cell arrays of numeric arrays.
cellfill - Fills missing data marked by INFs in a cell array.
cellgrid - Interpolate a cell array of numeric arrays onto a regular grid.
cellfirst - Returns the first element of each entry in a cell array.
Plotting
cellplot - Rapidly plot all element of a cell array of numeric arrays.
See also jVarfun.
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jCommon: Useful general-purpose functions, common to other JLAB modules
Array functions
aresame - Test whether two N-D arrays are the same.
arrayify - Converts a set of scalars or arrays into column arrays.
blocklen - Counts the lengths of 'blocks' in an array.
blocknum - Numbers the contiguous blocks of an array.
lnsd - Last non-singleton dimension of an array.
nonnan - Return all non-NAN elements of an array.
vectmult - Matrix multiplication for arrays of vectors.
File and directory tools
ncload - Load all variables from a NetCDF file and unpack any columns.
commentlines - Returns the comment lines from m-files.
findfiles - Returns all files in a directory with a specified extension.
findpath - Returns the full pathname of a directory on the Matlab search path.
jhelp - Opens linked JLAB help files in Matlab's internal web browser.
whichdir - Returns directory name containing file in search path.
standalone - Create stand-alone version of an m-file, including dependencies.
Mathematical aliases
choose - Binomial coefficient: CHOOSE(N,K) = N!K!/(N-K)!
frac - Fraction: FRAC(A,B)=A./B
imlog - Imaginary part of log: IMLOG(X)=UNWRAP(IMAG(LOG(X)))
iseven - True for even integer values; false otherwise.
isodd - True for odd integer values; false otherwise.
oprod - Outer product: OPROD(X,Y)=X*CONJ(Y')
res - Residual after flooring: RES(X)=X-FLOOR(X)
rot - Complex-valued rotation: ROT(X)=EXP(SQRT(-1)*X)
squared - Squares the modulus of its argument: SQUARED(X)=ABS(X).^2
Matrices, polynomials, and special functions
jmat2 - 2x2 rotation matrix through specified angle.
jmat3 - 3x3 rotation matrix through specified angle.
tmat - 2x2 complex grouping matrix. TMAT = [1 i; 1 -i] / SQRT(2)
bellpoly - Complete Bell polynomials.
jhermpoly - Hermite polynomials. [with F. Rekibi]
jhermfun - Orthonormal Hermite functions. [with F. Rekibi]
chisquared - The chi-squared distribution.
Dataset organization as structures
make - Create a structure containing named variables as fields.
matsave - Create and save structure of variables as a mat-file.
use - Copies structure fields into named variables in workspace.
catstruct - Concatenates the array elements of a cell array of structures.
structindex - Applies an index to all array-valued fields in a structure.
Statistics
cum2mom - Convert cumulants to moments.
mom2cum - Convert moments to cumulants.
pdfprops - Mean and variance associated with a probability distribution.
simplepdf - Gaussian, uniform, Cauchy, and exponential pdfs.
Filling bad data points
fillbad - Linearly interpolate over bad data points.
Date, time, and units
yearfrac - Converts a DATENUM into 'year.fraction' and 'month.fraction'.
cms2kmd - Converts centimeters per second to kilometers per day.
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jData: Routines for generating oceanographic datasets
make_goldaltimetry - Create a synthetic altimeter dataset and gridded statistics.
make_goldocean - Create quarter-degree gridded files from GOLD simulations.
make_betaeddyone - Create the BetaEddyOne nonlinear QG eddy simulation.
make_gomed - Create a drifter-derived eddy database for the Gulf of Mexico.
make_gulfdrifters - Create a drifter dataset for the Gulf of Mexico.
make_gulfflow - Create a gridded velocity dataset for the Gulf of Mexico.
make_jason - Create a reformatted version of the Beckley altimeter dataset.
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jEllipse: Analysis of modulated elliptical, or bivariate, signals
Elliptical signal properties
ellband - Bandwidth of modulated elliptical signals in two or three dimensions.
ellparams - Ellipse parameters of a modulated bivariate or trivariate oscillation.
ellvel - Average and instantaneous ellipse velocities.
ellrad - Average and instantaneous ellipse radius.
ellpol - Polarization parameters of an elliptical signal.
Elliptical signal generation and conversions
ellsig - Creates a modulated elliptical signal in two or three dimensions.
sig2latlon - Converts an oscillatory signal to lat/lon displacements.
elldiff - Differentiation of modulated elliptical signals.
Plotting tools
ellcurves - Returns curves corresponding to specified ellipse properties.
ellipseplot - Plot ellipses.
Basic ellipse properties
ab2kl - Converts A and B to ellipse parameters Kappa and Lambda.
kl2ab - Converts ellipse parameters Kappa and Lambda to A and B.
ecconv - Converts between eccentricity measures.
ellrossby - Ellipse Rossby number, for oceanographic applications.
See also jRidges, jSpectral, jWavelet.
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jFigures: A low-level directory containing routines for example figures.
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jGraph: Plotting tools and refinements for making high-quality figures
High-level graphical post-processing
fixlabels - Specify precision of axes labels.
fontsize - Rapidly set title, axes, label, and text fontsizes.
letterlabels - For automatically putting letter labels on subplots.
linecolor - Set line colors based on a property value within a colormap.
linestyle - Rapidly set color, style, and width properties of lines.
linering - Moves lines through the current line style order.
packfig - Squeeze together rows and/or columns of the current figure.
Oceanography-specific plotting tools
hodograph - Generate hodograph plots (simple and fancy).
provec - Generate progressive vector diagrams (simple and fancy).
stickvect - Plots "stick vectors" for multicomponent velocity time series.
[See also CELLPLOT, REGIONPLOT, TOPOPLOT]
Modified plotting functions
discretecolorbar - Plots a colorbar with discrete variation.
jpcolor - Modified version of PCOLOR appropriate for cell-centered grids.
patchcontourf - Generate filled contours using patches, with specified colors.
uvplot - Plots the real and imaginary parts of a signal on the same axis.
Figure tweaking
jfig - Shorthand for tweaking figures.
dlines - Add diagonal lines to a plot.
hlines - Add horizontal lines to a plot.
vlines - Add vertical lines to a plot.
nocontours - Removes contours from a CONTOURF plot.
noxlabels - Remove some or all x-axis tick mark labels.
noylabels - Remove some or all y-axis tick mark labels.
xoffset - Offsets lines in the x-direction after plotting.
yoffset - Offsets lines in the y-direction after plotting.
xtick - Sets locations of x-axis tick marks.
ytick - Sets locations of y-axis tick marks.
ztick - Sets locations of z-axis tick marks.
Color and colormaps
colorquant - Sets the color axis according to quantiles of the data.
lansey - The Lansey modification of Cynthia Brewer's "Spectral" colormap.
haxby - The Haxby colormap.
seminfhaxby - The seminf-Haxby colormap.
Printing
jprint - Print to a specified directory and crop the resulting file.
printall - Print and close all open figures.
Graphics aliases
boxoff - Sets 'box' property to 'off'.
boxon - Sets 'box' property to 'on'.
flipmap - Flips the current colormap upside-down.
flipx - Flips the direction of the x-axis
flipy - Flips the direction of the y-axis
inticks - Sets the 'tickdir' property of the current axis to 'in'.
outticks - Sets the 'tickdir' property of the current axis to 'out'.
xlin - Sets x-axis scale to linear.
xlog - Sets x-axis scale to logarithm.
ylin - Sets y-axis scale to linear.
ylog - Sets y-axis scale to log.
Low-level or specialized functions
axeshandles - Returns handles to all axes children.
crop - Gets rid of whitespace around an image. [by A. Bliss]
linehandles - Finds all line and patch handles from a given set of axes.
linestyleparse - Parses the input string to LINESTYLE.
gulf4plot - A four-panel circulation plot for the Gulf of Mexico.
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jMatern: Parametric spectral analysis based on the Matern process
Top-level functions
maternspec - Fourier spectrum of the Matern random process and variations.
materncov - Autocovariance of the Matern random process and variations.
maternimp - Impulse response function for the Matern random process.
maternoise - Realizations of the Matern process and variations, including fBm. [with A. Sykulski]
maternfit - Parametric spectral fit to the Matern form. [with A. Sykulski]
Other utilities
blurspec - Returns the blurred and aliased spectrum given the autocovariance.
fminsearchbnd - FMINSEARCH, but with bound constraints by transformation. [By J. D'Errico]
Low-level Matern functions
materncfun - Returns the normalization or C-function for a Matern process.
maternchol - Cholesky decomposition of Matern and fBm covariances. [with A. Sykulski]
maternedge - Long-time cutoff edge for the Matern impulse response function.
See also jSpectral, makefigs_matern.
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jMatfiles: Descriptions of included mat-files, mostly for testing and examples.
bravo94 - Labrador Sea mooring data from Lilly et. al (1999).
drifterbetty - Two-hour resolution drifter trajectory, AOML GDP id #44000.
ebasnfloats - "Meddy" float data analyzed in Lilly and Olhede (2009,10,11,12).
goldsnapshot - Snapshot from GOLD model, courtesy of Harper Simmons.
labseatpjaos - Altimeter data for the Labrador Sea, analyzed in Lilly (2017).
m1244 - The M1244 mooring from the Labrador Sea boundary current.
npg2006 - Float data analyzed in Lilly and Gascard (2006).
qgsnapshot - Snapshot of f-plane QG turbulence from a simulation by J. Early.
slasnapshot - Snapshot of AVISO 1/4 degree sea level anomaly on Jan. 1, 2007.
solomon - Solomon Islands Earthquake data analyzed in Lilly (2011).
vortex - QG model of a barotropic jet on a beta plane, by R. K. Scott.
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jOceans: Oceanography-specific data and model analysis tools
Conversions for Lagrangian trajectories
latlon2uv - Converts latitude and longitude to horizontal velocity.
uv2latlon - Integrates horizontal velocity to give latitude and longitude.
Manipulating Lagrangian trajectories [see also jCell]
trajextract - Extracts Lagrangian trajectory segments within given region.
trajunwrap - Unwraps Lagrangian trajectories from a periodic domain.
trajwrap - Wraps Lagrangian trajectories to fit within a periodic domain.
trajchunk - Chunks Lagrangian trajectories based on the Coriolis period.
griddrifters - Average drifter velocities onto a space/time 3D grid.
Idealized numerical model tools
psi2fields - Velocity and other fields from the streamfunction. [with P.E. Isachsen]
periodize - Returns a doubly periodic version of an input array.
Lagrangian eddy identification and analysis
eddyridges - Coherent eddy ridges from Lagrangian trajectories.
noisedrifters - Create a noise Lagrangian dataset matching mean and variance.
eddylevels - Eddy ridge significance levels using the survival function.
Eulerian eddy identification and analysis
inellipse - Locates points on the interior of ellipses.
closedcurves - Locate and interpolate closed curves in a possibly periodic domain.
curvemoments - Centroid, area, and many other moments of a closed curve.
divgeom - Geometric decomposition of eddy vorticity flux divergence.
eddyfit2d - Least squares fit of 2D velocity data to an eddy profile.
simpleddy - Streamfunction, velocity, and vorticity for various eddy profiles.
Plotting tools for mooring data
hodograph - Generate hodograph plots (simple and fancy).
provec - Generate progressive vector diagrams (simple and fancy).
stickvect - Plots "stick vectors" for multicomponent velocity time series.
Alongtrack altimetry tools
trackextract - Extracts alongtrack altimetry segments within given region.
Wind-driven surface currents
windtrans - Ekman-like transfer-functions for the wind-driven response.
NetCDF tools
ncinterp - One-line interpolation from 3D lat/lon/time field in NetCDF file.
Date and time
monthstats - Mean month and standard deviation using circular statistics.
Topography tools and data
jtopo.mat - One-sixth degree global topography, from Smith and Sandwell + IBCAO.
topoplot - Plot regional or global topography at one-sixth degree resolution.
Low-level functions
besselktilde - K-type Bessel function after factoring off exponential decay.
besselitilde - I-type Bessel function after factoring off exponential growth.
curveinterp - Interpolate a field or its gradient onto a set of curves.
orbitbreaks - Separate orbit into passes based on turning points.
topo_copyright - Copyright statement for the Smith and Sandwell topography.
See also jData.
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jPapers: Routines for generating figures from published papers.
makefigs_stokes - Make figures for Lilly et al. (2024).
makefigs_gulfcensus - Make figures for Lilly and Perez-Brunius (2021b).
makefigs_gulfdrifters - Make figures for Lilly and Perez-Brunius (2021a).
makefigs_transfer - Make figures for Lilly and Elipot (2021).
makefigs_kinematics - Make figures for Lilly (2018).
makefigs_matern - Make figures for Lilly et al. (2017).
makefigs_element - Make figures for Lilly (2017).
makefigs_superfamily - Make figures for Lilly and Olhede (2012b).
makefigs_multivariate - Make figures for Lilly and Olhede (2012a).
makefigs_ridges - Make figures for Lilly, Scott, and Olhede (2011).
makefigs_trivariate - Make figures for Lilly (2011).
makefigs_analytic - Make figures for Lilly and Olhede (2010b).
makefigs_bandwidth - Make figures for Lilly and Olhede (2010a).
makefigs_asilomar - Make figures for Lilly and Olhede (2009b).
makefigs_morsies - Make figures for Lilly and Olhede (2009a).
makefigs_vortex - Make figures for Lilly and Gascard (2006).
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jRidges: Wavelet ridge analysis of modulated oscillatory signals
Top-level functions
ridgewalk - Extract wavelet transform ridges, including bias estimates.
ridgemap - Maps ridge quantities back onto the time series.
instmom - Univariate and multivariate instantaneous moments.
Ridge utilities
ridgetrim - Trim edge effect regions from wavelet ridges.
ridgelen - Wavelet ridge length expressed as number of full cycles.
periodindex - Returns time index in increments of instantaneous period.
ridgemult - Ridge multiplicity, the number of simultaneous ridges present.
See also jEllipse, jWavelet, jOceans
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jSpectral: Multitaper spectral analysis, and other time series tools
Multitaper spectral analysis
sleptap - Calculate Slepian tapers.
mspec - Multitaper power and cross spectra.
mconf - Confidence intervals for the multitaper spectral estimate.
Multitaper polarization analysis
msvd - Singular value decomposition for polarization analysis.
polparams - Spectral matrix polarization parameters.
specdiag - Diagonalize a 2 x 2 spectral matrix.
Assorted other transforms
anatrans - Analytic part of signal.
wigdist - Wigner distribution (alias-free algorithm).
Time series analysis utilities
doublen - Interpolates a time series to double its length.
fourier - The one-sided Fourier frequencies for a given length time series.
sampletimes - Computes mean sampling intervals and their statistics.
Plotting tools
twospecplot - Plots a pair of rotary or Cartesian spectra.
See also jWavelet, jEllipse, jMatern.
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jSphere: Tools for latitude, longitude, and spherical geometry
Simple lat / lon conversions
deg180 - Converts degrees to the range [-180,180].
deg360 - Converts degrees to the range [0, 360].
degunwrap - Unwraps arrays given in degrees.
jdeg2rad - Converts degrees to radians.
jrad2deg - Converts radians to degrees.
Distances and regions
inregion - Tests whether lat/lon points lie within a specified box.
spheredist - Computes great circle distances on a sphere.
Earth constants and frequencies
radearth - The radius of the earth in kilometers.
corfreq - Coriolis frequency in radians per hour.
tidefreq - Frequencies of the eight major tidal components.
Coordinate transformations
latlon2xy - Converts latitude and longitude into tangent plane coordinates.
latlon2xyz - Converts latitude and longitude into 3D Cartesian coordinates.
xy2latlon - Converts tangent plane coordinates into latitude and longitude.
xyz2latlon - Converts 3D Cartesian coordinates into latitude and longitude.
sphere2uvw - Converts a 3D spherical vector to a 3D Cartesian vector.
Differential operators
spherecurl - Curl of a vector field on the surface of a sphere.
spherediv - Divergence of a vector field on the surface of a sphere.
spheregrad - Gradient of a field on the surface of a sphere.
spherelap - Laplacian of a field on the surface of a sphere.
Interpolation
interplatlon - Interpolation for working with latitude and longitude.
sphereinterp - Fast linear interpolation on the sphere from non-plaid grids.
Plotting tools
latratio - Set plot aspect ratio for latitude / longitude plot.
lonshift - Shifts longitude origin for plotting purposes.
regionplot - Plots a simple box indicating a latitude / longitude region.
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jStats: Fast statistical analysis of large datasets in two dimensions
twodhist - Two-dimensional histogram.
twodstats - Mean, variance, and covariance of functions of two variables.
twodmed - Median value of a function of two variables.
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jVarfun: Perform common operations on multiple variables simultaneously.
Sizes and statistics
vsize - Returns the sizes of multiple arguments.
vmean - Mean over non-NaN elements along a specified dimension.
vrms - Root-mean-square of non-NaN elements along a specified dimension.
vsum - Sum over non-NaN elements along a specified dimension.
vstd - Standard deviation over non-NaN elements along a specfied dimension.
vmoment - Central moment over non-NaN elements along a specfied dimension.
vmedian - Median over finite elements along a specified dimension.
Reshaping, shifting, swapping
vcolon - Condenses its arguments, like X(:).
vshift - Cycles the elements of an array along a specified dimension.
vsqueeze - Squeezes multiple input arguments simultaneously.
vrep - Replicates an array along a specified dimension.
vswap - VSWAP(X,A,B) replaces A with B in numeric array X.
vtranspose - Transpose multiple input arguments simultaneously.
Initializing
vzeros - Initializes multiple variables to arrays of zeros or nans.
vempty - Initializes multiple variables to empty sets or empty cell arrays.
Operations and indexing
vfilt - Filtering along rows without change in length.
vdiff - Length-preserving first central difference.
vindex - Indexes an N-D array along a specified dimension.
vindexinto - Indexes into N-D array along a specified dimension.
Reshaping dataset composed of irregular length segments
col2mat - Expands 'column-appended' data into a matrix.
colbreaks - Insert NANs into discontinuties in a vector.
mat2col - Compress NAN-padded matrix data into long columns.
Low-level functions
jhanning - Hanning window.
See also jCell.
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jWavelet: Continuous wavelet analysis using generalized Morse wavelets
Top-level wavelet transform functions
wavetrans - Continuous wavelet transform.
morsewave - Generalized Morse wavelets of Olhede and Walden (2002).
morsespace - Logarithmically-spaced frequencies for generalized Morse wavelets.
wavespecplot - Plot of wavelet spectra together with time series.
spheretrans - Wavelet transform for oscillations on the surface of a sphere.
Details of generalized Morse wavelets
morsearea - Time-frequency concentration area of Morse wavelets. [with F. Rekibi]
morsebox - Heisenberg time-frequency box for generalized Morse wavelets.
morsefreq - Frequency measures for generalized Morse wavelets. [with F. Rekibi]
morseprops - Properties of the demodulated generalized Morse wavelets.
morsexpand - Generalized Morse wavelets via time-domain Taylor series.
morsederiv - Frequency-domain derivatives of generalized Morse wavelets.
Element analysis using generalized Morse wavelets
transmax - Locates modulus maximum points of wavelet transform.
transmaxdist - Distributions of wavelet transform maxima in noise.
morseregion - Generalized Morse wavelet time-frequency concentration region.
isomax - Returns those transform maxima that are isolated from others.
maxprops - Returns properties of wavelet transform maxima.
max2eddy - Converts transform maxima into oceanic coherent eddy properties.
Low-level functions
morseafun - Returns the generalized Morse wavelet amplitude or a-function.
morsehigh - High-frequency cutoff of the generalized Morse wavelets.
morseproj - Projection coefficient for two generalized Morse wavelets.
morsemom - Frequency-domain moments of generalized Morse wavelets.
jdawson - The Dawson function. [By P.J. Acklam]
Morlet wavelet
morlwave - Morlet wavelet.
morlfreq - Compute Morlet wavelet carrier frequency given peak frequency.
See also jRidges, jSpectral, jEllipse.
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This is part of JLAB --- type 'help jlab' for more information
(C) 2015--2024 J.M. Lilly --- type 'help jlab_license' for details