JLAB_ALLHELP Displays the help comments for all JLAB modules. 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. __________________________________________________________________ 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. matmult - Matrix multiplication for arrays of matrices. 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. hermpoly - Hermite polynomials. [with F. Rekibi] hermfun - 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. __________________________________________________________________ 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. __________________________________________________________________ jFigures: A low-level directory containing routines for example figures. __________________________________________________________________ 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. __________________________________________________________________ jMap: Mapping scattered data using local polynomial fitting polysmooth - Smoothing scattered 2D data with local polynomial fitting. spheresort - Sorted great circle distances to nearby points on the earth. twodsort - Distances from data points to nearby grid points. Low level functions matinv - Fast inversion of arrays of small matrices. __________________________________________________________________ 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] makefigs_matern - Makes all figures for Lilly et al. 2017. 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. __________________________________________________________________ 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. __________________________________________________________________ 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. __________________________________________________________________ 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 __________________________________________________________________ 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 slidetrans - Sliding-window ('moving-window') Fourier transform. 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. __________________________________________________________________ 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. __________________________________________________________________ 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. __________________________________________________________________ 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. __________________________________________________________________ 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. __________________________________________________________________ This is part of JLAB --- type 'help jlab' for more information (C) 2015--2021 J.M. Lilly --- type 'help jlab_license' for details