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jlab_allhelp.m
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function[varargout]=jlab_allhelp(varargin)
% 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.
% 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.
% __________________________________________________________________
%
% 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.
% __________________________________________________________________
%
% 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.
% __________________________________________________________________
%
% 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.
% __________________________________________________________________
%
% 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.
% __________________________________________________________________
%
% 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).
% __________________________________________________________________
%
% 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
% 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--2024 J.M. Lilly --- type 'help jlab_license' for details
if nargin==0
help jlab_allhelp
else
if strcmpi(varargin{1},'--create')
jlab_allhelp_create;
return
end
end
function[]=jlab_allhelp_create
jlab_path=findpath('jlab');
dirlist=dir(jlab_path);
xx=[];
newlinestr=[ ' __________________________________________________________________' char(13) char(13)];
for i=1:length(dirlist)
if dirlist(i).isdir
if ~strcmpi(dirlist(i).name(1),'.')
if ~strcmpi(dirlist(i).name,'doc')&&~strcmpi(dirlist(i).name,'html')&&~strcmpi(dirlist(i).name,'figures')
eval(['xx=[xx help(''' dirlist(i).name ''') newlinestr];'])
end
end
end
end
xx=real(xx);
xx(xx==10)=nan;
xx(xx==13)=nan;
xx=xx';
xx=col2mat(xx);
xx(4:end+3,:)=xx;
xx(1,:)=10;
xx(2,:)=real('%');
xx(3,:)=real(' ');
xx=setstr(mat2col(xx))';
xx=xx(1:end-3);
disp(xx)