authoring-sf-programs-matlab

name	authoring-sf-programs-matlab
description	Use when authoring a Madagascar sf* main program in MATLAB.

When to use

Use this skill when a researcher already has MATLAB installed (licensed) and wants to write an sf<name> program as a .m script, leveraging existing MATLAB toolboxes (e.g. Signal Processing Toolbox, Optimization Toolbox) that would be cumbersome to replicate in C or Python.

File naming: the MATLAB main script must be named M<name>.m — same M prefix convention used by all Madagascar languages. There is no sf prefix in the source file; the installed binary is called sf<name>.

Important — compile-time requirement: the MEX backing library (rsf_create.mex*, rsf_read.mex*, etc.) is compiled at scons configure time only when MATLAB is detected on the build host. See api/matlab/SConstruct: the entire MEX build is gated on 'matlab' in env.get('API',[]). Without a licensed MATLAB on the build machine the API produces nothing and MATLAB programs cannot run.

Octave overlap: the .m extension is shared with Octave. The build system selects Matlab vs. Octave at configure time via the API variable; they are mutually exclusive at build time. For Octave programs see authoring-sf-programs-octave/SKILL.md.

Always load the shared skill alongside this one: skills/authoring-sf-programs/ — file naming, self-documentation, parameter conventions, error handling, and testing conventions that apply to every sf-program regardless of language.

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Skeleton

The canonical pattern is taken from api/matlab/test/clip.m. A MATLAB sf-program is a plain function (not a script) that receives RSF filenames as arguments:

function M<name>(in, out, param1)
%<NAME>  One-sentence synopsis (appears in sfdoc output).
%
% par1=default  description of parameter

% 1. Query dimensions of the input file.
dims = rsf_dim(in);          % returns column vector [n1; n2; ...]
n1   = dims(1);
n2   = prod(dims(2:end));

% 2. Read a named parameter from the input header.
clip = rsf_par(in, 'clip', 'f', 1.0);  % type 'f'=float, 'i'=int, 'b'=bool

% 3. Create output header, inheriting geometry from input.
rsf_create(out, in);         % copy header: rsf_create(outfile, infile)
% -- OR, specify sizes explicitly:
% rsf_create(out, [n1; n2]);

% 4. Allocate a trace-length working buffer.
trace = zeros(1, n1);

% 5. Loop over traces, reading and writing sequentially.
for i2 = 1:n2
    rsf_read(trace, in, 'same');          % read next n1 samples
    % ... process trace ...
    trace(trace >  clip) =  clip;
    trace(trace < -clip) = -clip;
    rsf_write(trace, out, 'same');        % write next n1 samples
end

The 'same' flag on rsf_read / rsf_write advances an internal file pointer so successive calls walk through the binary data sequentially — essential for loop-based trace processing.

For single-call whole-file I/O, prefer rsf_read_all / rsf_write_all (see cheat sheet below).

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API cheat sheet

All functions are MEX-compiled C entry points. nrhs = number of right-hand side (input) arguments; nlhs = number of left-hand side (output) arguments.

Function	MATLAB call	nrhs	nlhs	Notes
rsf_create	rsf_create(outfile, infile)	2	0	Create RSF header on disk; copies geometry from infile (string)
rsf_create	rsf_create(outfile, [n1;n2;...])	2	0	Create header; sizes from column vector of doubles
rsf_read	rsf_read(buf, infile)	2	0	Read numel(buf) samples from infile into pre-allocated double array buf
rsf_read	rsf_read(buf, infile, 'same')	3	0	Same, but advance internal file pointer (sequential trace loop)
rsf_read_all	[data,sz,d,o,lbl,unit] = rsf_read_all(file)	1	1–6	Read entire file; returns data array plus optional size/delta/origin/label/unit vectors
rsf_read_header	[sz,d,o,lbl,unit] = rsf_read_header(file)	1	1–5	Read header only (no data); returns size vector plus optional delta/origin/label/unit
rsf_write	rsf_write(buf, outfile)	2	0	Write double array buf to outfile (sets n1/n2/... from buf dimensions)
rsf_write	rsf_write(buf, outfile, 'same')	3	0	Append to existing binary; does not rewrite header
rsf_write_all	rsf_write_all(file, cmdargs, data)	3–7	0	Write full RSF file; cmdargs is cell array (e.g. {'out=stdout'}); optional delta/origin/label/unit row vectors
rsf_par

Type details for rsf_par: type string first character selects the branch — 'f' or 'r' → float, 'i' or 'd' → integer, 'l' or 'b' → logical. The return value is always a double scalar.

Complex data: rsf_read / rsf_write handle SF_COMPLEX files automatically when buf / data is a MATLAB complex array (mxIsComplex).

m8r MEX (m8r.c → m8r.mex*): exposes rsf_filter(cmd, data, deltas, origins, labels, units) — runs an arbitrary Madagascar binary as a filter on MATLAB data via temp files. Useful for calling existing sf* programs from within a MATLAB session.

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Build integration

The MEX binaries are built by api/matlab/SConstruct, which is invoked automatically by the top-level Madagascar scons when MATLAB is present:

# api/matlab/SConstruct (excerpt)
if 'matlab' in env.get('API',[]):
    mex = env.get('MEX')          # path to mex compiler, detected at configure time
    suffix = env.get('MEXSUFFIX') # platform suffix, e.g. .mexa64 / .mexmaci64
    if mex:
        mexcom = mex + " CC=$CC CFLAGS='$CFLAGS $_CCCOMCOM -fPIC' ..."
        for inp in Split('m8r par dim read_header read read_all write write_all create'):
            ...
            mfile = env.Command(cfile+suffix, cfile+'.c', mexcom)
            if root:
                install = env.Install(libdir, mfile)

MATLAB must be detectable by the configure step for this block to execute. If MATLAB is not installed, env.get('API',[]) will not contain 'matlab' and the entire block is skipped — no MEX files are produced and MATLAB programs will fail with "undefined function" errors at runtime.

No UserSconsTargets for MATLAB: the bldutil.UserSconsTargets() helper in framework/bldutil.py supports .c, .f90, .py, and .jl attributes — not .m. MATLAB programs are not automatically discovered or compiled by the standard user directory SConstruct machinery.

Deploying a new MATLAB program: place M<name>.m somewhere on MATLAB's path (or in the current directory) and ensure that the MEX binaries installed to libdir are also on MATLAB's path. The simplest approach:

addpath('/path/to/madagascar/lib')   % directory containing rsf_*.mex* files
addpath('/path/to/your/Mname.m')
M<name>(input_rsf, output_rsf, ...)

There is no automated install target for .m main programs analogous to the C or Python install targets.

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Pointers

Files in api/matlab/ with one-line descriptions:

File	Description
SConstruct	SCons build script; compiles all rsf_*.c and m8r.c to MEX when matlab is in API
rsf_create.c	MEX: create an RSF output header from a filename+infile or filename+dims vector
rsf_read.c	MEX: read samples from an RSF file into a pre-allocated MATLAB double buffer
rsf_read_all.c	MEX: read an entire RSF file in one call, returning data and optional header metadata
rsf_read_header.c	MEX: read RSF header only (sizes, deltas, origins, labels, units) without touching the binary
rsf_write.c	MEX: write a MATLAB double array to an RSF file, with optional 'same' append mode
rsf_write_all.c	MEX: write a complete RSF file (header + data) in one call with full metadata support
rsf_par.c	MEX: read a scalar parameter (int, float, or bool) from an RSF header by name
rsf_dim.c	MEX: return the axis-length vector [n1; n2; ...] for an RSF file
m8r.c	MEX: run any Madagascar sf* binary as a filter on MATLAB data via temp RSF files
test/clip.m	Example MATLAB sf-program: clips data to [-clip, clip] trace by trace using rsf_dim, rsf_create, rsf_read/rsf_write with 'same'

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Shared conventions

All Madagascar sf-programs — regardless of language — follow the same conventions for file naming, self-documentation comments, parameter style, error handling, and testing. See skills/authoring-sf-programs/ for the full shared reference.