Reads a MAT file structure from a connection or a file (2024)

readMat {R.matlab}

R Documentation

Description

Reads a MAT file structure from a connection or a file.Both the MAT version 4 and MAT version 5 file formats aresupported. The implementation is based on [1-5].Note: Do not mix up version numbers for the MATLAB software andthe MATLAB file formats.

Usage

## Default S3 method:readMat(con, maxLength=NULL, fixNames=TRUE, drop=c("singletonLists"), sparseMatrixClass=c("Matrix", "SparseM", "matrix"), verbose=FALSE, ...)

Arguments

`con`	Binary `connection` from which the MAT file structureshould be read.If a `character` string, it is interpreted as filename, which thenwill be opened (and closed afterwards).If a `raw` `vector`, it will be read via as a raw binary `connection`.
`maxLength`	The maximum number of bytes to be read from the inputstream, which should be equal to the length of the MAT file structure.If `NULL`, data will be read until End Of File has been reached.
`fixNames`	If `TRUE`, underscores within names of MATLAB variablesand fields are converted to periods.
`drop`	A `character` `vector` specifying cases when one or more dimensionsof elements should be dropped in order to decrease the amount of "nestedness"of the returned data structure. This only applies to the MAT v5 file format.
`sparseMatrixClass`	If `"matrix"`, a sparse matrix is expanded toa regular `matrix`. If either `"Matrix"` (default) or `"SparseM"`,the sparse matrix representation by the package of the same name will be used.These packages are only loaded if the a sparse matrix is read.
`verbose`	Either a `logical`, a `numeric`, or a `Verbose`object specifying how much verbose/debug information is written tostandard output. If a Verbose object, how detailed the information isis specified by the threshold level of the object. If a numeric, thevalue is used to set the threshold of a new Verbose object. If `TRUE`,the threshold is set to -1 (minimal). If `FALSE`, no output is written.
`...`	Not used.

Value

Returns a named list structure containing all variables in theMAT file structure.

Speed performance

This function uses a MAT file parser implemented completely usingpure R. For MAT files containing large vectorized objects, for instancelong vectors and large matrices, the R implementation is indeed fastenough because it can read and parse each such objects in one go.

MAT cell structures

For the MAT v5 format, cell structures are read intoR as a list structure.

Unicode strings

Recent versions of MATLAB store some strings using Unicodeencodings. If the R installation supports iconv,these strings will be read correctly. Otherwise non-ASCII codesare converted to NA. Saving to an earlier file format versionmay avoid this problem as well.

Reading compressed MAT files

From MATLAB v7, compressed MAT version 5 files are used bydefault [3-5], which is supported by this function.

If for some reason it fails, use save -V6 in MATLAB to writenon-compressed MAT v5 files (sic!).

About MAT files saved in MATLAB using '-v7.3'

MAT v7.3 files, saved using for instance save('foo.mat', '-v7.3'),stores the data in the Hierarchical Data Format (HDF5) [6, 7], whichis a format not supported by this function/package.However, there exist other R packages that can parse HDF5, e.g.CRAN package h5 and Bioconductor package rhdf5.

Reading MAT file structures input streams

Reads a MAT file structure from an input stream, either until End of Fileis detected or until maxLength bytes has been read.Using maxLength it is possible to read MAT file structure oversocket connections and other non-terminating input streams. In such casesthe maxLength has to be communicated before sending the actualMAT file structure.

Author(s)

Henrik Bengtsson.The internal MAT v4 reader was written byAndy Jacobson (Princeton University).Support for reading sparse matrices, UTF-encoded strings andcompressed files, was contributed by Jason Riedy (UC Berkeley).

References

[1] The MathWorks Inc., MATLAB - MAT-File Format, version 5, June 1999.
[2] The MathWorks Inc., MATLAB - Application Program Interface Guide, version 5, 1998.
[3] The MathWorks Inc., MATLAB - MAT-File Format, version 7, September 2009.
[4] The MathWorks Inc., MATLAB - MAT-File Format, version R2012a, September 2012.
[5] The MathWorks Inc., MATLAB - MAT-File Format, version R2015b, September 2015.
[6] The MathWorks Inc., MATLAB - MAT-File Versions, December 2015.https://www.mathworks.com/help/matlab/import_export/mat-file-versions.html
[7] Undocumented Matlab, Improving save performance, May 2013.https://undocumentedmatlab.com/articles/improving-save-performance/
[8] J. Gilbert et al., Sparse Matrices in MATLAB: Design and Implementation, SIAM J. Matrix Anal. Appl., 1992.https://www.mathworks.com/help/pdf_doc/otherdocs/simax.pdf
[9] J. Burkardt, HB Files: Harwell Boeing Sparse Matrix File Format, Apr 2010.https://people.sc.fsu.edu/~jburkardt/data/hb/hb.html

Examples

path <- system.file("mat-files", package = "R.matlab")pathname <- file.path(path, "ABC.mat")data <- readMat(pathname)print(data)

[Package R.matlab version 3.7.0 Index]