R.matlab (version 1.3.1)

readMat: Reads a MAT file structure from a connection or a file

Description

Reads a MAT file structure from an input stream, either until End of File is detected or until maxLength bytes has been read. Using maxLength it is possible to read MAT file structure over socket connections and other non-terminating input streams. In such cases the maxLength has to be communicated before sending the actual MAT file structure. Both the MAT version 4 and MAT version 5 file formats are supported. The implementation is based on [1]. From Matlab v7, compressed MAT version 5 files are used by default [3], which can be read (not written) if the Rcompression package is installed. See R.matlab for more details on that package. If Rcompression is not available, use save -V6 in Matlab to write a MAT file compatible with Matlab v6, that is, to write a non-compressed MAT version 5 file. Note: Do not mix up version numbers for the Matlab software and the Matlab file formats. Recent versions of Matlab store some strings using Unicode encodings. If the R installation supports iconv, these strings will be read correctly. Otherwise non-ASCII codes are converted to NA. Saving to an earlier file format version may avoid this problem as well.

Usage

## S3 method for class 'default':
readMat(con, maxLength=NULL, fixNames=TRUE, verbose=FALSE, sparseMatrixClass=c("Matrix", "SparseM", "matrix"), ...)

Arguments

con

Binary connection to which the MAT file structure should be written to. A string is interpreted as filename, which then will be opened (and closed afterwards).

maxLength

The maximum number of bytes to be read from the input stream, 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 variables and fields are converted to periods.

verbose

Either a logical, a numeric, or a Verbose object specifying how much verbose/debug infor

sparseMatrixClass

If "matrix", a sparse matrix is expanded to a regular matrix. If either "Matrix" (default) or "SparseM", the sparse matrix representation by the package

...

Not used.

Value

• Returns a named list structure containing all variables in the MAT file structure.

Details

For the MAT v5 format, cell structures are read into Ras a list structure.

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, http://www.mathworks.com/access/helpdesk/help/pdf_doc/matlab/matfile_format.pdf

See Also

writeMat().

Examples

path <- system.file("mat-files", package="R.matlab")

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Reading all example files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
for (version in 4:5) {
  cat("Loading all MAT v", version, "example files in ",
                                                path, "...
", sep="")

  pattern <- sprintf("-v%d[.]mat$", version)
  pathnames <- list.files(pattern=pattern, path=path, full.names=TRUE)

  for (pathname in pathnames) {
    cat("Reading MAT file: ", basename(pathname), "", sep="")
    mat <- readMat(pathname)
    if (interactive()) {
      cat("Press ENTER to view data:")
      readline()
    }
    print(mat)
  }
}

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Assert that signed and unsigned integers are read correctly
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
bs <- readMat(file.path(path, "unsignedByte.mat"))
if (!identical(as.vector(bs$A), as.double(126:255)))
  stop("Error reading unsigned bytes saved by Matlab.")

is <- readMat(file.path(path, "unsignedInt.mat"))
if (!identical(as.vector(is$B), as.double(127:256)))
  stop("Error reading unsigned ints saved by Matlab.")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Assert that sparse matrices are read identically in MAT v4 and v5
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
mat4 <- readMat(file.path(path, "SparseMatrix3-v4.mat"))
mat5 <- readMat(file.path(path, "SparseMatrix3-v5.mat"))
diff <- sum(abs(mat4$sparseM - mat5$sparseM))
if (diff > .Machine$double.eps)
  stop("Failed to read identical MAT v4 and MAT v5 sparse matrices.")


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Assert that sparse matrices can be read as 'Matrix' and 'SparseM'
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
pathname <- file.path(path, "SparseMatrix3-v4.mat")
mat4a <- readMat(pathname, sparseMatrixClass="matrix")

if (require("Matrix")) {
  mat4b <- readMat(pathname, sparseMatrixClass="Matrix")
  diff <- sum(abs(as.matrix(mat4b$sparseM) - mat4a$sparseM))
  if (diff > .Machine$double.eps)
    stop("Failed to read MAT v4 sparse matrix by class 'Matrix'.")
}

if (require("SparseM")) {
  mat4c <- readMat(pathname, sparseMatrixClass="SparseM");
  diff <- sum(abs(as.matrix(mat4c$sparseM) - mat4a$sparseM))
  if (diff > .Machine$double.eps)
    stop("Failed to read MAT v4 sparse matrix by class 'SparseM'.")
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Assert that compressed files can be read
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (require("Rcompression")) {
  # A particular compressed file
  pathname <- file.path(path, "StructWithSparseMatrix-v4,compressed.mat")
  mat4 <- readMat(pathname, sparseMatrixClass="matrix")

  # All compressed files
  pattern <- ",compressed[.]mat$"
  pathnames <- list.files(pattern=pattern, path=path, full.names=TRUE)
  for (pathname in pathnames) {
    cat("Reading MAT file: ", basename(pathname), "", sep="")
    mat <- readMat(pathname)
    if (interactive()) {
      cat("Press ENTER to view data:")
      readline()
    }
    print(mat)
  }
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Example of a Matlab struct
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# File was created by
# s = struct('type',{'big','little'},  'color','red',  'x',{3,4})
#  1x2 struct array with fields:
#      type
#      color
#      x
# save structLooped.mat s -v6
mat <- readMat(file.path(path, "structLooped.mat"))

# Extract the structure
s <- mat$s

# Field names are always in the first dimension
fields <- dimnames(s)[[1]]
cat("Field names: ", paste(fields, collapse=", "), "", sep="");

print(s)

# Get field 'type'
print(s["type",,])

# Get substructure s(:,2)
print(s[,,2])