Write object to an HDF5 file.

Writes an R object to an HDF5 file. This function can be used to write either full arrays/vectors or subarrays (hyperslabs) within an existing dataset.

h5write(obj, file, name, ...)

# S3 method for default
h5write(
  obj,
  file,
  name,
  createnewfile = TRUE,
  write.attributes = FALSE,
  ...,
  native = FALSE
)

h5writeDataset(obj, h5loc, name, ...)

# S3 method for data.frame
h5writeDataset(obj, h5loc, name, level = 6, chunk, DataFrameAsCompound = TRUE)

# S3 method for array
h5writeDataset(
  obj,
  h5loc,
  name,
  index = NULL,
  start = NULL,
  stride = NULL,
  block = NULL,
  count = NULL,
  size = NULL,
  variableLengthString = FALSE,
  encoding = NULL,
  level = 6
)

Arguments

obj: The R object to be written.
file: The filename (character) of the file in which the dataset will be located. For advanced programmers it is possible to provide an object of class H5IdComponent representing a H5 location identifier (file or group). See H5Fcreate, H5Fopen, H5Gcreate, H5Gopen to create an object of this kind.
name: The name of the dataset in the HDF5 file.
...: Further arguments passed to H5Dwrite.
createnewfile: If TRUE, a new file will be created if necessary.
write.attributes: (logical) If TRUE, all R-attributes attached to the object obj are written to the HDF5 file.
native: An object of class logical. If TRUE, array-like objects are treated as stored in HDF5 row-major rather than R column-major orientation. Using native = TRUE increases HDF5 file portability between programming languages. A file written with native = TRUE should also be read with native = TRUE
h5loc: An object of class H5IdComponent representing a H5 location identifier (file or group). See H5Fcreate, H5Fopen, H5Gcreate, H5Gopen to create an object of this kind.
level: The compression level. An integer value between 0 (no compression) and 9 (highest and slowest compression). Only used, if the dataset does not yet exist. See h5createDataset() to create an dataset.
chunk: Specifies the number of items to be include in an HDF5 chunk. If left unspecified the defaults is the smaller of: the total number of elements or the number of elements that fit within 4GB of memory. If DataFrameAsCompound=FALSE each row of the data.frame can be consider an "element".
DataFrameAsCompound: If true, a data.frame will be saved as a compound data type. Otherwise it is saved like a list. The advantage of saving a data.frame as a compound data type is that it can be read as a table from python or with a struct-type from C. The disadvantage is that the data has to be rearranged on disk and thus can slow down I/O. If fast reading is required, DataFrameAsCompound=FALSE is recommended.
index: List of indices for subsetting. The length of the list has to agree with the dimensional extension of the HDF5 array. Each list element is an integer vector of indices. A list element equal to NULL chooses all indices in this dimension. Counting is R-style 1-based.
start: The start coordinate of a hyperslab (similar to subsetting in R). Counting is R-style 1-based. This argument is ignored, if index is not NULL.
stride: The stride of the hypercube. Read the introduction http://ftp.hdfgroup.org/HDF5/Tutor/phypecont.html before using this argument. R behaves like Fortran in this example. This argument is ignored, if index is not NULL.
block: The block size of the hyperslab. Read the introduction http://ftp.hdfgroup.org/HDF5/Tutor/phypecont.html before using this argument. R behaves like Fortran in this example. This argument is ignored, if index is not NULL.
count: The number of blocks to be written. This argument is ignored, if index is not NULL.
size: The length of the fixed-width string data type, when obj is a character vector. If NULL, this is set to the length of the largest string.
variableLengthString: Whether character vectors should be written as variable-length strings into the attributes. If TRUE, size is ignored.
encoding: The encoding of the string data type. Valid options are "ASCII" or "UTF-8".

Value

h5write returns 0 if successful.

Details

Writes an R object to an HDF5 file. If none of the arguments start, stride, block, count is specified, the dataset has the same dimension in the HDF5 file and in memory. If the dataset already exists in the HDF5 file, one can write subarrays, (so called hyperslabs) to the HDF5 file. The arguments start, stride, block, count define the subset of the dataset in the HDF5 file that is to be written to. See these introductions to hyperslabs: https://support.hdfgroup.org/HDF5/Tutor/selectsimple.html, https://support.hdfgroup.org/HDF5/Tutor/select.html and http://ftp.hdfgroup.org/HDF5/Tutor/phypecont.html. Please note that in R the first dimension is the fastest changing dimension.

When viewing the HDF5 datasets with any C-program (e.g. HDFView), the order of dimensions is inverted. In the R interface counting starts with 1, whereas in the C-programs (e.g. HDFView) counting starts with 0.

References

https://portal.hdfgroup.org/display/HDF5

Author

Bernd Fischer, Mike Smith

Examples


h5File <- tempfile(fileext = ".h5")
h5createFile( h5File )

# write a matrix
B = array(seq(0.1,2.0,by=0.1),dim=c(5,2,2))
attr(B, "scale") <- "liter"
h5write(B, h5File,"B")

# write a submatrix
h5createDataset(h5File, "S", c(5,8), storage.mode = "integer", chunk=c(5,1), level=7)
h5write(matrix(1:5,nr=5,nc=1), file=h5File, name="S", index=list(NULL,1))