Lazy 'HDF5' file loader — LazyH5 • ieegio

Provides hybrid data structure for 'HDF5' file. The class is not intended for direct-use. Please see io_read_h5 and io_write_h5.

Public fields

quiet: whether to suppress messages

Methods

Public methods

LazyH5$do_finalize()
LazyH5$print()
LazyH5$new()
LazyH5$save()
LazyH5$open()
LazyH5$close()
LazyH5$subset()
LazyH5$get_dims()
LazyH5$get_type()

`LazyH5$do_finalize()`

garbage collection method

Usage

LazyH5$do_finalize()

Returns

none

`LazyH5$print()`

overrides print method

Usage

LazyH5$print()

Returns

self instance

`LazyH5$new()`

constructor

Usage

LazyH5$new(file_path, data_name, read_only = FALSE, quiet = FALSE)

Arguments

file_path: where data is stored in 'HDF5' format
data_name: the data stored in the file
read_only: whether to open the file in read-only mode. It's highly recommended to set this to be true, otherwise the file connection is exclusive.
quiet: whether to suppress messages, default is false

Returns

self instance

`LazyH5$save()`

save data to a 'HDF5' file

Usage

LazyH5$save(
  x,
  chunk = "auto",
  level = 7,
  replace = TRUE,
  new_file = FALSE,
  force = TRUE,
  ctype = NULL,
  size = NULL,
  ...
)

Arguments

x: vector, matrix, or array
chunk: chunk size, length should matches with data dimension
level: compress level, from 1 to 9
replace: if the data exists in the file, replace the file or not
new_file: remove the whole file if exists before writing?
force: if you open the file in read-only mode, then saving objects to the file will raise error. Use force=TRUE to force write data
ctype: data type, see mode, usually the data type of x. Try mode(x) or storage.mode(x) as hints.
size: deprecated, for compatibility issues
...: passed to self open() method

`LazyH5$open()`

open connection

Usage

LazyH5$open(new_dataset = FALSE, robj, ...)

Arguments

new_dataset: only used when the internal pointer is closed, or to write the data
robj: data array to save
...: passed to createDataSet in hdf5r package

`LazyH5$close()`

close connection

Usage

LazyH5$close(all = TRUE)

Arguments

all: whether to close all connections associated to the data file. If true, then all connections, including access from other programs, will be closed

`LazyH5$subset()`

subset data

Usage

LazyH5$subset(..., drop = FALSE, stream = FALSE, envir = parent.frame())

Arguments

drop: whether to apply drop the subset
stream: whether to read partial data at a time
envir: if i,j,... are expressions, where should the expression be evaluated
i, j, ...: index along each dimension

Returns

subset of data

`LazyH5$get_dims()`

get data dimension

Usage

LazyH5$get_dims(stay_open = TRUE)

Arguments

stay_open: whether to leave the connection opened

Returns

dimension of the array

`LazyH5$get_type()`

get data type

Usage

LazyH5$get_type(stay_open = TRUE)

Arguments

stay_open: whether to leave the connection opened

Returns

data type, currently only character, integer, raw, double, and complex are available, all other types will yield "unknown"