Nothing
R/codec.R
In zarr: Native and Extensible R Driver for 'Zarr'
#' Zarr codecs
#'
#' @description Zarr codecs encode data from the user data to stored data, using
#' one or more transformations, such as compression. Decoding of stored data is
#' the inverse process, whereby the codecs are applied in reverse order.
#' @docType class
zarr_codec <- R6::R6Class('zarr_codec',
inherit = zarr_extension,
cloneable = FALSE,
private = list(
# The configuration parameters of the codec
.configuration = list(),
# The input and output data object for the encoding operation
.from = 'array',
.to = 'bytes',
# Print the configuration of the codec. To be implemented by descendant classes.
print_configuration = function() {
}
),
public = list(
#' @description Create a new codec object.
#' @param name The name of the codec, a single character string.
#' @param configuration A list with the configuration parameters for this
#' codec.
#' @return An instance of this class.
initialize = function(name, configuration) {
super$initialize(name)
private$.configuration <- configuration
},
#' @description Create a new, independent copy of this codec.
#' @return This method always throws an error.
copy = function() {
stop('Class', class(self)[1L], 'must implement the `copy()` method.', call. = FALSE) # nocov
},
#' @description Print a summary of the codec to the console.
print = function() {
cat('<Zarr codec>', private$.name, '\n')
cat('Mode :', self$mode, '\n')
private$print_configuration()
invisible(self)
},
#' @description Return the metadata fragment that describes this codec.
#' @return A list with the metadata of this codec.
metadata_fragment = function() {
if (length(private$.configuration))
list(name = private$.name, configuration = private$.configuration)
else
list(name = private$.name)
},
#' @description This method encodes a data object but since this is the base
#' codec class the "encoding" is a no-op.
#' @param data The data to be encoded.
#' @return The encoded data object, unaltered.
encode = function(data) {
data
},
#' @description This method decodes a data object but since this is the base
#' codec class the "decoding" is a no-op.
#' @param data The data to be decoded.
#' @return The decoded data object, unaltered.
decode = function(data) {
data
}
),
active = list(
#' @field mode (read-only) Retrieve the operating mode of the encoding
#' operation of the codec in form of a string "array -> array", "array ->
#' bytes" or "bytes -> bytes".
mode = function(value) {
if (missing(value))
paste(private$.from, private$.to, sep = ' -> ')
},
#' @field from (read-only) Character string that indicates the source data
#' type of this codec, either "array" or "bytes".
from = function(value) {
if (missing(value))
private$.from
},
#' @field to (read-only) Character string that indicates the output data
#' type of this codec, either "array" or "bytes".
to = function(value) {
if (missing(value))
private$.to
},
#' @field configuration (read-only) A list with the configuration parameters
#' of the codec, exactly like they are defined in Zarr. This field is
#' read-only but each codec class has fields to set individual parameters.
configuration = function(value) {
if (missing(value))
private$.configuration
}
)
)
#' Zarr transpose codec
#'
#' @description The Zarr "transpose" codec registers the storage order of a data
#' object relative to the canonical row-major ordering of Zarr. If the
#' registered ordering is different from the native ordering on the platform
#' where the array is being read, the data object will be permuted upon
#' reading.
#'
#' R data is arranged in column-major order. The most efficient storage
#' arrangement between Zarr and R is thus column-major ordering, avoiding
#' encoding to the canonical row-major ordering during storage and decoding to
#' column-major ordering during a read. If the storage arrangement is not
#' row-major ordering, a transpose codec must be added to the array
#' definition. Note that within R, both writing and reading are no-ops when
#' data is stored in column-major ordering. On the other hand, when no
#' transpose codec is defined for the array, there will be an automatic
#' transpose of the data on writing and reading to maintain compatibility with
#' the Zarr specification. Using the [array_builder] will automatically add
#' the transpose codec to the array definition.
#'
#' For maximum portability (e.g. with Zarr implementations outside of R that
#' do not implement the transpose codec), data should be stored in row-major
#' order, which can be achieved by not including this codec in the array
#' definition.
#' @docType class
zarr_codec_transpose <- R6::R6Class('zarr_codec_transpose',
inherit = zarr_codec,
cloneable = FALSE,
private = list (
# Print the configuration information to the console. This is called by
# zarr_codec$print().
print_configuration = function() {
cat('Configuration:\n')
cat(' order: [', paste(private$.configuration$order, collapse = ', '), ']\n', sep = '')
},
# Check if the "order" argument is valid. Returns TRUE or FALSE. "order"
# must have been cast to integer.
check_order = function(order, len) {
!is.null(order) && is.integer(order) && length(order) == len &&
all(order >= 0L & order < len) && anyDuplicated(order) == 0L
}
),
public = list(
#' @description Create a new "transpose" codec object.
#' @param shape_length The length of the shape of the array that this codec
#' operates on.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec. The element `order` specifies the ordering of the
#' dimensions of the shape relative to the Zarr canonical arrangement. An
#' integer vector with a length equal to argument
#' `shape_length`. The ordering must be 0-based. If not given, the default R
#' ordering is used.
#' @return An instance of this class.
initialize = function(shape_length, configuration = list()) {
if (shape_length < 2L)
stop('Can only set a transpose codec on a matrix or array.', call. = FALSE) # nocov
if (!length(configuration))
configuration <- list(order = seq(shape_length - 1L, 0L, -1L))
else if (!private$check_order(configuration$order, shape_length))
stop('Dimension ordering does not match the shape.', call. = FALSE) # nocov
super$initialize('transpose', configuration)
private$.from <- 'array'
private$.to <- 'array'
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_transpose`.
copy = function() {
zarr_codec_transpose$new(length(private$.configuration$order), private$.configuration)
},
#' @description This method permutes a data object to match the desired
#' dimension ordering.
#' @param data The data to be permuted, an R matrix or array.
#' @return The permuted data object, a matrix or array in Zarr store
#' dimension order.
encode = function(data) {
if (all(diff(private$.configuration$order) == -1L))
# Store in native R order - no-op
data
else
aperm(data, perm = rev(private$.configuration$order) + 1L)
},
#' @description This method permutes a data object from a Zarr store to an
#' R matrix or array.
#' @param data The data to be permuted, from a Zarr store.
#' @return The permuted data object, an R matrix or array.
decode = function(data) {
if (all(diff(private$.order) == -1L))
# Stored in native R order - no-op
data
else
aperm(data, perm = rev(private$.configuration$order) + 1L)
}
),
active = list(
#' @field order Set or retrieve the 0-based ordering of the dimensions of
#' the array when storing
order = function(value) {
if (missing(value))
private$.configuration$order
else if (private$check_order(value, length(private$.configuration$order)))
private$.configuration$order <- value
else
stop('Dimension ordering does not match the shape.', call. = FALSE) # nocov
}
)
)
#' Zarr bytes codec
#'
#' @description The Zarr "bytes" codec encodes an R data object to a raw byte
#' string, and decodes a raw byte string to a R object, possibly inverting the
#' endianness of the data in the operation.
#' @docType class
zarr_codec_bytes <- R6::R6Class('zarr_codec_bytes',
inherit = zarr_codec,
cloneable = FALSE,
private = list(
# The data type of the object that this codec operates on, an instance of
# the data_type extension object.
.data_type = NULL,
# The shape of a chunk of array data, an integer vector.
.chunk_shape = NULL,
# Print the configuration information to the console. This is called by
# zarr_codec$print().
print_configuration = function() {
cat('Configuration:\n')
cat(' endian:', private$.configuration$endian, '\n')
}
),
public = list(
#' @description Create a new "bytes" codec object.
#' @param data_type The [zarr_data_type] instance of the Zarr array that
#' this codec is used for.
#' @param chunk_shape The shape of a chunk of data of the array, an integer
#' vector.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec. The element `endian` specifies the byte ordering of the
#' data type of the Zarr array. A string with value "big" or "little". If
#' not given, the default endianness of the platform is used.
#' @return An instance of this class.
initialize = function(data_type, chunk_shape, configuration = NULL) {
if (inherits(data_type, 'zarr_data_type'))
private$.data_type <- data_type
else
stop('Codec must be initialized with a `zarr_data_type` instance.', call. = FALSE) # nocov
if (is.integer(chunk_shape))
private$.chunk_shape <- chunk_shape
else
stop('Codec must be initialized with an integer vector giving the shape of a chunk of data.', call. = FALSE) # nocov
if (is.null(configuration))
configuration <- list(endian = .Platform$endian)
else if (!is.list(configuration))
stop('`configuration` parameter must be a list.', call. = FALSE) # nocov
super$initialize('bytes', configuration)
private$.from <- 'array'
private$.to <- 'bytes'
self$endian <- configuration$endian
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_bytes`.
copy = function() {
zarr_codec_bytes$new(private$.data_type, private$.chunk_shape, private$.configuration)
},
#' @description Return the metadata fragment that describes this codec.
#' @return A list with the metadata of this codec.
metadata_fragment = function() {
if (private$.data_type$size > 1L)
list(name = 'bytes',
configuration = list(endian = private$.configuration$endian))
else
list(name = 'bytes')
},
#' @description This method writes an R object to a raw vector in the data
#' type of the Zarr array. Prior to writing, any `NA` values are assigned
#' the `fill_value` of the `data_type` of the Zarr array. Note that the
#' logical type cannot encode `NA` in Zarr and any `NA` values are set to
#' `FALSE`.
#' @param data The data to be encoded.
#' @return A raw vector with the encoded data object.
encode = function(data) {
dt <- private$.data_type
data[is.na(data)] <- dt$fill_value
dim(data) <- NULL
if (dt$data_type == 'logical') {
as.raw(as.integer(data))
} else if (dt$data_type == 'integer64') {
writeBin(unclass(data), raw(), endian = private$.configuration$endian)
} else
writeBin(data, raw(), size = dt$size, endian = private$.configuration$endian)
},
#' @description This method takes a raw vector and converts it to an R
#' object of an appropriate type. For all types other than logical, any
#' data elements with the `fill_value` of the Zarr data type are set to
#' `NA`.
#' @param data The data to be decoded.
#' @return An R object with the shape of a chunk from the array.
decode = function(data) {
dt <- private$.data_type
Rtype <- dt$Rtype
n <- length(data) %/% dt$size
if (length(data) %% dt$size)
stop('Data length not a multiple of data type size.', call. = FALSE) # nocov
out <- if (Rtype == 'logical') {
as.logical(as.integer(data))
} else if (Rtype == 'integer64') {
vals <- readBin(data, what = 'double', n = n, endian = private$.configuration$endian)
class(vals) <- 'integer64'
vals
} else {
readBin(data, what = Rtype, size = dt$size, signed = dt$signed,
n = n, endian = private$.configuration$endian)
}
if (is.nan(dt$fill_value))
out[which(is.nan(out))] <- NA
else if (!(Rtype %in% c('logical', 'integer64')))
out[.near(out, dt$fill_value)] <- NA
dim(out) <- private$.chunk_shape
out
}
),
active = list(
#' @field endian Set or retrieve the endianness of the storage of the data
#' with this codec. A string with value of "big" or "little".
endian = function(value) {
if (missing(value))
private$.configuration$endian
else if (is.character(value) && length(value) == 1L && value %in% c("big", "little"))
private$.configuration$endian <- value
else
stop('Bad value for endianness of the data.', call. = FALSE) # nocov
}
)
)
#' Zarr blosc codec
#'
#' @description The Zarr "blosc" codec offers a number of compression options to
#' reduce the size of a raw vector prior to storing, and uncompressing when
#' reading.
#' @docType class
zarr_codec_blosc <- R6::R6Class('zarr_codec_blosc',
inherit = zarr_codec,
cloneable = FALSE,
private = list(
# The zarr_data_type of the array using this codec.
.data_type = NULL,
# Print the configuration information to the console. This is called by
# zarr_codec$print().
print_configuration = function() {
cat('Configuration:\n')
cat(' compressor:', private$.configuration$cname, '\n')
cat(' level :', private$.configuration$clevel, '\n')
cat(' shuffle :', private$.configuration$shuffle, '\n')
cat(' typesize :', private$.configuration$typesize, '\n')
cat(' blocksize :', private$.configuration$blocksize, '\n')
},
# Check the configuration parameters. Conf must be a list. If ok, the list
# is returned. If not ok, an error is thrown.
check_configuration = function(conf) {
if (is.null(conf$cname))
conf$cname <- 'zstd'
else if (!is.character(conf$cname) || !(length(conf$cname) == 1L) ||
!(conf$cname %in% c("blosclz", "lz4", "lz4hc", "zstd", "zlib")))
stop('Blosc configuration has bad compression name.', call. = FALSE) # nocov
if (is.null(conf$clevel))
conf$clevel <- 1L
else if (!is.numeric(conf$clevel) || !(length(conf$clevel) == 1L) ||
!(conf$clevel >= 0 && conf$clevel <= 9))
stop('Blosc parameter clevel must be a single integer value between 0 and 9.', call. = FALSE) # nocov
if (is.null(conf$shuffle))
conf$shuffle <-
if (private$.data_type$data_type %in% c('bool', 'int8', 'uint8')) 'noshuffle'
else if (private$.data_type$data_type %in% c('int16', 'uint16', 'int32', 'uint32', 'int64', 'float32')) 'shuffle'
else 'bitshuffle'
else if (!(length(conf$shuffle) == 1L))
stop('Blosc shuffle parameter must be a single value.', call. = FALSE)
else if ((is.character(conf$shuffle) && !(conf$shuffle %in% c('shuffle', 'noshuffle', 'bitshuffle'))) ||
(is.integer(conf$shuffle) && !(conf$shuffle %in% 0L:2L)))
stop(paste('Bad blosc shuffle parameter:', conf$shuffle), call. = FALSE) # nocov
if (is.null(conf$typesize))
conf$typesize <- private$.data_type$size
else if (!is.integer(conf$typesize) || !(length(conf$typesize) == 1L) ||
!(conf$typesize %in% c(1L, 2L, 4L, 8L)))
stop('Blosc typesize parameter must be 1, 2, 4 or 8.', call. = FALSE) # nocov
if (is.null(conf$blocksize))
conf$blocksize <- 0L
else if (!is.integer(conf$blocksize) || !(length(conf$blocksize) == 1L))
stop('Blosc blocksize parameter must be a single integer value.', call. = FALSE) # nocov
conf
}
),
public = list(
#' @description Create a new "blosc" codec object. The typesize argument is
#' taken from the data type of the array passed in through the `data_type`
#' argument and the shuffle argument is chosen based on the `data_type`.
#' @param data_type The [zarr_data_type] instance of the Zarr array that
#' this codec is used for.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec. If not given, the default compression of "zstd" with
#' level 1 will be used.
#' @return An instance of this class.
initialize = function(data_type, configuration = NULL) {
if (!requireNamespace('blosc'))
stop('Must install package "blosc" for this functionality', call. = FALSE) # nocov
if (!inherits(data_type, 'zarr_data_type'))
stop('Codec must be initialized with a `zarr_data_type` instance.', call. = FALSE) # nocov
else
private$.data_type <- data_type
if (is.null(configuration))
configuration <- list()
else if (!is.list(configuration))
stop('`configuration` parameter must be a list.', call. = FALSE) # nocov
configuration <- private$check_configuration(configuration)
super$initialize('blosc', configuration)
private$.from <- 'bytes'
private$.to <- 'bytes'
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_blosc`.
copy = function() {
zarr_codec_blosc$new(private$.data_type, private$.configuration)
},
#' @description This method compresses a data object using the "blosc"
#' compression library.
#' @param data The raw vector to be compressed.
#' @return A raw vector with compressed data.
encode = function(data) {
if (is.raw(data))
blosc::blosc_compress(data, compressor = private$.configuration$cname,
level = private$.configuration$clevel,
shuffle = private$.configuration$shuffle,
typesize = private$.configuration$typesize,
blocksize = private$.configuration$blocksize)
else
stop('Blosc codec should be passed a raw vector.', call. = FALSE)
},
#' @description This method decompresses a data object using the "blosc"
#' compression library.
#' @param data The raw vector to be decoded.
#' @return A raw vector with the decoded data.
decode = function(data) {
if (is.raw(data))
blosc::blosc_decompress(data)
else
stop('Blosc codec should be passed a raw vector.', call. = FALSE)
}
),
active = list(
#' @field cname Set or retrieve the name of the compression algorithm. Must
#' be one of "blosclz", "lz4", "lz4hc", "zstd" or "zlib".
cname = function(value) {
if (missing(value))
private$.configuration$cname
else {
conf <- private$.configuration
conf$cname <- value
private$.configuration <- private$check_configuration(conf)
}
},
#' @field clevel Set or retrieve the compression level. Must
#' be an integer between 0 (no compression) and 9 (maximum compression).
clevel = function(value) {
if (missing(value))
private$.configuration$clevel
else {
conf <- private$.configuration
conf$clevel <- as.integer(value)
private$.configuration <- private$check_configuration(conf)
}
},
#' @field shuffle Set or retrieve the data shuffling of the compression
#' algorithm. Must be one of "shuffle", "noshuffle" or "bitshuffle".
shuffle = function(value) {
if (missing(value))
private$.configuration$shuffle
else {
conf <- private$.configuration
conf$shuffle <- value
private$.configuration <- private$check_configuration(conf)
}
},
#' @field typesize Set or retrieve the size in bytes of the data type being
#' compressed. It is highly recommended to leave this at the automatically
#' determined value.
typesize = function(value) {
if (missing(value))
private$.configuration$typesize
else {
conf <- private$.configuration
conf$typesize <- value
private$.configuration <- private$check_configuration(conf)
}
},
#' @field blocksize Set or retrieve the size in bytes of the blocks being
#' compressed. It is highly recommended to leave this at a value of 0 such
#' that the blosc library will automatically determine the optimal value.
blocksize = function(value) {
if (missing(value))
private$.configuration$blocksize
else {
conf <- private$.configuration
conf$blocksize <- value
private$.configuration <- private$check_configuration(conf)
}
}
)
)
#' Zarr "zstd" codec
#'
#' @description This class provides the codec for "zstd" compression.
#' @docType class
zarr_codec_zstd <- R6::R6Class('zarr_codec_zstd',
inherit = zarr_codec,
cloneable = FALSE,
private = list(
# Print the configuration information to the console. This is called by
# zarr_codec$print().
print_configuration = function() {
cat('Configuration:\n')
cat(' level:', private$.configuration$level, '\n')
}
),
public = list(
#' @description Create a new "zstd" codec object.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec. The element `level` specifies the compression level of
#' this codec, ranging from 1 (no compression) to 20 (maximum compression).
#' @return An instance of this class.
initialize = function(configuration = NULL) {
if (!requireNamespace('qs2'))
stop('Must install package "qs2" for this functionality', call. = FALSE) # nocov
if (is.null(configuration))
configuration <- list(level = 6)
else if (!is.list(configuration) || is.null(configuration$level))
stop('`configuration` argument must be a list with a field `level`.', call. = FALSE) # nocov
else if (!is.numeric(configuration$level) || length(configuration$level) != 1L ||
!(configuration$level >= 1 && configuration$level <= 20))
stop('Configuration parameter `level` must be a single integer value between 1 and 20.', call. = FALSE) # nocov
super$initialize('zstd', configuration)
private$.from <- 'bytes'
private$.to <- 'bytes'
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_zstd`.
copy = function() {
zarr_codec_zstd$new(private$.configuration)
},
#' @description This method encodes a raw data object.
#' @param data The raw data to be encoded.
#' @return The encoded raw data object.
encode = function(data) {
qs2::zstd_compress_raw(data, compress_level = private$.configuration$level)
},
#' @description This method decodes a raw data object.
#' @param data The raw data to be decoded.
#' @return The decoded raw data object.
decode = function(data) {
qs2::zstd_decompress_raw(data)
}
),
active = list(
#' @field level The compression level of the zstd codec, an integer value
#' between 1L (fast) and 20 (maximum compression).
level = function(value) {
if (missing(value))
private$.configuration$level
else {
value <- as.integer(value)
if (length(value) == 1L && value >= 1 && value <= 20)
private$.configuration$level <- as.integer(value)
else
stop('Compression level of zstd must be an integer value between 1 and 20.', call. = FALSE) # nocov
}
}
)
)
#' Zarr gzip codec
#'
#' @description The Zarr "gzip" codec compresses a raw vector prior to storing,
#' and uncompresses the raw vector when reading.
#' @docType class
zarr_codec_gzip <- R6::R6Class('zarr_codec_gzip',
inherit = zarr_codec,
cloneable = FALSE,
private = list(
# Print the configuration information to the console. This is called by
# zarr_codec$print().
print_configuration = function() {
cat('Configuration:\n')
cat(' level:', private$.configuration$level, '\n')
}
),
public = list(
#' @description Create a new "gzip" codec object.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec. The element `level` specifies the compression level of
#' this codec, ranging from 0 (no compression) to 9 (maximum compression).
#' @return An instance of this class.
initialize = function(configuration = NULL) {
if (!requireNamespace('zlib'))
stop('Must install package "zlib" for this functionality', call. = FALSE) # nocov
if (is.null(configuration))
configuration <- list(level = 6)
else if (!is.list(configuration) || is.null(configuration$level))
stop('`configuration` argument must be a list with a field `level`.', call. = FALSE) # nocov
else if (!is.numeric(configuration$level) || length(configuration$level) != 1L ||
!(configuration$level >= 0 && configuration$level <= 9))
stop('Configuration parameter `level` must be a single integer value between 0 and 9.', call. = FALSE) # nocov
super$initialize('gzip', configuration)
private$.from <- 'bytes'
private$.to <- 'bytes'
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_gzip`.
copy = function() {
zarr_codec_gzip$new(private$.configuration)
},
#' @description This method encodes a data object.
#' @param data The data to be encoded.
#' @return The encoded data object.
encode = function(data) {
zlib::compress(data, level = private$.configuration$level, wbits = 31)
},
#' @description This method decodes a data object.
#' @param data The data to be decoded.
#' @return The decoded data object.
decode = function(data) {
zlib::decompress(data, wbits = 31)
}
),
active = list(
#' @field level The compression level of the gzip codec, an integer value
#' between 0L (no compression) and 9 (maximum compression).
level = function(value) {
if (missing(value))
private$.configuration$level
else {
value <- as.integer(value)
if (length(value) == 1L && value >= 0 && value <= 9)
private$.configuration$level <- as.integer(value)
else
stop('Compression level of gzip must be an integer value between 0 and 9.', call. = FALSE) # nocov
}
}
)
)
#' Zarr CRC32C codec
#'
#' @description The Zarr "CRC32C" codec computes a 32-bit checksum of a raw
#' vector. Upon encoding the codec appends the checksum to the end of the
#' vector. When decoding, the final 4 bytes from the raw vector are extracted
#' and compared to the checksum of the remainder of the raw vector - if the
#' two don't match a warning is generated.
#' @docType class
zarr_codec_crc32c <- R6::R6Class('zarr_codec_crc32c',
inherit = zarr_codec,
cloneable = FALSE,
public = list(
#' @description Create a new "crc32c" codec object.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec but since this codec doesn't have any the argument is
#' always ignored.
#' @return An instance of this class.
initialize = function() {
if (!requireNamespace('digest'))
stop('Must install package "digest" for this functionality', call. = FALSE) # nocov
super$initialize('crc32c', configuration = list())
private$.from <- 'bytes'
private$.to <- 'bytes'
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_crc32c`.
copy = function() {
zarr_codec_crc32c$new()
},
#' @description This method computes the CRC32C checksum of a data object
#' and appends it to the data object.
#' @param data A raw vector whose checksum to compute.
#' @return The input `data` raw vector with the 32-bit checksum appended to
#' it.
encode = function(data) {
dig <- writeBin(strtoi(digest::digest(data, 'crc32c', serialize = FALSE), base = 16L), raw())
c(data, dig)
},
#' @description This method extracts the CRC32C checksum from the trailing
#' 32-bits of a data object. It then computes the CRC32C checksum from the
#' data object (less the trailing 32-bits) and compares the two values. If
#' the values differ, a warning will be issued.
#' @param data The raw vector whose checksum to verify.
#' @return The `data` raw vector with the trailing 32-bits removed.
decode = function(data) {
len <- length(data)
out <- data[1:(len - 4L)]
chk_stored <- readBin(data[(len - 3L):len], 'integer')
chk_calc <- strtoi(digest::digest(out, 'crc32c', serialize = FALSE), base = 16L)
if (chk_stored != chk_calc)
warning('Checksum failed on raw data object!', call. = FALSE) # nocov
out
}
)
)
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#' Zarr codecs
#'
#' @description Zarr codecs encode data from the user data to stored data, using
#' one or more transformations, such as compression. Decoding of stored data is
#' the inverse process, whereby the codecs are applied in reverse order.
#' @docType class
zarr_codec <- R6::R6Class('zarr_codec',
inherit = zarr_extension,
cloneable = FALSE,
private = list(
# The configuration parameters of the codec
.configuration = list(),
# The input and output data object for the encoding operation
.from = 'array',
.to = 'bytes',
# Print the configuration of the codec. To be implemented by descendant classes.
print_configuration = function() {
}
),
public = list(
#' @description Create a new codec object.
#' @param name The name of the codec, a single character string.
#' @param configuration A list with the configuration parameters for this
#' codec.
#' @return An instance of this class.
initialize = function(name, configuration) {
super$initialize(name)
private$.configuration <- configuration
},
#' @description Create a new, independent copy of this codec.
#' @return This method always throws an error.
copy = function() {
stop('Class', class(self)[1L], 'must implement the `copy()` method.', call. = FALSE) # nocov
},
#' @description Print a summary of the codec to the console.
print = function() {
cat('<Zarr codec>', private$.name, '\n')
cat('Mode :', self$mode, '\n')
private$print_configuration()
invisible(self)
},
#' @description Return the metadata fragment that describes this codec.
#' @return A list with the metadata of this codec.
metadata_fragment = function() {
if (length(private$.configuration))
list(name = private$.name, configuration = private$.configuration)
else
list(name = private$.name)
},
#' @description This method encodes a data object but since this is the base
#' codec class the "encoding" is a no-op.
#' @param data The data to be encoded.
#' @return The encoded data object, unaltered.
encode = function(data) {
data
},
#' @description This method decodes a data object but since this is the base
#' codec class the "decoding" is a no-op.
#' @param data The data to be decoded.
#' @return The decoded data object, unaltered.
decode = function(data) {
data
}
),
active = list(
#' @field mode (read-only) Retrieve the operating mode of the encoding
#' operation of the codec in form of a string "array -> array", "array ->
#' bytes" or "bytes -> bytes".
mode = function(value) {
if (missing(value))
paste(private$.from, private$.to, sep = ' -> ')
},
#' @field from (read-only) Character string that indicates the source data
#' type of this codec, either "array" or "bytes".
from = function(value) {
if (missing(value))
private$.from
},
#' @field to (read-only) Character string that indicates the output data
#' type of this codec, either "array" or "bytes".
to = function(value) {
if (missing(value))
private$.to
},
#' @field configuration (read-only) A list with the configuration parameters
#' of the codec, exactly like they are defined in Zarr. This field is
#' read-only but each codec class has fields to set individual parameters.
configuration = function(value) {
if (missing(value))
private$.configuration
}
)
)
#' Zarr transpose codec
#'
#' @description The Zarr "transpose" codec registers the storage order of a data
#' object relative to the canonical row-major ordering of Zarr. If the
#' registered ordering is different from the native ordering on the platform
#' where the array is being read, the data object will be permuted upon
#' reading.
#'
#' R data is arranged in column-major order. The most efficient storage
#' arrangement between Zarr and R is thus column-major ordering, avoiding
#' encoding to the canonical row-major ordering during storage and decoding to
#' column-major ordering during a read. If the storage arrangement is not
#' row-major ordering, a transpose codec must be added to the array
#' definition. Note that within R, both writing and reading are no-ops when
#' data is stored in column-major ordering. On the other hand, when no
#' transpose codec is defined for the array, there will be an automatic
#' transpose of the data on writing and reading to maintain compatibility with
#' the Zarr specification. Using the [array_builder] will automatically add
#' the transpose codec to the array definition.
#'
#' For maximum portability (e.g. with Zarr implementations outside of R that
#' do not implement the transpose codec), data should be stored in row-major
#' order, which can be achieved by not including this codec in the array
#' definition.
#' @docType class
zarr_codec_transpose <- R6::R6Class('zarr_codec_transpose',
inherit = zarr_codec,
cloneable = FALSE,
private = list (
# Print the configuration information to the console. This is called by
# zarr_codec$print().
print_configuration = function() {
cat('Configuration:\n')
cat(' order: [', paste(private$.configuration$order, collapse = ', '), ']\n', sep = '')
},
# Check if the "order" argument is valid. Returns TRUE or FALSE. "order"
# must have been cast to integer.
check_order = function(order, len) {
!is.null(order) && is.integer(order) && length(order) == len &&
all(order >= 0L & order < len) && anyDuplicated(order) == 0L
}
),
public = list(
#' @description Create a new "transpose" codec object.
#' @param shape_length The length of the shape of the array that this codec
#' operates on.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec. The element `order` specifies the ordering of the
#' dimensions of the shape relative to the Zarr canonical arrangement. An
#' integer vector with a length equal to argument
#' `shape_length`. The ordering must be 0-based. If not given, the default R
#' ordering is used.
#' @return An instance of this class.
initialize = function(shape_length, configuration = list()) {
if (shape_length < 2L)
stop('Can only set a transpose codec on a matrix or array.', call. = FALSE) # nocov
if (!length(configuration))
configuration <- list(order = seq(shape_length - 1L, 0L, -1L))
else if (!private$check_order(configuration$order, shape_length))
stop('Dimension ordering does not match the shape.', call. = FALSE) # nocov
super$initialize('transpose', configuration)
private$.from <- 'array'
private$.to <- 'array'
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_transpose`.
copy = function() {
zarr_codec_transpose$new(length(private$.configuration$order), private$.configuration)
},
#' @description This method permutes a data object to match the desired
#' dimension ordering.
#' @param data The data to be permuted, an R matrix or array.
#' @return The permuted data object, a matrix or array in Zarr store
#' dimension order.
encode = function(data) {
if (all(diff(private$.configuration$order) == -1L))
# Store in native R order - no-op
data
else
aperm(data, perm = rev(private$.configuration$order) + 1L)
},
#' @description This method permutes a data object from a Zarr store to an
#' R matrix or array.
#' @param data The data to be permuted, from a Zarr store.
#' @return The permuted data object, an R matrix or array.
decode = function(data) {
if (all(diff(private$.order) == -1L))
# Stored in native R order - no-op
data
else
aperm(data, perm = rev(private$.configuration$order) + 1L)
}
),
active = list(
#' @field order Set or retrieve the 0-based ordering of the dimensions of
#' the array when storing
order = function(value) {
if (missing(value))
private$.configuration$order
else if (private$check_order(value, length(private$.configuration$order)))
private$.configuration$order <- value
else
stop('Dimension ordering does not match the shape.', call. = FALSE) # nocov
}
)
)
#' Zarr bytes codec
#'
#' @description The Zarr "bytes" codec encodes an R data object to a raw byte
#' string, and decodes a raw byte string to a R object, possibly inverting the
#' endianness of the data in the operation.
#' @docType class
zarr_codec_bytes <- R6::R6Class('zarr_codec_bytes',
inherit = zarr_codec,
cloneable = FALSE,
private = list(
# The data type of the object that this codec operates on, an instance of
# the data_type extension object.
.data_type = NULL,
# The shape of a chunk of array data, an integer vector.
.chunk_shape = NULL,
# Print the configuration information to the console. This is called by
# zarr_codec$print().
print_configuration = function() {
cat('Configuration:\n')
cat(' endian:', private$.configuration$endian, '\n')
}
),
public = list(
#' @description Create a new "bytes" codec object.
#' @param data_type The [zarr_data_type] instance of the Zarr array that
#' this codec is used for.
#' @param chunk_shape The shape of a chunk of data of the array, an integer
#' vector.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec. The element `endian` specifies the byte ordering of the
#' data type of the Zarr array. A string with value "big" or "little". If
#' not given, the default endianness of the platform is used.
#' @return An instance of this class.
initialize = function(data_type, chunk_shape, configuration = NULL) {
if (inherits(data_type, 'zarr_data_type'))
private$.data_type <- data_type
else
stop('Codec must be initialized with a `zarr_data_type` instance.', call. = FALSE) # nocov
if (is.integer(chunk_shape))
private$.chunk_shape <- chunk_shape
else
stop('Codec must be initialized with an integer vector giving the shape of a chunk of data.', call. = FALSE) # nocov
if (is.null(configuration))
configuration <- list(endian = .Platform$endian)
else if (!is.list(configuration))
stop('`configuration` parameter must be a list.', call. = FALSE) # nocov
super$initialize('bytes', configuration)
private$.from <- 'array'
private$.to <- 'bytes'
self$endian <- configuration$endian
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_bytes`.
copy = function() {
zarr_codec_bytes$new(private$.data_type, private$.chunk_shape, private$.configuration)
},
#' @description Return the metadata fragment that describes this codec.
#' @return A list with the metadata of this codec.
metadata_fragment = function() {
if (private$.data_type$size > 1L)
list(name = 'bytes',
configuration = list(endian = private$.configuration$endian))
else
list(name = 'bytes')
},
#' @description This method writes an R object to a raw vector in the data
#' type of the Zarr array. Prior to writing, any `NA` values are assigned
#' the `fill_value` of the `data_type` of the Zarr array. Note that the
#' logical type cannot encode `NA` in Zarr and any `NA` values are set to
#' `FALSE`.
#' @param data The data to be encoded.
#' @return A raw vector with the encoded data object.
encode = function(data) {
dt <- private$.data_type
data[is.na(data)] <- dt$fill_value
dim(data) <- NULL
if (dt$data_type == 'logical') {
as.raw(as.integer(data))
} else if (dt$data_type == 'integer64') {
writeBin(unclass(data), raw(), endian = private$.configuration$endian)
} else
writeBin(data, raw(), size = dt$size, endian = private$.configuration$endian)
},
#' @description This method takes a raw vector and converts it to an R
#' object of an appropriate type. For all types other than logical, any
#' data elements with the `fill_value` of the Zarr data type are set to
#' `NA`.
#' @param data The data to be decoded.
#' @return An R object with the shape of a chunk from the array.
decode = function(data) {
dt <- private$.data_type
Rtype <- dt$Rtype
n <- length(data) %/% dt$size
if (length(data) %% dt$size)
stop('Data length not a multiple of data type size.', call. = FALSE) # nocov
out <- if (Rtype == 'logical') {
as.logical(as.integer(data))
} else if (Rtype == 'integer64') {
vals <- readBin(data, what = 'double', n = n, endian = private$.configuration$endian)
class(vals) <- 'integer64'
vals
} else {
readBin(data, what = Rtype, size = dt$size, signed = dt$signed,
n = n, endian = private$.configuration$endian)
}
if (is.nan(dt$fill_value))
out[which(is.nan(out))] <- NA
else if (!(Rtype %in% c('logical', 'integer64')))
out[.near(out, dt$fill_value)] <- NA
dim(out) <- private$.chunk_shape
out
}
),
active = list(
#' @field endian Set or retrieve the endianness of the storage of the data
#' with this codec. A string with value of "big" or "little".
endian = function(value) {
if (missing(value))
private$.configuration$endian
else if (is.character(value) && length(value) == 1L && value %in% c("big", "little"))
private$.configuration$endian <- value
else
stop('Bad value for endianness of the data.', call. = FALSE) # nocov
}
)
)
#' Zarr blosc codec
#'
#' @description The Zarr "blosc" codec offers a number of compression options to
#' reduce the size of a raw vector prior to storing, and uncompressing when
#' reading.
#' @docType class
zarr_codec_blosc <- R6::R6Class('zarr_codec_blosc',
inherit = zarr_codec,
cloneable = FALSE,
private = list(
# The zarr_data_type of the array using this codec.
.data_type = NULL,
# Print the configuration information to the console. This is called by
# zarr_codec$print().
print_configuration = function() {
cat('Configuration:\n')
cat(' compressor:', private$.configuration$cname, '\n')
cat(' level :', private$.configuration$clevel, '\n')
cat(' shuffle :', private$.configuration$shuffle, '\n')
cat(' typesize :', private$.configuration$typesize, '\n')
cat(' blocksize :', private$.configuration$blocksize, '\n')
},
# Check the configuration parameters. Conf must be a list. If ok, the list
# is returned. If not ok, an error is thrown.
check_configuration = function(conf) {
if (is.null(conf$cname))
conf$cname <- 'zstd'
else if (!is.character(conf$cname) || !(length(conf$cname) == 1L) ||
!(conf$cname %in% c("blosclz", "lz4", "lz4hc", "zstd", "zlib")))
stop('Blosc configuration has bad compression name.', call. = FALSE) # nocov
if (is.null(conf$clevel))
conf$clevel <- 1L
else if (!is.numeric(conf$clevel) || !(length(conf$clevel) == 1L) ||
!(conf$clevel >= 0 && conf$clevel <= 9))
stop('Blosc parameter clevel must be a single integer value between 0 and 9.', call. = FALSE) # nocov
if (is.null(conf$shuffle))
conf$shuffle <-
if (private$.data_type$data_type %in% c('bool', 'int8', 'uint8')) 'noshuffle'
else if (private$.data_type$data_type %in% c('int16', 'uint16', 'int32', 'uint32', 'int64', 'float32')) 'shuffle'
else 'bitshuffle'
else if (!(length(conf$shuffle) == 1L))
stop('Blosc shuffle parameter must be a single value.', call. = FALSE)
else if ((is.character(conf$shuffle) && !(conf$shuffle %in% c('shuffle', 'noshuffle', 'bitshuffle'))) ||
(is.integer(conf$shuffle) && !(conf$shuffle %in% 0L:2L)))
stop(paste('Bad blosc shuffle parameter:', conf$shuffle), call. = FALSE) # nocov
if (is.null(conf$typesize))
conf$typesize <- private$.data_type$size
else if (!is.integer(conf$typesize) || !(length(conf$typesize) == 1L) ||
!(conf$typesize %in% c(1L, 2L, 4L, 8L)))
stop('Blosc typesize parameter must be 1, 2, 4 or 8.', call. = FALSE) # nocov
if (is.null(conf$blocksize))
conf$blocksize <- 0L
else if (!is.integer(conf$blocksize) || !(length(conf$blocksize) == 1L))
stop('Blosc blocksize parameter must be a single integer value.', call. = FALSE) # nocov
conf
}
),
public = list(
#' @description Create a new "blosc" codec object. The typesize argument is
#' taken from the data type of the array passed in through the `data_type`
#' argument and the shuffle argument is chosen based on the `data_type`.
#' @param data_type The [zarr_data_type] instance of the Zarr array that
#' this codec is used for.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec. If not given, the default compression of "zstd" with
#' level 1 will be used.
#' @return An instance of this class.
initialize = function(data_type, configuration = NULL) {
if (!requireNamespace('blosc'))
stop('Must install package "blosc" for this functionality', call. = FALSE) # nocov
if (!inherits(data_type, 'zarr_data_type'))
stop('Codec must be initialized with a `zarr_data_type` instance.', call. = FALSE) # nocov
else
private$.data_type <- data_type
if (is.null(configuration))
configuration <- list()
else if (!is.list(configuration))
stop('`configuration` parameter must be a list.', call. = FALSE) # nocov
configuration <- private$check_configuration(configuration)
super$initialize('blosc', configuration)
private$.from <- 'bytes'
private$.to <- 'bytes'
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_blosc`.
copy = function() {
zarr_codec_blosc$new(private$.data_type, private$.configuration)
},
#' @description This method compresses a data object using the "blosc"
#' compression library.
#' @param data The raw vector to be compressed.
#' @return A raw vector with compressed data.
encode = function(data) {
if (is.raw(data))
blosc::blosc_compress(data, compressor = private$.configuration$cname,
level = private$.configuration$clevel,
shuffle = private$.configuration$shuffle,
typesize = private$.configuration$typesize,
blocksize = private$.configuration$blocksize)
else
stop('Blosc codec should be passed a raw vector.', call. = FALSE)
},
#' @description This method decompresses a data object using the "blosc"
#' compression library.
#' @param data The raw vector to be decoded.
#' @return A raw vector with the decoded data.
decode = function(data) {
if (is.raw(data))
blosc::blosc_decompress(data)
else
stop('Blosc codec should be passed a raw vector.', call. = FALSE)
}
),
active = list(
#' @field cname Set or retrieve the name of the compression algorithm. Must
#' be one of "blosclz", "lz4", "lz4hc", "zstd" or "zlib".
cname = function(value) {
if (missing(value))
private$.configuration$cname
else {
conf <- private$.configuration
conf$cname <- value
private$.configuration <- private$check_configuration(conf)
}
},
#' @field clevel Set or retrieve the compression level. Must
#' be an integer between 0 (no compression) and 9 (maximum compression).
clevel = function(value) {
if (missing(value))
private$.configuration$clevel
else {
conf <- private$.configuration
conf$clevel <- as.integer(value)
private$.configuration <- private$check_configuration(conf)
}
},
#' @field shuffle Set or retrieve the data shuffling of the compression
#' algorithm. Must be one of "shuffle", "noshuffle" or "bitshuffle".
shuffle = function(value) {
if (missing(value))
private$.configuration$shuffle
else {
conf <- private$.configuration
conf$shuffle <- value
private$.configuration <- private$check_configuration(conf)
}
},
#' @field typesize Set or retrieve the size in bytes of the data type being
#' compressed. It is highly recommended to leave this at the automatically
#' determined value.
typesize = function(value) {
if (missing(value))
private$.configuration$typesize
else {
conf <- private$.configuration
conf$typesize <- value
private$.configuration <- private$check_configuration(conf)
}
},
#' @field blocksize Set or retrieve the size in bytes of the blocks being
#' compressed. It is highly recommended to leave this at a value of 0 such
#' that the blosc library will automatically determine the optimal value.
blocksize = function(value) {
if (missing(value))
private$.configuration$blocksize
else {
conf <- private$.configuration
conf$blocksize <- value
private$.configuration <- private$check_configuration(conf)
}
}
)
)
#' Zarr "zstd" codec
#'
#' @description This class provides the codec for "zstd" compression.
#' @docType class
zarr_codec_zstd <- R6::R6Class('zarr_codec_zstd',
inherit = zarr_codec,
cloneable = FALSE,
private = list(
# Print the configuration information to the console. This is called by
# zarr_codec$print().
print_configuration = function() {
cat('Configuration:\n')
cat(' level:', private$.configuration$level, '\n')
}
),
public = list(
#' @description Create a new "zstd" codec object.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec. The element `level` specifies the compression level of
#' this codec, ranging from 1 (no compression) to 20 (maximum compression).
#' @return An instance of this class.
initialize = function(configuration = NULL) {
if (!requireNamespace('qs2'))
stop('Must install package "qs2" for this functionality', call. = FALSE) # nocov
if (is.null(configuration))
configuration <- list(level = 6)
else if (!is.list(configuration) || is.null(configuration$level))
stop('`configuration` argument must be a list with a field `level`.', call. = FALSE) # nocov
else if (!is.numeric(configuration$level) || length(configuration$level) != 1L ||
!(configuration$level >= 1 && configuration$level <= 20))
stop('Configuration parameter `level` must be a single integer value between 1 and 20.', call. = FALSE) # nocov
super$initialize('zstd', configuration)
private$.from <- 'bytes'
private$.to <- 'bytes'
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_zstd`.
copy = function() {
zarr_codec_zstd$new(private$.configuration)
},
#' @description This method encodes a raw data object.
#' @param data The raw data to be encoded.
#' @return The encoded raw data object.
encode = function(data) {
qs2::zstd_compress_raw(data, compress_level = private$.configuration$level)
},
#' @description This method decodes a raw data object.
#' @param data The raw data to be decoded.
#' @return The decoded raw data object.
decode = function(data) {
qs2::zstd_decompress_raw(data)
}
),
active = list(
#' @field level The compression level of the zstd codec, an integer value
#' between 1L (fast) and 20 (maximum compression).
level = function(value) {
if (missing(value))
private$.configuration$level
else {
value <- as.integer(value)
if (length(value) == 1L && value >= 1 && value <= 20)
private$.configuration$level <- as.integer(value)
else
stop('Compression level of zstd must be an integer value between 1 and 20.', call. = FALSE) # nocov
}
}
)
)
#' Zarr gzip codec
#'
#' @description The Zarr "gzip" codec compresses a raw vector prior to storing,
#' and uncompresses the raw vector when reading.
#' @docType class
zarr_codec_gzip <- R6::R6Class('zarr_codec_gzip',
inherit = zarr_codec,
cloneable = FALSE,
private = list(
# Print the configuration information to the console. This is called by
# zarr_codec$print().
print_configuration = function() {
cat('Configuration:\n')
cat(' level:', private$.configuration$level, '\n')
}
),
public = list(
#' @description Create a new "gzip" codec object.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec. The element `level` specifies the compression level of
#' this codec, ranging from 0 (no compression) to 9 (maximum compression).
#' @return An instance of this class.
initialize = function(configuration = NULL) {
if (!requireNamespace('zlib'))
stop('Must install package "zlib" for this functionality', call. = FALSE) # nocov
if (is.null(configuration))
configuration <- list(level = 6)
else if (!is.list(configuration) || is.null(configuration$level))
stop('`configuration` argument must be a list with a field `level`.', call. = FALSE) # nocov
else if (!is.numeric(configuration$level) || length(configuration$level) != 1L ||
!(configuration$level >= 0 && configuration$level <= 9))
stop('Configuration parameter `level` must be a single integer value between 0 and 9.', call. = FALSE) # nocov
super$initialize('gzip', configuration)
private$.from <- 'bytes'
private$.to <- 'bytes'
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_gzip`.
copy = function() {
zarr_codec_gzip$new(private$.configuration)
},
#' @description This method encodes a data object.
#' @param data The data to be encoded.
#' @return The encoded data object.
encode = function(data) {
zlib::compress(data, level = private$.configuration$level, wbits = 31)
},
#' @description This method decodes a data object.
#' @param data The data to be decoded.
#' @return The decoded data object.
decode = function(data) {
zlib::decompress(data, wbits = 31)
}
),
active = list(
#' @field level The compression level of the gzip codec, an integer value
#' between 0L (no compression) and 9 (maximum compression).
level = function(value) {
if (missing(value))
private$.configuration$level
else {
value <- as.integer(value)
if (length(value) == 1L && value >= 0 && value <= 9)
private$.configuration$level <- as.integer(value)
else
stop('Compression level of gzip must be an integer value between 0 and 9.', call. = FALSE) # nocov
}
}
)
)
#' Zarr CRC32C codec
#'
#' @description The Zarr "CRC32C" codec computes a 32-bit checksum of a raw
#' vector. Upon encoding the codec appends the checksum to the end of the
#' vector. When decoding, the final 4 bytes from the raw vector are extracted
#' and compared to the checksum of the remainder of the raw vector - if the
#' two don't match a warning is generated.
#' @docType class
zarr_codec_crc32c <- R6::R6Class('zarr_codec_crc32c',
inherit = zarr_codec,
cloneable = FALSE,
public = list(
#' @description Create a new "crc32c" codec object.
#' @param configuration Optional. A list with the configuration parameters
#' for this codec but since this codec doesn't have any the argument is
#' always ignored.
#' @return An instance of this class.
initialize = function() {
if (!requireNamespace('digest'))
stop('Must install package "digest" for this functionality', call. = FALSE) # nocov
super$initialize('crc32c', configuration = list())
private$.from <- 'bytes'
private$.to <- 'bytes'
},
#' @description Create a new, independent copy of this codec.
#' @return An instance of `zarr_codec_crc32c`.
copy = function() {
zarr_codec_crc32c$new()
},
#' @description This method computes the CRC32C checksum of a data object
#' and appends it to the data object.
#' @param data A raw vector whose checksum to compute.
#' @return The input `data` raw vector with the 32-bit checksum appended to
#' it.
encode = function(data) {
dig <- writeBin(strtoi(digest::digest(data, 'crc32c', serialize = FALSE), base = 16L), raw())
c(data, dig)
},
#' @description This method extracts the CRC32C checksum from the trailing
#' 32-bits of a data object. It then computes the CRC32C checksum from the
#' data object (less the trailing 32-bits) and compares the two values. If
#' the values differ, a warning will be issued.
#' @param data The raw vector whose checksum to verify.
#' @return The `data` raw vector with the trailing 32-bits removed.
decode = function(data) {
len <- length(data)
out <- data[1:(len - 4L)]
chk_stored <- readBin(data[(len - 3L):len], 'integer')
chk_calc <- strtoi(digest::digest(out, 'crc32c', serialize = FALSE), base = 16L)
if (chk_stored != chk_calc)
warning('Checksum failed on raw data object!', call. = FALSE) # nocov
out
}
)
)
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