Package 'blosc'

Compress and decompress with Blosc

Description

Use the Blosc library to compress or decompress data.

Usage

blosc_compress(
  x,
  compressor = "blosclz",
  level = 7L,
  shuffle = "noshuffle",
  typesize = 4L,
  ...
)

blosc_decompress(x, ...)

Arguments

x	In case of blosc_decompress(), x should always be raw data to be decompressed. Use ... arguments to convert decompressed data to a specific data type. In case of blosc_compress(), x should either be raw data or a vector of data to be compressed. In the latter case, you need to specify dtype (see r_to_dtype()) in order to convert the data to raw information first. See vignette("blosc-compression") for more details.
compressor	The compression algorithm to be used. Can be any of "blosclz", "lz4", "lz4hc", "zlib", or "zstd".
level	An integer indicating the required level of compression. Needs to be between 0 (no compression) and 9 (maximum compression).
shuffle	A shuffle filter to be activated before compression. Should be one of "noshuffle", "shuffle", or "bitshuffle".
typesize	BLOSC compresses arrays of structured data. This argument specifies the size (integer) of the data structure / type in bytes. Default is 4L bytes (i.e. 32 bits), which would be suitable for compressing 32 bit integers.
...	Arguments passed to r_to_dtype().

Value

In case of blosc_compress() a vector of compressed raw data is returned. In case of blosc_decompress() returns a vector of decompressed raw data. Or in in case dtype (see dtype_to_r()) is specified, a vector of the specified type is returned.

Examples

my_dat        <- as.raw(sample.int(2L, 10L*1024L, replace = TRUE) - 1L)
my_dat_out    <- blosc_compress(my_dat, typesize = 1L)
my_dat_decomp <- blosc_decompress(my_dat_out)

## After compressing and decompressing the data is the same as the original:
all(my_dat == my_dat_decomp)

---

Information about compressed data

Description

Obtain information about raw data compressed with blosc.

Usage

blosc_info(x, ...)

Arguments

x	Raw data compressed with blosc_compress().
...	Ignored

Value

Returns a named list with information about blosc compressed data x.

Examples

data_compressed <-
  blosc_compress(volcano, typesize = 2, dtype = "<i2", compressor = "lz4",
                 shuffle = "bitshuffle")

blosc_info(data_compressed)

---

Convert from or to ZARR data types

Description

Use ZARR V2.0 data types to convert between R native types and raw data.

Usage

r_to_dtype(x, dtype, na_value = NA, ...)

dtype_to_r(x, dtype, na_value = NA, ...)

Arguments

x	Object to be converted
dtype	The data type used for encoding/decoding raw data. The dtype is a code consisting of at least 3 characters. The first character indicates the endianness of the data: '<' (little-endian), '>' (big-endian), or '|' (endianness not relevant). The second character represents the main data type ('b' boolean (logical), 'i' signed integer, 'u' unsigned integer, 'f' floating point number, 'c' complex number). 'M' is used for date-time objects and 'm' for delta time (see difftime()). 'S' for UTF8 encoded character strings and 'U' for UTF32 encoded character strings. The following characters are numerical indicating the byte size of the data type. For example: dtype = "<f4" means a 32 bit floating point number; dtype = "|b1" means an 8 bit logical value. An exception is the main type 'U', where the number indicates the number of characters, where each character is represented by 4 bytes. The main types 'M' and 'm' should always be ended with the time unit between square brackets for storing the date time (difference). A valid code would be ⁠"<M8[h]⁠. For more details about dtypes see ZARR V2.0 or vignette("dtypes").
na_value	When storing raw data, you may want to reserve a value to represent missing values. This is also what R does for NA values. Other software may use different values to represent missing values. Also, some data types have insufficient storage capacity to store R NA values. Therefore, you can use this argument to indicate which value should represent missing values. By default it uses R NA. When set to NULL, missing values are just processed as is, without any further notice or warning. For more details see vignette("dtypes").
...	Ignored

Details

One of the applications of BLOSC compression is in ZARR, which is used to store n-dimensional structured data. r_to_dtype() and dtype_to_r() are convenience functions that allows you to convert most common data types to R native types.

R natively only supports logical() (actually stored as 32 bit integer in memory), integer() (signed 32 bit integers), numeric() (64 bit floating points) and complex() (real and imaginary component both represented by a 64 bit floating point). R also has some more complex classes, but those are generally derivatives of the aforementioned types.

The functions documented here will attempt to convert raw data to R types (or vice versa). As not all 'dtypes' have an appropriate R type counterpart, some conversions will not be possible directly and will result in an error.

For more details see vignette("dtypes").

Value

In case of r_to_dtype() a vector of encoded raw data is returned. In case of dtype_to_r() a vector of an R type (appropriate for the specified dtype) is returned if possible.

Author(s)

Pepijn de Vries

Examples

## Encode volcano data to 16 bit floating point values
volcano_encoded <-
  r_to_dtype(volcano, dtype = "<f2")

## Decode the volcano format to its original
volcano_reconstructed <-
  dtype_to_r(volcano_encoded, dtype = "<f2")

## The reconstruction is the same as its original:
all(volcano_reconstructed == volcano)

## Encode a numeric sequence with a missing value represented by -999
r_to_dtype(c(1, 2, 3, NA, 4), dtype = "<i2", na_value = -999)

---