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libaec - Adaptive Entropy Coding library

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# libaec - Adaptive Entropy Coding library

Libaec provides fast lossless compression of 1 up to 32 bit wide
signed or unsigned integers (samples). The library achieves best
results for low entropy data as often encountered in space imaging
instrument data or numerical model output from weather or climate
simulations. While floating point representations are not directly
supported, they can also be efficiently coded by grouping exponents
and mantissa.

## Scope

Libaec implements extended
[Golomb-Rice](http://en.wikipedia.org/wiki/Golomb_coding) coding as
defined in the CCSDS recommended standard [121.0-B-3][1]. The library
covers the adaptive entropy coder and the preprocessor discussed in
sections 1 to 5.2.6 of the [standard][1].

## Downloads

The source code is available from the git repository at

https://github.com/Deutsches-Klimarechenzentrum/libaec

or

https://gitlab.dkrz.de/dkrz-sw/libaec.

## Patent considerations

As stated in section A3 of the current [standard][1]

> At time of publication, the specifications of this Recommended
> Standard are not known to be the subject of patent rights.

## Installation

See [INSTALL.md](INSTALL.md) for details.

## SZIP Compatibility

Libaec contains libsz which can replace SZIP.

## Encoding

In this context efficiency refers to the size of the encoded
data. Performance refers to the time it takes to encode data.

Suppose you have an array of 32 bit signed integers you want to
compress. The pointer pointing to the data shall be called `source`,
output goes into `dest`.

```c
#include <libaec.h>

...
    struct aec_stream strm;
    int32_t *source;
    unsigned char *dest;

/* input data is 32 bits wide */
    strm.bits_per_sample = 32;

/* define a block size of 16 */
    strm.block_size = 16;

/* the reference sample interval is set to 128 blocks */
    strm.rsi = 128;

/* input data is signed and needs to be preprocessed */
    strm.flags = AEC_DATA_SIGNED | AEC_DATA_PREPROCESS;

/* pointer to input */
    strm.next_in = (unsigned char *)source;

/* length of input in bytes */
    strm.avail_in = source_length * sizeof(int32_t);

/* pointer to output buffer */
    strm.next_out = dest;

/* length of output buffer in bytes */
    strm.avail_out = dest_length;

/* initialize encoding */
    if (aec_encode_init(&strm) != AEC_OK)
        return 1;

/* Perform encoding in one call and flush output. */
    /* In this example you must be sure that the output */
    /* buffer is large enough for all compressed output */
    if (aec_encode(&strm, AEC_FLUSH) != AEC_OK)
        return 1;

/* free all resources used by encoder */
    aec_encode_end(&strm);
...
```

See [libaec.h](include/libaec.h) for a detailed description of all
relevant structure members and constants.

`block_size` can vary from 8 to 64 samples. Smaller blocks allow the
compression to adapt more rapidly to changing source
statistics. Larger blocks create less overhead but can be less
efficient if source statistics change across the block.

`rsi` sets the reference sample interval in blocks. A large RSI will
improve performance and efficiency. It will also increase memory
requirements since internal buffering is based on RSI size. A smaller
RSI may be desirable in situations where errors could occur in the
transmission of encoded data and the resulting propagation of errors
in decoded data has to be minimized.

### Flags:

* `AEC_DATA_SIGNED`: input data are signed integers. Specifying this
  correctly increases compression efficiency. Default is unsigned.

* `AEC_DATA_PREPROCESS`: preprocessing input will improve compression
  efficiency if data samples are correlated. It will only cost
  performance for no gain in efficiency if the data is already
  uncorrelated.

* `AEC_DATA_MSB`: input data is stored most significant byte first
  i.e. big endian. Default is little endian on all architectures.

* `AEC_DATA_3BYTE`: the 17 to 24 bit input data is stored in three
  bytes. This flag has no effect for other sample sizes.

* `AEC_RESTRICTED`: use a restricted set of code options. This option is
  only valid for `bits_per_sample` <= 4.

### Data size:

The following rules apply for deducing storage size from sample size
(`bits_per_sample`):

**sample size**  | **storage size**
--- | ---
 1 -  8 bits  | 1 byte
 9 - 16 bits  | 2 bytes
17 - 24 bits  | 3 bytes (only if `AEC_DATA_3BYTE` is set)
25 - 32 bits  | 4 bytes (if `AEC_DATA_3BYTE` is set)
17 - 32 bits  | 4 bytes (if `AEC_DATA_3BYTE` is not set)

If a sample requires less bits than the storage size provides, then
you have to make sure that unused bits are not set. Libaec does not
enforce this for performance reasons and will produce undefined output
if unused bits are set. All input data must be a multiple of the
storage size in bytes. Remaining bytes which do not form a complete
sample will be ignored.

Libaec accesses `next_in` and `next_out` buffers only bytewise. There
are no alignment requirements for these buffers.

### Flushing:

`aec_encode` can be used in a streaming fashion by chunking input and
output and specifying `AEC_NO_FLUSH`. The function will return if
either the input runs empty or the output buffer is full. The calling
function can check `avail_in` and `avail_out` to see what
occurred. The last call to `aec_encode()` must set `AEC_FLUSH` to
drain all output. [graec.c](src/graec.c) is an example of streaming
usage of encoding and decoding.

### Output:

Encoded data will be written to the buffer submitted with
`next_out`. The length of the compressed data is `total_out`.

In rare cases, like for random data, `total_out` can be larger than
the size of the input data `total_in`. The following should hold true
even for pathological cases.

```
total_out <= total_in * 67 / 64 + 256
```

## Decoding

Using decoding is very similar to encoding, only the meaning of input
and output is reversed.

```c
#include <libaec.h>

...
    struct aec_stream strm;
    /* this is now the compressed data */
    unsigned char *source;
    /* here goes the uncompressed result */
    int32_t *dest;

strm.bits_per_sample = 32;
    strm.block_size = 16;
    strm.rsi = 128;
    strm.flags = AEC_DATA_SIGNED | AEC_DATA_PREPROCESS;
    strm.next_in = source;
    strm.avail_in = source_length;
    strm.next_out = (unsigned char *)dest;
    strm.avail_out = dest_lenth * sizeof(int32_t);
    if (aec_decode_init(&strm) != AEC_OK)
        return 1;
    if (aec_decode(&strm, AEC_FLUSH) != AEC_OK)
        return 1;
    aec_decode_end(&strm);
...
```

It is strongly recommended that the size of the output buffer
(`next_out`) is a multiple of the storage size in bytes. If the buffer
is not a multiple of the storage size and the buffer gets filled to
the last sample, the error code `AEC_MEM_ERROR` is returned.

It is essential for decoding that parameters like `bits_per_sample`,
`block_size`, `rsi`, and `flags` are exactly the same as they were for
encoding. Libaec does not store these parameters in the coded stream
so it is up to the calling program to keep the correct parameters
between encoding and decoding.

The actual values of coding parameters are in fact only relevant for
efficiency and performance. Data integrity only depends on consistency
of the parameters.

The exact length of the original data is not preserved and must also
be transmitted out of band. The decoder can produce additional output
depending on whether the original data ended on a block boundary or on
zero blocks. The output data must therefore be truncated to the
correct length. This can also be achieved by providing an output
buffer of just the correct length.

### Decoding data ranges

The Libaec library has functionality that allows individual data areas
to be decoded without having to decode the entire file. This allows
efficient access to the data.

This is possible because AEC-encoded data consists of independent
blocks. It is, therefore, possible to decode individual blocks if
their offsets are known. If the preprocessor requires reference
samples, then decoding can commence only at blocks containing a
reference sample. The Libaec library can capture the offsets when
encoding or decoding the data and make them available to the user.

The following example shows how to obtain the offsets.

```c
#include <libaec.h>

...
    struct aec_stream strm;
    int32_t *source;
    unsigned char *dest;
    size_t count_offsets;
    size_t *offsets;

strm.bits_per_sample = 32;
    strm.block_size = 16;
    strm.rsi = 128;
    strm.flags = AEC_DATA_SIGNED | AEC_DATA_PREPROCESS;
    strm.next_in = (unsigned char *)source;
    strm.avail_in = source_length * sizeof(int32_t);
    strm.next_out = dest;
    strm.avail_out = dest_length;
    if (aec_encode_init(&strm) != AEC_OK)
        return 1;
    /* Enable RSI offsets */
    if (aec_encode_enable_offsets(&strm) != AEC_OK)
        return 1;
    if (aec_encode(&strm, AEC_FLUSH) != AEC_OK)
        return 1;
    /* Count RSI offsets */
    if (aec_encode_count_offsets(&strm, &count_offsets) != AEC_OK)
        return 1;
    offsets = malloc(count_offsets * sizeof(*offsets));
    /* Get RSI offsets */
    if (aec_encode_get_offsets(&strm, offsets, offsets_count) != AEC_OK)
        return 1;

aec_encode_end(&strm);
    free(offsets);
...
```

The offsets can then be used to decode ranges of data. The procedure
is similar to the previous section, but use aec_decode_range() instead
of aec_decode() and pass the offsets and the range as parameters. The
decoded ranges are written to the buffer as a stream. When decoding
the ranges into the individual buffers, set strm.total_out to zero.

```c
#include <libaec.h>

...
    struct aec_stream strm;
    unsigned char *source;
    int32_t *dest;
    /* Suppose we got the offsets from the previous step */
    size_t count_offsets;
    size_t *offsets;

strm.bits_per_sample = 32;
    strm.block_size = 16;
    strm.rsi = 128;
    strm.flags = AEC_DATA_SIGNED | AEC_DATA_PREPROCESS;
    strm.next_in = (unsigned char *)source;
    strm.avail_in = source_length * sizeof(int32_t);
    strm.next_out = dest;
    strm.avail_out = dest_length;

if (aec_decode_init(&strm))
        return 1;

/* Decode data as stream of ranges*/
    if (aec_decode_range(&strm, offsets, count_offsets, 12, 16);
        return 1;
    if (aec_decode_range(&strm, offsets, count_offsets, 244, 255);
        return 1;

/* Decode data ranges to individual buffers */
    strm.avail_out = 12
    unsigned char buf_a[strm.avail_out];
    strm.next_out = buf_a;
    strm.total_out = 0;
    if (aec_decode_range(&strm, offsets, count_offsets, 12, strm.avail_out);
        return 1;

strm.avail_out = 255;
    unsigned char buf_b[strm.avail_out];
    strm.next_out = buf_b;
    strm.total_out = 0;
    if (aec_decode_range(&strm, offsets, count_offsets, 244, strm.avail_out);
        return 1;

aec_decode_end(&strm);
...
```

## References

[Lossless Data Compression. Recommendation for Space Data System
Standards, CCSDS 121.0-B-3. Blue Book. Issue 3. Washington, D.C.:
CCSDS, August 2020.][1]

[1]: https://public.ccsds.org/Pubs/121x0b3.pdf

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