Algorithm¶

zfp uses two different algorithms to support lossy and lossless compression. These algorithms are described in detail below.

Lossy Compression¶

The zfp lossy compression scheme is based on the idea of breaking a d-dimensional array into independent blocks of 4d values each, e.g., 4 × 4 × 4 values in three dimensions. Each block is compressed/decompressed entirely independently from all other blocks. In this sense, zfp is similar to current hardware texture compression schemes for image coding implemented on graphics cards and mobile devices.

The lossy compression scheme implemented in this version of zfp has evolved from the method described in the original paper, and can conceptually be thought of as consisting of eight sequential steps (in practice some steps are consolidated or exist only for illustrative purposes):

1. The d-dimensional array is partitioned into blocks of dimensions 4d. If the array dimensions are not multiples of four, then blocks near the boundary are padded to the next multiple of four. This padding is invisible to the application.
2. The independent floating-point values in a block are converted to what is known as a block-floating-point representation, which uses a single, common floating-point exponent for all 4d values. The effect of this conversion is to turn each floating-point value into a 31- or 63-bit signed integer. If the values in the block are all zero or are smaller in magnitude than the fixed-accuracy tolerance (see below), then only a single bit is stored with the block to indicate that it is “empty” and expands to all zeros. Note that the block-floating-point conversion and empty-block encoding are not performed if the input data is represented as integers rather than floating-point numbers.
3. The integers are decorrelated using a custom, high-speed, near orthogonal transform similar to the discrete cosine transform used in JPEG image coding. The transform exploits separability and is implemented efficiently in-place using the lifting scheme, requiring only 2.5 d integer additions and 1.5 d bit shifts by one per integer in d dimensions. If the data is “smooth,” then this transform will turn most integers into small signed values clustered around zero.
4. The signed integer coefficients are reordered in a manner similar to JPEG zig-zag ordering so that statistically they appear in a roughly monotonically decreasing order. Coefficients corresponding to low frequencies tend to have larger magnitude and are listed first. In 3D, coefficients corresponding to frequencies i, j, k in the three dimensions are ordered by i + j + k first and then by i2 + j2 + k2.
5. The two’s complement signed integers are converted to their negabinary (base negative two) representation using one addition and one bit-wise exclusive or per integer. Because negabinary has no single dedicated sign bit, these integers are subsequently treated as unsigned. Unlike sign-magnitude representations, the leftmost one-bit in negabinary simultaneously encodes the sign and approximate magnitude of a number. Moreover, unlike two’s complement, numbers small in magnitude have many leading zeros in negabinary regardless of sign, which facilitates encoding.
6. The bits that represent the list of 4d integers are transposed so that instead of being ordered by coefficient they are ordered by bit plane, from most to least significant bit. Viewing each bit plane as an unsigned integer, with the lowest bit corresponding to the lowest frequency coefficient, the anticipation is that the first several of these transposed integers are small, because the coefficients are assumed to be ordered by magnitude.
7. The transform coefficients are compressed losslessly using embedded coding by exploiting the property that the coefficients tend to have many leading zeros that need not be encoded explicitly. Each bit plane is encoded in two parts, from lowest to highest bit. First, the n lowest bits are emitted verbatim, where n is the smallest number such that the 4dn highest bits in all previous bit planes are all zero. Initially, n = 0. Then, a variable-length representation of the remaining 4dn bits, x, is encoded. For such an integer x, a single bit is emitted to indicate if x = 0, in which case we are done with the current bit plane. If not, then bits of x are emitted, starting from the lowest bit, until a one-bit is emitted. This triggers another test whether this is the highest set bit of x, and the result of this test is output as a single bit. If not, then the procedure repeats until all m of x’s value bits have been output, where 2m-1x < 2m. This can be thought of as a run-length encoding of the zeros of x, where the run lengths are expressed in unary. The total number of value bits, n, in this bit plane is then incremented by m before being passed to the next bit plane, which is encoded by first emitting its n lowest bits. The assumption is that these bits correspond to n coefficients whose most significant bits have already been output, i.e., these n bits are essentially random and not compressible. Following this, the remaining 4dn bits of the bit plane are run-length encoded as described above, which potentially results in n being increased.
8. The embedded coder emits one bit at a time, with each successive bit potentially improving the accuracy of the approximation. The early bits are most important and have the greatest impact on accuracy, with the last few bits providing very small changes. The resulting compressed bit stream can be truncated at any point and still allow for a valid approximate reconstruction of the original block of values. The final step truncates the bit stream in one of three ways: to a fixed number of bits (the fixed-rate mode); after some fixed number of bit planes have been encoded (the fixed-precision mode); or until a lowest bit plane number has been encoded, as expressed in relation to the common floating-point exponent within the block (the fixed-accuracy mode).

Various parameters are exposed for controlling the quality and compressed size of a block, and can be specified by the user at a very fine granularity. These parameters are discussed here.

Lossless Compression¶

The reversible (lossless) compression algorithm shares most steps with the lossy algorithm. The main differences are steps 2, 3, and 8, which are the only sources of error. Since step 2 may introduce loss in the conversion to zfp’s block-floating-point representation, the reversible algorithm adds a test to see if this conversion is lossless. It does so by converting the values back to the source format and testing the result for bitwise equality with the uncompressed data. If this test passes, then a modified decorrelating transform is performed in step 3 that uses reversible integer subtraction operations only. Finally, step 8 is modified so that no one-bits are truncated in the variable-length bit stream. However, all least significant bit planes with all-zero bits are truncated, and the number of encoded bit planes is recorded in step 7. As with lossy compression, a floating-point block consisting of all (“positive”) zeros is represented as a single bit, making it possible to efficiently encode sparse data.

If the block-floating-point transform is not lossless, then the reversible compression algorithm falls back on a simpler scheme that reinterprets floating-point values as integers via type punning. This lossless conversion from floating-point to integer data replaces step 2, and the algorithm proceeds from there with the modified step 3. Moreover, this conversion ensures that special values like infinities, NaNs, and negative zero are preserved.

The lossless algorithm handles integer data also, for which step 2 is omitted.