// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute // SPDX-License-Identifier: GPL-3.0-only #pragma once #include #include #include #include #include #include #include "BitShuffleBlock.h" #include "CBFByteOffset.h" #include "../compression/CompressionAlgorithmEnum.h" #include "../common/JFJochException.h" #include "../common/CompressedImage.h" extern "C" { uint64_t bshuf_read_uint64_BE(const void* buf); }; // Decode the bitshuffle blocks one after another and hand each to block_done(first_element, data, // nelements), in element order. With output set, each block is decoded in place into output; with // output = nullptr, into a block-sized buffer that is reused for the next block, so a caller that // consumes the block straight away reads it from cache and the whole image is never written out. template size_t JFJochDecompressHperfBlocks(uint8_t *output, CompressionAlgorithm algorithm, const uint8_t *source, size_t source_size, size_t nelements, size_t elem_size, size_t block_size, F &&block_done) { if ((algorithm != CompressionAlgorithm::BSHUF_LZ4) && (algorithm != CompressionAlgorithm::BSHUF_ZSTD) && (algorithm != CompressionAlgorithm::BSHUF_ZSTD_RLE) && (algorithm != CompressionAlgorithm::BSHUF_ZSTD_RLE_HUFF)) throw JFJochException(JFJochExceptionCategory::Compression, "Algorithm not supported by hperf decompressor"); if ((block_size == 0) || ((block_size % BSHUF_BLOCKED_MULT) != 0)) throw JFJochException(JFJochExceptionCategory::Compression, "Invalid block size"); std::vector decompressed_block(block_size * elem_size); std::vector scratch(block_size * elem_size); std::vector unshuffled(output ? 0 : block_size * elem_size); const uint8_t *src_ptr = source; const uint8_t *const source_end = source + source_size; size_t first_element = 0; const size_t num_full_blocks = nelements / block_size; const size_t reminder_size = nelements - num_full_blocks * block_size; const size_t last_block_size = reminder_size - reminder_size % BSHUF_BLOCKED_MULT; auto decode_block = [&](size_t current_nelements) { // Both the block length and the block itself come from the stream, which for the CBOR path // and for the XDS plugin is data we did not produce. if (source_end - src_ptr < 4) throw JFJochException(JFJochExceptionCategory::Compression, "Truncated compressed block header"); const auto compressed_size = static_cast(bshuf_read_uint32_BE(src_ptr)); src_ptr += 4; if (static_cast(source_end - src_ptr) < compressed_size) throw JFJochException(JFJochExceptionCategory::Compression, "Compressed block extends past the input buffer"); const size_t expected_size = current_nelements * elem_size; size_t decompressed_size = 0; switch (algorithm) { case CompressionAlgorithm::BSHUF_LZ4: { const int ret = LZ4_decompress_safe(reinterpret_cast(src_ptr), decompressed_block.data(), static_cast(compressed_size), static_cast(expected_size)); if (ret < 0 || static_cast(ret) != expected_size) throw JFJochException(JFJochExceptionCategory::Compression, "LZ4 decompression error"); decompressed_size = static_cast(ret); break; } case CompressionAlgorithm::BSHUF_ZSTD: case CompressionAlgorithm::BSHUF_ZSTD_RLE: case CompressionAlgorithm::BSHUF_ZSTD_RLE_HUFF: { const size_t ret = ZSTD_decompress(decompressed_block.data(), expected_size, src_ptr, compressed_size); if (ZSTD_isError(ret) || ret != expected_size) throw JFJochException(JFJochExceptionCategory::Compression, "ZSTD decompression error"); decompressed_size = ret; break; } default: throw JFJochException(JFJochExceptionCategory::Compression, "Algorithm not supported"); } uint8_t *dst_ptr = output ? output + first_element * elem_size : unshuffled.data(); if (JFJochBitUnshuffleBlock(reinterpret_cast(dst_ptr), decompressed_block.data(), scratch.data(), current_nelements, elem_size) < 0) throw JFJochException(JFJochExceptionCategory::Compression, "bitshuffle block decode error"); block_done(first_element, dst_ptr, current_nelements); src_ptr += compressed_size; first_element += decompressed_size / elem_size; }; for (size_t i = 0; i < num_full_blocks; ++i) decode_block(block_size); if (last_block_size > 0) decode_block(last_block_size); const size_t leftover_bytes = (reminder_size % BSHUF_BLOCKED_MULT) * elem_size; if (leftover_bytes > 0) { if (static_cast(source_end - src_ptr) < leftover_bytes) throw JFJochException(JFJochExceptionCategory::Compression, "Truncated trailing bytes"); uint8_t *dst_ptr = output ? output + first_element * elem_size : unshuffled.data(); memcpy(dst_ptr, src_ptr, leftover_bytes); block_done(first_element, dst_ptr, leftover_bytes / elem_size); src_ptr += leftover_bytes; } return static_cast(src_ptr - source); } inline size_t JFJochDecompressHperfPtr(uint8_t *output, CompressionAlgorithm algorithm, const uint8_t *source, size_t source_size, size_t nelements, size_t elem_size, size_t block_size) { return JFJochDecompressHperfBlocks(output, algorithm, source, source_size, nelements, elem_size, block_size, [](size_t, const uint8_t *, size_t) {}); } // Plain LZ4, HDF5 filter 32004, as DECTRIS Eiger firmware 1.x wrote it. The framing is the same as // bitshuffle's - a 64-bit big-endian total size, a 32-bit big-endian block size IN BYTES, then each // block prefixed by its 32-bit big-endian compressed size - and the only difference is that no bit // shuffle was applied, so each block decompresses straight into place. It cannot go through the // bitshuffle path: that one requires the block to be a multiple of BSHUF_BLOCKED_MULT elements, and // these files put the WHOLE image in one block (measured: 40666360 bytes, i.e. 10166590 uint32). inline void JFJochDecompressLZ4Ptr(uint8_t *output, const uint8_t *source, size_t source_size, size_t nelements, size_t elem_size) { const size_t expected_total = nelements * elem_size; if (source_size < 12) throw JFJochException(JFJochExceptionCategory::Compression, "Buffer too short for the LZ4 header"); if (bshuf_read_uint64_BE(const_cast(source)) != expected_total) throw JFJochException(JFJochExceptionCategory::Compression, "Mismatch in size"); size_t block_bytes = bshuf_read_uint32_BE(source + 8); if (block_bytes == 0) block_bytes = expected_total; // some writers leave it zero and mean "one block" const uint8_t *src_ptr = source + 12; const uint8_t *const source_end = source + source_size; size_t written = 0; while (written < expected_total) { if (source_end - src_ptr < 4) throw JFJochException(JFJochExceptionCategory::Compression, "Truncated LZ4 block header"); const auto compressed_size = static_cast(bshuf_read_uint32_BE(src_ptr)); src_ptr += 4; if (compressed_size == 0 || static_cast(source_end - src_ptr) < compressed_size) throw JFJochException(JFJochExceptionCategory::Compression, "LZ4 block extends past the input buffer"); const size_t this_block = std::min(block_bytes, expected_total - written); const int ret = LZ4_decompress_safe(reinterpret_cast(src_ptr), reinterpret_cast(output + written), static_cast(compressed_size), static_cast(this_block)); if (ret < 0 || static_cast(ret) != this_block) throw JFJochException(JFJochExceptionCategory::Compression, "LZ4 decompression error"); src_ptr += compressed_size; written += this_block; } } // Check the 12-byte bitshuffle header and return the block size (in elements) it gives. inline size_t JFJochBitshuffleHeaderBlockSize(const uint8_t *source, size_t source_size, size_t nelements, size_t elem_size) { // The header must be there before it can be read, and before source_size - 12 is handed to the // decompressors. if (source_size < 12) throw JFJochException(JFJochExceptionCategory::Compression, "Buffer too short for the bitshuffle header"); if (bshuf_read_uint64_BE(const_cast(source)) != nelements * elem_size) throw JFJochException(JFJochExceptionCategory::Compression, "Mismatch in size"); return bshuf_read_uint32_BE(source + 8) / elem_size; } inline bool JFJochIsBitshuffle(CompressionAlgorithm algorithm) { return (algorithm == CompressionAlgorithm::BSHUF_LZ4) || (algorithm == CompressionAlgorithm::BSHUF_ZSTD) || (algorithm == CompressionAlgorithm::BSHUF_ZSTD_RLE) || (algorithm == CompressionAlgorithm::BSHUF_ZSTD_RLE_HUFF); } // A bitshuffle-compressed image, handed block by block to block_done(first_element, data, nelements) // in element order (see JFJochDecompressHperfBlocks), without the image ever being written out whole. template void JFJochDecompressBlocks(CompressionAlgorithm algorithm, const uint8_t *source, size_t source_size, size_t nelements, size_t elem_size, F &&block_done) { const size_t block_size = JFJochBitshuffleHeaderBlockSize(source, source_size, nelements, elem_size); if (JFJochDecompressHperfBlocks(nullptr, algorithm, source + 12, source_size - 12, nelements, elem_size, block_size, block_done) != source_size - 12) throw JFJochException(JFJochExceptionCategory::Compression, "Decompression error"); } inline void JFJochDecompressPtr(uint8_t *output, CompressionAlgorithm algorithm, const uint8_t *source, size_t source_size, size_t nelements, size_t elem_size, bool use_hperf = true) { if (algorithm == CompressionAlgorithm::LZ4_NO_SHUFFLE) { JFJochDecompressLZ4Ptr(output, source, source_size, nelements, elem_size); return; } if (algorithm == CompressionAlgorithm::CBF_BYTE_OFFSET) { if (elem_size != sizeof(int32_t)) throw JFJochException(JFJochExceptionCategory::Compression, "CBF byte offset decodes to int32"); DecodeCBFByteOffset(source, source_size, reinterpret_cast(output), nelements); return; } if (algorithm == CompressionAlgorithm::UINT16_WIDENED) { if (elem_size != sizeof(int32_t) || source_size != nelements * sizeof(uint16_t)) throw JFJochException(JFJochExceptionCategory::Compression, "Mismatch in size"); const auto *src = reinterpret_cast(source); auto *dst = reinterpret_cast(output); for (size_t i = 0; i < nelements; i++) dst[i] = src[i]; return; } size_t block_size = 0; if (algorithm != CompressionAlgorithm::NO_COMPRESSION) block_size = JFJochBitshuffleHeaderBlockSize(source, source_size, nelements, elem_size); switch (algorithm) { case CompressionAlgorithm::NO_COMPRESSION: if (source_size != nelements * elem_size) throw JFJochException(JFJochExceptionCategory::Compression, "Mismatch in size"); memcpy(output, source, source_size); break; case CompressionAlgorithm::BSHUF_LZ4: if (use_hperf) { if (JFJochDecompressHperfPtr(output, algorithm, source + 12, source_size - 12, nelements, elem_size, block_size) != source_size - 12) throw JFJochException(JFJochExceptionCategory::Compression, "Decompression error"); } else { if (bshuf_decompress_lz4(source + 12, output, nelements, elem_size, block_size) != source_size - 12) throw JFJochException(JFJochExceptionCategory::Compression, "Decompression error"); } break; case CompressionAlgorithm::BSHUF_ZSTD_RLE: case CompressionAlgorithm::BSHUF_ZSTD_RLE_HUFF: case CompressionAlgorithm::BSHUF_ZSTD: if (use_hperf) { if (JFJochDecompressHperfPtr(output, algorithm, source + 12, source_size - 12, nelements, elem_size, block_size) != source_size - 12) throw JFJochException(JFJochExceptionCategory::Compression, "Decompression error"); } else { if (bshuf_decompress_zstd(source + 12, output, nelements, elem_size, block_size) != source_size - 12) throw JFJochException(JFJochExceptionCategory::Compression, "Decompression error"); } break; default: throw JFJochException(JFJochExceptionCategory::Compression, "Not implemented algorithm"); } } template void JFJochDecompress(std::vector &output, CompressionAlgorithm algorithm, const Ts *source_v, size_t source_size, size_t nelements, bool use_hperf = true) { output.resize(nelements); JFJochDecompressPtr((uint8_t *) output.data(), algorithm, (uint8_t *) source_v, source_size, nelements, sizeof(Td), use_hperf); } template void JFJochDecompress(std::vector &output, CompressionAlgorithm algorithm, const std::vector source_v, size_t nelements, bool use_hperf = true) { JFJochDecompress(output, algorithm, source_v.data(), source_v.size() * sizeof(Ts), nelements, use_hperf); }