leonarski_fandClaude Opus 5
26fc4b02b3
The adopted space group travelled the pipeline as a bare int and was rebuilt downstream with find_spacegroup_by_number, which returns the reference setting. So every setting a number cannot name was destroyed one line after it was determined: P 1 1 2 came back as P 1 2 1, I 1 1 2 as C 1 2 1, R 3:R as R 3:H. DatasetSettings now holds the gemmi::SpaceGroup itself, DiffractionExperiment exposes it as GetGemmiSpaceGroup() / GetSpaceGroupOrP1(), and everything that used to take an int - HKLKeyGenerator (its int constructor is gone, so the compiler finds the callers), the merge, the R-free flags, French-Wilson, the reindexing ambiguity, the completeness enumeration, the MTZ and mmCIF exports, the model validation - takes the group. -S keeps the setting the symbol names rather than reducing it to a number. The end message carries both spellings and a reader prefers the name, since only the name keeps the setting while the number is what a reader written before the name understands. It carries them over CBOR too: the determined group was never serialised at all, so a group rugnux chose reached the master file only when the same process wrote it, and an online writer fell back to whatever the user had supplied at the start. Both keys are optional additions, so an older reader skips them and a newer one reads an older sender. On disk the master's /entry/sample/space_group carries the extended Hermann-Mauguin name and is what the reader takes the group from, so a setting survives a _process.h5 and the --mode scale that re-reads it; the number stays beside it and is the fallback for files written before. Every one of the 230 reference settings the old writer could produce reads back as itself, so older files are unaffected. Stage A and Stage B of the search still enumerate reference settings only, so this determines no group differently today - it is what the enumeration needs before it can be widened. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
1015 lines
47 KiB
C++
1015 lines
47 KiB
C++
// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include "CBORStream2Serializer.h"
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#include "tinycbor/cbor.h"
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#include "CborErr.h"
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#include "CborUtil.h"
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#include "../compression/JFJochCompressor.h"
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#include <nlohmann/json.hpp>
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const char* value) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_text_stringz(&encoder, value));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::string &value) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_text_stringz(&encoder, value.c_str()));
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}
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inline void CBOR_ENC_DATE(CborEncoder &encoder, const char* key, const std::string &value) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cbor_encode_tag(&encoder, CborDateTimeStringTag);
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cborErr(cbor_encode_text_stringz(&encoder, value.c_str()));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, float value) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_float(&encoder, value));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, bool value) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_boolean(&encoder, value));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, uint64_t value) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_uint(&encoder, value));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, int64_t value) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_int(&encoder, value));
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}
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template <class T>
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void CBOR_ENC(CborEncoder &encoder, const char* key, const std::optional<T> &value) {
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if (value)
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CBOR_ENC(encoder, key, value.value());
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}
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void CBOR_ENC_COMPRESSED(CborEncoder &encoder,
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const void *image, size_t image_size,
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CompressionAlgorithm algorithm,
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size_t elem_size) {
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if (algorithm == CompressionAlgorithm::NO_COMPRESSION)
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cborErr(cbor_encode_byte_string(&encoder, (uint8_t *) image, image_size));
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else {
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cbor_encode_tag(&encoder, TagDECTRISCompression);
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CborEncoder arrayEncoder;
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cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, 3));
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switch (algorithm) {
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case CompressionAlgorithm::BSHUF_LZ4:
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cborErr(cbor_encode_text_stringz(&arrayEncoder, "bslz4"));
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break;
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case CompressionAlgorithm::BSHUF_ZSTD:
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case CompressionAlgorithm::BSHUF_ZSTD_RLE:
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case CompressionAlgorithm::BSHUF_ZSTD_RLE_HUFF:
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cborErr(cbor_encode_text_stringz(&arrayEncoder, "bszstd"));
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break;
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default:
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throw JFJochException(JFJochExceptionCategory::CBORError, "Unsupported compression algorithm");
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}
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cborErr(cbor_encode_uint(&arrayEncoder, elem_size));
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cborErr(cbor_encode_byte_string(&arrayEncoder, (uint8_t *) image, image_size));
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cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
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}
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}
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inline void CBOR_ENC_2D_TYPED_ARRAY(CborEncoder &encoder, const CompressedImage& image) {
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//if ((algorithm == CompressionAlgorithm::NO_COMPRESSION) && (xpixel * ypixel != image_size / elem_size))
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// throw JFJochException(JFJochExceptionCategory::CBORError, "Mismatch in array size");
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CborEncoder arrayEncoder, arrayEncoder_2;
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cborErr(cbor_encode_text_stringz(&encoder, image.GetChannel().c_str()));
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cbor_encode_tag(&encoder, TagMultiDimArray);
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cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, 2));
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if (image.GetMode() == CompressedImageMode::RGB) {
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cborErr(cbor_encoder_create_array(&arrayEncoder, &arrayEncoder_2, 3));
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cborErr(cbor_encode_uint(&arrayEncoder_2, 3));
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cborErr(cbor_encode_uint(&arrayEncoder_2, image.GetHeight()));
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cborErr(cbor_encode_uint(&arrayEncoder_2, image.GetWidth()));
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cborErr(cbor_encoder_close_container(&arrayEncoder, &arrayEncoder_2));
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} else {
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cborErr(cbor_encoder_create_array(&arrayEncoder, &arrayEncoder_2, 2));
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cborErr(cbor_encode_uint(&arrayEncoder_2, image.GetHeight()));
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cborErr(cbor_encode_uint(&arrayEncoder_2, image.GetWidth()));
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cborErr(cbor_encoder_close_container(&arrayEncoder, &arrayEncoder_2));
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}
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CborTag typed_array_tag;
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switch (image.GetMode()) {
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case CompressedImageMode::RGB:
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case CompressedImageMode::Uint8:
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typed_array_tag = TagUnsignedInt8Bit;
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break;
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case CompressedImageMode::Uint16:
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typed_array_tag = TagUnsignedInt16BitLE;
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break;
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case CompressedImageMode::Uint32:
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typed_array_tag = TagUnsignedInt32BitLE;
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break;
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case CompressedImageMode::Int8:
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typed_array_tag = TagSignedInt8Bit;
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break;
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case CompressedImageMode::Int16:
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typed_array_tag = TagSignedInt16BitLE;
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break;
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case CompressedImageMode::Int32:
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typed_array_tag = TagSignedInt32BitLE;
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break;
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case CompressedImageMode::Float16:
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typed_array_tag = TagHalfLE;
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break;
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case CompressedImageMode::Float32:
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typed_array_tag = TagFloatLE;
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break;
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case CompressedImageMode::Float64:
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typed_array_tag = TagDoubleLE;
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break;
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default:
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throw JFJochException(JFJochExceptionCategory::CBORError, "Image mode not supported");
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}
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cbor_encode_tag(&arrayEncoder, typed_array_tag);
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CBOR_ENC_COMPRESSED(arrayEncoder, image.GetCompressed(),
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image.GetCompressedSize(), image.GetCompressionAlgorithm(),
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image.GetByteDepth());
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cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<float>& v) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_tag(&encoder, TagFloatLE));
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cborErr(cbor_encode_byte_string(&encoder, (uint8_t *) v.data(), v.size() * sizeof(float)));
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}
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inline void CBOR_ENC_FLOAT_ARRAY_NOKEY(CborEncoder &encoder, const std::vector<float>& v) {
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cborErr(cbor_encode_tag(&encoder, TagFloatLE));
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cborErr(cbor_encode_byte_string(&encoder, (uint8_t *) v.data(), v.size() * sizeof(float)));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<uint8_t>& v) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_tag(&encoder, TagUnsignedInt8Bit));
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cborErr(cbor_encode_byte_string(&encoder, v.data(), v.size() * sizeof(uint8_t)));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<int32_t>& v) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_tag(&encoder, TagSignedInt32BitLE));
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cborErr(cbor_encode_byte_string(&encoder, reinterpret_cast<const uint8_t *>(v.data()), v.size() * sizeof(int32_t)));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<int64_t>& v) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_tag(&encoder, TagSignedInt64BitLE));
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cborErr(cbor_encode_byte_string(&encoder, reinterpret_cast<const uint8_t *>(v.data()), v.size() * sizeof(int64_t)));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<uint64_t>& v) {
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encode_tag(&encoder, TagUnsignedInt64BitLE));
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cborErr(cbor_encode_byte_string(&encoder, (uint8_t *) v.data(), v.size() * sizeof(uint64_t)));
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}
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inline void CBOR_ENC_RATIONAL(CborEncoder &encoder, const char* key, uint64_t numerator, uint64_t denominator) {
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CborEncoder arrayEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, 2));
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cborErr(cbor_encode_uint(&arrayEncoder, numerator));
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cborErr(cbor_encode_uint(&arrayEncoder, denominator));
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cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::map<std::string, float> &val) {
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CborEncoder mapEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, val.size()));
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for (auto &[map_key, map_val]: val)
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CBOR_ENC(mapEncoder, map_key.c_str(), map_val);
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cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
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}
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inline void CBOR_ENC_RAD_INT_RESULT(CborEncoder &encoder, const char* key,
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const std::map<std::string, std::vector<float>> &az_int_result) {
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CborEncoder mapEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, az_int_result.size()));
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for (auto &[map_key, map_val]: az_int_result)
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CBOR_ENC(mapEncoder, map_key.c_str(), map_val);
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cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
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}
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inline void CBOR_ENC_ADU_HIST(CborEncoder &encoder, const char* key,
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const std::map<std::string, std::vector<uint64_t>> &adu_histogram) {
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CborEncoder mapEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, adu_histogram.size()));
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for (auto &[map_key, map_val]: adu_histogram)
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CBOR_ENC(mapEncoder, map_key.c_str(), map_val);
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cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const SpotToSave& spot) {
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CborEncoder mapEncoder;
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cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
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CBOR_ENC(mapEncoder, "x", spot.x);
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CBOR_ENC(mapEncoder, "y", spot.y);
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CBOR_ENC(mapEncoder, "I", spot.intensity);
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CBOR_ENC(mapEncoder, "maxc", spot.maxc);
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CBOR_ENC(mapEncoder, "ice_ring", spot.ice_ring);
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CBOR_ENC(mapEncoder, "indexed", spot.indexed);
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CBOR_ENC(mapEncoder, "latt", spot.lattice);
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CBOR_ENC(mapEncoder, "image", spot.image);
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if (spot.indexed) {
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CBOR_ENC(mapEncoder, "h", spot.h);
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CBOR_ENC(mapEncoder, "k", spot.k);
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CBOR_ENC(mapEncoder, "l", spot.l);
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CBOR_ENC(mapEncoder, "dist_ewald", spot.dist_ewald_sphere);
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}
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cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const XrayFluorescenceSpectrum& f) {
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if (f.empty())
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return;
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CborEncoder mapEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
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CBOR_ENC(mapEncoder, "data", f.GetData());
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CBOR_ENC(mapEncoder, "energy", f.GetEnergy_eV());
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cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const Reflection& r) {
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CborEncoder mapEncoder;
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cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
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CBOR_ENC(mapEncoder, "h", static_cast<int64_t>(r.h));
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CBOR_ENC(mapEncoder, "k", static_cast<int64_t>(r.k));
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CBOR_ENC(mapEncoder, "l", static_cast<int64_t>(r.l));
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CBOR_ENC(mapEncoder, "phi", r.delta_phi_deg);
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CBOR_ENC(mapEncoder, "x", r.predicted_x);
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CBOR_ENC(mapEncoder, "y", r.predicted_y);
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CBOR_ENC(mapEncoder, "obs_x", r.observed_x);
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CBOR_ENC(mapEncoder, "obs_y", r.observed_y);
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CBOR_ENC(mapEncoder, "d", r.d);
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CBOR_ENC(mapEncoder, "I", r.I);
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CBOR_ENC(mapEncoder, "bkg", r.bkg);
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CBOR_ENC(mapEncoder, "var_bkg", r.var_bkg);
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CBOR_ENC(mapEncoder, "sigma", r.sigma);
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CBOR_ENC(mapEncoder, "image", r.image_number);
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CBOR_ENC(mapEncoder, "rp", r.dist_ewald);
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CBOR_ENC(mapEncoder, "rlp", r.rlp);
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CBOR_ENC(mapEncoder, "partiality", r.partiality);
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CBOR_ENC(mapEncoder, "zeta", r.zeta);
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CBOR_ENC(mapEncoder, "image_scale_corr", r.image_scale_corr);
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cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const Coord& coord) {
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CborEncoder arrayEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, 3));
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cborErr(cbor_encode_float(&arrayEncoder, coord[0]));
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cborErr(cbor_encode_float(&arrayEncoder, coord[1]));
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cborErr(cbor_encode_float(&arrayEncoder, coord[2]));
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cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<SpotToSave>& spots) {
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CborEncoder arrayEncoder, mapEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, spots.size()));
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for (auto spot : spots)
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CBOR_ENC(arrayEncoder, spot);
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cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<Reflection>& refs) {
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CborEncoder arrayEncoder, mapEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, refs.size()));
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for (auto r: refs)
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CBOR_ENC(arrayEncoder, r);
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cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
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}
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inline void CBOR_ENC(CborEncoder &encoder, const char* key, const CompressedImage& message) {
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CborEncoder mapEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 1));
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CBOR_ENC_2D_TYPED_ARRAY(mapEncoder, message);
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cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
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}
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inline void CBOR_ENC_AXIS(CborEncoder &encoder, const char* key, const float det_translation[3]) {
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CborEncoder arrayEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, 3));
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for (int i = 0; i < 3; i++)
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cborErr(cbor_encode_float(&arrayEncoder, det_translation[i]));
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cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
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}
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inline void CBOR_ENC_GONIOMETER(CborEncoder &encoder, const GoniometerAxis &g) {
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CborEncoder mapEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, g.GetName().c_str()));
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cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
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CBOR_ENC(mapEncoder, "increment", g.GetIncrement_deg());
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CBOR_ENC(mapEncoder, "start", g.GetStart_deg());
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CBOR_ENC(mapEncoder, "axis", g.GetAxis());
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CBOR_ENC(mapEncoder, "screening_wedge", g.GetScreeningWedge());
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if (g.GetHelicalStep().has_value())
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CBOR_ENC(mapEncoder, "helical_step", g.GetHelicalStep().value());
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cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
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}
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inline void CBOR_ENC_GRID_SCAN(CborEncoder &encoder, const char* key, const GridScanSettings &g) {
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CborEncoder mapEncoder;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 6));
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CBOR_ENC(mapEncoder, "n_fast", g.GetNFast());
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CBOR_ENC(mapEncoder, "n_slow", g.GetNSlow());
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CBOR_ENC(mapEncoder, "step_x_axis", g.GetGridStepX_um() * 1e-6f);
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CBOR_ENC(mapEncoder, "step_y_axis", g.GetGridStepY_um() * 1e-6f);
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CBOR_ENC(mapEncoder, "snake_scan", g.IsSnakeScan());
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CBOR_ENC(mapEncoder, "vertical_scan", g.IsVerticalScan());
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cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
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}
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inline void CBOR_ENC_TRANSFORMATIONS(CborEncoder &encoder, const char* key,
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const std::vector<DetectorTransformation> &chain) {
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if (chain.empty())
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return;
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|
|
CborEncoder arrayEncoder, mapEncoder;
|
|
cborErr(cbor_encode_text_stringz(&encoder, key));
|
|
// An ARRAY, not a map: the chain is ordered, base first, and a CBOR map carries no order a
|
|
// consumer may rely on - RFC 8949 has deterministic encoders sort map keys.
|
|
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, chain.size()));
|
|
for (const auto &axis: chain) {
|
|
cborErr(cbor_encoder_create_map(&arrayEncoder, &mapEncoder, CborIndefiniteLength));
|
|
CBOR_ENC(mapEncoder, "name", axis.GetName());
|
|
CBOR_ENC(mapEncoder, "transformation_type", axis.IsRotation() ? "rotation" : "translation");
|
|
CBOR_ENC(mapEncoder, "units", axis.GetUnits());
|
|
CBOR_ENC(mapEncoder, "vector", axis.GetVector());
|
|
CBOR_ENC(mapEncoder, "offset", axis.GetOffset());
|
|
CBOR_ENC(mapEncoder, "depends_on", axis.GetDependsOn());
|
|
if (!axis.GetEquipment().empty())
|
|
CBOR_ENC(mapEncoder, "equipment", axis.GetEquipment());
|
|
if (!axis.GetEquipmentComponent().empty())
|
|
CBOR_ENC(mapEncoder, "equipment_component", axis.GetEquipmentComponent());
|
|
CBOR_ENC(mapEncoder, "values", axis.GetValues());
|
|
cborErr(cbor_encoder_close_container(&arrayEncoder, &mapEncoder));
|
|
}
|
|
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
|
|
}
|
|
|
|
inline void CBOR_ENC_GONIOMETER_MAP(CborEncoder &encoder, const char* key, const StartMessage &msg) {
|
|
CborEncoder mapEncoder;
|
|
|
|
if (msg.goniometer) {
|
|
cborErr(cbor_encode_text_stringz(&encoder, key));
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 1));
|
|
CBOR_ENC_GONIOMETER(mapEncoder, msg.goniometer.value());
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
}
|
|
}
|
|
|
|
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<std::string> &v) {
|
|
CborEncoder arrayEncoder;
|
|
|
|
cborErr(cbor_encode_text_stringz(&encoder, key));
|
|
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, v.size()));
|
|
for (const auto &i: v)
|
|
cborErr(cbor_encode_text_stringz(&arrayEncoder, i.c_str()));
|
|
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
|
|
}
|
|
|
|
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const ROIMessage &val) {
|
|
CborEncoder mapEncoder;
|
|
|
|
cborErr(cbor_encode_text_stringz(&encoder, key));
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 6));
|
|
CBOR_ENC(mapEncoder, "sum", val.sum);
|
|
CBOR_ENC(mapEncoder, "sum_square", val.sum_square);
|
|
CBOR_ENC(mapEncoder, "max_count", val.max_count);
|
|
CBOR_ENC(mapEncoder, "pixels", val.pixels);
|
|
CBOR_ENC(mapEncoder, "x_weighted_sum", val.x_weighted);
|
|
CBOR_ENC(mapEncoder, "y_weighted_sum", val.y_weighted);
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
}
|
|
|
|
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::map<std::string, ROIMessage> &map) {
|
|
CborEncoder mapEncoder;
|
|
|
|
if (map.empty())
|
|
return;
|
|
|
|
cborErr(cbor_encode_text_stringz(&encoder, key));
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, map.size()));
|
|
for (const auto &[x, y]: map)
|
|
CBOR_ENC(mapEncoder, x.c_str(), y);
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
}
|
|
|
|
inline void CBOR_ENC_PIXEL_MASK(CborEncoder &encoder, const StartMessage &msg) {
|
|
if (msg.pixel_mask.empty())
|
|
return;
|
|
|
|
CborEncoder mapEncoder;
|
|
|
|
cborErr(cbor_encode_text_stringz(&encoder, "pixel_mask"));
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, msg.pixel_mask.size()));
|
|
for (const auto &[key, value]: msg.pixel_mask) {
|
|
if (value.size() != msg.image_size_x * msg.image_size_y)
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"Mismatch in size of pixel mask");
|
|
|
|
JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
|
|
auto mask_compressed = compressor.Compress(value);
|
|
CompressedImage image(mask_compressed.data(), mask_compressed.size(),
|
|
msg.image_size_x, msg.image_size_y,
|
|
CompressedImageMode::Uint32,
|
|
CompressionAlgorithm::BSHUF_LZ4,
|
|
key);
|
|
CBOR_ENC_2D_TYPED_ARRAY(mapEncoder, image);
|
|
}
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
}
|
|
|
|
inline void CBOR_ENC_AZINT_MAP(CborEncoder &encoder, const StartMessage &msg) {
|
|
if (msg.az_int_map.empty())
|
|
return;
|
|
|
|
if (msg.az_int_map.size() != msg.image_size_x * msg.image_size_y)
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"Mismatch in size of pixel mask");
|
|
|
|
JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
|
|
auto mask_compressed = compressor.Compress(msg.az_int_map);
|
|
CompressedImage image(mask_compressed.data(), mask_compressed.size(),
|
|
msg.image_size_x, msg.image_size_y,
|
|
CompressedImageMode::Uint16,
|
|
CompressionAlgorithm::BSHUF_LZ4, "az_int_map");
|
|
CBOR_ENC_2D_TYPED_ARRAY(encoder, image);
|
|
}
|
|
|
|
inline void CBOR_ENC_ROI_MAP(CborEncoder &encoder, const StartMessage &msg) {
|
|
if (msg.roi_map.empty())
|
|
return;
|
|
|
|
if (msg.roi_map.size() != msg.image_size_x * msg.image_size_y)
|
|
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
|
"Mismatch in size of ROI map");
|
|
|
|
JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
|
|
auto mask_compressed = compressor.Compress(msg.roi_map);
|
|
CompressedImage image(mask_compressed.data(), mask_compressed.size(),
|
|
msg.image_size_x, msg.image_size_y,
|
|
CompressedImageMode::Uint16,
|
|
CompressionAlgorithm::BSHUF_LZ4, "roi_map");
|
|
CBOR_ENC_2D_TYPED_ARRAY(encoder, image);
|
|
}
|
|
|
|
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const UnitCell &val) {
|
|
CborEncoder mapEncoder;
|
|
|
|
cborErr(cbor_encode_text_stringz(&encoder, key));
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 6));
|
|
CBOR_ENC(mapEncoder, "a", val.a);
|
|
CBOR_ENC(mapEncoder, "b", val.b);
|
|
CBOR_ENC(mapEncoder, "c", val.c);
|
|
CBOR_ENC(mapEncoder, "alpha", val.alpha);
|
|
CBOR_ENC(mapEncoder, "beta", val.beta);
|
|
CBOR_ENC(mapEncoder, "gamma", val.gamma);
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
}
|
|
|
|
// Add encoder for LatticeMessage
|
|
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const LatticeMessage &val) {
|
|
CborEncoder mapEncoder;
|
|
cborErr(cbor_encode_text_stringz(&encoder, key));
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 3));
|
|
CBOR_ENC(mapEncoder, "centering", std::string(1, val.centering));
|
|
CBOR_ENC(mapEncoder, "niggli_class", val.niggli_class);
|
|
const char* cs_name = "triclinic";
|
|
switch (val.crystal_system) {
|
|
case gemmi::CrystalSystem::Triclinic: cs_name = "triclinic"; break;
|
|
case gemmi::CrystalSystem::Monoclinic: cs_name = "monoclinic"; break;
|
|
case gemmi::CrystalSystem::Orthorhombic:cs_name = "orthorhombic";break;
|
|
case gemmi::CrystalSystem::Tetragonal: cs_name = "tetragonal"; break;
|
|
case gemmi::CrystalSystem::Trigonal: cs_name = "trigonal"; break;
|
|
case gemmi::CrystalSystem::Hexagonal: cs_name = "hexagonal"; break;
|
|
case gemmi::CrystalSystem::Cubic: cs_name = "cubic"; break;
|
|
}
|
|
CBOR_ENC(mapEncoder, "system", std::string(cs_name));
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
}
|
|
|
|
inline nlohmann::json CBOR_ENC_ROI_CONFIG(const std::vector<ROIConfig> &roi) {
|
|
nlohmann::json j;
|
|
for (const auto &r: roi) {
|
|
nlohmann::json jr;
|
|
jr["name"] = r.name;
|
|
switch (r.type) {
|
|
case ROIConfig::ROIType::Box:
|
|
jr["type"] = "box";
|
|
jr["xmin"] = r.box.xmin;
|
|
jr["xmax"] = r.box.xmax;
|
|
jr["ymin"] = r.box.ymin;
|
|
jr["ymax"] = r.box.ymax;
|
|
break;
|
|
case ROIConfig::ROIType::Circle:
|
|
jr["type"] = "circle";
|
|
jr["r"] = r.circle.r;
|
|
jr["x"] = r.circle.x;
|
|
jr["y"] = r.circle.y;
|
|
break;
|
|
case ROIConfig::ROIType::Azim:
|
|
jr["type"] = "azim";
|
|
jr["qmin"] = r.azim.qmin;
|
|
jr["qmax"] = r.azim.qmax;
|
|
// phi_min == phi_max means a full ring; only emit a sector.
|
|
if (r.azim.phi_min != r.azim.phi_max) {
|
|
jr["phi_min"] = r.azim.phi_min;
|
|
jr["phi_max"] = r.azim.phi_max;
|
|
}
|
|
break;
|
|
}
|
|
j.push_back(jr);
|
|
}
|
|
return j;
|
|
}
|
|
|
|
inline void CBOR_ENC_START_USER_DATA(CborEncoder& encoder, const char* key,
|
|
const StartMessage& message) {
|
|
nlohmann::json j;
|
|
j["file_prefix"] = message.file_prefix;
|
|
j["images_per_file"] = message.images_per_file;
|
|
j["source_name"] = message.source_name;
|
|
if (!message.source_type.empty())
|
|
j["source_type"] = message.source_type;
|
|
j["instrument_name"] = message.instrument_name;
|
|
j["sample_name"] = message.sample_name;
|
|
if (!message.user_data.empty())
|
|
j["user"] = message.user_data;
|
|
if (message.attenuator_transmission)
|
|
j["attenuator_transmission"] = message.attenuator_transmission.value();
|
|
if (message.total_flux)
|
|
j["total_flux"] = message.total_flux.value();
|
|
if (message.space_group_number)
|
|
j["space_group_number"] = message.space_group_number.value();
|
|
|
|
j["roi"] = CBOR_ENC_ROI_CONFIG(message.rois);
|
|
|
|
j["gain_file_names"] = message.gain_file_names;
|
|
if (message.write_master_file)
|
|
j["write_master_file"] = message.write_master_file.value();
|
|
if (message.write_images)
|
|
j["write_images"] = message.write_images.value();
|
|
if (message.data_reduction_factor_serialmx)
|
|
j["data_reduction_factor_serialmx"] = message.data_reduction_factor_serialmx.value();
|
|
j["experiment_group"] = message.experiment_group;
|
|
j["jfjoch_release"] = message.jfjoch_release;
|
|
if (message.socket_number)
|
|
j["socket_number"] = message.socket_number.value();
|
|
if (message.bit_depth_readout)
|
|
j["bit_depth_readout"] = message.bit_depth_readout.value();
|
|
if (message.underload_value)
|
|
j["underload_value"] = message.underload_value.value();
|
|
if (!message.writer_notification_zmq_addr.empty())
|
|
j["writer_notification_zmq_addr"] = message.writer_notification_zmq_addr;
|
|
if (message.summation_mode.has_value())
|
|
j["summation_mode"] = message.summation_mode.value();
|
|
if (message.overwrite.has_value())
|
|
j["overwrite"] = message.overwrite.value();
|
|
if (message.xfel_pulse_id.has_value())
|
|
j["xfel_pulse_id"] = message.xfel_pulse_id.value();
|
|
if (message.ring_current_mA.has_value())
|
|
j["ring_current_mA"] = message.ring_current_mA.value();
|
|
if (message.sample_temperature_K.has_value())
|
|
j["sample_temperature_K"] = message.sample_temperature_K.value();
|
|
if (message.file_format.has_value())
|
|
j["file_format"] = static_cast<int>(message.file_format.value());
|
|
|
|
if (message.images_per_trigger.has_value())
|
|
j["images_per_trigger"] = message.images_per_trigger.value();
|
|
|
|
if (message.poni_rot1.has_value())
|
|
j["poni_rot1"] = message.poni_rot1.value();
|
|
if (message.poni_rot2.has_value())
|
|
j["poni_rot2"] = message.poni_rot2.value();
|
|
if (message.poni_rot3.has_value())
|
|
j["poni_rot3"] = message.poni_rot3.value();
|
|
|
|
if (message.detect_ice_rings.has_value())
|
|
j["detect_ice_rings"] = message.detect_ice_rings.value();
|
|
|
|
switch(message.indexing_algorithm) {
|
|
case IndexingAlgorithmEnum::FFBIDX:
|
|
j["indexing_algorithm"] = "ffbidx";
|
|
break;
|
|
case IndexingAlgorithmEnum::FFT:
|
|
j["indexing_algorithm"] = "fft";
|
|
break;
|
|
case IndexingAlgorithmEnum::FFTW:
|
|
j["indexing_algorithm"] = "fftw";
|
|
break;
|
|
default:
|
|
j["indexing_algorithm"] = "none";
|
|
break;
|
|
}
|
|
|
|
switch (message.geom_refinement_algorithm) {
|
|
case GeomRefinementAlgorithmEnum::BeamCenter:
|
|
j["geom_refinement_algorithm"] = "beam_center";
|
|
break;
|
|
default:
|
|
j["geom_refinement_algorithm"] = "none";
|
|
break;
|
|
}
|
|
|
|
if (message.smargon_position.has_value()) {
|
|
j["smargon"]["chi_deg"] = message.smargon_position->chi_deg;
|
|
j["smargon"]["phi_deg"] = message.smargon_position->phi_deg;
|
|
j["smargon"]["chi_axis"] = {message.smargon_position->chi_axis.x,
|
|
message.smargon_position->chi_axis.y,
|
|
message.smargon_position->chi_axis.z};
|
|
j["smargon"]["phi_axis"] = {message.smargon_position->phi_axis.x,
|
|
message.smargon_position->phi_axis.y,
|
|
message.smargon_position->phi_axis.z};
|
|
}
|
|
|
|
auto str = j.dump();
|
|
|
|
CBOR_ENC(encoder, key, str);
|
|
}
|
|
|
|
CBORStream2Serializer::CBORStream2Serializer(uint8_t *in_buffer, size_t buffer_size) :
|
|
buffer(in_buffer), max_buffer_size(buffer_size), curr_size(0) {}
|
|
|
|
size_t CBORStream2Serializer::GetBufferSize() const {
|
|
return curr_size;
|
|
}
|
|
|
|
void CBORStream2Serializer::SerializeSequenceStart(const StartMessage& message) {
|
|
CborEncoder encoder, mapEncoder;
|
|
|
|
cbor_encoder_init(&encoder, buffer, max_buffer_size, 0);
|
|
cborErr(cbor_encode_tag(&encoder, CborSignatureTag ));
|
|
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
|
|
|
|
CBOR_ENC(mapEncoder, "type", "start");
|
|
CBOR_ENC(mapEncoder, "magic_number", user_data_magic_number);
|
|
|
|
CBOR_ENC(mapEncoder, "detector_distance", message.detector_distance);
|
|
CBOR_ENC_AXIS(mapEncoder, "detector_translation", message.detector_translation);
|
|
CBOR_ENC(mapEncoder, "beam_center_x", message.beam_center_x);
|
|
CBOR_ENC(mapEncoder, "beam_center_y", message.beam_center_y);
|
|
CBOR_ENC(mapEncoder, "countrate_correction_enabled", message.countrate_correction_enabled);
|
|
CBOR_ENC(mapEncoder, "flatfield_enabled", message.flatfield_enabled);
|
|
CBOR_ENC(mapEncoder, "number_of_images", message.number_of_images);
|
|
CBOR_ENC(mapEncoder, "image_size_x", message.image_size_x);
|
|
CBOR_ENC(mapEncoder, "image_size_y", message.image_size_y);
|
|
|
|
CBOR_ENC(mapEncoder, "incident_energy", message.incident_energy);
|
|
CBOR_ENC(mapEncoder, "incident_wavelength", message.incident_wavelength);
|
|
CBOR_ENC(mapEncoder, "incident_wavelength_spread", message.incident_wavelength_spread);
|
|
|
|
CBOR_ENC(mapEncoder, "frame_time", message.frame_time);
|
|
CBOR_ENC(mapEncoder, "count_time", message.count_time);
|
|
|
|
CBOR_ENC(mapEncoder, "saturation_value", message.saturation_value);
|
|
CBOR_ENC(mapEncoder, "error_value", message.error_value);
|
|
CBOR_ENC(mapEncoder, "pixel_size_x", message.pixel_size_x);
|
|
CBOR_ENC(mapEncoder, "pixel_size_y", message.pixel_size_y);
|
|
CBOR_ENC(mapEncoder, "sensor_thickness", message.sensor_thickness);
|
|
CBOR_ENC(mapEncoder, "sensor_material", message.sensor_material);
|
|
CBOR_ENC_DATE(mapEncoder, "arm_date", message.arm_date);
|
|
CBOR_ENC(mapEncoder, "pixel_mask_enabled", message.pixel_mask_enabled);
|
|
CBOR_ENC(mapEncoder, "detector_description", message.detector_description);
|
|
CBOR_ENC(mapEncoder, "detector_serial_number", message.detector_serial_number);
|
|
CBOR_ENC(mapEncoder, "series_unique_id", message.run_name);
|
|
CBOR_ENC(mapEncoder, "series_id", message.run_number);
|
|
CBOR_ENC(mapEncoder, "fluorescence", message.fluorescence_spectrum);
|
|
|
|
if (message.goniometer)
|
|
CBOR_ENC_GONIOMETER_MAP(mapEncoder, "goniometer", message);
|
|
if (message.grid_scan)
|
|
CBOR_ENC_GRID_SCAN(mapEncoder, "grid_scan", message.grid_scan.value());
|
|
|
|
CBOR_ENC(mapEncoder, "jungfrau_conversion_enabled", message.jungfrau_conversion_enabled);
|
|
CBOR_ENC(mapEncoder, "jungfrau_conversion_factor", message.jungfrau_conversion_factor);
|
|
CBOR_ENC(mapEncoder, "geometry_transformation_enabled", message.geometry_transformation_enabled);
|
|
// Not a DECTRIS field - stream2 has nothing for the row direction, so a consumer that does not
|
|
// know this key simply skips it and gets today's behaviour, which is what absence means.
|
|
CBOR_ENC(mapEncoder, "mirror_y", message.mirror_y);
|
|
// Also not a DECTRIS field, and also skipped by a consumer that does not know it - absence means
|
|
// the identity, which is what every stream written before these keys existed carries.
|
|
CBOR_ENC(mapEncoder, "detector_orientation_mirror_y", message.detector_orientation_mirror_y);
|
|
CBOR_ENC(mapEncoder, "detector_orientation_quarter_turns",
|
|
message.detector_orientation_quarter_turns);
|
|
|
|
CBOR_ENC_PIXEL_MASK(mapEncoder, message);
|
|
CBOR_ENC_AZINT_MAP(mapEncoder, message);
|
|
CBOR_ENC_ROI_MAP(mapEncoder, message);
|
|
|
|
CBOR_ENC(mapEncoder, "channels", message.channels);
|
|
CBOR_ENC(mapEncoder, "max_spot_count", message.max_spot_count);
|
|
CBOR_ENC(mapEncoder, "max_extra_lattices", message.max_extra_lattices);
|
|
CBOR_ENC(mapEncoder, "storage_cell_number", message.storage_cell_number);
|
|
CBOR_ENC_RATIONAL(mapEncoder, "storage_cell_delay", message.storage_cell_delay_ns, 1000*1000*1000UL);
|
|
CBOR_ENC(mapEncoder, "threshold_energy", message.threshold_energy);
|
|
|
|
switch (message.bit_depth_image) {
|
|
case 8:
|
|
CBOR_ENC(mapEncoder, "image_dtype", message.pixel_signed ? "int8" : "uint8");
|
|
break;
|
|
case 16:
|
|
CBOR_ENC(mapEncoder, "image_dtype", message.pixel_signed ? "int16" : "uint16");
|
|
break;
|
|
case 32:
|
|
CBOR_ENC(mapEncoder, "image_dtype", message.pixel_signed ? "int32" : "uint32");
|
|
break;
|
|
}
|
|
|
|
CBOR_ENC(mapEncoder, "unit_cell", message.unit_cell);
|
|
CBOR_ENC(mapEncoder, "az_int_q_bin_count", message.az_int_q_bin_count);
|
|
CBOR_ENC(mapEncoder, "az_int_phi_bin_count", message.az_int_phi_bin_count);
|
|
CBOR_ENC(mapEncoder, "az_int_bin_to_q", message.az_int_bin_to_q);
|
|
CBOR_ENC(mapEncoder, "az_int_bin_to_two_theta", message.az_int_bin_to_two_theta);
|
|
if (!message.az_int_bin_to_phi.empty())
|
|
CBOR_ENC(mapEncoder, "az_int_bin_to_phi", message.az_int_bin_to_phi);
|
|
CBOR_ENC(mapEncoder, "summation", message.summation);
|
|
|
|
CBOR_ENC_START_USER_DATA(mapEncoder, "user_data", message);
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
curr_size = cbor_encoder_get_buffer_size(&encoder, buffer);
|
|
}
|
|
|
|
void CBORStream2Serializer::SerializeSequenceEnd(const EndMessage& message) {
|
|
CborEncoder encoder, mapEncoder;
|
|
cbor_encoder_init(&encoder, buffer, max_buffer_size, 0);
|
|
cborErr(cbor_encode_tag(&encoder, CborSignatureTag));
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
|
|
|
|
CBOR_ENC(mapEncoder, "type", "end");
|
|
CBOR_ENC(mapEncoder, "magic_number", user_data_magic_number);
|
|
|
|
CBOR_ENC(mapEncoder, "series_unique_id", message.run_name);
|
|
CBOR_ENC(mapEncoder, "series_id", message.run_number);
|
|
CBOR_ENC(mapEncoder, "end_date", message.end_date);
|
|
|
|
CBOR_ENC(mapEncoder, "max_image_number", message.max_image_number);
|
|
// Optional: absent means the writer builds the same chain from the start message itself.
|
|
CBOR_ENC_TRANSFORMATIONS(mapEncoder, "transformations", message.transformations);
|
|
CBOR_ENC(mapEncoder, "images_collected", message.images_collected_count);
|
|
CBOR_ENC(mapEncoder, "images_sent_to_write", message.images_sent_to_write_count);
|
|
CBOR_ENC(mapEncoder, "data_collection_efficiency", message.efficiency);
|
|
CBOR_ENC_RAD_INT_RESULT(mapEncoder, "az_int_result", message.az_int_result);
|
|
CBOR_ENC_ADU_HIST(mapEncoder, "adu_histogram", message.adu_histogram);
|
|
CBOR_ENC(mapEncoder, "adu_histogram_bin_width", message.adu_histogram_bin_width);
|
|
CBOR_ENC(mapEncoder, "max_receiver_delay", message.max_receiver_delay);
|
|
CBOR_ENC(mapEncoder, "indexing_rate", message.indexing_rate);
|
|
CBOR_ENC(mapEncoder, "bkg_estimate", message.bkg_estimate);
|
|
|
|
CBOR_ENC(mapEncoder, "rotation_lattice_type", message.rotation_lattice_type);
|
|
if (message.rotation_lattice.has_value())
|
|
CBOR_ENC(mapEncoder, "rotation_lattice", message.rotation_lattice->GetVector());
|
|
if (!message.rotation_extra_lattices.empty()) {
|
|
CborEncoder arrayEncoder;
|
|
cborErr(cbor_encode_text_stringz(&mapEncoder, "rotation_extra_lattices"));
|
|
cborErr(cbor_encoder_create_array(&mapEncoder, &arrayEncoder, message.rotation_extra_lattices.size()));
|
|
for (const auto &el : message.rotation_extra_lattices)
|
|
CBOR_ENC_FLOAT_ARRAY_NOKEY(arrayEncoder, el.GetVector());
|
|
cborErr(cbor_encoder_close_container(&mapEncoder, &arrayEncoder));
|
|
}
|
|
CBOR_ENC(mapEncoder, "data_collection_efficiency_image", message.data_collection_efficiency);
|
|
CBOR_ENC(mapEncoder, "spot_count", message.spot_count);
|
|
CBOR_ENC(mapEncoder, "spot_count_ice_ring", message.spot_count_ice_ring);
|
|
CBOR_ENC(mapEncoder, "spot_count_low_res", message.spot_count_low_res);
|
|
CBOR_ENC(mapEncoder, "spot_count_indexed", message.spot_count_indexed);
|
|
CBOR_ENC(mapEncoder, "image_indexed", message.image_indexed);
|
|
CBOR_ENC(mapEncoder, "v_bkg_estimate", message.v_bkg_estimate);
|
|
CBOR_ENC(mapEncoder, "ice_ring_score", message.ice_ring_score);
|
|
CBOR_ENC(mapEncoder, "ice_ring_score_mean", message.ice_ring_score_mean);
|
|
CBOR_ENC(mapEncoder, "spot_count_ice_control", message.spot_count_ice_control);
|
|
CBOR_ENC(mapEncoder, "profile_radius", message.profile_radius);
|
|
CBOR_ENC(mapEncoder, "mosaicity", message.mosaicity);
|
|
CBOR_ENC(mapEncoder, "bFactor", message.bFactor);
|
|
CBOR_ENC(mapEncoder, "resolution_estimate", message.resolution_estimate);
|
|
CBOR_ENC(mapEncoder, "min_viable_pixel_value", message.min_viable_pixel_value);
|
|
CBOR_ENC(mapEncoder, "max_viable_pixel_value", message.max_viable_pixel_value);
|
|
CBOR_ENC(mapEncoder, "saturated_pixel_count", message.saturated_pixel_count);
|
|
CBOR_ENC(mapEncoder, "error_pixel_count", message.error_pixel_count);
|
|
CBOR_ENC(mapEncoder, "indexed_lattice_count", message.indexed_lattice_count);
|
|
CBOR_ENC(mapEncoder, "image_scale_factor", message.image_scale_factor);
|
|
CBOR_ENC(mapEncoder, "image_scale_cc", message.image_scale_cc);
|
|
CBOR_ENC(mapEncoder, "image_scale_mosaicity", message.image_scale_mosaicity);
|
|
CBOR_ENC(mapEncoder, "integrated_reflections", message.integrated_reflections);
|
|
CBOR_ENC(mapEncoder, "niggli_class", message.niggli_class);
|
|
CBOR_ENC(mapEncoder, "pixel_sum", message.pixel_sum);
|
|
CBOR_ENC(mapEncoder, "unit_cell", message.unit_cell);
|
|
// Both spellings of the determined group. The name carries the setting and is what a reader
|
|
// should take; the number is beside it for a reader written before the name existed.
|
|
CBOR_ENC(mapEncoder, "space_group_name", message.space_group_name);
|
|
CBOR_ENC(mapEncoder, "space_group_number", message.space_group_number);
|
|
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
|
|
curr_size = cbor_encoder_get_buffer_size(&encoder, buffer);
|
|
}
|
|
|
|
void CBORStream2Serializer::SerializeImageInternal(CborEncoder &mapEncoder, const DataMessage &message, bool metadata_only) {
|
|
CBOR_ENC(mapEncoder, "image_id", message.number);
|
|
|
|
CBOR_ENC(mapEncoder, "original_image_id", message.original_number);
|
|
|
|
CBOR_ENC_RATIONAL(mapEncoder, "real_time", message.exptime, message.exptime_base);
|
|
CBOR_ENC_RATIONAL(mapEncoder, "start_time", message.timestamp, message.timestamp_base);
|
|
CBOR_ENC_RATIONAL(mapEncoder, "end_time", message.timestamp + message.exptime, message.timestamp_base);
|
|
|
|
CBOR_ENC(mapEncoder, "spot_count", message.spot_count);
|
|
CBOR_ENC(mapEncoder, "spot_count_ice_rings", message.spot_count_ice_rings);
|
|
CBOR_ENC(mapEncoder, "spot_count_ice_control", message.spot_count_ice_control);
|
|
CBOR_ENC(mapEncoder, "spot_count_low_res", message.spot_count_low_res);
|
|
CBOR_ENC(mapEncoder, "spot_count_indexed", message.spot_count_indexed);
|
|
CBOR_ENC(mapEncoder, "az_int_profile", message.az_int_profile);
|
|
if (!message.az_int_profile_std.empty())
|
|
CBOR_ENC(mapEncoder, "az_int_profile_std", message.az_int_profile_std);
|
|
CBOR_ENC(mapEncoder, "az_int_profile_count", message.az_int_profile_count);
|
|
|
|
CBOR_ENC(mapEncoder, "indexing_result", message.indexing_result);
|
|
CBOR_ENC(mapEncoder, "indexing_lattice_count", message.indexing_lattice_count);
|
|
if (message.indexing_lattice)
|
|
CBOR_ENC(mapEncoder, "indexing_lattice", message.indexing_lattice->GetVector());
|
|
if (!message.indexing_extra_lattices.empty()) {
|
|
CborEncoder arrayEncoder;
|
|
cborErr(cbor_encode_text_stringz(&mapEncoder, "indexing_extra_lattices"));
|
|
cborErr(cbor_encoder_create_array(&mapEncoder, &arrayEncoder, message.indexing_extra_lattices.size()));
|
|
for (const auto &el : message.indexing_extra_lattices)
|
|
CBOR_ENC_FLOAT_ARRAY_NOKEY(arrayEncoder, el.GetVector());
|
|
cborErr(cbor_encoder_close_container(&mapEncoder, &arrayEncoder));
|
|
}
|
|
CBOR_ENC(mapEncoder, "profile_radius", message.profile_radius);
|
|
CBOR_ENC(mapEncoder, "mosaicity", message.mosaicity_deg);
|
|
CBOR_ENC(mapEncoder, "integrated_reflections", message.integrated_reflections);
|
|
CBOR_ENC(mapEncoder, "b_factor", message.b_factor);
|
|
CBOR_ENC(mapEncoder, "indexing_time", message.indexing_time_s);
|
|
CBOR_ENC(mapEncoder, "processing_time", message.processing_time_s);
|
|
CBOR_ENC(mapEncoder, "azint_time", message.azint_time_s);
|
|
CBOR_ENC(mapEncoder, "spot_finding_time", message.spot_finding_time_s);
|
|
CBOR_ENC(mapEncoder, "bragg_prediction_time", message.bragg_prediction_time_s);
|
|
CBOR_ENC(mapEncoder, "integration_time", message.integration_time_s);
|
|
CBOR_ENC(mapEncoder, "refinement_time", message.refinement_time_s);
|
|
CBOR_ENC(mapEncoder, "preprocessing_time", message.preprocessing_time_s);
|
|
CBOR_ENC(mapEncoder, "compression_time", message.compression_time_s);
|
|
CBOR_ENC(mapEncoder, "image_scale_time", message.image_scale_time_s);
|
|
CBOR_ENC(mapEncoder, "index_analysis_time", message.index_analysis_time_s);
|
|
CBOR_ENC(mapEncoder, "indexing_unit_cell", message.indexing_unit_cell);
|
|
CBOR_ENC(mapEncoder, "xfel_pulse_id", message.xfel_pulse_id);
|
|
CBOR_ENC(mapEncoder, "xfel_event_code", message.xfel_event_code);
|
|
if (message.lattice_type)
|
|
CBOR_ENC(mapEncoder, "lattice_type", message.lattice_type.value());
|
|
CBOR_ENC(mapEncoder, "jf_info", message.jf_info);
|
|
CBOR_ENC(mapEncoder, "receiver_aq_dev_delay", message.receiver_aq_dev_delay);
|
|
CBOR_ENC(mapEncoder, "receiver_free_send_buf", message.receiver_buf_available);
|
|
CBOR_ENC(mapEncoder, "receiver_buf_in_sending", message.receiver_buf_in_sending);
|
|
CBOR_ENC(mapEncoder, "receiver_buf_in_preparation", message.receiver_buf_in_preparation);
|
|
CBOR_ENC(mapEncoder, "storage_cell", message.storage_cell);
|
|
CBOR_ENC(mapEncoder, "saturated_pixel_count", message.saturated_pixel_count);
|
|
CBOR_ENC(mapEncoder, "pixel_sum", message.pixel_sum);
|
|
CBOR_ENC(mapEncoder, "error_pixel_count", message.error_pixel_count);
|
|
CBOR_ENC(mapEncoder, "strong_pixel_count", message.strong_pixel_count);
|
|
CBOR_ENC(mapEncoder, "min_viable_pixel_value", message.min_viable_pixel_value);
|
|
CBOR_ENC(mapEncoder, "max_viable_pixel_value", message.max_viable_pixel_value);
|
|
CBOR_ENC(mapEncoder, "resolution_estimate", message.resolution_estimate);
|
|
CBOR_ENC(mapEncoder, "data_collection_efficiency", message.image_collection_efficiency);
|
|
CBOR_ENC(mapEncoder, "packets_expected", message.packets_expected);
|
|
CBOR_ENC(mapEncoder, "packets_received", message.packets_received);
|
|
CBOR_ENC(mapEncoder, "bkg_estimate", message.bkg_estimate);
|
|
CBOR_ENC(mapEncoder, "ice_ring_score", message.ice_ring_score);
|
|
CBOR_ENC(mapEncoder, "adu_histogram", message.adu_histogram);
|
|
CBOR_ENC(mapEncoder, "roi_integrals", message.roi);
|
|
CBOR_ENC(mapEncoder, "beam_corr_x", message.beam_corr_x);
|
|
CBOR_ENC(mapEncoder, "beam_corr_y", message.beam_corr_y);
|
|
CBOR_ENC(mapEncoder, "image_scale_factor", message.image_scale_factor);
|
|
CBOR_ENC(mapEncoder, "image_scale_mosaicity", message.image_scale_mosaicity);
|
|
CBOR_ENC(mapEncoder, "image_scale_cc", message.image_scale_cc);
|
|
CBOR_ENC(mapEncoder, "user_data", message.user_data.dump());
|
|
|
|
if (!metadata_only) {
|
|
CBOR_ENC(mapEncoder, "spots", message.spots);
|
|
CBOR_ENC(mapEncoder, "reflections", message.reflections);
|
|
CBOR_ENC(mapEncoder, "data", message.image);
|
|
}
|
|
}
|
|
|
|
void CBORStream2Serializer::SerializeImage(const DataMessage& message) {
|
|
CborEncoder encoder, mapEncoder;
|
|
cbor_encoder_init(&encoder, buffer, max_buffer_size, 0);
|
|
|
|
cborErr(cbor_encode_tag(&encoder, CborSignatureTag ));
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
|
|
|
|
CBOR_ENC(mapEncoder, "type", "image");
|
|
CBOR_ENC(mapEncoder, "magic_number", user_data_magic_number);
|
|
CBOR_ENC(mapEncoder, "series_unique_id", message.run_name);
|
|
CBOR_ENC(mapEncoder, "series_id", message.run_number);
|
|
|
|
SerializeImageInternal(mapEncoder, message, false);
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
|
|
curr_size = cbor_encoder_get_buffer_size(&encoder, buffer);
|
|
}
|
|
|
|
void CBORStream2Serializer::SerializeMetadata(const MetadataMessage &messages) {
|
|
if (messages.images.empty())
|
|
throw JFJochException(JFJochExceptionCategory::CBORError,
|
|
"Cannot serialize empty metadata packet");
|
|
CborEncoder encoder, mapEncoder, arrayEncoder;
|
|
cbor_encoder_init(&encoder, buffer, max_buffer_size, 0);
|
|
|
|
cborErr(cbor_encode_tag(&encoder, CborSignatureTag ));
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
|
|
CBOR_ENC(mapEncoder, "type", "metadata");
|
|
CBOR_ENC(mapEncoder, "magic_number", user_data_magic_number);
|
|
CBOR_ENC(mapEncoder, "series_unique_id", messages.run_name);
|
|
CBOR_ENC(mapEncoder, "series_id", messages.run_number);
|
|
cborErr(cbor_encode_text_stringz(&mapEncoder, "images"));
|
|
cborErr(cbor_encoder_create_array(&mapEncoder, &arrayEncoder, messages.images.size()));
|
|
|
|
for (const auto &image: messages.images) {
|
|
CborEncoder localEncoder;
|
|
|
|
cborErr(cbor_encoder_create_map(&arrayEncoder, &localEncoder, CborIndefiniteLength));
|
|
|
|
SerializeImageInternal(localEncoder, image, true);
|
|
cborErr(cbor_encoder_close_container(&arrayEncoder, &localEncoder));
|
|
}
|
|
|
|
cborErr(cbor_encoder_close_container(&mapEncoder, &arrayEncoder));
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
curr_size = cbor_encoder_get_buffer_size(&encoder, buffer);
|
|
}
|
|
|
|
void CBORStream2Serializer::SerializeCalibration(const CompressedImage &image) {
|
|
CborEncoder encoder, mapEncoder;
|
|
cbor_encoder_init(&encoder, buffer, max_buffer_size, 0);
|
|
|
|
cborErr(cbor_encode_tag(&encoder, CborSignatureTag ));
|
|
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
|
|
CBOR_ENC(mapEncoder, "type", "calibration");
|
|
CBOR_ENC(mapEncoder, "magic_number", user_data_magic_number);
|
|
CBOR_ENC(mapEncoder, "data", image);
|
|
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
|
|
|
|
curr_size = cbor_encoder_get_buffer_size(&encoder, buffer);
|
|
}
|
|
|
|
size_t CBORStream2Serializer::GetImageAppendOffset() const {
|
|
return curr_size + sizeof(size_t) - 1;
|
|
}
|
|
|
|
void CBORStream2Serializer::AppendImage(size_t image_size) {
|
|
if (curr_size + image_size + sizeof(size_t) + 1 >= max_buffer_size)
|
|
throw JFJochException(JFJochExceptionCategory::CBORError, "No space to extend the image");
|
|
|
|
buffer[curr_size - 2] = 0x40 + 27;
|
|
curr_size--;
|
|
// CBOR encodes the byte-string length as a big-endian 64-bit integer (major
|
|
// type 2, additional info 27). Write it big-endian byte-by-byte so the result
|
|
// is correct on any host endianness and needs no compiler-specific byte-swap
|
|
// intrinsic (__builtin_bswap64 is GCC/Clang-only; MSVC lacks it).
|
|
const uint64_t image_size_be = image_size;
|
|
for (size_t k = 0; k < sizeof(uint64_t); ++k)
|
|
buffer[curr_size + k] = static_cast<uint8_t>(image_size_be >> (8 * (sizeof(uint64_t) - 1 - k)));
|
|
curr_size += sizeof(size_t);
|
|
curr_size += image_size + 0;
|
|
buffer[curr_size] = 0xFF;
|
|
curr_size++;
|
|
}
|