leonarski_fandClaude Opus 5
db9cc9106f
The factor multiplied into each integrated intensity was called rlp, for reciprocal Lorentz-polarization, and until this week that is all it held. It now also carries the sensor efficiency at the angle the beam arrives, and on the stills path it holds that efficiency and the polarization with no Lorentz term at all - correctly, since the Lorentz factor of a still is one. Three different products under one name that promises exactly one of them, in code where the neighbouring member is the total correction. Rename it prescaling_corr: multiplicative, applied before scaling, therefore not a scale, and silent about its contents - which is the point, since the contents have now grown twice. It is also what DIALS calls the same product. The stills refinement member spelled "1 / rlp" becomes inv_corr, and the comments and usage text that promised "the Lorentz-polarization factor and nothing else" now say what is actually there. The Lorentz term keeps its own name where it is computed, because that name is correct. The two external spellings are untouched: the CBOR key and the reflection dataset are a published format, and a reader that meets an unknown key would take the factor as zero, which both the merge key and the ingest treat as a reflection to drop - so every reflection would vanish and the run would still exit zero. No output changes: the merged and unmerged files of two full runs are byte for byte what the previous binary wrote, four stored files from before the efficiency correction still re-scale identically, and the reflection datasets of the process file are unchanged. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
1025 lines
48 KiB
C++
1025 lines
48 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.prescaling_corr);
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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;
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cborErr(cbor_encode_text_stringz(&encoder, key));
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// An ARRAY, not a map: the chain is ordered, base first, and a CBOR map carries no order a
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// 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);
|
|
// Not a DECTRIS field, and skipped by a consumer that does not know it. beam_center_x/y above is
|
|
// the PONI, which is not where the beam lands once the detector is tilted; these two are.
|
|
CBOR_ENC(mapEncoder, "direct_beam_x", message.direct_beam_x);
|
|
CBOR_ENC(mapEncoder, "direct_beam_y", message.direct_beam_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, "beam_size_x", message.beam_size_x);
|
|
CBOR_ENC(mapEncoder, "beam_size_y", message.beam_size_y);
|
|
|
|
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, "spindle_blind_fraction", message.spindle_blind_fraction);
|
|
CBOR_ENC(mapEncoder, "spindle_lost_unique_fraction", message.spindle_lost_unique_fraction);
|
|
|
|
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, "v_spindle_blind_fraction", message.v_spindle_blind_fraction);
|
|
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, "spindle_blind_fraction", message.spindle_blind_fraction);
|
|
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++;
|
|
}
|