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Jungfraujoch/frame_serialize/CBORStream2Serializer.cpp
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leonarski_fandClaude Opus 5 d2f57975e8 Record whether the image is mirrored in Y, and label the .poni orientation 
Which way the detector's rows run was decided once, in the module assembly, and
never stated again: not on the wire, not in the file, nowhere a consumer could
read it. mirror_y was consumed inside the DetectorGeometryModular constructor and
discarded. It is now a declared property of the detector setup, carried into the
start message, written to HDF5 under detectorSpecific, and read back. Absence
means true, which is the MX convention and the only thing Jungfraujoch has ever
produced.

Deliberately a boolean and not a corner enum: the assembled image can only be
flipped in Y, so a four-corner value would encode states that cannot occur.

DECTRIS stream2 has no field for this - checked against the specification - so
the key is new rather than an extension of theirs, and a consumer that does not
know it skips it and behaves exactly as before.

The .poni file gains pyFAI's orientation. Without it pyFAI applies its own
default, 3 (bottom left), and believes increasing row means physically upwards.
The numbers still agreed - a mirror preserves 2theta, so radial integration was
never affected - but the azimuth came out with the opposite sense, which matters
for cake and sector integration.

Declaring orientation 2 is not a one-line addition: it re-anchors Poni1 to the
top edge and reverses rot2 and rot3, a row flip being improper. Measured against
pyFAI 2026.5.0 by searching all four orientations, both Poni1 anchorings and all
eight sign combinations: exactly two combinations reproduce the lab position
DiffractionGeometry computes to 1.4e-17 m - the unlabelled form written before,
and (orientation 2, Poni1 = height-1-beam_y, +rot1/+rot2/-rot3), which is now
written. Calibration_PoniFileAxisConvention pins it.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-08-22 22:54:50 +02:00

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// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "CBORStream2Serializer.h"
#include "tinycbor/cbor.h"
#include "CborErr.h"
#include "CborUtil.h"
#include "../compression/JFJochCompressor.h"
#include <nlohmann/json.hpp>
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const char* value) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_text_stringz(&encoder, value));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::string &value) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_text_stringz(&encoder, value.c_str()));
}
inline void CBOR_ENC_DATE(CborEncoder &encoder, const char* key, const std::string &value) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cbor_encode_tag(&encoder, CborDateTimeStringTag);
cborErr(cbor_encode_text_stringz(&encoder, value.c_str()));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, float value) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_float(&encoder, value));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, bool value) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_boolean(&encoder, value));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, uint64_t value) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_uint(&encoder, value));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, int64_t value) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_int(&encoder, value));
}
template <class T>
void CBOR_ENC(CborEncoder &encoder, const char* key, const std::optional<T> &value) {
if (value)
CBOR_ENC(encoder, key, value.value());
}
void CBOR_ENC_COMPRESSED(CborEncoder &encoder,
const void *image, size_t image_size,
CompressionAlgorithm algorithm,
size_t elem_size) {
if (algorithm == CompressionAlgorithm::NO_COMPRESSION)
cborErr(cbor_encode_byte_string(&encoder, (uint8_t *) image, image_size));
else {
cbor_encode_tag(&encoder, TagDECTRISCompression);
CborEncoder arrayEncoder;
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, 3));
switch (algorithm) {
case CompressionAlgorithm::BSHUF_LZ4:
cborErr(cbor_encode_text_stringz(&arrayEncoder, "bslz4"));
break;
case CompressionAlgorithm::BSHUF_ZSTD:
case CompressionAlgorithm::BSHUF_ZSTD_RLE:
case CompressionAlgorithm::BSHUF_ZSTD_RLE_HUFF:
cborErr(cbor_encode_text_stringz(&arrayEncoder, "bszstd"));
break;
default:
throw JFJochException(JFJochExceptionCategory::CBORError, "Unsupported compression algorithm");
}
cborErr(cbor_encode_uint(&arrayEncoder, elem_size));
cborErr(cbor_encode_byte_string(&arrayEncoder, (uint8_t *) image, image_size));
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
}
}
inline void CBOR_ENC_2D_TYPED_ARRAY(CborEncoder &encoder, const CompressedImage& image) {
//if ((algorithm == CompressionAlgorithm::NO_COMPRESSION) && (xpixel * ypixel != image_size / elem_size))
// throw JFJochException(JFJochExceptionCategory::CBORError, "Mismatch in array size");
CborEncoder arrayEncoder, arrayEncoder_2;
cborErr(cbor_encode_text_stringz(&encoder, image.GetChannel().c_str()));
cbor_encode_tag(&encoder, TagMultiDimArray);
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, 2));
if (image.GetMode() == CompressedImageMode::RGB) {
cborErr(cbor_encoder_create_array(&arrayEncoder, &arrayEncoder_2, 3));
cborErr(cbor_encode_uint(&arrayEncoder_2, 3));
cborErr(cbor_encode_uint(&arrayEncoder_2, image.GetHeight()));
cborErr(cbor_encode_uint(&arrayEncoder_2, image.GetWidth()));
cborErr(cbor_encoder_close_container(&arrayEncoder, &arrayEncoder_2));
} else {
cborErr(cbor_encoder_create_array(&arrayEncoder, &arrayEncoder_2, 2));
cborErr(cbor_encode_uint(&arrayEncoder_2, image.GetHeight()));
cborErr(cbor_encode_uint(&arrayEncoder_2, image.GetWidth()));
cborErr(cbor_encoder_close_container(&arrayEncoder, &arrayEncoder_2));
}
CborTag typed_array_tag;
switch (image.GetMode()) {
case CompressedImageMode::RGB:
case CompressedImageMode::Uint8:
typed_array_tag = TagUnsignedInt8Bit;
break;
case CompressedImageMode::Uint16:
typed_array_tag = TagUnsignedInt16BitLE;
break;
case CompressedImageMode::Uint32:
typed_array_tag = TagUnsignedInt32BitLE;
break;
case CompressedImageMode::Int8:
typed_array_tag = TagSignedInt8Bit;
break;
case CompressedImageMode::Int16:
typed_array_tag = TagSignedInt16BitLE;
break;
case CompressedImageMode::Int32:
typed_array_tag = TagSignedInt32BitLE;
break;
case CompressedImageMode::Float16:
typed_array_tag = TagHalfLE;
break;
case CompressedImageMode::Float32:
typed_array_tag = TagFloatLE;
break;
case CompressedImageMode::Float64:
typed_array_tag = TagDoubleLE;
break;
default:
throw JFJochException(JFJochExceptionCategory::CBORError, "Image mode not supported");
}
cbor_encode_tag(&arrayEncoder, typed_array_tag);
CBOR_ENC_COMPRESSED(arrayEncoder, image.GetCompressed(),
image.GetCompressedSize(), image.GetCompressionAlgorithm(),
image.GetByteDepth());
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<float>& v) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_tag(&encoder, TagFloatLE));
cborErr(cbor_encode_byte_string(&encoder, (uint8_t *) v.data(), v.size() * sizeof(float)));
}
inline void CBOR_ENC_FLOAT_ARRAY_NOKEY(CborEncoder &encoder, const std::vector<float>& v) {
cborErr(cbor_encode_tag(&encoder, TagFloatLE));
cborErr(cbor_encode_byte_string(&encoder, (uint8_t *) v.data(), v.size() * sizeof(float)));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<uint8_t>& v) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_tag(&encoder, TagUnsignedInt8Bit));
cborErr(cbor_encode_byte_string(&encoder, v.data(), v.size() * sizeof(uint8_t)));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<int32_t>& v) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_tag(&encoder, TagSignedInt32BitLE));
cborErr(cbor_encode_byte_string(&encoder, reinterpret_cast<const uint8_t *>(v.data()), v.size() * sizeof(int32_t)));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<int64_t>& v) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_tag(&encoder, TagSignedInt64BitLE));
cborErr(cbor_encode_byte_string(&encoder, reinterpret_cast<const uint8_t *>(v.data()), v.size() * sizeof(int64_t)));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<uint64_t>& v) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encode_tag(&encoder, TagUnsignedInt64BitLE));
cborErr(cbor_encode_byte_string(&encoder, (uint8_t *) v.data(), v.size() * sizeof(uint64_t)));
}
inline void CBOR_ENC_RATIONAL(CborEncoder &encoder, const char* key, uint64_t numerator, uint64_t denominator) {
CborEncoder arrayEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, 2));
cborErr(cbor_encode_uint(&arrayEncoder, numerator));
cborErr(cbor_encode_uint(&arrayEncoder, denominator));
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::map<std::string, float> &val) {
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, val.size()));
for (auto &[map_key, map_val]: val)
CBOR_ENC(mapEncoder, map_key.c_str(), map_val);
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC_RAD_INT_RESULT(CborEncoder &encoder, const char* key,
const std::map<std::string, std::vector<float>> &az_int_result) {
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, az_int_result.size()));
for (auto &[map_key, map_val]: az_int_result)
CBOR_ENC(mapEncoder, map_key.c_str(), map_val);
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC_ADU_HIST(CborEncoder &encoder, const char* key,
const std::map<std::string, std::vector<uint64_t>> &adu_histogram) {
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, adu_histogram.size()));
for (auto &[map_key, map_val]: adu_histogram)
CBOR_ENC(mapEncoder, map_key.c_str(), map_val);
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const SpotToSave& spot) {
CborEncoder mapEncoder;
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
CBOR_ENC(mapEncoder, "x", spot.x);
CBOR_ENC(mapEncoder, "y", spot.y);
CBOR_ENC(mapEncoder, "I", spot.intensity);
CBOR_ENC(mapEncoder, "maxc", spot.maxc);
CBOR_ENC(mapEncoder, "ice_ring", spot.ice_ring);
CBOR_ENC(mapEncoder, "indexed", spot.indexed);
CBOR_ENC(mapEncoder, "latt", spot.lattice);
CBOR_ENC(mapEncoder, "image", spot.image);
if (spot.indexed) {
CBOR_ENC(mapEncoder, "h", spot.h);
CBOR_ENC(mapEncoder, "k", spot.k);
CBOR_ENC(mapEncoder, "l", spot.l);
CBOR_ENC(mapEncoder, "dist_ewald", spot.dist_ewald_sphere);
}
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const XrayFluorescenceSpectrum& f) {
if (f.empty())
return;
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
CBOR_ENC(mapEncoder, "data", f.GetData());
CBOR_ENC(mapEncoder, "energy", f.GetEnergy_eV());
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const Reflection& r) {
CborEncoder mapEncoder;
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
CBOR_ENC(mapEncoder, "h", static_cast<int64_t>(r.h));
CBOR_ENC(mapEncoder, "k", static_cast<int64_t>(r.k));
CBOR_ENC(mapEncoder, "l", static_cast<int64_t>(r.l));
CBOR_ENC(mapEncoder, "phi", r.delta_phi_deg);
CBOR_ENC(mapEncoder, "x", r.predicted_x);
CBOR_ENC(mapEncoder, "y", r.predicted_y);
CBOR_ENC(mapEncoder, "obs_x", r.observed_x);
CBOR_ENC(mapEncoder, "obs_y", r.observed_y);
CBOR_ENC(mapEncoder, "d", r.d);
CBOR_ENC(mapEncoder, "I", r.I);
CBOR_ENC(mapEncoder, "bkg", r.bkg);
CBOR_ENC(mapEncoder, "var_bkg", r.var_bkg);
CBOR_ENC(mapEncoder, "sigma", r.sigma);
CBOR_ENC(mapEncoder, "image", r.image_number);
CBOR_ENC(mapEncoder, "rp", r.dist_ewald);
CBOR_ENC(mapEncoder, "rlp", r.rlp);
CBOR_ENC(mapEncoder, "partiality", r.partiality);
CBOR_ENC(mapEncoder, "zeta", r.zeta);
CBOR_ENC(mapEncoder, "image_scale_corr", r.image_scale_corr);
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const Coord& coord) {
CborEncoder arrayEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, 3));
cborErr(cbor_encode_float(&arrayEncoder, coord[0]));
cborErr(cbor_encode_float(&arrayEncoder, coord[1]));
cborErr(cbor_encode_float(&arrayEncoder, coord[2]));
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<SpotToSave>& spots) {
CborEncoder arrayEncoder, mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, spots.size()));
for (auto spot : spots)
CBOR_ENC(arrayEncoder, spot);
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<Reflection>& refs) {
CborEncoder arrayEncoder, mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, refs.size()));
for (auto r: refs)
CBOR_ENC(arrayEncoder, r);
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const CompressedImage& message) {
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 1));
CBOR_ENC_2D_TYPED_ARRAY(mapEncoder, message);
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC_AXIS(CborEncoder &encoder, const char* key, const float det_translation[3]) {
CborEncoder arrayEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, 3));
for (int i = 0; i < 3; i++)
cborErr(cbor_encode_float(&arrayEncoder, det_translation[i]));
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
}
inline void CBOR_ENC_GONIOMETER(CborEncoder &encoder, const GoniometerAxis &g) {
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, g.GetName().c_str()));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
CBOR_ENC(mapEncoder, "increment", g.GetIncrement_deg());
CBOR_ENC(mapEncoder, "start", g.GetStart_deg());
CBOR_ENC(mapEncoder, "axis", g.GetAxis());
CBOR_ENC(mapEncoder, "screening_wedge", g.GetScreeningWedge());
if (g.GetHelicalStep().has_value())
CBOR_ENC(mapEncoder, "helical_step", g.GetHelicalStep().value());
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC_GRID_SCAN(CborEncoder &encoder, const char* key, const GridScanSettings &g) {
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 6));
CBOR_ENC(mapEncoder, "n_fast", g.GetNFast());
CBOR_ENC(mapEncoder, "n_slow", g.GetNSlow());
CBOR_ENC(mapEncoder, "step_x_axis", g.GetGridStepX_um() * 1e-6f);
CBOR_ENC(mapEncoder, "step_y_axis", g.GetGridStepY_um() * 1e-6f);
CBOR_ENC(mapEncoder, "snake_scan", g.IsSnakeScan());
CBOR_ENC(mapEncoder, "vertical_scan", g.IsVerticalScan());
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
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);
// Both, when both are present - the decoder has always read the two keys independently.
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);
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);
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);
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++;
}
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