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5b8ce26c83bc506146796cfc9541c00307925b54
Jungfraujoch/frame_serialize/CBORStream2Serializer.cpp
T
leonarski_fandClaude Opus 5 5b8ce26c83 integration: the flight path between the sample and the detector is corrected for, and named 
A reflection arriving at an angle to the detector normal crosses D/cos(alpha) of
whatever lies between the sample and the sensor, not D, so it is attenuated more than
one arriving head-on and reads low. That is the same geometry as the sensor crossing
already corrected here and the opposite sign, and it was missing.

The factor is exp(D/L*(1/cos(alpha)-1)) from the NIST attenuation coefficient of the
medium, the stated distance and the stated wavelength. Nothing in it is fitted, and
it is not justified by any measured amplitude: the flight path and the sensor
crossing are collinear to better than 0.998 over the angular range any single
experiment samples, so no fit of one can be evidence for the other. It is the
tabulated absorption of a known thickness of a known material over a known path.

The medium cannot be detected. No field of the NXmx application definition describes
it, none of the masters this program reads carries one, and it cannot be inferred
from the implied transmission either - in this corpus a station confirmed to use
helium sits at 51% implied air transmission and one confirmed to use air at 63%, so
any rule separating them is a threshold fitted between two points. It is therefore
assumed, stated, and overridable: --flight-path air|helium|vacuum, defaulting to air.
Helium is its own material rather than an alias for vacuum, attenuating about a six
hundredth of air rather than nothing.

On an untilted detector the correction is a function of resolution alone, so its
entire effect on merged data is a shift in the Wilson B - which is what the report
now prints beside the assumption, accurate to better than a tenth of an angstrom
squared against measurement from 0.05 up to 28. Where that shift is large the report
warns, because a wrong medium is then the largest number in the run: applied to data
from the confirmed helium station it returns a B of 14 A^2 at 3.0 A resolution, which
is not a value a crystal can have.

The corpus contains its own control. One crystal, one station, three collections a
quarter of an hour apart at falling energy through the same air: corrected, the
Wilson B rises monotonically with the dose, as it must.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
2026-09-05 17:55:43 +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.prescaling_corr);
CBOR_ENC(mapEncoder, "qe", r.qe_corr);
CBOR_ENC(mapEncoder, "flight", r.flight_corr);
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_TRANSFORMATIONS(CborEncoder &encoder, const char* key,
const std::vector<DetectorTransformation> &chain) {
if (chain.empty())
return;
CborEncoder arrayEncoder, mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
// An ARRAY, not a map: the chain is ordered, base first, and a CBOR map carries no order a
// consumer may rely on - RFC 8949 has deterministic encoders sort map keys.
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, chain.size()));
for (const auto &axis: chain) {
cborErr(cbor_encoder_create_map(&arrayEncoder, &mapEncoder, CborIndefiniteLength));
CBOR_ENC(mapEncoder, "name", axis.GetName());
CBOR_ENC(mapEncoder, "transformation_type", axis.IsRotation() ? "rotation" : "translation");
CBOR_ENC(mapEncoder, "units", axis.GetUnits());
CBOR_ENC(mapEncoder, "vector", axis.GetVector());
CBOR_ENC(mapEncoder, "offset", axis.GetOffset());
CBOR_ENC(mapEncoder, "depends_on", axis.GetDependsOn());
if (!axis.GetEquipment().empty())
CBOR_ENC(mapEncoder, "equipment", axis.GetEquipment());
if (!axis.GetEquipmentComponent().empty())
CBOR_ENC(mapEncoder, "equipment_component", axis.GetEquipmentComponent());
CBOR_ENC(mapEncoder, "values", axis.GetValues());
cborErr(cbor_encoder_close_container(&arrayEncoder, &mapEncoder));
}
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
}
inline void CBOR_ENC_GONIOMETER_MAP(CborEncoder &encoder, const char* key, const StartMessage &msg) {
CborEncoder mapEncoder;
if (msg.goniometer) {
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 1));
CBOR_ENC_GONIOMETER(mapEncoder, msg.goniometer.value());
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::vector<std::string> &v) {
CborEncoder arrayEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_array(&encoder, &arrayEncoder, v.size()));
for (const auto &i: v)
cborErr(cbor_encode_text_stringz(&arrayEncoder, i.c_str()));
cborErr(cbor_encoder_close_container(&encoder, &arrayEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const ROIMessage &val) {
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 6));
CBOR_ENC(mapEncoder, "sum", val.sum);
CBOR_ENC(mapEncoder, "sum_square", val.sum_square);
CBOR_ENC(mapEncoder, "max_count", val.max_count);
CBOR_ENC(mapEncoder, "pixels", val.pixels);
CBOR_ENC(mapEncoder, "x_weighted_sum", val.x_weighted);
CBOR_ENC(mapEncoder, "y_weighted_sum", val.y_weighted);
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const std::map<std::string, ROIMessage> &map) {
CborEncoder mapEncoder;
if (map.empty())
return;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, map.size()));
for (const auto &[x, y]: map)
CBOR_ENC(mapEncoder, x.c_str(), y);
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC_PIXEL_MASK(CborEncoder &encoder, const StartMessage &msg) {
if (msg.pixel_mask.empty())
return;
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, "pixel_mask"));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, msg.pixel_mask.size()));
for (const auto &[key, value]: msg.pixel_mask) {
if (value.size() != msg.image_size_x * msg.image_size_y)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Mismatch in size of pixel mask");
JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
auto mask_compressed = compressor.Compress(value);
CompressedImage image(mask_compressed.data(), mask_compressed.size(),
msg.image_size_x, msg.image_size_y,
CompressedImageMode::Uint32,
CompressionAlgorithm::BSHUF_LZ4,
key);
CBOR_ENC_2D_TYPED_ARRAY(mapEncoder, image);
}
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline void CBOR_ENC_AZINT_MAP(CborEncoder &encoder, const StartMessage &msg) {
if (msg.az_int_map.empty())
return;
if (msg.az_int_map.size() != msg.image_size_x * msg.image_size_y)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Mismatch in size of pixel mask");
JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
auto mask_compressed = compressor.Compress(msg.az_int_map);
CompressedImage image(mask_compressed.data(), mask_compressed.size(),
msg.image_size_x, msg.image_size_y,
CompressedImageMode::Uint16,
CompressionAlgorithm::BSHUF_LZ4, "az_int_map");
CBOR_ENC_2D_TYPED_ARRAY(encoder, image);
}
inline void CBOR_ENC_ROI_MAP(CborEncoder &encoder, const StartMessage &msg) {
if (msg.roi_map.empty())
return;
if (msg.roi_map.size() != msg.image_size_x * msg.image_size_y)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Mismatch in size of ROI map");
JFJochBitShuffleCompressor compressor(CompressionAlgorithm::BSHUF_LZ4);
auto mask_compressed = compressor.Compress(msg.roi_map);
CompressedImage image(mask_compressed.data(), mask_compressed.size(),
msg.image_size_x, msg.image_size_y,
CompressedImageMode::Uint16,
CompressionAlgorithm::BSHUF_LZ4, "roi_map");
CBOR_ENC_2D_TYPED_ARRAY(encoder, image);
}
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const UnitCell &val) {
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 6));
CBOR_ENC(mapEncoder, "a", val.a);
CBOR_ENC(mapEncoder, "b", val.b);
CBOR_ENC(mapEncoder, "c", val.c);
CBOR_ENC(mapEncoder, "alpha", val.alpha);
CBOR_ENC(mapEncoder, "beta", val.beta);
CBOR_ENC(mapEncoder, "gamma", val.gamma);
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
// Add encoder for LatticeMessage
inline void CBOR_ENC(CborEncoder &encoder, const char* key, const LatticeMessage &val) {
CborEncoder mapEncoder;
cborErr(cbor_encode_text_stringz(&encoder, key));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, 3));
CBOR_ENC(mapEncoder, "centering", std::string(1, val.centering));
CBOR_ENC(mapEncoder, "niggli_class", val.niggli_class);
const char* cs_name = "triclinic";
switch (val.crystal_system) {
case gemmi::CrystalSystem::Triclinic: cs_name = "triclinic"; break;
case gemmi::CrystalSystem::Monoclinic: cs_name = "monoclinic"; break;
case gemmi::CrystalSystem::Orthorhombic:cs_name = "orthorhombic";break;
case gemmi::CrystalSystem::Tetragonal: cs_name = "tetragonal"; break;
case gemmi::CrystalSystem::Trigonal: cs_name = "trigonal"; break;
case gemmi::CrystalSystem::Hexagonal: cs_name = "hexagonal"; break;
case gemmi::CrystalSystem::Cubic: cs_name = "cubic"; break;
}
CBOR_ENC(mapEncoder, "system", std::string(cs_name));
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
}
inline nlohmann::json CBOR_ENC_ROI_CONFIG(const std::vector<ROIConfig> &roi) {
nlohmann::json j;
for (const auto &r: roi) {
nlohmann::json jr;
jr["name"] = r.name;
switch (r.type) {
case ROIConfig::ROIType::Box:
jr["type"] = "box";
jr["xmin"] = r.box.xmin;
jr["xmax"] = r.box.xmax;
jr["ymin"] = r.box.ymin;
jr["ymax"] = r.box.ymax;
break;
case ROIConfig::ROIType::Circle:
jr["type"] = "circle";
jr["r"] = r.circle.r;
jr["x"] = r.circle.x;
jr["y"] = r.circle.y;
break;
case ROIConfig::ROIType::Azim:
jr["type"] = "azim";
jr["qmin"] = r.azim.qmin;
jr["qmax"] = r.azim.qmax;
// phi_min == phi_max means a full ring; only emit a sector.
if (r.azim.phi_min != r.azim.phi_max) {
jr["phi_min"] = r.azim.phi_min;
jr["phi_max"] = r.azim.phi_max;
}
break;
}
j.push_back(jr);
}
return j;
}
inline void CBOR_ENC_START_USER_DATA(CborEncoder& encoder, const char* key,
const StartMessage& message) {
nlohmann::json j;
j["file_prefix"] = message.file_prefix;
j["images_per_file"] = message.images_per_file;
j["source_name"] = message.source_name;
if (!message.source_type.empty())
j["source_type"] = message.source_type;
j["instrument_name"] = message.instrument_name;
j["sample_name"] = message.sample_name;
if (!message.user_data.empty())
j["user"] = message.user_data;
if (message.attenuator_transmission)
j["attenuator_transmission"] = message.attenuator_transmission.value();
if (message.total_flux)
j["total_flux"] = message.total_flux.value();
if (message.space_group_number)
j["space_group_number"] = message.space_group_number.value();
j["roi"] = CBOR_ENC_ROI_CONFIG(message.rois);
j["gain_file_names"] = message.gain_file_names;
if (message.write_master_file)
j["write_master_file"] = message.write_master_file.value();
if (message.write_images)
j["write_images"] = message.write_images.value();
if (message.data_reduction_factor_serialmx)
j["data_reduction_factor_serialmx"] = message.data_reduction_factor_serialmx.value();
j["experiment_group"] = message.experiment_group;
j["jfjoch_release"] = message.jfjoch_release;
if (message.socket_number)
j["socket_number"] = message.socket_number.value();
if (message.bit_depth_readout)
j["bit_depth_readout"] = message.bit_depth_readout.value();
if (message.underload_value)
j["underload_value"] = message.underload_value.value();
if (!message.writer_notification_zmq_addr.empty())
j["writer_notification_zmq_addr"] = message.writer_notification_zmq_addr;
if (message.summation_mode.has_value())
j["summation_mode"] = message.summation_mode.value();
if (message.overwrite.has_value())
j["overwrite"] = message.overwrite.value();
if (message.xfel_pulse_id.has_value())
j["xfel_pulse_id"] = message.xfel_pulse_id.value();
if (message.ring_current_mA.has_value())
j["ring_current_mA"] = message.ring_current_mA.value();
if (message.sample_temperature_K.has_value())
j["sample_temperature_K"] = message.sample_temperature_K.value();
if (message.file_format.has_value())
j["file_format"] = static_cast<int>(message.file_format.value());
if (message.images_per_trigger.has_value())
j["images_per_trigger"] = message.images_per_trigger.value();
if (message.poni_rot1.has_value())
j["poni_rot1"] = message.poni_rot1.value();
if (message.poni_rot2.has_value())
j["poni_rot2"] = message.poni_rot2.value();
if (message.poni_rot3.has_value())
j["poni_rot3"] = message.poni_rot3.value();
if (message.detect_ice_rings.has_value())
j["detect_ice_rings"] = message.detect_ice_rings.value();
switch(message.indexing_algorithm) {
case IndexingAlgorithmEnum::FFBIDX:
j["indexing_algorithm"] = "ffbidx";
break;
case IndexingAlgorithmEnum::FFT:
j["indexing_algorithm"] = "fft";
break;
case IndexingAlgorithmEnum::FFTW:
j["indexing_algorithm"] = "fftw";
break;
default:
j["indexing_algorithm"] = "none";
break;
}
switch (message.geom_refinement_algorithm) {
case GeomRefinementAlgorithmEnum::BeamCenter:
j["geom_refinement_algorithm"] = "beam_center";
break;
default:
j["geom_refinement_algorithm"] = "none";
break;
}
if (message.smargon_position.has_value()) {
j["smargon"]["chi_deg"] = message.smargon_position->chi_deg;
j["smargon"]["phi_deg"] = message.smargon_position->phi_deg;
j["smargon"]["chi_axis"] = {message.smargon_position->chi_axis.x,
message.smargon_position->chi_axis.y,
message.smargon_position->chi_axis.z};
j["smargon"]["phi_axis"] = {message.smargon_position->phi_axis.x,
message.smargon_position->phi_axis.y,
message.smargon_position->phi_axis.z};
}
auto str = j.dump();
CBOR_ENC(encoder, key, str);
}
CBORStream2Serializer::CBORStream2Serializer(uint8_t *in_buffer, size_t buffer_size) :
buffer(in_buffer), max_buffer_size(buffer_size), curr_size(0) {}
size_t CBORStream2Serializer::GetBufferSize() const {
return curr_size;
}
void CBORStream2Serializer::SerializeSequenceStart(const StartMessage& message) {
CborEncoder encoder, mapEncoder;
cbor_encoder_init(&encoder, buffer, max_buffer_size, 0);
cborErr(cbor_encode_tag(&encoder, CborSignatureTag ));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
CBOR_ENC(mapEncoder, "type", "start");
CBOR_ENC(mapEncoder, "magic_number", user_data_magic_number);
CBOR_ENC(mapEncoder, "detector_distance", message.detector_distance);
CBOR_ENC_AXIS(mapEncoder, "detector_translation", message.detector_translation);
CBOR_ENC(mapEncoder, "beam_center_x", message.beam_center_x);
CBOR_ENC(mapEncoder, "beam_center_y", message.beam_center_y);
// 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++;
}
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