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Jungfraujoch/frame_serialize/CBORStream2Serializer.cpp
T
leonarski_fandClaude Opus 5 fed077e683 geometry: hold the detector plane as axis vectors, and give the discrete part its own home 
The detector plane was three PONI angles and nothing else, so the two things it
cannot express - an image mirrored in Y, and one mounted at a multiple of 90
degrees - had no home at all. They are now the DetectorOrientation carried by the
detector setup, composed with the PONI rotation into one orthogonal matrix whose
columns ARE the fast axis, the slow axis and the sample->PONI normal:

    lab = R(rot1, rot2, rot3) * Delta * ( (x-bx)*p , (y-by)*p , distance )

GetFastAxis/GetSlowAxis/GetNormalAxis read those columns and DetectorAxes() sets
the plane from them, decomposing back to the angles; PoniRotMatrix and
PoniAnglesFromMatrix are the conversion in both directions, exact on the canonical
branch (rot2 in [-pi/2, pi/2]) and with a stated convention at gimbal lock. The
angles stay stored rather than re-derived, so a geometry given as angles is
written back as the same angles, to the bit.

Delta is never inferred. In particular an arbitrary rot3 is NOT decomposed into a
quarter turn plus a residual: rot3 is a fitted quantity, and a least-squares step
must not be able to turn the stored image. It is set only where something states
it - the detector setup, --detector-mirror-y / --detector-quarter-turns, or the
value a file this system wrote records - and defaults to the identity, which makes
the whole change a no-op for every existing detector and every existing file.

It is a different setting from DetectorSetup::mirror_y, which flips the MODULE
LAYOUT while an image is assembled and so decides what the stored pixels are.
Merging the two would apply the mirror twice for every modular detector, or change
the pixel content of every file written; both are ruled out. The new one earns its
keep exactly where the old one is a no-op: a detector whose image arrives already
assembled has no layout to flip.

Both generators are signed permutations of the in-plane offset, so they preserve
the distance from the PONI. That is why almost nothing downstream changes:
everything needing an azimuth already goes through LabCoord, and everything that
does not needs only a radius. The two hand-written copies of the rotation -
XtalResidual and RingOptimizer - take the discrete part as four constants next to
cos_rot3/sin_rot3, since it acts in the detector frame where rot3 acts in the
laboratory and cannot be folded into it. RingOptimizer needs it despite being a
radial fit: it fits the tilt, and the discrete part changes which way the tilt
tips a ring.

Carried as two optional CBOR keys and two detectorSpecific datasets, both
back-compatible; the NXmx module axis vectors and the translation direction stop
being hardcoded and are computed from it, reproducing today's values exactly at
the identity. GetPoniRotMatrix is renamed GetDetectorMatrix, because it is no
longer only the PONI rotation.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Lc5JG6kJqZoCWaoZ43JGTW
2026-08-29 23:00:35 +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_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);
CBOR_ENC(mapEncoder, "countrate_correction_enabled", message.countrate_correction_enabled);
CBOR_ENC(mapEncoder, "flatfield_enabled", message.flatfield_enabled);
CBOR_ENC(mapEncoder, "number_of_images", message.number_of_images);
CBOR_ENC(mapEncoder, "image_size_x", message.image_size_x);
CBOR_ENC(mapEncoder, "image_size_y", message.image_size_y);
CBOR_ENC(mapEncoder, "incident_energy", message.incident_energy);
CBOR_ENC(mapEncoder, "incident_wavelength", message.incident_wavelength);
CBOR_ENC(mapEncoder, "incident_wavelength_spread", message.incident_wavelength_spread);
CBOR_ENC(mapEncoder, "frame_time", message.frame_time);
CBOR_ENC(mapEncoder, "count_time", message.count_time);
CBOR_ENC(mapEncoder, "saturation_value", message.saturation_value);
CBOR_ENC(mapEncoder, "error_value", message.error_value);
CBOR_ENC(mapEncoder, "pixel_size_x", message.pixel_size_x);
CBOR_ENC(mapEncoder, "pixel_size_y", message.pixel_size_y);
CBOR_ENC(mapEncoder, "sensor_thickness", message.sensor_thickness);
CBOR_ENC(mapEncoder, "sensor_material", message.sensor_material);
CBOR_ENC_DATE(mapEncoder, "arm_date", message.arm_date);
CBOR_ENC(mapEncoder, "pixel_mask_enabled", message.pixel_mask_enabled);
CBOR_ENC(mapEncoder, "detector_description", message.detector_description);
CBOR_ENC(mapEncoder, "detector_serial_number", message.detector_serial_number);
CBOR_ENC(mapEncoder, "series_unique_id", message.run_name);
CBOR_ENC(mapEncoder, "series_id", message.run_number);
CBOR_ENC(mapEncoder, "fluorescence", message.fluorescence_spectrum);
if (message.goniometer)
CBOR_ENC_GONIOMETER_MAP(mapEncoder, "goniometer", message);
if (message.grid_scan)
CBOR_ENC_GRID_SCAN(mapEncoder, "grid_scan", message.grid_scan.value());
CBOR_ENC(mapEncoder, "jungfrau_conversion_enabled", message.jungfrau_conversion_enabled);
CBOR_ENC(mapEncoder, "jungfrau_conversion_factor", message.jungfrau_conversion_factor);
CBOR_ENC(mapEncoder, "geometry_transformation_enabled", message.geometry_transformation_enabled);
// Not a DECTRIS field - stream2 has nothing for the row direction, so a consumer that does not
// know this key simply skips it and gets today's behaviour, which is what absence means.
CBOR_ENC(mapEncoder, "mirror_y", message.mirror_y);
// Also not a DECTRIS field, and also skipped by a consumer that does not know it - absence means
// the identity, which is what every stream written before these keys existed carries.
CBOR_ENC(mapEncoder, "detector_orientation_mirror_y", message.detector_orientation_mirror_y);
CBOR_ENC(mapEncoder, "detector_orientation_quarter_turns",
message.detector_orientation_quarter_turns);
CBOR_ENC_PIXEL_MASK(mapEncoder, message);
CBOR_ENC_AZINT_MAP(mapEncoder, message);
CBOR_ENC_ROI_MAP(mapEncoder, message);
CBOR_ENC(mapEncoder, "channels", message.channels);
CBOR_ENC(mapEncoder, "max_spot_count", message.max_spot_count);
CBOR_ENC(mapEncoder, "max_extra_lattices", message.max_extra_lattices);
CBOR_ENC(mapEncoder, "storage_cell_number", message.storage_cell_number);
CBOR_ENC_RATIONAL(mapEncoder, "storage_cell_delay", message.storage_cell_delay_ns, 1000*1000*1000UL);
CBOR_ENC(mapEncoder, "threshold_energy", message.threshold_energy);
switch (message.bit_depth_image) {
case 8:
CBOR_ENC(mapEncoder, "image_dtype", message.pixel_signed ? "int8" : "uint8");
break;
case 16:
CBOR_ENC(mapEncoder, "image_dtype", message.pixel_signed ? "int16" : "uint16");
break;
case 32:
CBOR_ENC(mapEncoder, "image_dtype", message.pixel_signed ? "int32" : "uint32");
break;
}
CBOR_ENC(mapEncoder, "unit_cell", message.unit_cell);
CBOR_ENC(mapEncoder, "az_int_q_bin_count", message.az_int_q_bin_count);
CBOR_ENC(mapEncoder, "az_int_phi_bin_count", message.az_int_phi_bin_count);
CBOR_ENC(mapEncoder, "az_int_bin_to_q", message.az_int_bin_to_q);
CBOR_ENC(mapEncoder, "az_int_bin_to_two_theta", message.az_int_bin_to_two_theta);
if (!message.az_int_bin_to_phi.empty())
CBOR_ENC(mapEncoder, "az_int_bin_to_phi", message.az_int_bin_to_phi);
CBOR_ENC(mapEncoder, "summation", message.summation);
CBOR_ENC_START_USER_DATA(mapEncoder, "user_data", message);
cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
curr_size = cbor_encoder_get_buffer_size(&encoder, buffer);
}
void CBORStream2Serializer::SerializeSequenceEnd(const EndMessage& message) {
CborEncoder encoder, mapEncoder;
cbor_encoder_init(&encoder, buffer, max_buffer_size, 0);
cborErr(cbor_encode_tag(&encoder, CborSignatureTag));
cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
CBOR_ENC(mapEncoder, "type", "end");
CBOR_ENC(mapEncoder, "magic_number", user_data_magic_number);
CBOR_ENC(mapEncoder, "series_unique_id", message.run_name);
CBOR_ENC(mapEncoder, "series_id", message.run_number);
CBOR_ENC(mapEncoder, "end_date", message.end_date);
CBOR_ENC(mapEncoder, "max_image_number", message.max_image_number);
// Optional: absent means the writer builds the same chain from the start message itself.
CBOR_ENC_TRANSFORMATIONS(mapEncoder, "transformations", message.transformations);
CBOR_ENC(mapEncoder, "images_collected", message.images_collected_count);
CBOR_ENC(mapEncoder, "images_sent_to_write", message.images_sent_to_write_count);
CBOR_ENC(mapEncoder, "data_collection_efficiency", message.efficiency);
CBOR_ENC_RAD_INT_RESULT(mapEncoder, "az_int_result", message.az_int_result);
CBOR_ENC_ADU_HIST(mapEncoder, "adu_histogram", message.adu_histogram);
CBOR_ENC(mapEncoder, "adu_histogram_bin_width", message.adu_histogram_bin_width);
CBOR_ENC(mapEncoder, "max_receiver_delay", message.max_receiver_delay);
CBOR_ENC(mapEncoder, "indexing_rate", message.indexing_rate);
CBOR_ENC(mapEncoder, "bkg_estimate", message.bkg_estimate);
CBOR_ENC(mapEncoder, "rotation_lattice_type", message.rotation_lattice_type);
if (message.rotation_lattice.has_value())
CBOR_ENC(mapEncoder, "rotation_lattice", message.rotation_lattice->GetVector());
if (!message.rotation_extra_lattices.empty()) {
CborEncoder arrayEncoder;
cborErr(cbor_encode_text_stringz(&mapEncoder, "rotation_extra_lattices"));
cborErr(cbor_encoder_create_array(&mapEncoder, &arrayEncoder, message.rotation_extra_lattices.size()));
for (const auto &el : message.rotation_extra_lattices)
CBOR_ENC_FLOAT_ARRAY_NOKEY(arrayEncoder, el.GetVector());
cborErr(cbor_encoder_close_container(&mapEncoder, &arrayEncoder));
}
CBOR_ENC(mapEncoder, "data_collection_efficiency_image", message.data_collection_efficiency);
CBOR_ENC(mapEncoder, "spot_count", message.spot_count);
CBOR_ENC(mapEncoder, "spot_count_ice_ring", message.spot_count_ice_ring);
CBOR_ENC(mapEncoder, "spot_count_low_res", message.spot_count_low_res);
CBOR_ENC(mapEncoder, "spot_count_indexed", message.spot_count_indexed);
CBOR_ENC(mapEncoder, "image_indexed", message.image_indexed);
CBOR_ENC(mapEncoder, "v_bkg_estimate", message.v_bkg_estimate);
CBOR_ENC(mapEncoder, "ice_ring_score", message.ice_ring_score);
CBOR_ENC(mapEncoder, "ice_ring_score_mean", message.ice_ring_score_mean);
CBOR_ENC(mapEncoder, "spot_count_ice_control", message.spot_count_ice_control);
CBOR_ENC(mapEncoder, "profile_radius", message.profile_radius);
CBOR_ENC(mapEncoder, "mosaicity", message.mosaicity);
CBOR_ENC(mapEncoder, "bFactor", message.bFactor);
CBOR_ENC(mapEncoder, "resolution_estimate", message.resolution_estimate);
CBOR_ENC(mapEncoder, "min_viable_pixel_value", message.min_viable_pixel_value);
CBOR_ENC(mapEncoder, "max_viable_pixel_value", message.max_viable_pixel_value);
CBOR_ENC(mapEncoder, "saturated_pixel_count", message.saturated_pixel_count);
CBOR_ENC(mapEncoder, "error_pixel_count", message.error_pixel_count);
CBOR_ENC(mapEncoder, "indexed_lattice_count", message.indexed_lattice_count);
CBOR_ENC(mapEncoder, "image_scale_factor", message.image_scale_factor);
CBOR_ENC(mapEncoder, "image_scale_cc", message.image_scale_cc);
CBOR_ENC(mapEncoder, "image_scale_mosaicity", message.image_scale_mosaicity);
CBOR_ENC(mapEncoder, "integrated_reflections", message.integrated_reflections);
CBOR_ENC(mapEncoder, "niggli_class", message.niggli_class);
CBOR_ENC(mapEncoder, "pixel_sum", message.pixel_sum);
CBOR_ENC(mapEncoder, "unit_cell", message.unit_cell);
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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