Program Listing for File serialization.h¶
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#ifndef AMICI_SERIALIZATION_H
#define AMICI_SERIALIZATION_H
#include "amici/rdata.h"
#include "amici/model.h"
#include "amici/solver.h"
#include "amici/solver_cvodes.h"
#include <cassert>
#include <fstream>
#include <iostream>
#include <chrono>
#include <boost/serialization/array.hpp>
#include <boost/serialization/vector.hpp>
#include <boost/archive/binary_iarchive.hpp>
#include <boost/archive/binary_oarchive.hpp>
#include <boost/archive/text_iarchive.hpp>
#include <boost/archive/text_oarchive.hpp>
#include <boost/iostreams/device/back_inserter.hpp>
#include <boost/iostreams/stream.hpp>
namespace boost {
namespace serialization {
template <class Archive, typename T>
void archiveVector(Archive &ar, T **p, int size) {
if (Archive::is_loading::value) {
if(*p != nullptr)
delete[] *p;
ar &size;
*p = size ? new T[size] : nullptr;
} else {
size = *p == nullptr ? 0 : size;
ar &size;
}
ar &make_array<T>(*p, size);
}
#ifndef EXHALE_DOXYGEN_SHOULD_SKIP_THIS
template <class Archive>
void serialize(Archive &ar, amici::Solver &s, const unsigned int /*version*/) {
ar &s.sensi_;
ar &s.atol_;
ar &s.rtol_;
ar &s.atolB_;
ar &s.rtolB_;
ar &s.atol_fsa_;
ar &s.rtol_fsa_;
ar &s.quad_atol_;
ar &s.quad_rtol_;
ar &s.ss_atol_;
ar &s.ss_rtol_;
ar &s.ss_atol_sensi_;
ar &s.ss_rtol_sensi_;
ar &s.maxsteps_;
ar &s.maxstepsB_;
ar &s.requires_preequilibration_;
ar &s.newton_maxsteps_;
ar &s.newton_maxlinsteps_;
ar &s.newton_damping_factor_mode_;
ar &s.newton_damping_factor_lower_bound_;
ar &s.ism_;
ar &s.sensi_meth_;
ar &s.linsol_;
ar &s.interp_type_;
ar &s.lmm_;
ar &s.iter_;
ar &s.stldet_;
ar &s.ordering_;
ar &s.cpu_time_;
ar &s.cpu_timeB_;
ar &s.rdata_mode_;
ar &s.maxtime_;
}
template <class Archive, class Period, class Rep>
void serialize(Archive &ar, std::chrono::duration<Period, Rep> &d, const unsigned int /*version*/) {
Period tmp_period;
if (Archive::is_loading::value) {
ar &tmp_period;
d = std::chrono::duration<Period, Rep>(tmp_period);
} else {
tmp_period = d.count();
ar &tmp_period;
}
}
template <class Archive>
void serialize(Archive &ar, amici::CVodeSolver &s, const unsigned int /*version*/) {
ar & static_cast<amici::Solver&>(s);
}
template <class Archive>
void serialize(Archive &ar, amici::Model &m, const unsigned int /*version*/) {
ar &dynamic_cast<amici::ModelDimensions&>(m);
ar &m.simulation_parameters_;
ar &m.o2mode;
ar &m.z2event_;
ar &m.idlist;
ar &m.state_.h;
ar &m.state_.unscaledParameters;
ar &m.state_.fixedParameters;
ar &m.state_.plist;
ar &m.x0data_;
ar &m.sx0data_;
ar &m.nmaxevent_;
ar &m.state_is_non_negative_;
ar &m.pythonGenerated;
ar &m.min_sigma_;
ar &m.sigma_res_;
}
template <class Archive>
void serialize(Archive &ar, amici::SimulationParameters &s, const unsigned int /*version*/) {
ar &s.fixedParameters;
ar &s.fixedParametersPreequilibration;
ar &s.fixedParametersPresimulation;
ar &s.parameters;
ar &s.x0;
ar &s.sx0;
ar &s.pscale;
ar &s.plist;
ar &s.ts_;
ar &s.tstart_;
ar &s.t_presim;
ar &s.reinitializeFixedParameterInitialStates;
}
template <class Archive>
void serialize(Archive &ar, amici::ReturnData &r, const unsigned int /*version*/) {
ar &dynamic_cast<amici::ModelDimensions&>(r);
ar &r.nx;
ar &r.nxtrue;
ar &r.nplist;
ar &r.nmaxevent;
ar &r.nt;
ar &r.newton_maxsteps;
ar &r.pscale;
ar &r.o2mode;
ar &r.sensi;
ar &r.sensi_meth;
ar &r.ts;
ar &r.xdot;
ar &r.J;
ar &r.w;
ar &r.z & r.sigmaz;
ar &r.sz &r.ssigmaz;
ar &r.rz;
ar &r.srz;
ar &r.s2rz;
ar &r.x;
ar &r.sx;
ar &r.y & r.sigmay;
ar &r.sy & r.ssigmay;
ar &r.numsteps;
ar &r.numstepsB;
ar &r.numrhsevals;
ar &r.numrhsevalsB;
ar &r.numerrtestfails;
ar &r.numerrtestfailsB;
ar &r.numnonlinsolvconvfails;
ar &r.numnonlinsolvconvfailsB;
ar &r.order;
ar &r.cpu_time;
ar &r.cpu_timeB;
ar &r.preeq_cpu_time;
ar &r.preeq_cpu_timeB;
ar &r.preeq_status;
ar &r.preeq_numsteps;
ar &r.preeq_numlinsteps;
ar &r.preeq_wrms;
ar &r.preeq_t;
ar &r.posteq_cpu_time;
ar &r.posteq_cpu_timeB;
ar &r.posteq_status;
ar &r.posteq_numsteps;
ar &r.posteq_numlinsteps;
ar &r.posteq_wrms;
ar &r.posteq_t;
ar &r.x0;
ar &r.sx0;
ar &r.llh;
ar &r.chi2;
ar &r.sllh;
ar &r.s2llh;
ar &r.status;
}
template <class Archive>
void serialize(Archive &ar, amici::ModelDimensions &m, const unsigned int /*version*/) {
ar &m.nx_rdata;
ar &m.nxtrue_rdata;
ar &m.nx_solver;
ar &m.nxtrue_solver;
ar &m.nx_solver_reinit;
ar &m.np;
ar &m.nk;
ar &m.ny;
ar &m.nytrue;
ar &m.nz;
ar &m.nztrue;
ar &m.ne;
ar &m.nw;
ar &m.ndwdx;
ar &m.ndwdp;
ar &m.ndwdw;
ar &m.ndxdotdw;
ar &m.ndJydy;
ar &m.nnz;
ar &m.nJ;
ar &m.ubw;
ar &m.lbw;
}
#endif
} // namespace serialization
} // namespace boost
namespace amici {
template <typename T>
char *serializeToChar(T const& data, int *size) {
try {
std::string serialized;
::boost::iostreams::back_insert_device<std::string> inserter(serialized);
::boost::iostreams::stream<::boost::iostreams::back_insert_device<std::string>>
s(inserter);
::boost::archive::binary_oarchive oar(s);
oar << data;
s.flush();
char *charBuffer = new char[serialized.size()];
memcpy(charBuffer, serialized.data(), serialized.size());
if (size)
*size = serialized.size();
return charBuffer;
} catch(boost::archive::archive_exception const& e) {
throw AmiException("Serialization to char failed: %s", e.what());
}
}
template <typename T>
T deserializeFromChar(const char *buffer, int size) {
namespace ba = ::boost::archive;
namespace bio = ::boost::iostreams;
bio::basic_array_source<char> device(buffer, size);
bio::stream<bio::basic_array_source<char>> s(device);
T data;
try {
// archive must be destroyed BEFORE returning
ba::binary_iarchive iar(s);
iar >> data;
} catch(ba::archive_exception const& e) {
throw AmiException("Deserialization from char failed: %s", e.what());
}
return data;
}
template <typename T>
std::string serializeToString(T const& data) {
namespace ba = ::boost::archive;
namespace bio = ::boost::iostreams;
std::string serialized;
bio::back_insert_device<std::string> inserter(serialized);
bio::stream<bio::back_insert_device<std::string>> os(inserter);
try {
// archive must be destroyed BEFORE returning
ba::binary_oarchive oar(os);
oar << data;
} catch(ba::archive_exception const& e) {
throw AmiException("Serialization to string failed: %s", e.what());
}
return serialized;
}
template <typename T>
std::vector<char> serializeToStdVec(T const& data) {
namespace ba = ::boost::archive;
namespace bio = ::boost::iostreams;
std::vector<char> buffer;
bio::stream<
bio::back_insert_device<
std::vector<char>>> os(buffer);
try{
// archive must be destroyed BEFORE returning
ba::binary_oarchive oar(os);
oar << data;
} catch(ba::archive_exception const& e) {
throw AmiException("Serialization to std::vector failed: %s", e.what());
}
return buffer;
}
template <typename T>
T deserializeFromString(std::string const& serialized) {
namespace ba = ::boost::archive;
namespace bio = ::boost::iostreams;
bio::basic_array_source<char> device(serialized.data(), serialized.size());
bio::stream<bio::basic_array_source<char>> os(device);
T deserialized;
try{
// archive must be destroyed BEFORE returning
ba::binary_iarchive iar(os);
iar >> deserialized;
} catch(ba::archive_exception const& e) {
throw AmiException("Deserialization from std::string failed: %s",
e.what());
}
return deserialized;
}
} // namespace amici
#endif // AMICI_SERIALIZATION_H