Program Listing for File edata.h
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#ifndef AMICI_EDATA_H
#define AMICI_EDATA_H
#include "amici/defines.h"
#include "amici/misc.h"
#include "amici/simulation_parameters.h"
#include <vector>
namespace amici {
class Model;
class ReturnData;
class ExpData : public SimulationParameters {
public:
ExpData() = default;
// needs to be declared to be wrapped by SWIG
ExpData(ExpData const&) = default;
ExpData(int nytrue, int nztrue, int nmaxevent);
ExpData(int nytrue, int nztrue, int nmaxevent, std::vector<realtype> ts);
ExpData(
int nytrue, int nztrue, int nmaxevent, std::vector<realtype> ts,
std::vector<realtype> fixedParameters
);
ExpData(
int nytrue, int nztrue, int nmaxevent, std::vector<realtype> ts,
std::vector<realtype> const& observedData,
std::vector<realtype> const& observedDataStdDev,
std::vector<realtype> const& observedEvents,
std::vector<realtype> const& observedEventsStdDev
);
explicit ExpData(Model const& model);
ExpData(ReturnData const& rdata, realtype sigma_y, realtype sigma_z);
ExpData(
ReturnData const& rdata, std::vector<realtype> sigma_y,
std::vector<realtype> sigma_z
);
~ExpData() = default;
friend inline bool operator==(ExpData const& lhs, ExpData const& rhs);
int nytrue() const;
int nztrue() const;
int nmaxevent() const;
int nt() const;
void setTimepoints(std::vector<realtype> const& ts);
std::vector<realtype> const& getTimepoints() const;
realtype getTimepoint(int it) const;
void setObservedData(std::vector<realtype> const& observedData);
void setObservedData(std::vector<realtype> const& observedData, int iy);
bool isSetObservedData(int it, int iy) const;
std::vector<realtype> const& getObservedData() const;
realtype const* getObservedDataPtr(int it) const;
void setObservedDataStdDev(std::vector<realtype> const& observedDataStdDev);
void setObservedDataStdDev(realtype stdDev);
void setObservedDataStdDev(
std::vector<realtype> const& observedDataStdDev, int iy
);
void setObservedDataStdDev(realtype stdDev, int iy);
bool isSetObservedDataStdDev(int it, int iy) const;
std::vector<realtype> const& getObservedDataStdDev() const;
realtype const* getObservedDataStdDevPtr(int it) const;
void setObservedEvents(std::vector<realtype> const& observedEvents);
void setObservedEvents(std::vector<realtype> const& observedEvents, int iz);
bool isSetObservedEvents(int ie, int iz) const;
std::vector<realtype> const& getObservedEvents() const;
realtype const* getObservedEventsPtr(int ie) const;
void
setObservedEventsStdDev(std::vector<realtype> const& observedEventsStdDev);
void setObservedEventsStdDev(realtype stdDev);
void setObservedEventsStdDev(
std::vector<realtype> const& observedEventsStdDev, int iz
);
void setObservedEventsStdDev(realtype stdDev, int iz);
bool isSetObservedEventsStdDev(int ie, int iz) const;
std::vector<realtype> const& getObservedEventsStdDev() const;
realtype const* getObservedEventsStdDevPtr(int ie) const;
void clear_observations();
std::string id;
protected:
void applyDimensions();
void applyDataDimension();
void applyEventDimension();
void checkDataDimension(
std::vector<realtype> const& input, char const* fieldname
) const;
void checkEventsDimension(
std::vector<realtype> const& input, char const* fieldname
) const;
int nytrue_{0};
int nztrue_{0};
int nmaxevent_{0};
std::vector<realtype> observed_data_;
std::vector<realtype> observed_data_std_dev_;
std::vector<realtype> observed_events_;
std::vector<realtype> observed_events_std_dev_;
};
inline bool operator==(ExpData const& lhs, ExpData const& rhs) {
return *dynamic_cast<SimulationParameters const*>(&lhs)
== *dynamic_cast<SimulationParameters const*>(&rhs)
&& lhs.id == rhs.id && lhs.nytrue_ == rhs.nytrue_
&& lhs.nztrue_ == rhs.nztrue_ && lhs.nmaxevent_ == rhs.nmaxevent_
&& is_equal(lhs.observed_data_, rhs.observed_data_)
&& is_equal(lhs.observed_data_std_dev_, rhs.observed_data_std_dev_)
&& is_equal(lhs.observed_events_, rhs.observed_events_)
&& is_equal(
lhs.observed_events_std_dev_, rhs.observed_events_std_dev_
);
};
void checkSigmaPositivity(
std::vector<realtype> const& sigmaVector, char const* vectorName
);
void checkSigmaPositivity(realtype sigma, char const* sigmaName);
class ConditionContext : public ContextManager {
public:
explicit ConditionContext(
Model* model, ExpData const* edata = nullptr,
FixedParameterContext fpc = FixedParameterContext::simulation
);
ConditionContext& operator=(ConditionContext const& other) = delete;
~ConditionContext();
void applyCondition(ExpData const* edata, FixedParameterContext fpc);
void restore();
private:
Model* model_ = nullptr;
std::vector<realtype> original_x0_;
std::vector<realtype> original_sx0_;
std::vector<realtype> original_parameters_;
std::vector<realtype> original_fixed_parameters_;
realtype original_tstart_;
std::vector<realtype> original_timepoints_;
std::vector<int> original_parameter_list_;
std::vector<amici::ParameterScaling> original_scaling_;
bool original_reinitialize_fixed_parameter_initial_states_;
std::vector<int> original_reinitialization_state_idxs;
};
} // namespace amici
#endif /* AMICI_EDATA_H */