Class MultiConditionDataProviderDefault

Inheritance Relationships

Base Type

Class Documentation

class MultiConditionDataProviderDefault : public parpe::MultiConditionDataProvider

In-memory data.

!!Very limited implementation, currently only for testing!!

Public Functions

MultiConditionDataProviderDefault(std::unique_ptr<amici::Model> model, std::unique_ptr<amici::Solver> solver)
~MultiConditionDataProviderDefault() override = default
virtual int getNumberOfSimulationConditions() const override

Provides the number of conditions for which data is available and simulations need to be run. This is determined from the dimensions of the MultiConditionDataProviderDefault::hdf5MeasurementPath dataset.

Returns:

Number of conditions

virtual std::vector<int> getSimulationToOptimizationParameterMapping(int conditionIdx) const override

Get mapping vector simulation_parameter_idx -> optimization_parameter_idx for the given condition index.

Parameters:

conditionIdx –

Returns:

Mapping vector

virtual void mapSimulationToOptimizationGradientAddMultiply(int conditionIdx, gsl::span<double const> simulation, gsl::span<double> optimization, gsl::span<const double> parameters, double coefficient = 1.0) const override
virtual void mapAndSetOptimizationToSimulationVariables(int conditionIdx, gsl::span<double const> optimization, gsl::span<double> simulation, gsl::span<amici::ParameterScaling> optimizationScale, gsl::span<amici::ParameterScaling> simulationScale) const override
virtual std::vector<amici::ParameterScaling> getParameterScaleOpt() const override
virtual amici::ParameterScaling getParameterScaleOpt(int optimizationParameterIndex) const override

Get the parameter scale for the given optimization parameter.

Parameters:

simulationIdx –

Returns:

Parameter scale

virtual amici::ParameterScaling getParameterScaleSim(int simulationIdx, int optimizationParameterIndex) const override

Get the parameter scale for the given parameter and simulation.

Parameters:

simulationIdx –

Returns:

virtual std::vector<amici::ParameterScaling> getParameterScaleSim(int) const override

Get the parameter scale vector for the given simulation.

Parameters:

simulationIdx –

Returns:

virtual void updateSimulationParametersAndScale(int conditionIndex, gsl::span<const double> optimizationParams, amici::Model &model) const override
virtual std::unique_ptr<amici::ExpData> getExperimentalDataForCondition(int conditionIdx) const override
virtual std::vector<std::vector<double>> getAllMeasurements() const override
virtual std::vector<std::vector<double>> getAllSigmas() const override
virtual int getNumOptimizationParameters() const override

Returns the number of optimization parameters of this problem.

Returns:

Number of parameters

virtual std::unique_ptr<amici::Model> getModel() const override

Returns a pointer to the underlying AMICI model.

Returns:

The model

virtual std::unique_ptr<amici::Solver> getSolver() const override
virtual std::vector<std::string> getProblemParameterIds() const override

Public Members

std::vector<amici::ExpData> edata_