Class MultiConditionDataProviderDefault

• Defined in File multiConditionDataProvider.h

Inheritance Relationships

Base Type

• public parpe::MultiConditionDataProvider (Class MultiConditionDataProvider)

Class Documentation

class parpe::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)

virtual ~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 hdf5MeasurementPath dataset.

Return

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.

Return

Mapping vector

Parameters

• conditionIdx:

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.

Return

Parameter scale

Parameters

• simulationIdx:

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

Get the parameter scale for the given parameter and simulation.

Return

Parameters

• simulationIdx:

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

Get the parameter scale vector for the given simulation.

Return

Parameters

• simulationIdx:

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.

Return

Number of parameters

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

Returns a pointer to the underlying AMICI model.

Return

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_