Class SimulationResultWriter¶
Defined in File simulationResultWriter.h
Class Documentation¶
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class parpe::SimulationResultWriter¶
The SimulationResultWriter class saves AMICI simulation results for one or multiple conditions to an HDF5 file.
Will write to existing file or create new one. Will fail if the dataset to be written already exist.
Structure is
rootPath/ +- yMes/$conditionIdx [double: nt x ny] (nt may be condition-specific) +- ySim/$conditionIdx [double: nt x ny] (nt may be condition-specific) +- llh [double: nConditions] +- ...
Public Functions
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SimulationResultWriter() = default¶
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SimulationResultWriter(const H5::H5File &file, std::string rootPath)¶
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- Parameters
file – HDF5 file object to write to
rootPath – Path prefix inside HDF5 file
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SimulationResultWriter(std::string const &hdf5FileName, std::string rootPath)¶
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- Parameters
hdf5FileName – HDF5 file to create or open for appending
rootPath – Path prefix inside HDF5 file
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SimulationResultWriter(SimulationResultWriter const&) = delete¶
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~SimulationResultWriter()¶
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void createDatasets(hsize_t numSimulations)¶
Create results datasets.
Must be called before first call to
save*
- Parameters
numSimulations –
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void createDatasets(int numberOfSimulations = 1)¶
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void saveSimulationResults(const amici::ExpData *edata, const amici::ReturnData *rdata, int simulationIdx)¶
Save results for a single simulation to HDF5 file.
- Parameters
edata –
rdata –
simulationIdx – If >= 0: write results in the selected position of the result data sets (-> createDatasets)
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void saveTimepoints(gsl::span<const double> timepoints, int simulationIdx) const¶
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void saveMeasurements(gsl::span<const double> measurements, int nt, int nytrue, int simulationIdx) const¶
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void saveModelOutputs(gsl::span<const double> outputs, int nt, int nytrue, int simulationIdx) const¶
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void saveStates(gsl::span<const double> states, int nt, int nx, int simulationIdx) const¶
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void saveParameters(gsl::span<const double> parameters, int simulationIdx) const¶
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void saveLikelihood(double llh, int simulationIdx) const¶
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H5::H5File reopenFile()¶
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SimulationResultWriter() = default¶