Class HDF5DataGenerator¶
Defined in File hdf5_pe_input.py
Class Documentation¶
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class
HDF5DataGenerator
¶ Generate HDF5 file with fixed parameters and measurements for an AMICI-imported SBML model based on a PEtab problem. Attributes: amici_model: AMICI model for which to estimate parameters petab_problem: PEtab optimization problem (will be modified in place) compression: h5py compression to be used condition_ids: numpy.array condition IDs (different condition vectors, both simulation and preequilibration) num_condition_vectors: Number of condition vectors, including simulation and preequilibration. Not necessarily equal to the number of simulations. unique_timepoints: time points for which there is data f: h5py.File hdf5 file which is being created
Public Functions
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__init__
()¶
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generate_file
()¶
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get_index_mapping_for_par
()¶
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create_fixed_parameter_dataset_and_write_attributes
()¶
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write_measurements
(self self)¶ Write measurements to hdf5 dataset
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handle_offset_parameter
(self self, offset_candidates offset_candidates)¶ Write list of offset parameters selected for hierarchical optimization
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