Class HDF5DataGenerator¶

Defined in File hdf5_pe_input.py

Class Documentation¶

class parpe.hdf5_pe_input.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

__init__()¶

generate_file()¶

get_index_mapping_for_par()¶

create_fixed_parameter_dataset_and_write_attributes()¶

write_measurements(self)¶

Write measurements to hdf5 dataset

handle_offset_parameter(self, offset_candidates)¶

Write list of offset parameters selected for hierarchical optimization

Public Members

condition_ids¶

unique_timepoints¶

condition_map¶

observable_ids¶

verbose¶

compression¶

f¶

num_condition_vectors¶

condition_id_to_index¶

problem_parameter_ids¶

parameter_mapping¶

optimization_parameter_name_to_index¶

nk¶

ny¶