Storage¶

Saving and loading traces and results objects.

class pypesto.store.OptimizationResultHDF5Reader(storage_filename: str)[source]¶

Bases: object

Reader of the HDF5 result files written by class OptimizationResultHDF5Writer.

storage_filename¶: HDF5 result file name

__init__(storage_filename: str)[source]¶

Parameters: storage_filename (str) – HDF5 result file name

read() → pypesto.result.Result [source]¶: Read HDF5 result file and return pyPESTO result object.

class pypesto.store.OptimizationResultHDF5Writer(storage_filename: str)[source]¶

Bases: object

Writer of the HDF5 result files.

storage_filename¶: HDF5 result file name

__init__(storage_filename: str)[source]¶

Parameters: storage_filename (str) – HDF5 result file name

write(result: pypesto.result.Result, overwrite=False)[source]¶: Write HDF5 result file from pyPESTO result object.

class pypesto.store.ProblemHDF5Reader(storage_filename: str)[source]¶

Bases: object

Reader of the HDF5 problem files written by class ProblemHDF5Writer.

storage_filename¶: HDF5 problem file name

__init__(storage_filename: str)[source]¶

Parameters: storage_filename (str) – HDF5 problem file name

read(objective: Optional[pypesto.objective.base.ObjectiveBase] = None) → pypesto.problem.Problem [source]¶

Read HDF5 problem file and return pyPESTO problem object.

Parameters: objective – Objective function which is currently not saved to storage.
Returns: A problem instance with all attributes read in.
Return type: problem

class pypesto.store.ProblemHDF5Writer(storage_filename: str)[source]¶

Bases: object

Writer of the HDF5 problem files.

storage_filename¶: HDF5 result file name

__init__(storage_filename: str)[source]¶

Parameters: storage_filename (str) – HDF5 problem file name

write(problem, overwrite: bool = False)[source]¶: Write HDF5 problem file from pyPESTO problem object.

class pypesto.store.ProfileResultHDF5Reader(storage_filename: str)[source]¶

Bases: object

Reader of the HDF5 result files written by class OptimizationResultHDF5Writer.

storage_filename¶: HDF5 result file name

__init__(storage_filename: str)[source]¶

Parameters: storage_filename (str) – HDF5 result file name

read() → pypesto.result.Result [source]¶: Read HDF5 result file and return pyPESTO result object.

class pypesto.store.ProfileResultHDF5Writer(storage_filename: str)[source]¶

Bases: object

Writer of the HDF5 result files.

storage_filename¶: HDF5 result file name

__init__(storage_filename: str)[source]¶

Parameters: storage_filename (str) – HDF5 result file name

write(result: pypesto.result.Result, overwrite: bool = False)[source]¶: Write HDF5 result file from pyPESTO result object.

class pypesto.store.SamplingResultHDF5Reader(storage_filename: str)[source]¶

Bases: object

Reader of the HDF5 result files written by class SamplingResultHDF5Writer.

storage_filename¶: HDF5 result file name

__init__(storage_filename: str)[source]¶

Parameters: storage_filename (str) – HDF5 result file name

read() → pypesto.result.Result [source]¶: Read HDF5 result file and return pyPESTO result object.

class pypesto.store.SamplingResultHDF5Writer(storage_filename: str)[source]¶

Bases: object

Writer of the HDF5 sampling files.

storage_filename¶: HDF5 result file name

__init__(storage_filename: str)[source]¶

Parameters: storage_filename (str) – HDF5 result file name

write(result: pypesto.result.Result, overwrite: bool = False)[source]¶: Write HDF5 sampling file from pyPESTO result object.

pypesto.store.get_or_create_group(f: Union[h5py._hl.files.File, h5py._hl.group.Group], group_path: str) → h5py._hl.group.Group[source]¶

Helper function that returns a group object for the group with group_path relative to f. Creates it if it doesn’t exist.

pypesto.store.f¶

should be checked

Type: file or group where existence of a group with the path group_path

pypesto.store.group_path¶

Type: the path or simply the name of the group that should exist in f

Returns: hdf5 group object with specified path.
Return type: grp

pypesto.store.load_objective_config(filename: str)[source]¶

Load the objective information stored in f

Parameters

filename – The name of the file in which the information are stored.
Returns – A dictionary of the information, stored instead of the actual objective in problem.objective.

pypesto.store.optimization_result_from_history(filename: str)[source]¶

Converts a saved hdf5 History to an optimization result. Used for interrupted optimization runs.

Parameters

filename – The name of the file in which the information are stored.
Returns – A result object in which the optimization result is constructed from history. But missing “Time, Message and Exitflag” keys.

pypesto.store.read_result(filename: str, problem: bool = True, optimize: bool = False, profile: bool = False, sample: bool = False) → pypesto.result.Result [source]¶

This is a function that saves the whole pypesto.Result object in an HDF5 file. With booleans one can choose more detailed what to save.

Parameters

filename – The HDF5 filename.
problem – Read the problem.
optimize – Read the optimize result.
profile – Read the profile result.
sample – Read the sample result.

Returns

Result object containing the results stored in HDF5 file.

Return type

result

pypesto.store.write_array(f: h5py._hl.group.Group, path: str, values: Collection) → None [source]¶

Write array to hdf5

Parameters

f – h5py.Group where dataset should be created
path – path of the dataset to create
values – array to write

pypesto.store.write_result(result: pypesto.result.Result, filename: str, overwrite: bool = False, problem: bool = True, optimize: bool = True, profile: bool = True, sample: bool = True)[source]¶

Save whole pypesto.Result to hdf5 file.

Boolean indicators allow specifying what to save.

Parameters

result – The pypesto.Result object to be saved.
filename – The HDF5 filename.
overwrite – Boolean, whether already existing results should be overwritten.
problem – Read the problem.
optimize – Read the optimize result.
profile – Read the profile result.
sample – Read the sample result.