simulation_analysis.py¶

`SimulationAnalysis` ¶

Interface to make plots of multiple hdf5 files generated with Simulation.

All plot methods of the Analysis class are available in the SimulationAnalysis class.

Important

When calling an Analysis method from a SimulationAnalysis object every instance of "$id" in a str parameter will be replaced with the identifier of that hdf5, this can be useful to use with parameters like filename or title.

Example:

from comorbuss import SimulationAnalysis

analysis = SimulationAnalysis.from_folder("/data/folder")
analysis.plot_SEIR(filename="$id.pdf")
analysis.close()

`empty_from_files(filenames)` `classmethod` ¶

Instances an empty SimulationAnalysis object from a list/array/tuples of hdf5 filenames

Parameters:

Name	Type	Description	Default
`filenames`		A list/numpy.array/tuple array of filenames	required

Returns:

Type	Description
`SimulationAnalysis`	SimulationAnalysis object.

Source code in comorbuss/lab/simulation_analysis.py

@classmethod
def empty_from_files(cls, filenames):
    """Instances an empty SimulationAnalysis object from a list/array/tuples of hdf5 filenames

    Args:
        filenames: A list/numpy.array/tuple array of filenames

    Returns:
        SimulationAnalysis: SimulationAnalysis object.
    """
    As = {}
    for simid, hdf5 in enumerate(filenames):
        As[simid] = Analysis({}, {}, False)
        As[simid].filename = hdf5
    return cls(As)

`from_exp_parameters(*args, **kwargs)` `classmethod` ¶

Instance an SimulationAnalysis object from experiment parameters. Accepts same parameters as the Simulation class.

Returns:

Type	Description
`SimulationAnalysis`	SimulationAnalysis object.

Source code in comorbuss/lab/simulation_analysis.py

@classmethod
def from_exp_parameters(cls, *args, **kwargs):
    """Instance an SimulationAnalysis object from experiment parameters. Accepts same
        parameters as the [Simulation class](#comorbuss.lab.Simulation.__init__).

    Returns:
        SimulationAnalysis: SimulationAnalysis object.
    """
    sim = Simulation(*args, **kwargs)
    return SimulationAnalysis.from_sim(sim)

`from_files(filenames)` `classmethod` ¶

Instances a SimulationAnalysis object from a list/array/tuples of hdf5 filenames

Parameters:

Name	Type	Description	Default
`filenames`		A list/numpy.array/tuple array of filenames	required

Returns:

Type	Description
`SimulationAnalysis`	SimulationAnalysis object.

Source code in comorbuss/lab/simulation_analysis.py

@classmethod
def from_files(cls, filenames):
    """Instances a SimulationAnalysis object from a list/array/tuples of hdf5 filenames

    Args:
        filenames: A list/numpy.array/tuple array of filenames

    Returns:
        SimulationAnalysis: SimulationAnalysis object.
    """
    As = {}
    for simid, hdf5 in enumerate(filenames):
        As[simid] = Analysis.from_hdf5(hdf5)
    return cls(As)

`from_folder(folder, strings_to_ignore=[])` `classmethod` ¶

Instance an SimulationAnalysis object from all hdf5 files in a folder.

Parameters:

Name	Type	Description	Default
`folder`	`str`	Path to the folder where the hdf5 files are stored.	required

Returns:

Type	Description
`SimulationAnalysis`	SimulationAnalysis object.

Source code in comorbuss/lab/simulation_analysis.py

@classmethod
def from_folder(cls, folder, strings_to_ignore=[]):
    """Instance an SimulationAnalysis object from all hdf5 files in a folder.

    Args:
        folder (str): Path to the folder where the hdf5 files are stored.

    Returns:
        SimulationAnalysis: SimulationAnalysis object.
    """
    files = os.listdir(path=folder)
    files.sort(key=lambda f: os.path.getctime(os.path.join(folder, f)))
    As = {}
    for f in files:
        ignore = any([s in f for s in strings_to_ignore])
        if f.lower()[-5:] == ".hdf5" and not ignore:
            hdf5 = os.path.join(folder, f)
            simid = os.path.split(f)[-1][:-5]
            As[simid] = Analysis.from_hdf5(hdf5)
    return cls(As)

`from_sim(sim)` `classmethod` ¶

Instance an SimulationAnalysis object from a Simulation object.

Parameters:

Name	Type	Description	Default
`sim`	`Simulation`	Simulation object to load data.	required

Returns:

Type	Description
`SimulationAnalysis`	SimulationAnalysis object.

Source code in comorbuss/lab/simulation_analysis.py

@classmethod
def from_sim(cls, sim):
    """Instance an SimulationAnalysis object from a Simulation object.

    Args:
        sim (Simulation): Simulation object to load data.

    Returns:
        SimulationAnalysis: SimulationAnalysis object.
    """
    As = {}
    for simid, hdf5 in sim.get_hdf5_files().items():
        As[simid] = Analysis.from_hdf5(hdf5)
    return cls(As)

`caller` ¶

Stores a function to further calls.

simulation_analysis.py¶