pymcmcstat.utilities package

pymcmcstat.utilities.NumpyEncoder module

Created on Mon Apr 2 08:42:56 2018

@author: prmiles

class pymcmcstat.utilities.NumpyEncoder.NumpyEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]

Bases: json.encoder.JSONEncoder

Encoder used for storing numpy arrays in json files.


Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
        iterable = iter(o)
    except TypeError:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)

pymcmcstat.utilities.general module

Created on Tue Jun 26 06:16:02 2018

General functions used throughout package

@author: prmiles

pymcmcstat.utilities.general.check_settings(default_settings, user_settings=None)[source]

Check user settings with default.

Recursively checks elements of user settings against the defaults and updates settings as it goes. If a user setting does not exist in the default, then the user setting is added to the settings. If the setting is defined in both the user and default settings, then the user setting overrides the default. Otherwise, the default settings persist.

  • default_settings (dict): Default settings for particular method.

  • user_settings (dict): User defined settings.

  • (dict): Updated settings.


Format number for display

  • number (float): Number to be formatted

  • (str): Formatted string display

pymcmcstat.utilities.general.message(verbosity, level, printthis)[source]

Display message

  • verbosity (int): Verbosity of display output.

  • level (int): Print level relative to verbosity.

  • printthis (str): String to be printed.

pymcmcstat.utilities.general.removekey(d, key)[source]

Removed elements from dictionary and return the remainder.

  • d (dict): Original dictionary.

  • key (str): Keyword to be removed.

  • r (dict): Updated dictionary without the keyword, value pair.

pymcmcstat.utilities.progressbar module


Simulation progress bar.

A simple progress bar to monitor MCMC sampling progress. Modified from original code by Corey Goldberg (2010).

  • iters (int): Number of iterations in simulation.

Example display:

[--------         21%                  ] 2109 of 10000 complete in 0.5 sec


Will display a progress bar as simulation runs, providing feedback as to the status of the simulation. Depending on the available resources, the appearance of the progress bar may differ.