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Utilities

utils.py

Module to provide utilities for the hallmd package.

Includes

  • ModelRunException - Used to note when a model has encountered an unknown error.
  • data_write() - Convenience function for writing .json data to file.
  • plot_qoi() - Convenience plotting tool for showing QoI with UQ bounds

ModelRunException

Bases: Exception

Custom exception to note when a model has encountered an unknown error while executing.

data_write(data, filename, write_dir='.')

Convenience function to write .json data files.

Source code in src/hallmd/utils.py 
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def data_write(data, filename, write_dir='.'):
    """Convenience function to write .json data files."""
    with open(Path(write_dir) / filename, 'w', encoding='utf-8') as fd:
        json.dump(data, fd, ensure_ascii=False, indent=4)

model_config_dir()

Return a path to the model configuration directory

Source code in src/hallmd/utils.py 
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def model_config_dir():
    """Return a path to the model configuration directory"""
    return resources.files('hallmd.models.config')

plot_qoi(ax, x, qoi, xlabel, ylabel, legend=False)

Plot a quantity of interest with 5%, 50%, 95% percentiles against x.

PARAMETER DESCRIPTION
ax

matplotlib Axes object to plot on
x

(Nx,) array to plot on x axis
qoi

(Nx, Ns,) samples of the QOI at each x location
xlabel

label for the x-axis
ylabel

label for the y-axis
legend

whether to plot a legend

DEFAULT: False

Source code in src/hallmd/utils.py 
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def plot_qoi(ax, x, qoi, xlabel, ylabel, legend=False):
    """ Plot a quantity of interest with 5%, 50%, 95% percentiles against `x`.

    :param ax: matplotlib Axes object to plot on
    :param x: `(Nx,)` array to plot on `x` axis
    :param qoi: `(Nx, Ns,)` samples of the QOI at each `x` location
    :param xlabel: label for the x-axis
    :param ylabel: label for the y-axis
    :param legend: whether to plot a legend
    """
    p5 = np.percentile(qoi, 5, axis=1)
    med = np.percentile(qoi, 50, axis=1)
    p95 = np.percentile(qoi, 95, axis=1)
    ax.plot(x, med, '-k', label='Model')
    ax.fill_between(x, p5, p95, alpha=0.4, edgecolor=(0.4, 0.4, 0.4), facecolor=(0.8, 0.8, 0.8))
    ax_default(ax, xlabel, ylabel, legend=legend)