Source code for pints._util

#
# Utility classes for Pints
#
# This file is part of PINTS (https://github.com/pints-team/pints/) which is
# released under the BSD 3-clause license. See accompanying LICENSE.md for
# copyright notice and full license details.
#
import pints
import numpy as np
import timeit




def strfloat(x):
    """
    Converts a float to a string, with maximum precision.
    """
    return pints.FLOAT_FORMAT.format(float(x))





class Timer(object):
    """
    Provides accurate timing.

    Example
    -------
    ::

        timer = pints.Timer()
        print(timer.format(timer.time()))

    """
    def __init__(self, output=None):
        self._start = timeit.default_timer()
        self._methods = {}



    def format(self, time=None):
        """
        Formats a (non-integer) number of seconds, returns a string like
        "5 weeks, 3 days, 1 hour, 4 minutes, 9 seconds", or "0.0019 seconds".
        """
        if time is None:
            time = self.time()
        if time < 1e-2:
            return str(time) + ' seconds'
        elif time < 60:
            return str(round(time, 2)) + ' seconds'
        output = []
        time = int(round(time))
        units = [
            (604800, 'week'),
            (86400, 'day'),
            (3600, 'hour'),
            (60, 'minute'),
        ]
        for k, name in units:
            f = time // k
            if f > 0 or output:
                output.append(str(f) + ' ' + (name if f == 1 else name + 's'))
            time -= f * k
        output.append('1 second' if time == 1 else str(time) + ' seconds')
        return ', '.join(output)




    def reset(self):
        """
        Resets this timer's start time.
        """
        self._start = timeit.default_timer()




    def time(self):
        """
        Returns the time (in seconds) since this timer was created, or since
        meth:`reset()` was last called.
        """
        return timeit.default_timer() - self._start






def vector(x):
    """
    Copies ``x`` and returns a 1d read-only NumPy array of floats with shape
    ``(n,)``.

    Raises a ``ValueError`` if ``x`` has an incompatible shape.
    """
    if np.isscalar(x):
        x = np.array([float(x)])
    else:
        x = np.array(x, copy=True, dtype=float)
    x.setflags(write=False)
    if x.ndim != 1:
        n = np.max(x.shape)
        if np.prod(x.shape) != n:
            raise ValueError(
                'Unable to convert to 1d vector of scalar values.')
        x = x.reshape((n,))
    return x





def matrix2d(x):
    """
    Copies ``x`` and returns a 2d read-only NumPy array of floats with shape
    ``(m, n)``.

    Raises a ``ValueError`` if ``x`` has an incompatible shape.
    """
    x = np.array(x, copy=True, dtype=float)
    if x.ndim == 1:
        x = x.reshape((len(x), 1))
    elif x.ndim != 2:
        raise ValueError('Unable to convert to 2d matrix.')
    x.setflags(write=False)
    return x