3999396905

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[merge before other PRs] ruff updates (#580)

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26.23

/mdsuite/time_series/base.py

"""
MDSuite: A Zincwarecode package.

License
-------
This program and the accompanying materials are made available under the terms
of the Eclipse Public License v2.0 which accompanies this distribution, and is
available at https://www.eclipse.org/legal/epl-v20.html

SPDX-License-Identifier: EPL-2.0

Copyright Contributors to the Zincwarecode Project.

Contact Information
-------------------
email: zincwarecode@gmail.com
github: https://github.com/zincware
web: https://zincwarecode.com/

Citation
--------
If you use this module please cite us with:

Summary
-------
"""
from __future__ import annotations

from typing import TYPE_CHECKING

import matplotlib.pyplot as plt
import numpy as np
import tensorflow as tf

from mdsuite.database.simulation_database import Database

if TYPE_CHECKING:
    from mdsuite import Experiment


def running_mean(x, size):
    """Perform a rolling window mean."""
    cumsum = np.cumsum(np.insert(x, 0, 0))
    return (cumsum[size:] - cumsum[:-size]) / float(size)


class TimeSeries:
    """Time Series class."""

    def __init__(self, experiment: Experiment):
        """

        Parameters
        ----------
        experiment: Experiment
            The parent experiment class to perform the time series operation on
        """
        self.experiment = experiment

        self.loaded_property = None
        self.fig_labels = {"x": None, "y": None}
        self.species = experiment.species
        self.rolling_window = 0
        self.reduce_sum = True

        # Properties
        self._database = None
        self._data = None

    def __call__(self, species: list = None, rolling_window: int = 0):
        if species is not None:
            self.species = species
        self.rolling_window = rolling_window
        self.plot()

    @property
    def database(self):
        """Get the database."""
        if self._database is None:
            self._database = Database(self.experiment.database_path / "database.hdf5")
        return self._database

    @property
    def data(self):
        """Get the data for all species and timesteps for the loaded_property."""
        if self._data is None:
            self._data = tf.concat(
                [
                    self.database.load_data([f"{species}/{self.loaded_property}"])
                    for species in self.species
                ],
                axis=0,
            )
        return self._data

    @property
    def preprocess_data(self):
        """Perform some data preprocessing before plotting it."""
        data = self.data
        if self.reduce_sum:
            data = tf.einsum("atx -> t", data)
            # perform a reduce sum over atoms "a" and property dimension "x" to
            # yield time steps "t"
        if self.rolling_window > 0:
            data = running_mean(data, self.rolling_window)

        return data

    def plot(self):
        """Plot the data over timesteps."""
        fig, ax = plt.subplots()
        ax.plot(self.preprocess_data)
        ax.set_xlabel(self.fig_labels["x"])
        ax.set_ylabel(self.fig_labels["y"])
        fig.show()

1	"""
2	MDSuite: A Zincwarecode package.
3
4	License
5	-------
6	This program and the accompanying materials are made available under the terms
7	of the Eclipse Public License v2.0 which accompanies this distribution, and is
8	available at https://www.eclipse.org/legal/epl-v20.html
9
10	SPDX-License-Identifier: EPL-2.0
11
12	Copyright Contributors to the Zincwarecode Project.
13
14	Contact Information
15	-------------------
16	email: zincwarecode@gmail.com
17	github: https://github.com/zincware
18	web: https://zincwarecode.com/
19
20	Citation
21	--------
22	If you use this module please cite us with:
23
24	Summary
25	-------
26	"""
27	from __future__ import annotations	4✔
28
29	from typing import TYPE_CHECKING	4✔
30
31	import matplotlib.pyplot as plt	4✔
32	import numpy as np	4✔
33	import tensorflow as tf	4✔
34
35	from mdsuite.database.simulation_database import Database	4✔
36
37	if TYPE_CHECKING:	4!
38	from mdsuite import Experiment	×
39
40
41	def running_mean(x, size):	4✔
42	"""Perform a rolling window mean."""
43	cumsum = np.cumsum(np.insert(x, 0, 0))	×
44	return (cumsum[size:] - cumsum[:-size]) / float(size)	×
45
46
47	class TimeSeries:	4✔
48	"""Time Series class."""
49
50	def __init__(self, experiment: Experiment):	4✔
51	"""
52
53	Parameters
54	----------
55	experiment: Experiment
56	The parent experiment class to perform the time series operation on
57	"""
58	self.experiment = experiment	×
59
60	self.loaded_property = None	×
61	self.fig_labels = {"x": None, "y": None}	×
62	self.species = experiment.species	×
63	self.rolling_window = 0	×
64	self.reduce_sum = True	×
65
66	# Properties
67	self._database = None	×
68	self._data = None	×
69
70	def __call__(self, species: list = None, rolling_window: int = 0):	4✔
71	if species is not None:	×
72	self.species = species	×
73	self.rolling_window = rolling_window	×
74	self.plot()	×
75
76	@property	4✔
77	def database(self):	3✔
78	"""Get the database."""
79	if self._database is None:	×
80	self._database = Database(self.experiment.database_path / "database.hdf5")	×
81	return self._database	×
82
83	@property	4✔
84	def data(self):	3✔
85	"""Get the data for all species and timesteps for the loaded_property."""
86	if self._data is None:	×
87	self._data = tf.concat(	×
88	[
89	self.database.load_data([f"{species}/{self.loaded_property}"])
90	for species in self.species
91	],
92	axis=0,
93	)
94	return self._data	×
95
96	@property	4✔
97	def preprocess_data(self):	3✔
98	"""Perform some data preprocessing before plotting it."""
99	data = self.data	×
100	if self.reduce_sum:	×
101	data = tf.einsum("atx -> t", data)	×
102	# perform a reduce sum over atoms "a" and property dimension "x" to
103	# yield time steps "t"
104	if self.rolling_window > 0:	×
105	data = running_mean(data, self.rolling_window)	×
106
107	return data	×
108
109	def plot(self):	4✔
110	"""Plot the data over timesteps."""
111	fig, ax = plt.subplots()	×
112	ax.plot(self.preprocess_data)	×
113	ax.set_xlabel(self.fig_labels["x"])	×
114	ax.set_ylabel(self.fig_labels["y"])	×
115	fig.show()	×

zincware / MDSuite / 3999396905

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