#
# NumpyArray class
#
from __future__ import annotations
import numpy as np
from scipy.sparse import csr_matrix, issparse
import pybamm
from pybamm.type_definitions import DomainType, AuxiliaryDomainType, DomainsType
import sympy
[docs]
class Array(pybamm.Symbol):
"""
Node in the expression tree that holds an tensor type variable
(e.g. :class:`numpy.array`)
Parameters
----------
entries : numpy.array or list
the array associated with the node. If a list is provided, it is converted to a
numpy array
name : str, optional
the name of the node
domain : iterable of str, optional
list of domains the parameter is valid over, defaults to empty list
auxiliary_domains : dict, optional
dictionary of auxiliary domains, defaults to empty dict
domains : dict
A dictionary equivalent to {'primary': domain, auxiliary_domains}. Either
'domain' and 'auxiliary_domains', or just 'domains', should be provided
(not both). In future, the 'domain' and 'auxiliary_domains' arguments may be
deprecated.
entries_string : str
String representing the entries (slow to recalculate when copying)
"""
def __init__(
self,
entries: np.ndarray | list[float] | csr_matrix,
name: str | None = None,
domain: DomainType = None,
auxiliary_domains: AuxiliaryDomainType = None,
domains: DomainsType = None,
entries_string: str | None = None,
) -> None:
# if
if isinstance(entries, list):
entries = np.array(entries)
if entries.ndim == 1:
entries = entries[:, np.newaxis]
if name is None:
name = f"Array of shape {entries.shape!s}"
self._entries = entries.astype(float)
# Use known entries string to avoid re-hashing, where possible
self.entries_string = entries_string
super().__init__(
name, domain=domain, auxiliary_domains=auxiliary_domains, domains=domains
)
@classmethod
def _from_json(cls, snippet: dict):
if isinstance(snippet["entries"], dict):
matrix = csr_matrix(
(
snippet["entries"]["data"],
snippet["entries"]["row_indices"],
snippet["entries"]["column_pointers"],
),
shape=snippet["entries"]["shape"],
)
else:
matrix = snippet["entries"]
return cls(
matrix,
name=snippet["name"],
domains=snippet["domains"],
)
@property
def entries(self):
return self._entries
@property
def ndim(self):
"""returns the number of dimensions of the tensor."""
return self._entries.ndim
@property
def shape(self):
"""returns the number of entries along each dimension."""
return self._entries.shape
@property
def entries_string(self):
return self._entries_string
@entries_string.setter
def entries_string(self, value: None | tuple):
# We must include the entries in the hash, since different arrays can be
# indistinguishable by class, name and domain alone
# Slightly different syntax for sparse and non-sparse matrices
if value is not None:
self._entries_string = value
else:
entries = self._entries
if issparse(entries):
dct = entries.__dict__
entries_string = ["shape", str(dct["_shape"])]
for key in ["data", "indices", "indptr"]:
entries_string += [key, dct[key].tobytes()]
self._entries_string = tuple(entries_string)
# self._entries_string = str(entries.__dict__)
else:
self._entries_string = (entries.tobytes(),)
[docs]
def set_id(self):
"""See :meth:`pybamm.Symbol.set_id()`."""
self._id = hash(
(self.__class__, self.name, *self.entries_string, *tuple(self.domain))
)
def _jac(self, variable) -> pybamm.Matrix:
"""See :meth:`pybamm.Symbol._jac()`."""
# Return zeros of correct size
jac = csr_matrix((self.size, variable.evaluation_array.count(True)))
return pybamm.Matrix(jac)
[docs]
def create_copy(self):
"""See :meth:`pybamm.Symbol.new_copy()`."""
return self.__class__(
self.entries,
self.name,
domains=self.domains,
entries_string=self.entries_string,
)
def _base_evaluate(
self,
t: float | None = None,
y: np.ndarray | None = None,
y_dot: np.ndarray | None = None,
inputs: dict | str | None = None,
):
"""See :meth:`pybamm.Symbol._base_evaluate()`."""
return self._entries
[docs]
def is_constant(self):
"""See :meth:`pybamm.Symbol.is_constant()`."""
return True
[docs]
def to_equation(self) -> sympy.Array:
"""Returns the value returned by the node when evaluated."""
entries_list = self.entries.tolist()
return sympy.Array(entries_list)
[docs]
def to_json(self):
"""
Method to serialise an Array object into JSON.
"""
if isinstance(self.entries, np.ndarray):
matrix = self.entries.tolist()
elif isinstance(self.entries, csr_matrix):
matrix = {
"shape": self.entries.shape,
"data": self.entries.data.tolist(),
"row_indices": self.entries.indices.tolist(),
"column_pointers": self.entries.indptr.tolist(),
}
json_dict = {
"name": self.name,
"id": self.id,
"domains": self.domains,
"entries": matrix,
}
return json_dict
[docs]
def linspace(start: float, stop: float, num: int = 50, **kwargs) -> pybamm.Array:
"""
Creates a linearly spaced array by calling `numpy.linspace` with keyword
arguments 'kwargs'. For a list of 'kwargs' see the
`numpy linspace documentation <https://tinyurl.com/yc4ne47x>`_
"""
return pybamm.Array(np.linspace(start, stop, num, **kwargs))
[docs]
def meshgrid(
x: pybamm.Array, y: pybamm.Array, **kwargs
) -> tuple[pybamm.Array, pybamm.Array]:
"""
Return coordinate matrices as from coordinate vectors by calling
`numpy.meshgrid` with keyword arguments 'kwargs'. For a list of 'kwargs'
see the `numpy meshgrid documentation <https://tinyurl.com/y8azewrj>`_
"""
[X, Y] = np.meshgrid(x.entries, y.entries)
X = pybamm.Array(X)
Y = pybamm.Array(Y)
return X, Y
