"""Module for observable reader abstract class"""
from abc import abstractmethod, ABC
from typing import Union, Any, TYPE_CHECKING
import numpy as np
from MDMC.common import units
from MDMC.common.decorators import repr_decorator, unit_decorator
from MDMC.readers.reader import Reader
if TYPE_CHECKING:
from MDMC.trajectory_analysis.observables.obs import Observable
[docs]@repr_decorator('data')
class ObservableReader(Reader):
"""
Abstract class that defines methods common to all readers for observables
ObservableReaders are created using ObservableReaderFactory
"""
[docs] def assign(self, observable: 'Observable') -> None:
# disable pylint warning about writing to the `Observable`
#pylint: disable=protected-access
"""
Abstract method to assign the parsed information into the `Observable`
Parameters
----------
observable : `Observable`
An MDMC `Observable` that will be assigned the data parsed by the reader.
"""
observable._independent_variables = self.independent_variables
observable._dependent_variables = self.dependent_variables
observable._errors = self.errors
@property
def data(self) -> dict:
"""
A dictionary of dictionaries containing the independent variables,
dependent variables and the associated errors.
Returns
-------
dict
The independent variables, dependent variables and the errors on
the dependent variables
"""
return {"independent": self.independent_variables,
"dependent": self.dependent_variables,
"errors": self.errors}
@property
@abstractmethod
def independent_variables(self) -> dict:
"""
The independent variables
Returns
-------
dict
A dictionary of the independent variables
"""
raise NotImplementedError
@property
@abstractmethod
def dependent_variables(self) -> None:
"""
The dependent variables
Returns
-------
dict
A dictionary of the dependent variables
"""
raise NotImplementedError
@property
@abstractmethod
def errors(self) -> None:
"""
The errors on the dependent variables
Returns
-------
dict
A dictionary of the errors on the dependent variables
"""
raise NotImplementedError
@staticmethod
def _make_float(i: Any) -> Union[float, None]:
"""
Casts the input to a `float`, or passes if the input cannot be cast
Parameters
----------
i : numeric
Input to be cast to `float`
Returns
-------
float
A non-negative `float`, if the input can be converted to a `float`.
"""
try:
return np.float64(i)
except ValueError:
return None
[docs]class SQwReader(ObservableReader, ABC):
"""Abstract base subclass that adds attributes & methods common to all SQw readers"""
# pylint: disable=attribute-defined-outside-init
# to avoid it flagging up on private attributes in getters
def __init__(self, file_name: str):
super().__init__(file_name)
self.SQw = None
self.SQw_err = None
@property
def independent_variables(self) -> dict:
"""
Get the independent variables, Q (in ``Ang^-1``) and E (``meV``)
Returns
-------
dict
The independent variables Q and E
"""
return {"Q": self.Q, "E": self.E}
@property
def dependent_variables(self) -> dict:
"""
Get the dependent variables, SQw (in ``arb``)
Returns
-------
dict
The dependent variables, SQw (in ``arb``)
"""
return {"SQw": [self.SQw]}
@property
def errors(self) -> dict:
"""
Get the errors on the dependent variables
Returns
-------
dict
The error on SQw (in ``arb``)
"""
return {"SQw": [self.SQw_err]}
@property
def w(self) -> float:
"""
Get or set the energy transfer expressed in angular frequency, w, in
``1 / ps``
Returns
-------
array
Energy transfer as angular frequency, w, in ``1 / ps``
"""
return self._w
@w.setter
@unit_decorator(unit=units.Unit('ps') ** -1)
def w(self, value: float) -> None:
self._w = value
@property
def E(self) -> float:
"""
Get or set the energy transfer, E, in ``meV``
Returns
-------
array
Energy transfer, E, in ``meV``
"""
return self._E
@E.setter
@unit_decorator(unit=units.ENERGY_TRANSFER)
def E(self, value: float) -> None:
self._E = value
@property
def Q(self) -> float:
"""
Get or set the momentum transfer, Q, in ``Ang^-1``
Returns
-------
array
Momentum transfer, Q, in ``Ang^-1``
"""
return self._Q
@Q.setter
@unit_decorator(unit=units.LENGTH ** -1)
def Q(self, value: float) -> None:
self._Q = value
[docs]class PDFReader(ObservableReader, ABC):
"""Abstract base subclass that adds attributes & methods common to all PDF readers"""
def __init__(self, file_name: str):
super().__init__(file_name)
self.PDF = None
self.PDF_err = None
self.partial_pdfs = None
@property
def independent_variables(self) -> dict:
"""
Get the independent variable r (in ``Ang^-1``)
Returns
-------
dict
The independent variable r (in ``Ang^-1``)
"""
return {"r": self.r}
@property
def dependent_variables(self) -> dict:
"""
Get the dependent variable PDF, the pair distribution function (in ``barn``)
Returns
-------
dict
The dependent variable, PDF (in ``barn``)
"""
return {"PDF": self.PDF}
@property
def errors(self) -> dict:
"""
Get the errors on the dependent variable
Returns
-------
dict
The error on PDF (in ``barn``)
"""
return {"PDF": self.PDF_err}
@property
def r(self) -> float:
"""
Get or set the value of the atomic separation distance (in ``Ang``)
"""
return self._r
@r.setter
@unit_decorator(unit=units.Unit('Ang'))
def r(self, value) -> None:
self._r = value
@property
def PDF(self) -> np.ndarray:
"""
Get or set the total pair distribution function between pairs (in ``barn``)
Returns
-------
numpy.ndarray
total pair distribution function (in ``barn``)
"""
return self._PDF
@PDF.setter
@unit_decorator(unit=units.Unit('barn'))
def PDF(self, value: float) -> None:
self._PDF = value
@property
def PDF_err(self) -> np.ndarray:
"""
Get or set the error on the total pair distribution function between pairs (in ``barn``)
Returns
-------
numpy.ndarray
error on the total pair distribution function (in ``barn``)
"""
return self._PDF_err
@PDF_err.setter
@unit_decorator(unit=units.Unit('barn'))
def PDF_err(self, value: float) -> None:
self._PDF_err = value