Source code for qiskit_experiments.curve_analysis.curve_data

# This code is part of Qiskit.
# (C) Copyright IBM 2021.
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at
# Any modifications or derivative works of this code must retain this
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# that they have been altered from the originals.

Curve data classes.
import dataclasses
import itertools
import inspect
from typing import Any, Dict, Union, List, Tuple, Optional, Iterable, Callable

import numpy as np
import uncertainties
from uncertainties.unumpy import uarray

from qiskit.utils.deprecation import deprecate_func

from qiskit_experiments.exceptions import AnalysisError

[docs] @dataclasses.dataclass(frozen=True) class SeriesDef: """A dataclass to describe the definition of the curve. Attributes: fit_func: A callable that defines the fit model of this curve. The argument names in the callable are parsed to create the fit parameter list, which will appear in the analysis results. The first argument should be ``x`` that represents X-values that the experiment sweeps. filter_kwargs: Optional. Dictionary of properties that uniquely identifies this series. This dictionary is used for data processing. This must be provided when the curve analysis consists of multiple series. name: Optional. Name of this series. plot_color: Optional. String representation of the color that is used to draw fit data and data points in the output figure. This depends on the drawer class being set to the curve analysis options. Usually this conforms to the Matplotlib color names. plot_symbol: Optional. String representation of the marker shape that is used to draw data points in the output figure. This depends on the drawer class being set to the curve analysis options. Usually this conforms to the Matplotlib symbol names. canvas: Optional. Index of sub-axis in the output figure that draws this curve. This option is valid only when the drawer instance provides multi-axis drawing. model_description: Optional. Arbitrary string representation of this fit model. This string will appear in the analysis results as a part of metadata. """ fit_func: Callable filter_kwargs: Dict[str, Any] = dataclasses.field(default_factory=dict) name: str = "Series-0" plot_color: str = "black" plot_symbol: str = "o" canvas: Optional[int] = None model_description: Optional[str] = None signature: Tuple[str, ...] = dataclasses.field(init=False) @deprecate_func( since="0.5", additional_msg="SeriesDef has been replaced by the LMFIT module.", removal_timeline="after 0.6", package_name="qiskit-experiments", ) def __init__(self, *args, **kwargs): self.args = args self.kwargs = kwargs def __post_init__(self): """Parse the fit function signature to extract the names of the variables. Fit functions take arguments F(x, p0, p1, p2, ...) thus the first value should be excluded. """ signature = list(inspect.signature(self.fit_func).parameters.keys()) fitparams = tuple(signature[1:]) # Note that this dataclass is frozen object.__setattr__(self, "signature", fitparams)
[docs] @dataclasses.dataclass(frozen=True) class CurveData: """A dataclass that manages the multiple arrays comprising the dataset for fitting. This dataset can consist of X, Y values from multiple series. To extract curve data of the particular series, :meth:`get_subset_of` can be used. Attributes: x: X-values that experiment sweeps. y: Y-values that observed and processed by the data processor. y_err: Uncertainty of the Y-values which is created by the data processor. Usually this assumes standard error. shots: Number of shots used in the experiment to obtain the Y-values. data_allocation: List with identical size with other arrays. The value indicates the series index of the corresponding element. This is classified based upon the matching of :attr:`SeriesDef.filter_kwargs` with the circuit metadata of the corresponding data index. If metadata doesn't match with any series definition, element is filled with ``-1``. labels: List of curve labels. The list index corresponds to the series index. """ x: np.ndarray y: np.ndarray y_err: np.ndarray shots: np.ndarray data_allocation: np.ndarray labels: List[str] @deprecate_func( since="0.6", additional_msg="CurveData is replaced by `ScatterTable`'s DataFrame representation.", removal_timeline="after 0.7", package_name="qiskit-experiments", ) def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs)
[docs] def get_subset_of(self, index: Union[str, int]) -> "CurveData": """Filter data by series name or index. Args: index: Series index of name. Returns: A subset of data corresponding to a particular series. """ if isinstance(index, int): _index = index _name = self.labels[index] else: _index = self.labels.index(index) _name = index locs = self.data_allocation == _index return CurveData( x=self.x[locs], y=self.y[locs], y_err=self.y_err[locs], shots=self.shots[locs], data_allocation=np.full(np.count_nonzero(locs), _index), labels=[_name], )
[docs] class CurveFitResult: """Result of Qiskit Experiment curve analysis.""" def __init__( self, method: Optional[str] = None, model_repr: Optional[Dict[str, str]] = None, success: Optional[bool] = True, nfev: Optional[int] = None, message: Optional[str] = "", dof: Optional[float] = None, init_params: Optional[Dict[str, float]] = None, chisq: Optional[float] = None, reduced_chisq: Optional[float] = None, aic: Optional[float] = None, bic: Optional[float] = None, params: Optional[Dict[str, float]] = None, var_names: Optional[List[str]] = None, x_data: Optional[np.ndarray] = None, y_data: Optional[np.ndarray] = None, covar: Optional[np.ndarray] = None, ): """Create new Qiskit curve analysis result object. Args: method: A name of fitting algorithm used for the curve fitting. model_repr: String representation of fit functions of each curve. success: True when the fitting is successfully performed. nfev: Number of fit function evaluation until the solution is obtained. message: Any message from the fitting software. dof: Degree of freedom in this fitting, i.e. number of free parameters. init_params: Initial parameters provided to the fitter. chisq: Chi-squared value. reduced_chisq: Reduced Chi-squared value. aic: Akaike's information criterion. bic: Bayesian information criterion. params: Estimated fitting parameters keyed on the parameter names in the fit function. var_names: Name of variables, i.e. fixed parameters are excluded from the list. x_data: X values used for the fitting. y_data: Y values used for the fitting. covar: Covariance matrix of fitting variables. """ self.method = method self.model_repr = model_repr self.success = success self.nfev = nfev self.message = message self.dof = dof self.init_params = init_params self.chisq = chisq self.reduced_chisq = reduced_chisq self.aic = aic self.bic = bic self.params = params self.var_names = var_names self.x_data = x_data self.y_data = y_data self.covar = covar @property def x_range(self) -> Tuple[float, float]: """Range of x_data values.""" return min(self.x_data), max(self.x_data) @property def y_range(self) -> Tuple[float, float]: """Range of y_data values.""" return min(self.y_data), max(self.y_data) @property def ufloat_params(self) -> Dict[str, uncertainties.UFloat]: """UFloat representation of fit parameters.""" if hasattr(self, "_ufloat_params"): # Return cache return getattr(self, "_ufloat_params") if self.params is None: ufloat_params = None else: if self.covar is not None: ufloat_fitvals = uncertainties.correlated_values( nom_values=[self.params[name] for name in self.var_names], covariance_mat=self.covar, tags=self.var_names, ) else: # Invalid covariance matrix. Std dev is set to nan, i.e. not computed. with np.errstate(invalid="ignore"): # Setting std_devs to NaN will trigger floating point exceptions # which we can ignore. See ufloat_fitvals = uarray( nominal_values=[self.params[name] for name in self.var_names], std_devs=np.full(len(self.var_names), np.nan), ) # Combine fixed params and fitting variables into a single dictionary # Fixed parameter has zero std_dev ufloat_params = {} for name in self.params.keys(): try: uind = self.var_names.index(name) ufloat_params[name] = ufloat_fitvals[uind] except ValueError: ufloat_params[name] = uncertainties.ufloat(self.params[name], std_dev=0.0) setattr(self, "_ufloat_params", ufloat_params) return ufloat_params @property def correl(self): """Correlation matrix of fit parameters.""" if hasattr(self, "_correl"): # Return cache return getattr(self, "_correl") if self.covar is not None: # This is how uncertainties computes correlation matrix stdevs = np.sqrt(np.diag(self.covar)) correl = self.covar / stdevs / stdevs[:, np.newaxis] else: correl = None setattr(self, "_correl", correl) return correl def __str__(self): ret = "CurveFitResult:" ret += f"\n - fitting method: {self.method}" ret += f"\n - number of sub-models: {len(self.model_repr)}" for model_name, model_expr in self.model_repr.items(): if len(model_expr) > 60: model_expr = f"{model_expr[:60]}..." ret += f"\n * F_{model_name}(x) = {model_expr}" ret += f"\n - success: {self.success}" ret += f"\n - number of function evals: {self.nfev}" ret += f"\n - degree of freedom: {self.dof}" ret += f"\n - chi-square: {self.chisq}" ret += f"\n - reduced chi-square: {self.reduced_chisq}" ret += f"\n - Akaike info crit.: {self.aic}" ret += f"\n - Bayesian info crit.: {self.bic}" if self.init_params is not None: ret += "\n - init params:" for name, value in self.init_params.items(): ret += f"\n * {name} = {value}" if self.ufloat_params is not None: ret += "\n - fit params:" for name, param in self.ufloat_params.items(): if np.isfinite(param.std_dev): ret += f"\n * {name} = {param.nominal_value} ± {param.std_dev}" else: ret += f"\n * {name} = {param.nominal_value}" if self.correl is not None: ret += "\n - correlations:" correlated = {} for pi, pj in itertools.combinations(range(len(self.var_names)), 2): correlated[(pi, pj)] = self.correl[pi, pj] for (pi, pj), corr in sorted(correlated.items(), key=lambda item: item[1]): ret += f"\n * ({self.var_names[pi]}, {self.var_names[pj]}) = {corr}" return ret def __copy__(self): instance = CurveFitResult(**self.__json_encode__()) # Copying ufloat invalidate parameter correlation. # Note that ufloat object has `self._linear_part.linear_combo` dictionary # to store parameter correlation keyed on the ufloat objects. # Copying the ufloat object may change object id, which is the identifier # of ufloat value, thus it invalidates the `linear_combo` dictionary. # To avoid missing correlation, the copy invalidate ufloat parameter object cache. return instance def __deepcopy__(self, memo): return self.__copy__() def __json_encode__(self): return { "method": self.method, "model_repr": self.model_repr, "success": self.success, "nfev": self.nfev, "message": self.message, "dof": self.dof, "init_params": self.init_params, "chisq": self.chisq, "reduced_chisq": self.reduced_chisq, "aic": self.aic, "bic": self.bic, "params": self.params, "var_names": self.var_names, "x_data": self.x_data, "y_data": self.y_data, "covar": self.covar, } @classmethod def __json_decode__(cls, value): return cls(**value)
@dataclasses.dataclass(frozen=True) class FitData: """A dataclass to store the outcome of the fitting. Attributes: popt: List of optimal parameter values with uncertainties if available. popt_keys: List of parameter names being fit. pcov: Covariance matrix from the least square fitting. reduced_chisq: Reduced Chi-squared value for the fit curve. dof: Degree of freedom in this fit model. x_data: X-values provided to the fitter. y_data: Y-values provided to the fitter. """ popt: List[uncertainties.UFloat] popt_keys: List[str] pcov: np.ndarray reduced_chisq: float dof: int x_data: np.ndarray y_data: np.ndarray @deprecate_func( since="0.5", additional_msg="Fit data is replaced with 'CurveFitResult' based on LMFIT minimizer result.", removal_timeline="after 0.6", package_name="qiskit-experiments", ) def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) @property def x_range(self) -> Tuple[float, float]: """Range of x values.""" return np.min(self.x_data), np.max(self.x_data) @property def y_range(self) -> Tuple[float, float]: """Range of y values.""" return np.min(self.y_data), np.max(self.y_data) def fitval(self, key: str) -> uncertainties.UFloat: """A helper method to get fit value object from parameter key name. Args: key: Name of parameters to extract. Returns: A UFloat object which functions as a standard Python float object but with automatic error propagation. Raises: ValueError: When specified parameter is not defined. """ try: index = self.popt_keys.index(key) return self.popt[index] except ValueError as ex: raise ValueError(f"Parameter {key} is not defined.") from ex
[docs] @dataclasses.dataclass class ParameterRepr: """Detailed description of fitting parameter. Attributes: name: Original name of the fit parameter being defined in the fit model. repr: Optional. Human-readable parameter name shown in the analysis result and in the figure. unit: Optional. Physical unit of this parameter if applicable. """ # Fitter argument name name: str # Unicode representation repr: Optional[str] = None # Unit unit: Optional[str] = None
class OptionsDict(dict): """General extended dictionary for fit options. This dictionary provides several extra features. - A value setting method which validates the dict key and value. - Dictionary keys are limited to those specified in the constructor as ``parameters``. """ def __init__( self, parameters: List[str], defaults: Optional[Union[Iterable[Any], Dict[str, Any]]] = None, ): """Create new dictionary. Args: parameters: List of parameter names used in the fit model. defaults: Default values. Raises: AnalysisError: When defaults is provided as array-like but the number of element doesn't match with the number of fit parameters. """ if defaults is not None: if not isinstance(defaults, dict): if len(defaults) != len(parameters): raise AnalysisError( f"Default parameter {defaults} is provided with array-like " "but the number of element doesn't match. " f"This fit requires {len(parameters)} parameters." ) defaults = dict(zip(parameters, defaults)) full_options = {p: self.format(defaults.get(p, None)) for p in parameters} else: full_options = {p: None for p in parameters} super().__init__(**full_options) def __setitem__(self, key, value): """Set value with validations. Raises: AnalysisError: When key is not previously defined. """ if key not in self: raise AnalysisError(f"Parameter {key} is not defined in this fit model.") super().__setitem__(key, self.format(value)) def __hash__(self): return hash(tuple(sorted(self.items()))) def set_if_empty(self, **kwargs): """Set value to the dictionary if not assigned. Args: kwargs: Key and new value to assign. """ for key, value in kwargs.items(): if self.get(key) is None: self[key] = value @staticmethod def format(value: Any) -> Any: """Format dictionary value. Subclasses may override this method to provide their own validation. Args: value: New value to assign. Returns: Formatted value. """ return value class InitialGuesses(OptionsDict): """Dictionary providing a float validation for initial guesses.""" @staticmethod def format(value: Any) -> Optional[float]: """Validate that value is float a float or None. Args: value: New value to assign. Returns: Formatted value. Raises: AnalysisError: When value is not a float or None. """ if value is None: return None try: return float(value) except (TypeError, ValueError) as ex: raise AnalysisError(f"Input value {value} is not valid initial guess. ") from ex class Boundaries(OptionsDict): """Dictionary providing a validation for boundaries.""" @staticmethod def format(value: Any) -> Optional[Tuple[float, float]]: """Validate if value is a min-max value tuple. Args: value: New value to assign. Returns: Formatted value. Raises: AnalysisError: When value is invalid format. """ if value is None: return None try: minv, maxv = value if minv >= maxv: raise AnalysisError( f"The first value is greater than the second value {minv} >= {maxv}." ) return float(minv), float(maxv) except (TypeError, ValueError) as ex: raise AnalysisError(f"Input boundary {value} is not a min-max value tuple.") from ex # pylint: disable=invalid-name
[docs] class FitOptions: """Collection of fitting options. This class is initialized with a list of parameter names used in the fit model and corresponding default values provided by users. This class is hashable, and generates fitter keyword arguments. """ def __init__( self, parameters: List[str], default_p0: Optional[Union[Iterable[float], Dict[str, float]]] = None, default_bounds: Optional[Union[Iterable[Tuple], Dict[str, Tuple]]] = None, **extra, ): # These are private members so that user cannot directly override values # without implicitly implemented validation logic. No setter will be provided. self.__p0 = InitialGuesses(parameters, default_p0) self.__bounds = Boundaries(parameters, default_bounds) self.__extra = extra def __hash__(self): return hash((self.__p0, self.__bounds, tuple(sorted(self.__extra.items())))) def __eq__(self, other): if isinstance(other, FitOptions): checks = [ self.__p0 == other.__p0, self.__bounds == other.__bounds, self.__extra == other.__extra, ] return all(checks) return False
[docs] def add_extra_options(self, **kwargs): """Add more fitter options.""" self.__extra.update(kwargs)
[docs] def copy(self): """Create copy of this option.""" return FitOptions( parameters=list(self.__p0.keys()), default_p0=dict(self.__p0), default_bounds=dict(self.__bounds), **self.__extra, )
@property def p0(self) -> InitialGuesses: """Return initial guess dictionary.""" return self.__p0 @property def bounds(self) -> Boundaries: """Return bounds dictionary.""" return self.__bounds @property def fitter_opts(self) -> Boundaries: """Return fitter options dictionary.""" return self.__extra @property def options(self): """Generate keyword arguments of the curve fitter.""" bounds = {k: v if v is not None else (-np.inf, np.inf) for k, v in self.__bounds.items()} return {"p0": dict(self.__p0), "bounds": bounds, **self.__extra}