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 http://www.apache.org/licenses/LICENSE-2.0.
#
# Any modifications or derivative works of this code must retain this
# copyright notice, and modified files need to carry a notice indicating
# that they have been altered from the originals.

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

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

from qiskit_experiments.exceptions import AnalysisError




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,
        weighted_residuals: Optional[np.ndarray] = None,
        residuals: 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.
            weighted_residuals: The residuals from the fitting after assigning weights for each ydata.
            residuals: residuals of the fitted model.
            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.weighted_residuals = weighted_residuals
        self.residuals = residuals
        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 https://stackoverflow.com/q/75656026
                    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
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


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



    def add_extra_options(self, **kwargs):
        """Add more fitter options."""
        self.__extra.update(kwargs)




    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}