sqil-core 0.0.1__py3-none-any.whl → 0.1.0__py3-none-any.whl

sqil_core/fit/_core.py

@@ -0,0 +1,936 @@
+import inspect
+import warnings
+from functools import wraps
+
+import numpy as np
+import scipy.optimize as spopt
+from lmfit.model import ModelResult
+
+from sqil_core.utils import print_fit_metrics as _print_fit_metrics
+from sqil_core.utils import print_fit_params as _print_fit_params
+from sqil_core.utils._utils import _count_function_parameters
+
+
+class FitResult:
+    """
+    Stores the result of a fitting procedure.
+
+    This class encapsulates the fitted parameters, their standard errors, optimizer output,
+    and fit quality metrics. It also provides functionality for summarizing the results and
+    making predictions using the fitted model.
+
+    Parameters
+    ----------
+    params : dict
+        Array of fitted parameters.
+    std_err : dict
+        Array of standard errors of the fitted parameters.
+    fit_output : any
+        Raw output from the optimization routine.
+    metrics : dict, optional
+        Dictionary of fit quality metrics (e.g., R-squared, reduced chi-squared).
+    predict : callable, optional
+        Function of x that returns predictions based on the fitted parameters.
+        If not provided, an exception will be raised when calling it.
+    param_names : list, optional
+        List of parameter names, defaulting to a range based on the number of parameters.
+    metadata : dict, optional
+        Additional information that can be passed in the fit result.
+
+    Methods
+    -------
+    summary()
+        Prints a detailed summary of the fit results, including parameter values,
+        standard errors, and fit quality metrics.
+    _no_prediction()
+        Raises an exception when no prediction function is available.
+    """
+
+    def __init__(
+        self,
+        params,
+        std_err,
+        fit_output,
+        metrics=None,
+        predict=None,
+        param_names=None,
+        metadata={},
+    ):
+        self.params = params
+        self.std_err = std_err
+        self.output = fit_output
+        self.metrics = metrics
+        self.predict = predict or self._no_prediction
+        self.param_names = param_names or list(range(len(params)))
+        self.metadata = metadata
+
+    def __repr__(self):
+        return (
+            f"FitResult(\n"
+            f"  params={self.params},\n"
+            f"  std_err={self.std_err},\n"
+            f"  metrics={self.metrics}\n)"
+        )
+
+    def summary(self):
+        """Prints a detailed summary of the fit results."""
+        _print_fit_metrics(self.metrics)
+        _print_fit_params(
+            self.param_names,
+            self.params,
+            self.std_err,
+            self.std_err / self.params * 100,
+        )
+
+    def _no_prediction(self):
+        raise Exception("No predition function available")
+
+
+def fit_output(fit_func):
+    """
+    Decorator to standardize the output of fitting functions.
+
+    This decorator processes the raw output of various fitting libraries
+    (such as SciPy's curve_fit, least_squares leastsq, and minimize, as well as lmfit)
+    and converts it into a unified `FitResult` object. It extracts
+    optimized parameters, their standard errors, fit quality metrics,
+    and a prediction function.
+
+    Parameters
+    ----------
+    fit_func : Callable
+        A function that performs fitting and returns raw fit output,
+        possibly along with metadata.
+
+    Returns
+    -------
+    Callable
+        A wrapped function that returns a `FitResult` object containing:
+        - `params` : list
+            Optimized parameter values.
+        - `std_err` : list or None
+            Standard errors of the fitted parameters.
+        - `metrics` : dict or None
+            Dictionary of fit quality metrics (e.g., reduced chi-squared).
+        - `predict` : Callable or None
+            A function that predicts values using the optimized parameters.
+        - `output` : object
+            The raw optimizer output from the fitting process.
+        - `param_names` : list or None
+            Names of the fitted parameters.
+        - `metadata` : dict
+            A dictionary containing extra information. Advanced uses include passing
+            functions that get evaluated after fit result has been processed.
+            See the documentation, Notebooks/The fit_output decorator
+
+    Raises
+    ------
+    TypeError
+        If the fitting function's output format is not recognized.
+
+    Notes
+    -----
+    - If the fit function returns a tuple `(raw_output, metadata)`,
+      the metadata is extracted and applied to enhance the fit results.
+      In case of any conflicts, the metadata overrides the computed values.
+
+    Examples
+    --------
+    >>> @fit_output
+    ... def my_fitting_function(x, y):
+    ...     return some_raw_fit_output
+    ...
+    >>> fit_result = my_fitting_function(x_data, y_data)
+    >>> print(fit_result.params)
+    """
+
+    @wraps(fit_func)
+    def wrapper(*args, **kwargs):
+        # Perform the fit
+        fit_result = fit_func(*args, **kwargs)
+
+        # Extract information from function arguments
+        x_data, y_data = _get_xy_data_from_fit_args(*args, **kwargs)
+        sigma = kwargs.get("sigma", None)
+        has_sigma = isinstance(sigma, (list, np.ndarray))
+
+        # Initilize variables
+        sqil_keys = ["params", "std_err", "metrics", "predict", "output", "param_names"]
+        sqil_dict = {key: None for key in sqil_keys}
+        metadata = {}
+        formatted = None
+        # Set the default parameters to an empty array instead of None
+        sqil_dict["params"] = []
+
+        # Check if the fit output is a tuple and separate it into raw_fit_ouput and metadata
+        if (
+            isinstance(fit_result, tuple)
+            and (len(fit_result) == 2)
+            and isinstance(fit_result[1], dict)
+        ):
+            raw_fit_output, metadata = fit_result
+        else:
+            raw_fit_output = fit_result
+        sqil_dict["output"] = raw_fit_output
+
+        # Format the raw_fit_output into a standardized dict
+        # Scipy tuple (curve_fit, leastsq)
+        if _is_scipy_tuple(raw_fit_output):
+            formatted = _format_scipy_tuple(raw_fit_output, has_sigma=has_sigma)
+
+        # Scipy least squares
+        elif _is_scipy_least_squares(raw_fit_output):
+            formatted = _format_scipy_least_squares(raw_fit_output, has_sigma=has_sigma)
+
+        # Scipy minimize
+        elif _is_scipy_minimize(raw_fit_output):
+            residuals = None
+            predict = metadata.get("predict", None)
+            if predict and callable(predict):
+                residuals = y_data - metadata["predict"](x_data, *raw_fit_output.x)
+            formatted = _format_scipy_minimize(
+                raw_fit_output, residuals=residuals, has_sigma=has_sigma
+            )
+
+        # lmfit
+        elif _is_lmfit(raw_fit_output):
+            formatted = _format_lmfit(raw_fit_output)
+
+        # Custom fit output
+        elif isinstance(raw_fit_output, dict):
+            formatted = raw_fit_output
+
+        else:
+            raise TypeError(
+                "Couldn't recognize the output.\n"
+                + "Are you using scipy? Did you forget to set `full_output=True` in your fit method?"
+            )
+
+        # Update sqil_dict with the formatted fit_output
+        if formatted is not None:
+            sqil_dict.update(formatted)
+
+        # Add/override fileds using metadata
+        sqil_dict.update(metadata)
+
+        # Process metadata
+        metadata = _process_metadata(metadata, sqil_dict)
+        # Remove fields already present in sqil_dict from metadata
+        filtered_metadata = {k: v for k, v in metadata.items() if k not in sqil_keys}
+
+        # Assign the optimized parameters to the prediction function
+        if sqil_dict["predict"] is not None:
+            params = sqil_dict["params"]
+            predict = sqil_dict["predict"]
+            n_inputs = _count_function_parameters(predict)
+            if n_inputs == 1 + len(params):
+                sqil_dict["predict"] = lambda x: predict(x, *params)
+
+        return FitResult(
+            params=sqil_dict.get("params", []),
+            std_err=sqil_dict.get("std_err", None),
+            fit_output=raw_fit_output,
+            metrics=sqil_dict.get("metrics", None),
+            predict=sqil_dict.get("predict", None),
+            param_names=sqil_dict.get("param_names", None),
+            metadata=filtered_metadata,
+        )
+
+    return wrapper
+
+
+# TODO: make a function that handles the bounds for lmfit.
+# Such a function will take the bounds as they are returned by @fit_input, i.e lower and upper bounds
+# and it will iterated through the lmfit parameters to apply the bounds.
+def fit_input(fit_func):
+    """
+    Decorator to handle optional fitting inputs like initial guesses, bounds, and fixed parameters
+    for a fitting function.
+
+    - `guess` : list or np.ndarray, optional, default=None
+        The initial guess for the fit. If None it's not passed to the fit function.
+    - `bounds` : list or np.ndarray, optional, default=(-np.inf, np.inf)
+        The bounds on the fit parameters in the form [(min, max), (min, max), ...].
+    - `fixed_params` : list or np.ndarray, optional, default=None
+        Indices of the parameters that must remain fixed during the optimization.
+        For example fitting `f(x, a, b)`, if we want to fix the value of `a` we would pass
+        `fit_f(guess=[a_guess, b_guess], fixed_params=[0])`
+    - `fixed_bound_factor` : float, optional, default=1e-6
+        The relative tolerance allowed for parameters that must remain fixed (`fixed_params`).
+
+    IMPORTANT: This decorator requires the x and y input vectors to be named `x_data` and `y_data`.
+        The initial guess must be called `guess` and the bounds `bounds`.
+
+    Parameters
+    ----------
+    fit_func : callable
+        The fitting function to be decorated. This function should accept `x_data` and `y_data` as
+        mandatory parameters and may optionally accept `guess` and `bounds` (plus any other additional
+        parameter).
+
+    Returns
+    -------
+    callable
+        A wrapper function that processes the input arguments and then calls the original fitting
+        function with the preprocessed inputs. This function also handles warnings if unsupported
+        parameters are passed to the fit function.
+
+    Notes
+    -----
+    - The parameters in `guess`, `bounds` and `fixed_params` must be in the same order as in the
+      modeled function definition.
+    - The decorator can fix certain parameters by narrowing their bounds based on an initial guess
+      and a specified `fixed_bound_factor`.
+    - The decorator processes bounds by setting them as `(-np.inf, np.inf)` if they are not specified (`None`).
+
+    Examples
+    -------
+    >>> @fit_input
+    ... def my_fit_func(x_data, y_data, guess=None, bounds=None, fixed_params=None):
+    ...     # Perform fitting...
+    ...     return fit_result
+    >>> x_data = np.linspace(0, 10, 100)
+    >>> y_data = np.sin(x_data) + np.random.normal(0, 0.1, 100)
+    >>> result = my_fit_func(x_data, y_data, guess=[1, 1], bounds=[(0, 5), (-np.inf, np.inf)])
+    """
+
+    @wraps(fit_func)
+    def wrapper(
+        x_data,
+        y_data,
+        guess=None,
+        bounds=None,
+        fixed_params=None,
+        fixed_bound_factor=1e-6,
+        **kwargs,
+    ):
+        # Inspect function to check if it requires guess and bounds
+        func_params = inspect.signature(fit_func).parameters
+
+        # Check if the user passed parameters that are not supported by the fit fun
+        if guess and ("guess" not in func_params):
+            warnings.warn("The fit function doesn't allow any initial guess.")
+        if bounds and ("bounds" not in func_params):
+            warnings.warn("The fit function doesn't allow any bounds.")
+        if fixed_params and (not guess):
+            raise ValueError("Using fixed_params requires an initial guess.")
+
+        # Process bounds if the function accepts it
+        if bounds and ("bounds" in func_params):
+            processed_bounds = np.array(
+                [(-np.inf, np.inf) if b is None else b for b in bounds],
+                dtype=np.float64,
+            )
+            lower_bounds, upper_bounds = (
+                processed_bounds[:, 0],
+                processed_bounds[:, 1],
+            )
+        else:
+            lower_bounds, upper_bounds = None, None
+
+        # Fix parameters by setting a very tight bound
+        if (fixed_params is not None) and (guess is not None):
+            if bounds is None:
+                lower_bounds = -np.inf * np.ones(len(guess))
+                upper_bounds = np.inf * np.ones(len(guess))
+            for idx in fixed_params:
+                tolerance = (
+                    abs(guess[idx]) * fixed_bound_factor
+                    if guess[idx] != 0
+                    else fixed_bound_factor
+                )
+                lower_bounds[idx] = guess[idx] - tolerance
+                upper_bounds[idx] = guess[idx] + tolerance
+
+        # Prepare arguments dynamically
+        fit_args = {"x_data": x_data, "y_data": y_data, **kwargs}
+
+        if guess is not None and "guess" in func_params:
+            fit_args["guess"] = guess
+        if (
+            (bounds is not None) or (fixed_params is not None)
+        ) and "bounds" in func_params:
+            fit_args["bounds"] = (lower_bounds, upper_bounds)
+
+        # Call the wrapped function with preprocessed inputs
+        return fit_func(**fit_args)
+
+    return wrapper
+
+
+def _process_metadata(metadata: dict, sqil_dict: dict):
+    """Process metadata by computing values that cannot be calculated before having
+    the sqil_dict. For example use the standard errors to compute a different metric.
+
+    Treats items whose key starts with @ as functions that take sqil_dict as input.
+    So it evaluates them and renames the key removing the @.
+    """
+    res = metadata.copy()
+    for key, value in metadata.items():
+        if key.startswith("@"):
+            res[key[1:]] = value(sqil_dict)
+            del res[key]
+    return res
+
+
+def compute_adjusted_standard_errors(
+    pcov: np.ndarray,
+    residuals: np.ndarray,
+    red_chi2=None,
+    cov_rescaled=True,
+    sigma=None,
+) -> np.ndarray:
+    """
+    Compute adjusted standard errors for fitted parameters.
+
+    This function adjusts the covariance matrix based on the reduced chi-squared
+    value and calculates the standard errors for each parameter. It accounts for
+    cases where the covariance matrix is not available or the fit is nearly perfect.
+
+    Parameters
+    ----------
+    pcov : np.ndarray
+        Covariance matrix of the fitted parameters, typically obtained from an
+        optimization routine.
+    residuals : np.ndarray
+        Residuals of the fit, defined as the difference between observed and
+        model-predicted values.
+    red_chi2 : float, optional
+        Precomputed reduced chi-squared value. If `None`, it is computed from
+        `residuals` and `sigma`.
+    cov_rescaled : bool, default=True
+        Whether the fitting process already rescales the covariance matrix with
+        the reduced chi-squared.
+    sigma : np.ndarray, optional
+        Experimental uncertainties. Only used if `cov_rescaled=False` AND
+        known experimental errors are available.
+
+    Returns
+    -------
+    np.ndarray
+        Standard errors for each fitted parameter. If the covariance matrix is
+        undefined, returns `None`.
+
+    Warnings
+    --------
+    - If the covariance matrix is not available (`pcov is None`), the function
+      issues a warning about possible numerical instability or a near-perfect fit.
+    - If the reduced chi-squared value is `NaN`, the function returns `NaN` for
+      all standard errors.
+
+    Notes
+    -----
+    - The covariance matrix is scaled by the reduced chi-squared value to adjust
+      for under- or overestimation of uncertainties.
+    - If `red_chi2` is not provided, it is computed internally using the residuals.
+    - If a near-perfect fit is detected (all residuals close to zero), the function
+      warns that standard errors may not be necessary.
+
+    Examples
+    --------
+    >>> pcov = np.array([[0.04, 0.01], [0.01, 0.09]])
+    >>> residuals = np.array([0.1, -0.2, 0.15])
+    >>> compute_adjusted_standard_errors(pcov, residuals)
+    array([0.2, 0.3])
+    """
+    # Check for invalid covariance
+    if pcov is None:
+        if np.allclose(residuals, 0, atol=1e-10):
+            warnings.warn(
+                "Covariance matrix could not be estimated due to an almost perfect fit. "
+                "Standard errors are undefined but may not be necessary in this case."
+            )
+        else:
+            warnings.warn(
+                "Covariance matrix could not be estimated. This could be due to poor model fit "
+                "or numerical instability. Review the data or model configuration."
+            )
+        return None
+
+    # Calculate reduced chi-squared
+    n_params = len(np.diag(pcov))
+    if red_chi2 is None:
+        _, red_chi2 = compute_chi2(
+            residuals, n_params, cov_rescaled=cov_rescaled, sigma=sigma
+        )
+
+    # Rescale the covariance matrix
+    if np.isnan(red_chi2):
+        pcov_rescaled = np.nan
+    else:
+        pcov_rescaled = pcov * red_chi2
+
+    # Calculate standard errors for each parameter
+    if np.any(np.isnan(pcov_rescaled)):
+        standard_errors = np.full(n_params, np.nan, dtype=float)
+    else:
+        standard_errors = np.sqrt(np.diag(pcov_rescaled))
+
+    return standard_errors
+
+
+def compute_chi2(residuals, n_params=None, cov_rescaled=True, sigma: np.ndarray = None):
+    """
+    Compute the chi-squared (χ²) and reduced chi-squared (χ²_red) statistics.
+
+    This function calculates the chi-squared value based on residuals and an
+    estimated or provided uncertainty (`sigma`). If the number of model parameters
+    (`n_params`) is specified, it also computes the reduced chi-squared.
+
+    Parameters
+    ----------
+    residuals : np.ndarray
+        The difference between observed and model-predicted values.
+    n_params : int, optional
+        Number of fitted parameters. If provided, the function also computes
+        the reduced chi-squared (χ²_red).
+    cov_rescaled : bool, default=True
+        Whether the covariance matrix has been already rescaled by the fit method.
+        If `True`, the function assumes proper uncertainty scaling. Otherwise,
+        it estimates uncertainty from the standard deviation of the residuals.
+    sigma : np.ndarray, optional
+        Experimental uncertainties. Should only be used when the fitting process
+        does not account for experimental errors AND known uncertainties are available.
+
+    Returns
+    -------
+    chi2 : float
+        The chi-squared statistic (χ²), which measures the goodness of fit.
+    red_chi2 : float (if `n_params` is provided)
+        The reduced chi-squared statistic (χ²_red), computed as χ² divided by
+        the degrees of freedom (N - p). If `n_params` is `None`, only χ² is returned.
+
+    Warnings
+    --------
+    - If the degrees of freedom (N - p) is non-positive, a warning is issued,
+      and χ²_red is set to NaN. This may indicate overfitting or an insufficient
+      number of data points.
+    - If any uncertainty value in `sigma` is zero, it is replaced with machine epsilon
+      to prevent division by zero.
+
+    Notes
+    -----
+    - If `sigma` is not provided and `cov_rescaled=False`, the function estimates
+      the uncertainty using the standard deviation of residuals.
+    - The reduced chi-squared value (χ²_red) should ideally be close to 1 for a good fit.
+      Values significantly greater than 1 indicate underfitting, while values much less
+      than 1 suggest overfitting.
+
+    Examples
+    --------
+    >>> residuals = np.array([0.1, -0.2, 0.15, -0.05])
+    >>> compute_chi2(residuals, n_params=2)
+    (0.085, 0.0425)  # Example output
+    """
+    # If the optimization does not account for th experimental sigma,
+    # approximate it with the std of the residuals
+    S = 1 if cov_rescaled else np.std(residuals)
+    # If the experimental error is provided, use that instead
+    if sigma is not None:
+        S = sigma
+
+    # Replace 0 elements of S with the machine epsilon to avoid divisions by 0
+    if not np.isscalar(S):
+        S_safe = np.where(S == 0, np.finfo(float).eps, S)
+    else:
+        S_safe = np.finfo(float).eps if S == 0 else S
+
+    # Compute chi squared
+    chi2 = np.sum((residuals / S_safe) ** 2)
+    # If number of parameters is not provided return just chi2
+    if n_params is None:
+        return chi2
+
+    # Reduced chi squared
+    dof = len(residuals) - n_params  # degrees of freedom (N - p)
+    if dof <= 0:
+        warnings.warn(
+            "Degrees of freedom (dof) is non-positive. This may indicate overfitting or insufficient data."
+        )
+        red_chi2 = np.nan
+    else:
+        red_chi2 = np.sum(residuals**2) / dof
+
+    return chi2, red_chi2
+
+
+def _is_scipy_tuple(result):
+    """
+    Check whether the given result follows the expected structure of a SciPy optimization tuple.
+    """
+    if isinstance(result, tuple):
+        if len(result) < 3:
+            raise TypeError(
+                "Fit result is a tuple, but couldn't recognize it.\n"
+                + "Are you using scipy? Did you forget to set `full_output=True` in your fit method?"
+            )
+        popt = result[0]
+        cov_ish = result[1]
+        infodict = result[2]
+        keys_to_check = ["fvec"]
+
+        if cov_ish is not None:
+            cov_check = isinstance(cov_ish, np.ndarray) and cov_ish.ndim == 2
+        else:
+            cov_check = True
+        return (
+            isinstance(popt, np.ndarray)
+            and cov_check
+            and (all(key in infodict for key in keys_to_check))
+        )
+    return False
+
+
+def _is_scipy_minimize(result):
+    """
+    Check whether the given result follows the expected structure of a SciPy minimize.
+    """
+    return (
+        isinstance(result, spopt.OptimizeResult)
+        and hasattr(result, "fun")
+        and np.isscalar(result.fun)
+        and hasattr(result, "jac")
+    )
+
+
+def _is_scipy_least_squares(result):
+    """
+    Check whether the given result follows the expected structure of a SciPy least_squares.
+    """
+    return (
+        isinstance(result, spopt.OptimizeResult)
+        and hasattr(result, "cost")
+        and hasattr(result, "fun")
+        and hasattr(result, "jac")
+    )
+
+
+def _is_lmfit(result):
+    """
+    Check whether the given result follows the expected structure of a lmfit fit.
+    """
+    return isinstance(result, ModelResult)
+
+
+def _format_scipy_tuple(result, has_sigma=False):
+    """
+    Formats the output of a SciPy fitting function into a standardized dictionary.
+
+    This function takes the tuple returned by SciPy optimization functions (e.g., `curve_fit`, `leastsq`)
+    and extracts relevant fitting parameters, standard errors, and reduced chi-squared values. It ensures
+    the result is structured consistently for further processing.
+
+    Parameters
+    ----------
+    result : tuple
+        A tuple containing the fitting results from a SciPy function. Expected structure:
+        - `result[0]`: `popt` (optimized parameters, NumPy array)
+        - `result[1]`: `pcov` (covariance matrix, NumPy array or None)
+        - `result[2]`: `infodict` (dictionary containing residuals, required for error computation)
+
+    has_sigma : bool, optional
+        Indicates whether the fitting procedure considered experimental errors (`sigma`).
+        If `True`, the covariance matrix (`pcov`) does not need rescaling.
+
+    Returns
+    -------
+    dict
+        A dictionary containing:
+        - `"params"`: The optimized parameters (`popt`).
+        - `"std_err"`: The standard errors computed from the covariance matrix (`pcov`).
+        - `"metrics"`: A dictionary containing the reduced chi-squared (`red_chi2`).
+    """
+    if not isinstance(result, tuple):
+        raise TypeError("Fit result must be a tuple")
+
+    std_err = None
+    popt, pcov, infodict = None, None, None
+
+    # Extract output parameters
+    length = len(result)
+    popt = result[0]
+    pcov = result[1] if length > 1 else None
+    infodict = result[2] if length > 2 else None
+
+    if infodict is not None:
+        residuals = infodict["fvec"]
+        _, red_chi2 = compute_chi2(
+            residuals, n_params=len(popt), cov_rescaled=has_sigma
+        )
+        if pcov is not None:
+            std_err = compute_adjusted_standard_errors(
+                pcov, residuals, cov_rescaled=has_sigma, red_chi2=red_chi2
+            )
+
+    return {"params": popt, "std_err": std_err, "metrics": {"red_chi2": red_chi2}}
+
+
+def _format_scipy_least_squares(result, has_sigma=False):
+    """
+    Formats the output of a SciPy least-squares optimization into a standardized dictionary.
+
+    This function processes the result of a SciPy least-squares fitting function (e.g., `scipy.optimize.least_squares`)
+    and structures the fitting parameters, standard errors, and reduced chi-squared values for consistent downstream use.
+
+    Parameters
+    ----------
+    result : `scipy.optimize.OptimizeResult`
+        The result of a least-squares optimization (e.g., from `scipy.optimize.least_squares`).
+        It must contain the following fields:
+        - `result.x`: Optimized parameters (NumPy array)
+        - `result.fun`: Residuals (array of differences between the observed and fitted data)
+        - `result.jac`: Jacobian matrix (used to estimate covariance)
+
+    has_sigma : bool, optional
+        Indicates whether the fitting procedure considered experimental errors (`sigma`).
+        If `True`, the covariance matrix does not need rescaling.
+
+    Returns
+    -------
+    dict
+        A dictionary containing:
+        - `"params"`: Optimized parameters (`result.x`).
+        - `"std_err"`: Standard errors computed from the covariance matrix and residuals.
+        - `"metrics"`: A dictionary containing the reduced chi-squared (`red_chi2`).
+    """
+    params = result.x
+    residuals = result.fun
+    cov = np.linalg.inv(result.jac.T @ result.jac)
+    _, red_chi2 = compute_chi2(residuals, n_params=len(params), cov_rescaled=has_sigma)
+    std_err = compute_adjusted_standard_errors(
+        cov, residuals, cov_rescaled=has_sigma, red_chi2=red_chi2
+    )
+
+    return {"params": params, "std_err": std_err, "metrics": {"red_chi2": red_chi2}}
+
+
+def _format_scipy_minimize(result, residuals=None, has_sigma=False):
+    """
+    Formats the output of a SciPy minimize optimization into a standardized dictionary.
+
+    This function processes the result of a SciPy minimization optimization (e.g., `scipy.optimize.minimize`)
+    and structures the fitting parameters, standard errors, and reduced chi-squared values for consistent downstream use.
+
+    Parameters
+    ----------
+    result : `scipy.optimize.OptimizeResult`
+        The result of a minimization optimization (e.g., from `scipy.optimize.minimize`).
+        It must contain the following fields:
+        - `result.x`: Optimized parameters (NumPy array).
+        - `result.hess_inv`: Inverse Hessian matrix used to estimate the covariance.
+
+    residuals : array-like, optional
+        The residuals (differences between observed data and fitted model).
+        If not provided, standard errors will be computed based on the inverse Hessian matrix.
+
+    has_sigma : bool, optional
+        Indicates whether the fitting procedure considered experimental errors (`sigma`).
+        If `True`, the covariance matrix does not need rescaling.
+
+    Returns
+    -------
+    dict
+        A dictionary containing:
+        - `"params"`: Optimized parameters (`result.x`).
+        - `"std_err"`: Standard errors computed either from the Hessian matrix or based on the residuals.
+        - `"metrics"`: A dictionary containing the reduced chi-squared (`red_chi2`), if residuals are provided.
+    """
+    params = result.x
+    cov = _get_covariance_from_scipy_optimize_result(result)
+    metrics = None
+
+    if residuals is None:
+        std_err = np.sqrt(np.abs(result.hess_inv.diagonal()))
+    else:
+        std_err = compute_adjusted_standard_errors(
+            cov, residuals, cov_rescaled=has_sigma
+        )
+        _, red_chi2 = compute_chi2(
+            residuals, n_params=len(params), cov_rescaled=has_sigma
+        )
+        metrics = {"red_chi2": red_chi2}
+
+    return {"params": params, "std_err": std_err, "metrics": metrics}
+
+
+def _format_lmfit(result: ModelResult):
+    """
+    Formats the output of an lmfit model fitting result into a standardized dictionary.
+
+    This function processes the result of an lmfit model fitting (e.g., from `lmfit.Model.fit`) and
+    structures the fitting parameters, their standard errors, reduced chi-squared, and a prediction function.
+
+    Parameters
+    ----------
+    result : `lmfit.ModelResult`
+        The result of an lmfit model fitting procedure. It must contain the following fields:
+        - `result.params`: A dictionary of fitted parameters and their values.
+        - `result.redchi`: The reduced chi-squared value.
+        - `result.eval`: A method to evaluate the fitted model using independent variable values.
+        - `result.userkws`: Dictionary of user-supplied keywords that includes the independent variable.
+        - `result.model.independent_vars`: List of independent variable names in the model.
+
+    Returns
+    -------
+    dict
+        A dictionary containing:
+        - `"params"`: Optimized parameters (as a NumPy array).
+        - `"std_err"`: Standard errors of the parameters.
+        - `"metrics"`: A dictionary containing the reduced chi-squared (`red_chi2`).
+        - `"predict"`: A function that predicts the model's output given an input (using optimized parameters).
+        - `"param_names"`: List of parameter names.
+
+    Notes
+    -----
+    - lmfit already rescales standard errors by the reduced chi-squared, so no further adjustments are made.
+    - The independent variable name used in the fit is determined from `result.userkws` and `result.model.independent_vars`.
+    - The function creates a prediction function (`predict`) from the fitted model.
+    """
+    params = np.array([param.value for param in result.params.values()])
+    param_names = list(result.params.keys())
+    std_err = np.array(
+        [
+            param.stderr if param.stderr is not None else np.nan
+            for param in result.params.values()
+        ]
+    )
+    # Determine the independent variable name used in the fit
+    independent_var = result.userkws.keys() & result.model.independent_vars
+    independent_var = (
+        independent_var.pop() if independent_var else result.model.independent_vars[0]
+    )
+    fit_function = lambda x: result.eval(**{independent_var: x})
+
+    return {
+        "params": params,
+        "std_err": std_err,
+        "metrics": {"red_chi2": result.redchi},
+        "predict": fit_function,
+        "param_names": param_names,
+    }
+
+
+def _get_covariance_from_scipy_optimize_result(
+    result: spopt.OptimizeResult,
+) -> np.ndarray:
+    """
+    Extracts the covariance matrix (or an approximation) from a scipy optimization result.
+
+    This function attempts to retrieve the covariance matrix of the fitted parameters from the
+    result object returned by a scipy optimization method. It first checks for the presence of
+    the inverse Hessian (`hess_inv`), which is used to estimate the covariance. If it's not available,
+    the function attempts to compute the covariance using the Hessian matrix (`hess`).
+
+    Parameters
+    ----------
+    result : `scipy.optimize.OptimizeResult`
+        The result object returned by a scipy optimization function, such as `scipy.optimize.minimize` or `scipy.optimize.curve_fit`.
+        This object contains the optimization results, including the Hessian or its inverse.
+
+    Returns
+    -------
+    np.ndarray or None
+        The covariance matrix of the optimized parameters, or `None` if it cannot be computed.
+        If the inverse Hessian (`hess_inv`) is available, it will be returned directly.
+        If the Hessian matrix (`hess`) is available and not singular, its inverse will be computed and returned.
+        If neither is available, the function returns `None`.
+
+    Notes
+    -----
+    - If the Hessian matrix (`hess`) is singular or nearly singular, the covariance matrix cannot be computed.
+    - In some cases, the inverse Hessian (`hess_inv`) is directly available and provides the covariance without further computation.
+    """
+    if hasattr(result, "hess_inv"):
+        hess_inv = result.hess_inv
+
+        # Handle different types of hess_inv
+        if isinstance(hess_inv, np.ndarray):
+            return hess_inv
+        elif hasattr(hess_inv, "todense"):
+            return hess_inv.todense()
+
+    if hasattr(result, "hess") and result.hess is not None:
+        try:
+            return np.linalg.inv(result.hess)
+        except np.linalg.LinAlgError:
+            pass  # Hessian is singular, cannot compute covariance
+
+    return None
+
+
+def _get_xy_data_from_fit_args(*args, **kwargs):
+    """
+    Extracts x and y data from the given arguments and keyword arguments.
+
+    This helper function retrieves the x and y data (1D vectors) from the function's arguments or keyword arguments.
+    The function checks for common keyword names like "x_data", "xdata", "x", "y_data", "ydata", and "y", and returns
+    the corresponding data. If no keyword arguments are found, it attempts to extract the first two consecutive 1D
+    vectors from the positional arguments.
+
+    Parameters
+    ----------
+    *args : variable length argument list
+        The positional arguments passed to the function, potentially containing the x and y data.
+
+    **kwargs : keyword arguments
+        The keyword arguments passed to the function, potentially containing keys such as "x_data", "x", "y_data", or "y".
+
+    Returns
+    -------
+    tuple of (np.ndarray, np.ndarray)
+        A tuple containing the x data and y data as 1D numpy arrays or lists. If no valid data is found, returns (None, None).
+
+    Raises
+    ------
+    ValueError
+        If both x and y data cannot be found in the input arguments.
+
+    Notes
+    -----
+    - The function looks for the x and y data in the keyword arguments first, in the order of x_keys and y_keys.
+    - If both x and y data are not found in keyword arguments, the function will look for the first two consecutive
+      1D vectors in the positional arguments.
+    - If the data cannot be found, the function will return (None, None).
+    - The function validates that the extracted x and y data are 1D vectors (either lists or numpy arrays).
+    """
+    # Possible keyword names for x and y data
+    x_keys = ["x_data", "xdata", "x"]
+    y_keys = ["y_data", "ydata", "y"]
+
+    # Validate if an object is a 1D vector
+    def is_valid_vector(obj):
+        return isinstance(obj, (list, np.ndarray)) and np.ndim(obj) == 1
+
+    x_data, y_data = None, None
+
+    # Look for x_data in keyword arguments
+    for key in x_keys:
+        if key in kwargs and is_valid_vector(kwargs[key]):
+            x_data = kwargs[key]
+            break
+    # Look for y_data in keyword arguments
+    for key in y_keys:
+        if key in kwargs and is_valid_vector(kwargs[key]):
+            y_data = kwargs[key]
+            break
+
+    # If both parameters were found, return them
+    if (x_data is not None) and (y_data is not None):
+        return x_data, y_data
+
+    # If the args have only 1 entry
+    if len(args) == 1 and is_valid_vector(args[0]):
+        if y_data is not None:
+            x_data = args[0]
+        else:
+            y_data = args[0]
+
+    # If x and y were not found, try finding the first two consecutive vectors in args
+    if x_data is None or y_data is None:
+        # Check pairs of consecutive elements
+        for i in range(len(args) - 1):
+            if is_valid_vector(args[i]) and is_valid_vector(args[i + 1]):
+                x_data, y_data = args[i], args[i + 1]
+                break
+
+    return x_data, y_data