# This code is part of Qiskit.
#
# (C) Copyright IBM 2022.
#
# 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.
"""
Base class of curve analysis.
"""
import warnings
from abc import ABC, abstractmethod
from typing import Dict, List, Union
import lmfit
from qiskit.utils.deprecation import deprecate_func
from qiskit_experiments.data_processing import DataProcessor
from qiskit_experiments.data_processing.processor_library import get_processor
from qiskit_experiments.framework import (
AnalysisResultData,
BaseAnalysis,
ExperimentData,
Options,
)
from qiskit_experiments.visualization import (
BaseDrawer,
BasePlotter,
CurvePlotter,
LegacyCurveCompatDrawer,
MplDrawer,
)
from .curve_data import CurveFitResult, ParameterRepr
from .scatter_table import ScatterTable
PARAMS_ENTRY_PREFIX = "@Parameters_"
DATA_ENTRY_PREFIX = "@Data_"
[docs]
class BaseCurveAnalysis(BaseAnalysis, ABC):
"""Abstract superclass of curve analysis base classes.
Note that this class doesn't define the :meth:`_run_analysis` method,
and no actual fitting protocol is implemented in this base class.
However, this class defines several common methods that can be reused.
A curve analysis subclass can construct proper fitting protocol
by combining following methods, i.e. subroutines.
See :ref:`curve_analysis_workflow` for how these subroutines are called.
Subclass must implement following methods.
.. rubric:: _run_data_processing
This method performs data processing and returns the processed dataset.
Input data is a list of dictionaries, where each entry represents an outcome
of circuit sampling along with the metadata attached to it.
.. rubric:: _format_data
This method consumes the processed dataset and outputs the formatted dataset.
For example, this may include averaging Y values over the same X data points.
.. rubric:: _run_curve_fit
This method performs the fitting with the predefined fit models and the formatted dataset.
This is a core functionality of the :meth:`_run_analysis` method
that creates fit result objects from the formatted dataset.
Optionally, a subclass may override following methods.
These methods have default implementations as described below.
.. rubric:: _evaluate_quality
This method evaluates the quality of the fit based on the fit result.
This returns "good" when reduced chi-squared is less than 3.0.
Usually it returns string "good" or "bad" according to the evaluation.
This criterion can be updated by subclass.
.. rubric:: _run_curve_fit
This method performs the fitting with predefined fit models and the formatted dataset.
This method internally calls :meth:`_generate_fit_guesses` method.
Note that this is a core functionality of the :meth:`_run_analysis` method,
that creates fit result object from the formatted dataset.
.. rubric:: _create_analysis_results
This method creates analysis results for important fit parameters
that might be defined by analysis options ``result_parameters``.
.. rubric:: _create_figures
This method creates figures by consuming the scatter table data.
Figures are created when the analysis option ``plot`` is ``True``.
.. rubric:: _initialize
This method initializes analysis options against input experiment data.
Usually this method is called before other methods are called.
"""
@property
@abstractmethod
def parameters(self) -> List[str]:
"""Return parameters estimated by this analysis."""
@property
@abstractmethod
def name(self) -> str:
"""Return name of this analysis."""
@property
@abstractmethod
def models(self) -> List[lmfit.Model]:
"""Return fit models."""
@property
def plotter(self) -> BasePlotter:
"""A short-cut to the curve plotter instance."""
return self._options.plotter
@property
@deprecate_func(
since="0.5",
additional_msg="Use `plotter` from the new visualization module.",
removal_timeline="after 0.6",
package_name="qiskit-experiments",
)
def drawer(self) -> BaseDrawer:
"""A short-cut for curve drawer instance, if set. ``None`` otherwise."""
if isinstance(self.plotter.drawer, LegacyCurveCompatDrawer):
return self.plotter.drawer._curve_drawer
else:
return None
@classmethod
def _default_options(cls) -> Options:
"""Return default analysis options.
Analysis Options:
plotter (BasePlotter): A curve plotter instance to visualize
the analysis result.
plot_raw_data (bool): Set ``True`` to draw processed data points,
dataset without formatting, on canvas. This is ``False`` by default.
plot (bool): Set ``True`` to create figure for fit result or ``False`` to
not create a figure. This overrides the behavior of ``generate_figures``.
return_fit_parameters (bool): (Deprecated) Set ``True`` to return all fit model parameters
with details of the fit outcome. Default to ``False``.
return_data_points (bool): (Deprecated) Set ``True`` to include in the analysis result
the formatted data points given to the fitter. Default to ``False``.
data_processor (Callable): A callback function to format experiment data.
This can be a :class:`.DataProcessor`
instance that defines the `self.__call__` method.
normalization (bool): Set ``True`` to normalize y values within range [-1, 1].
Default to ``False``.
average_method (Literal["sample", "iwv", "shots_weighted"]): Method
to average the y values when the same x values
appear multiple times. One of "sample", "iwv" (i.e. inverse
weighted variance), "shots_weighted". See :func:`.mean_xy_data`
for details. Default to "shots_weighted".
p0 (Dict[str, float]): Initial guesses for the fit parameters.
The dictionary is keyed on the fit parameter names.
bounds (Dict[str, Tuple[float, float]]): Boundary of fit parameters.
The dictionary is keyed on the fit parameter names and
values are the tuples of (min, max) of each parameter.
fit_method (str): Fit method that LMFIT minimizer uses.
Default to ``least_squares`` method which implements the
Trust Region Reflective algorithm to solve the minimization problem.
See LMFIT documentation for available options.
lmfit_options (Dict[str, Any]): Options that are passed to the
LMFIT minimizer. Acceptable options depend on fit_method.
x_key (str): Circuit metadata key representing a scanned value.
fit_category (str): Name of dataset in the scatter table to fit.
result_parameters (List[Union[str, ParameterRepr]): Parameters reported in the
database as a dedicated entry. This is a list of parameter representation
which is either string or ParameterRepr object. If you provide more
information other than name, you can specify
``[ParameterRepr("alpha", "\u03B1", "a.u.")]`` for example.
The parameter name should be defined in the series definition.
Representation should be printable in standard output, i.e. no latex syntax.
extra (Dict[str, Any]): A dictionary that is appended to all database entries
as extra information.
fixed_parameters (Dict[str, Any]): Fitting model parameters that are fixed
during the curve fitting. This should be provided with default value
keyed on one of the parameter names in the series definition.
filter_data (Dict[str, Any]): Dictionary of experiment data metadata to filter.
Experiment outcomes with metadata that matches with this dictionary
are used in the analysis. If not specified, all experiment data are
input to the curve fitter. By default, no filtering condition is set.
data_subfit_map (Dict[str, Dict[str, Any]]): The mapping of experiment result data
to sub-fit models. This dictionary is keyed on the LMFIT model name,
and the value is a sorting key-value pair that filters the experiment results,
and the filtering is done based on the circuit metadata.
"""
options = super()._default_options()
options.plotter = CurvePlotter(MplDrawer())
options.plot_raw_data = False
options.return_fit_parameters = True
options.return_data_points = False
options.data_processor = None
options.normalization = False
options.average_method = "shots_weighted"
options.x_key = "xval"
options.fit_category = "formatted"
options.result_parameters = []
options.extra = {}
options.fit_method = "least_squares"
options.lmfit_options = {}
options.p0 = {}
options.bounds = {}
options.fixed_parameters = {}
options.filter_data = {}
options.data_subfit_map = {}
# Set automatic validator for particular option values
options.set_validator(field="data_processor", validator_value=DataProcessor)
options.set_validator(field="plotter", validator_value=BasePlotter)
return options
@abstractmethod
def _run_data_processing(
self,
raw_data: List[Dict],
category: str = "raw",
) -> ScatterTable:
"""Perform data processing from the experiment result payload.
Args:
raw_data: Payload in the experiment data.
category: Category string of the output dataset.
Returns:
Processed data that will be sent to the formatter method.
"""
@abstractmethod
def _format_data(
self,
curve_data: ScatterTable,
category: str = "formatted",
) -> ScatterTable:
"""Postprocessing for preparing the fitting data.
Args:
curve_data: Processed dataset created from experiment results.
category: Category string of the output dataset.
Returns:
New scatter table instance including fit data.
"""
@abstractmethod
def _run_curve_fit(
self,
curve_data: ScatterTable,
) -> CurveFitResult:
"""Perform curve fitting on given data collection and fit models.
Args:
curve_data: Formatted data to fit.
Returns:
The best fitting outcome with minimum reduced chi-squared value.
"""
def _evaluate_quality(
self,
fit_data: CurveFitResult,
) -> Union[str, None]:
"""Evaluate quality of the fit result.
Args:
fit_data: Fit outcome.
Returns:
String that represents fit result quality. Usually "good" or "bad".
"""
if 0 < fit_data.reduced_chisq < 3.0:
return "good"
return "bad"
def _create_analysis_results(
self,
fit_data: CurveFitResult,
quality: str,
**metadata,
) -> List[AnalysisResultData]:
"""Create analysis results for important fit parameters.
Args:
fit_data: Fit outcome.
quality: Quality of fit outcome.
Returns:
List of analysis result data.
"""
outcomes = []
# Create entries for important parameters
for param_repr in self.options.result_parameters:
if isinstance(param_repr, ParameterRepr):
p_name = param_repr.name
p_repr = param_repr.repr or param_repr.name
unit = param_repr.unit
else:
p_name = param_repr
p_repr = param_repr
unit = None
if unit:
par_metadata = metadata.copy()
par_metadata["unit"] = unit
else:
par_metadata = metadata
outcome = AnalysisResultData(
name=p_repr,
value=fit_data.ufloat_params[p_name],
chisq=fit_data.reduced_chisq,
quality=quality,
extra=par_metadata,
)
outcomes.append(outcome)
return outcomes
# pylint: disable=unused-argument
def _create_curve_data(
self,
curve_data: ScatterTable,
**metadata,
) -> List[AnalysisResultData]:
"""Create analysis results for raw curve data.
Args:
curve_data: Formatted data that is used for the fitting.
Returns:
List of analysis result data.
"""
samples = []
for model_name, sub_data in list(curve_data.groupby("model_name")):
raw_datum = AnalysisResultData(
name=DATA_ENTRY_PREFIX + self.__class__.__name__,
value={
"xdata": sub_data.xval.to_numpy(),
"ydata": sub_data.yval.to_numpy(),
"sigma": sub_data.yerr.to_numpy(),
},
extra={
"name": model_name,
**metadata,
},
)
samples.append(raw_datum)
return samples
def _create_figures(
self,
curve_data: ScatterTable,
) -> List["matplotlib.figure.Figure"]:
"""Create a list of figures from the curve data.
Args:
curve_data: Scatter data table containing all data points.
Returns:
A list of figures.
"""
return []
def _initialize(
self,
experiment_data: ExperimentData,
):
"""Initialize curve analysis with experiment data.
This method is called ahead of other processing.
Args:
experiment_data: Experiment data to analyze.
"""
# Initialize data processor
# TODO move this to base analysis in follow-up
data_processor = self.options.data_processor or get_processor(experiment_data, self.options)
if not data_processor.is_trained:
data_processor.train(data=experiment_data.data())
self.set_options(data_processor=data_processor)
# Check if a model contains legacy data mapping option.
data_subfit_map = {}
for model in self.models:
if "data_sort_key" in model.opts:
data_subfit_map[model._name] = model.opts["data_sort_key"]
del model.opts["data_sort_key"]
if data_subfit_map:
warnings.warn(
"Setting 'data_sort_key' to an LMFIT model constructor is no longer "
"valid configuration of the model. "
"Use 'data_subfit_map' option in the analysis options. "
"This warning will be dropped in v0.6 along with the support for the "
"'data_sort_key' in the LMFIT model options.",
DeprecationWarning,
)
self.set_options(data_subfit_map=data_subfit_map)