Cleanup composite analysis (#1397)

### Summary

Thanks to #1342 we can cleanup internals of `CompositeCurveAnalysis`.
Not API break and no feature upgrade with this PR.

### Details and comments

Previously the curve data and fit summary data are internally created in
`CurveAnalysis` but immediately discarded. The implementation in
`CurveAnalysis._run_analysis` is manually copied to
`CompositeCurveAnalysis._run_analysis` to access these artifact data to
create composite artifact data from them. This makes code fragile since
developers needed to manually update both base classes. With this PR,
implementation of component analysis is encapsulated.

Author: nkanazawa1989

qiskit_experiments/curve_analysis/base_curve_analysis.py

@@ -356,7 +356,7 @@ def _create_curve_data(
         """
         samples = []
 
-        for model_name, sub_data in list(curve_data.groupby("model_name")):
+        for model_name, sub_data in list(curve_data.dataframe.groupby("model_name")):
             raw_datum = AnalysisResultData(
                 name=DATA_ENTRY_PREFIX + self.__class__.__name__,
                 value={

qiskit_experiments/curve_analysis/composite_curve_analysis.py

@@ -16,11 +16,11 @@
 # pylint: disable=invalid-name
 import warnings
 from typing import Dict, List, Optional, Tuple, Union
+from collections import defaultdict
 
 import lmfit
 import numpy as np
 import pandas as pd
-from uncertainties import unumpy as unp
 
 from qiskit.utils.deprecation import deprecate_func
 
@@ -39,10 +39,9 @@
 )
 
 from qiskit_experiments.framework.containers import FigureType, ArtifactData
-from .base_curve_analysis import DATA_ENTRY_PREFIX, BaseCurveAnalysis, PARAMS_ENTRY_PREFIX
+from .base_curve_analysis import BaseCurveAnalysis
 from .curve_data import CurveFitResult
 from .scatter_table import ScatterTable
-from .utils import eval_with_uncertainties
 
 
 class CompositeCurveAnalysis(BaseAnalysis):
@@ -344,123 +343,64 @@ def _run_analysis(
         else:
             plot = getattr(self, "_generate_figures", "always")
 
-        fit_dataset = {}
-        curve_data_set = []
-        for analysis in self._analyses:
-            analysis._initialize(experiment_data)
-            analysis.set_options(plot=False)
-
-            metadata = analysis.options.extra.copy()
+        sub_artifacts = defaultdict(list)
+        for source_analysis in self._analyses:
+            analysis = source_analysis.copy()
+            metadata = analysis.options.extra
             metadata["group"] = analysis.name
+            analysis.set_options(
+                plot=False,
+                extra=metadata,
+                return_fit_parameters=self.options.return_fit_parameters,
+                return_data_points=self.options.return_data_points,
+            )
+            results, _ = analysis._run_analysis(experiment_data)
+            for res in results:
+                if isinstance(res, ArtifactData):
+                    sub_artifacts[res.name].append((analysis.name, res.data))
+                else:
+                    result_data.append(res)
+
+        if "curve_data" in sub_artifacts:
+            combined_curve_data = ScatterTable.from_dataframe(
+                data=pd.concat([d.dataframe for _, d in sub_artifacts["curve_data"]])
+            )
+            artifacts.append(ArtifactData(name="curve_data", data=combined_curve_data))
+        else:
+            combined_curve_data = None
 
-            table = analysis._format_data(analysis._run_data_processing(experiment_data.data()))
-            formatted_subset = table.filter(category=analysis.options.fit_category)
-            fit_data = analysis._run_curve_fit(formatted_subset)
-            fit_dataset[analysis.name] = fit_data
-
-            if fit_data.success:
-                quality = analysis._evaluate_quality(fit_data)
-            else:
-                quality = "bad"
-
-            if self.options.return_fit_parameters:
-                # Store fit status overview entry regardless of success.
-                # This is sometime useful when debugging the fitting code.
-                overview = AnalysisResultData(
-                    name=PARAMS_ENTRY_PREFIX + analysis.name,
-                    value=fit_data,
-                    quality=quality,
-                    extra=metadata,
-                )
-                result_data.append(overview)
-
-            if fit_data.success:
-                # Add fit data to curve data table
-                model_names = analysis.model_names()
-                for series_id, sub_data in formatted_subset.iter_by_series_id():
-                    xval = sub_data.x
-                    if len(xval) == 0:
-                        # If data is empty, skip drawing this model.
-                        # This is the case when fit model exist but no data to fit is provided.
-                        continue
-                    # Compute X, Y values with fit parameters.
-                    xval_arr_fit = np.linspace(np.min(xval), np.max(xval), num=100, dtype=float)
-                    uval_arr_fit = eval_with_uncertainties(
-                        x=xval_arr_fit,
-                        model=analysis.models[series_id],
-                        params=fit_data.ufloat_params,
-                    )
-                    yval_arr_fit = unp.nominal_values(uval_arr_fit)
-                    if fit_data.covar is not None:
-                        yerr_arr_fit = unp.std_devs(uval_arr_fit)
-                    else:
-                        yerr_arr_fit = np.zeros_like(xval_arr_fit)
-                    for xval, yval, yerr in zip(xval_arr_fit, yval_arr_fit, yerr_arr_fit):
-                        table.add_row(
-                            xval=xval,
-                            yval=yval,
-                            yerr=yerr,
-                            series_name=model_names[series_id],
-                            series_id=series_id,
-                            category="fitted",
-                            analysis=analysis.name,
-                        )
-                result_data.extend(
-                    analysis._create_analysis_results(
-                        fit_data=fit_data,
-                        quality=quality,
-                        **metadata.copy(),
-                    )
-                )
-
-            if self.options.return_data_points:
-                # Add raw data points
-                warnings.warn(
-                    f"{DATA_ENTRY_PREFIX + self.name} has been moved to experiment data artifacts. "
-                    "Saving this result with 'return_data_points'=True will be disabled in "
-                    "Qiskit Experiments 0.7.",
-                    DeprecationWarning,
-                )
-                result_data.extend(
-                    analysis._create_curve_data(curve_data=formatted_subset, **metadata)
-                )
-
-            curve_data_set.append(table)
-
-        combined_curve_data = ScatterTable.from_dataframe(
-            pd.concat([d.dataframe for d in curve_data_set])
-        )
-        total_quality = self._evaluate_quality(fit_dataset)
+        if "fit_summary" in sub_artifacts:
+            combined_summary = dict(sub_artifacts["fit_summary"])
+            artifacts.append(ArtifactData(name="fit_summary", data=combined_summary))
+            total_quality = self._evaluate_quality(combined_summary)
+        else:
+            combined_summary = None
+            total_quality = "No Information"
 
         # After the quality is determined, plot can become a boolean flag for whether
         # to generate the figure
         plot_bool = plot == "always" or (plot == "selective" and total_quality == "bad")
 
         # Create analysis results by combining all fit data
-        if all(fit_data.success for fit_data in fit_dataset.values()):
+        if combined_summary and all(fit_data.success for fit_data in combined_summary.values()):
             composite_results = self._create_analysis_results(
-                fit_data=fit_dataset, quality=total_quality, **self.options.extra.copy()
+                fit_data=combined_summary,
+                quality=total_quality,
+                **self.options.extra.copy(),
             )
             result_data.extend(composite_results)
         else:
             composite_results = []
 
-        artifacts.append(
-            ArtifactData(
-                name="curve_data",
-                data=combined_curve_data,
-            )
-        )
-        artifacts.append(
-            ArtifactData(
-                name="fit_summary",
-                data=fit_dataset,
-            )
-        )
-
-        if plot_bool:
+        if plot_bool and combined_curve_data:
+            if combined_summary:
+                red_chi_dict = {
+                    k: v.reduced_chisq for k, v in combined_summary.items() if v.success
+                }
+            else:
+                red_chi_dict = {}
             self.plotter.set_supplementary_data(
-                fit_red_chi={k: v.reduced_chisq for k, v in fit_dataset.items() if v.success},
+                fit_red_chi=red_chi_dict,
                 primary_results=composite_results,
             )
             figures.extend(self._create_figures(curve_data=combined_curve_data))