Merge pull request #809 from chriseclectic/0.3.1

Prepare 0.3.1 patch

docs/_ext/autodoc_experiment.py

@@ -27,14 +27,12 @@ class ExperimentDocumenter(ClassDocumenter):
     """Sphinx extension for the custom documentation of the standard experiment class."""
 
     objtype = "experiment"
-    directivetype = 'class'
+    directivetype = "class"
     priority = 10 + ClassDocumenter.priority
     option_spec = dict(ClassDocumenter.option_spec)
 
     @classmethod
-    def can_document_member(
-        cls, member: Any, membername: str, isattr: bool, parent: Any
-    ) -> bool:
+    def can_document_member(cls, member: Any, membername: str, isattr: bool, parent: Any) -> bool:
         return isinstance(member, BaseExperiment)
 
     def add_content(self, more_content: Any, no_docstring: bool = False) -> None:

docs/conf.py

@@ -47,7 +47,7 @@
 # The short X.Y version
 version = "0.3"
 # The full version, including alpha/beta/rc tags
-release = "0.3.0"
+release = "0.3.1"
 
 rst_prolog = """
 .. raw:: html

qiskit_experiments/VERSION.txt

@@ -1 +1 @@
-0.3.0
+0.3.1

qiskit_experiments/curve_analysis/curve_analysis.py

@@ -174,10 +174,11 @@ def _run_analysis(
         formatted_data = self._format_data(processed_data)
         if self.options.plot:
             for s in self.__series__:
+                sub_data = formatted_data.get_subset_of(s.name)
                 self.drawer.draw_formatted_data(
-                    x_data=formatted_data.x,
-                    y_data=formatted_data.y,
-                    y_err_data=formatted_data.y_err,
+                    x_data=sub_data.x,
+                    y_data=sub_data.y,
+                    y_err_data=sub_data.y_err,
                     name=s.name,
                     ax_index=s.canvas,
                     color=s.plot_color,
@@ -244,13 +245,14 @@ def _run_analysis(
                                 alpha=alpha,
                                 color=s.plot_color,
                             )
-                    # Write fitting report
-                    report_description = ""
-                    for res in analysis_results:
-                        if isinstance(res.value, (float, UFloat)):
-                            report_description += f"{analysis_result_to_repr(res)}\n"
-                    report_description += r"Fit $\chi^2$ = " + f"{fit_data.reduced_chisq: .4g}"
-                    self.drawer.draw_fit_report(description=report_description)
+
+                # Write fitting report
+                report_description = ""
+                for res in analysis_results:
+                    if isinstance(res.value, (float, UFloat)):
+                        report_description += f"{analysis_result_to_repr(res)}\n"
+                report_description += r"Fit $\chi^2$ = " + f"{fit_data.reduced_chisq: .4g}"
+                self.drawer.draw_fit_report(description=report_description)
 
         # Add raw data points
         analysis_results.extend(self._create_curve_data(formatted_data, self.__series__))

qiskit_experiments/database_service/db_experiment_data.py

@@ -1835,8 +1835,6 @@ def __json_encode__(self):
         for att in [
             "_metadata",
             "_source",
-            "_service",
-            "_backend",
             "_id",
             "_parent_id",
             "_type",
@@ -1861,6 +1859,15 @@ def __json_encode__(self):
         # Handle non-serializable objects
         json_value["_jobs"] = self._safe_serialize_jobs()
 
+        # the attribute self._service in charge of the connection and communication with the
+        #  experiment db. It doesn't have meaning in the json format so there is no need to serialize
+        #  it.
+        for att in ["_service", "_backend"]:
+            json_value[att] = None
+            value = getattr(self, att)
+            if value is not None:
+                LOG.info("%s cannot be JSON serialized", str(type(value)))
+
         return json_value
 
     @classmethod

qiskit_experiments/framework/__init__.py

@@ -176,6 +176,11 @@
 - :meth:`BaseExperiment._metadata`
   to add any experiment metadata to the result data.
 
+Furthermore, some characterization and calibration experiments can be run with restless
+measurements, i.e. measurements where the qubits are not reset and circuits are executed
+immediately after the previous measurement. Here, the :class:`.RestlessMixin` can help
+to set the appropriate run options and data processing chain.
+
 Analysis Subclasses
 *******************
 
@@ -232,6 +237,14 @@
     BaseExperiment
     BaseAnalysis
 
+Mix-ins
+*******
+
+.. autosummary::
+    :toctree: ../stubs/
+
+    RestlessMixin
+
 .. _create-experiment:
 """
 from qiskit.providers.options import Options
@@ -252,3 +265,4 @@
     CompositeAnalysis,
 )
 from .json import ExperimentEncoder, ExperimentDecoder
+from .restless_mixin import RestlessMixin

qiskit_experiments/framework/composite/composite_analysis.py

@@ -16,6 +16,7 @@
 from typing import List, Dict, Union, Optional, Tuple
 import numpy as np
 from qiskit.result import marginal_counts
+from qiskit.result.postprocess import format_counts_memory
 from qiskit_experiments.framework import BaseAnalysis, ExperimentData
 from qiskit_experiments.framework.analysis_result_data import AnalysisResultData
 from qiskit_experiments.framework.base_analysis import _requires_copy
@@ -111,7 +112,7 @@ def run(
 
     def _run_analysis(self, experiment_data: ExperimentData):
         # Return list of experiment data containers for each component experiment
-        # containing the marginalied data from the composite experiment
+        # containing the marginalized data from the composite experiment
         component_expdata = self._component_experiment_data(experiment_data)
 
         # Run the component analysis on each component data
@@ -194,6 +195,10 @@ def _marginalized_component_data(self, composite_data: List[Dict]) -> List[List[
                 composite_clbits = metadata["composite_clbits"]
             else:
                 composite_clbits = None
+
+            # Pre-process the memory if any to avoid redundant calls to format_counts_memory
+            f_memory = self._format_memory(datum, composite_clbits)
+
             for i, index in enumerate(metadata["composite_index"]):
                 if index not in marginalized_data:
                     # Initialize data list for marginalized
@@ -206,16 +211,44 @@ def _marginalized_component_data(self, composite_data: List[Dict]) -> List[List[
                         sub_data["counts"] = datum["counts"]
                 if "memory" in datum:
                     if composite_clbits is not None:
-                        sub_data["memory"] = (
-                            np.array(datum["memory"])[composite_clbits[i]]
-                        ).tolist()
+                        # level 2
+                        if f_memory is not None:
+                            idx = slice(
+                                -1 - composite_clbits[i][-1], -composite_clbits[i][0] or None
+                            )
+                            sub_data["memory"] = [shot[idx] for shot in f_memory]
+                        # level 1
+                        else:
+                            mem = np.array(datum["memory"])
+
+                            # Averaged level 1 data
+                            if len(mem.shape) == 2:
+                                sub_data["memory"] = mem[composite_clbits[i]].tolist()
+                            # Single-shot level 1 data
+                            if len(mem.shape) == 3:
+                                sub_data["memory"] = mem[:, composite_clbits[i]].tolist()
                     else:
                         sub_data["memory"] = datum["memory"]
                 marginalized_data[index].append(sub_data)
 
         # Sort by index
         return [marginalized_data[i] for i in sorted(marginalized_data.keys())]
 
+    @staticmethod
+    def _format_memory(datum: Dict, composite_clbits: List):
+        """A helper method to convert level 2 memory (if it exists) to bit-string format."""
+        f_memory = None
+        if (
+            "memory" in datum
+            and composite_clbits is not None
+            and isinstance(datum["memory"][0], str)
+        ):
+            num_cbits = 1 + max(cbit for cbit_list in composite_clbits for cbit in cbit_list)
+            header = {"memory_slots": num_cbits}
+            f_memory = list(format_counts_memory(shot, header) for shot in datum["memory"])
+
+        return f_memory
+
     def _add_child_data(self, experiment_data: ExperimentData):
         """Save empty component experiment data as child data.
 

qiskit_experiments/framework/json.py

@@ -456,6 +456,8 @@ def default(self, obj: Any) -> Any:  # pylint: disable=arguments-differ
             return {"__type__": "spmatrix", "__value__": value}
         if isinstance(obj, bytes):
             return _serialize_bytes(obj)
+        if isinstance(obj, np.number):
+            return obj.item()
         if dataclasses.is_dataclass(obj):
             return _serialize_object(obj, settings=dataclasses.asdict(obj))
         if isinstance(obj, uncertainties.UFloat):

qiskit_experiments/library/characterization/cr_hamiltonian.py

@@ -157,22 +157,21 @@ def __init__(
         Raises:
             QiskitError: When ``qubits`` length is not 2.
         """
-        super().__init__(qubits, analysis=CrossResonanceHamiltonianAnalysis(), backend=backend)
+        # backend parameters required to run this experiment
+        # random values are populated here but these are immediately updated after backend is set
+        # this is to keep capability of generating circuits just for checking
+        self._dt = 1
+        self._cr_channel = 0
+        self._granularity = 1
+        self._cr_gate = cr_gate
 
         if len(qubits) != 2:
             raise QiskitError(
                 "Length of qubits is not 2. Please provide index for control and target qubit."
             )
 
+        super().__init__(qubits, analysis=CrossResonanceHamiltonianAnalysis(), backend=backend)
         self.set_experiment_options(flat_top_widths=flat_top_widths, **kwargs)
-        self._cr_gate = cr_gate
-
-        # backend parameters required to run this experiment
-        # random values are populated here but these are immediately updated after backend is set
-        # this is to keep capability of generating circuits just for checking
-        self._dt = 1
-        self._cr_channel = 0
-        self._granularity = 1
 
     @classmethod
     def _default_experiment_options(cls) -> Options:

qiskit_experiments/test/__init__.py

@@ -26,9 +26,6 @@
     :toctree: ../stubs/
 
     MockIQBackend
-    MockRamseyXY
-    MockFineAmp
-    DragBackend
     T1Backend
     T2RamseyBackend
     FakeJob
@@ -37,7 +34,7 @@
 """
 
 from .utils import FakeJob
-from .mock_iq_backend import MockIQBackend, MockRamseyXY, MockFineAmp, DragBackend
+from .mock_iq_backend import MockIQBackend
 from .t1_backend import T1Backend
 from .t2ramsey_backend import T2RamseyBackend
 from .fake_service import FakeService