Data processor with uncertainties package (#481)

* fix SVD shape * fix docs * fix comment * fix var name * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * comments * update except for SVD * update note tests * fix processor logic * documentation * lint * add reno use np.testing * fix test * Update qiskit_experiments/data_processing/data_action.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/data_action.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/data_action.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/data_action.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/data_processor.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/data_processor.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/data_processor.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/data_processor.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/data_processor.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * add description for correlation * remove typehint for trainable node * update return doc * add type check * detail for full array * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * add comment * fix document * black * Update qiskit_experiments/data_processing/__init__.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/data_processor.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/data_processor.py Co-authored-by: Daniel J. Egger <[email protected]> * update docs * update docs * restrict count validation * update return type of data processor * lint * add svd test * update average node * Update qiskit_experiments/data_processing/data_processor.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * Update qiskit_experiments/data_processing/nodes.py Co-authored-by: Daniel J. Egger <[email protected]> * add comment * add handling for level2 memory * black * lint Co-authored-by: Daniel J. Egger <[email protected]>
qiskit-community · Dec 1, 2021 · e9297ad · e9297ad
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diff --git a/qiskit_experiments/curve_analysis/curve_analysis.py b/qiskit_experiments/curve_analysis/curve_analysis.py
@@ -21,6 +21,7 @@
 import warnings
 from abc import ABC
 from typing import Any, Dict, List, Tuple, Callable, Union, Optional
+from uncertainties import unumpy as unp
 
 import numpy as np
 from qiskit.providers import Backend
@@ -577,30 +578,29 @@ def _is_target_series(datum, **filters):
 
         x_key = self._get_option("x_key")
         try:
-            x_values = [datum["metadata"][x_key] for datum in data]
+            x_values = np.asarray([datum["metadata"][x_key] for datum in data], dtype=float)
         except KeyError as ex:
             raise DataProcessorError(
                 f"X value key {x_key} is not defined in circuit metadata."
             ) from ex
 
         if isinstance(data_processor, DataProcessor):
-            y_values, y_sigmas = data_processor(data)
-            if y_sigmas is None:
-                y_sigmas = np.full(y_values.shape, np.nan)
+            y_data = data_processor(data)
+
+            y_nominals = unp.nominal_values(y_data)
+            y_stderrs = unp.std_devs(y_data)
         else:
-            y_values, y_sigmas = zip(*map(data_processor, data))
+            y_nominals, y_stderrs = zip(*map(data_processor, data))
+
+            y_nominals = np.asarray(y_nominals, dtype=float)
+            y_stderrs = np.asarray(y_stderrs, dtype=float)
 
         # Store metadata
         metadata = np.asarray([datum["metadata"] for datum in data], dtype=object)
 
         # Store shots
         shots = np.asarray([datum.get("shots", np.nan) for datum in data])
 
-        # Format data
-        x_values = np.asarray(x_values, dtype=float)
-        y_values = np.asarray(y_values, dtype=float)
-        y_sigmas = np.asarray(y_sigmas, dtype=float)
-
         # Find series (invalid data is labeled as -1)
         data_index = np.full(x_values.size, -1, dtype=int)
         for idx, series_def in enumerate(self.__series__):
@@ -613,8 +613,8 @@ def _is_target_series(datum, **filters):
         raw_data = CurveData(
             label="raw_data",
             x=x_values,
-            y=y_values,
-            y_err=y_sigmas,
+            y=y_nominals,
+            y_err=y_stderrs,
             shots=shots,
             data_index=data_index,
             metadata=metadata,

diff --git a/qiskit_experiments/data_processing/__init__.py b/qiskit_experiments/data_processing/__init__.py
@@ -16,10 +16,32 @@
 
 .. currentmodule:: qiskit_experiments.data_processing
 
-Data processing is the act of taking taking the data returned by the backend and
-converting it into a format that can be analyzed. For instance, counts can be
-converted to a probability while two-dimensional IQ data may be converted to a
-one-dimensional signal.
+Data processing is the act of taking the data returned by the backend and
+converting it into a format that can be analyzed.
+It is implemented as a chain of data processing steps that transform various input data,
+e.g. IQ data, into a desired format, e.g. population, which can be analyzed.
+
+These data transformations may consist of multiple steps, such as kerneling and discrimination.
+Each step is implemented by a :class:`~qiskit_experiments.data_processing.data_action.DataAction`
+also called a `node`.
+
+The data processor implements the :meth:`__call__` method. Once initialized, it
+can thus be used as a standard python function:
+
+.. code-block:: python
+
+    processor = DataProcessor(input_key="memory", [Node1(), Node2(), ...])
+    out_data = processor(in_data)
+
+The data input to the processor is a sequence of dictionaries each representing the result
+of a single circuit. The output of the processor is a numpy array whose shape and data type
+depend on the combination of the nodes in the data processor.
+
+Uncertainties that arise from quantum measurements or finite sampling can be taken into account
+in the nodes: a standard error can be generated in a node and can be propagated
+through the subsequent nodes in the data processor.
+Correlation between computed values is also considered.
+
 
 Classes
 =======

diff --git a/qiskit_experiments/data_processing/data_action.py b/qiskit_experiments/data_processing/data_action.py
@@ -13,66 +13,65 @@
 """Defines the steps that can be used to analyse data."""
 
 from abc import ABCMeta, abstractmethod
-from typing import Any, List, Optional, Tuple
+
+import numpy as np
 
 
 class DataAction(metaclass=ABCMeta):
-    """
-    Abstract action done on measured data to process it. Each subclass of DataAction must
-    define the way it formats, validates and processes data.
+    """Abstract action done on measured data to process it.
+
+    Each subclass of DataAction must define the way it formats, validates and processes data.
     """
 
     def __init__(self, validate: bool = True):
-        """
+        """Create new node.
+
         Args:
             validate: If set to False the DataAction will not validate its input.
         """
         self._validate = validate
 
     @abstractmethod
-    def _process(self, datum: Any, error: Optional[Any] = None) -> Tuple[Any, Any]:
-        """
-        Applies the data processing step to the datum.
+    def _process(self, data: np.ndarray) -> np.ndarray:
+        """Applies the data processing step to the data.
 
         Args:
-            datum: A single item of data which will be processed.
-            error: An optional error estimation on the datum that can be further propagated.
+            data: A data array to process. This is a single numpy array containing
+                all circuit results input to the data processor.
+                If the elements are ufloat objects consisting of a nominal value and
+                a standard error, then the error propagation is automatically computed.
 
         Returns:
-            processed data: The data that has been processed along with the propagated error.
+            The processed data.
         """
 
-    @abstractmethod
-    def _format_data(self, datum: Any, error: Optional[Any] = None) -> Tuple[Any, Any]:
+    def _format_data(self, data: np.ndarray) -> np.ndarray:
         """Format and validate the input.
 
-        Check that the given data and error has the correct structure. This method may
+        Check that the given data has the correct structure. This method may
         additionally change the data type, e.g. converting a list to a numpy array.
 
         Args:
-            datum: The data instance to check and format.
-            error: An optional error estimation on the datum to check and format.
+            data: A data array to format. This is a single numpy array containing
+                all circuit results input to the data processor.
 
         Returns:
-            datum, error: The formatted datum and its optional error.
-
-        Raises:
-            DataProcessorError: If either the data or the error do not have the proper format.
+            The data that has been validated and formatted.
         """
+        return data
 
-    def __call__(self, data: Any, error: Optional[Any] = None) -> Tuple[Any, Any]:
-        """Call the data action of this node on the data and propagate the error.
+    def __call__(self, data: np.ndarray) -> np.ndarray:
+        """Call the data action of this node on the data.
 
         Args:
-            data: The data to process. The action nodes in the data processor will
-                raise errors if the data does not have the appropriate format.
-            error: An optional error estimation on the datum that can be further processed.
+            data: A numpy array with arbitrary dtype. If the elements are ufloat objects
+                consisting of a nominal value and a standard error, then the error propagation
+                is done automatically.
 
         Returns:
-            processed data: The data processed by self as a tuple of processed datum and
-                optionally the propagated error estimate.
+            The processed data.
         """
-        return self._process(*self._format_data(data, error))
+        return self._process(self._format_data(data))
 
     def __repr__(self):
         """String representation of the node."""
@@ -94,11 +93,13 @@ def is_trained(self) -> bool:
         """
 
     @abstractmethod
-    def train(self, data: List[Any]):
+    def train(self, data: np.ndarray):
         """Train a DataAction.
 
         Certain data processing nodes, such as a SVD, require data to first train.
 
         Args:
-            data: A list of datum. Each datum is a point used to train the node.
+            data: A data array for training. This is a single numpy array containing
+                all circuit results input to the data processor :meth:`~qiskit_experiments.\
+                data_processing.data_processor.DataProcessor#train` method.
         """