multielectrode_grasp/code/python-neo/neo/core/dataobject.py

# -*- coding: utf-8 -*-
"""
This module defines :class:`DataObject`, the abstract base class
used by all :module:`neo.core` classes that can contain data (i.e. are not container classes).
It contains basic functionality that is shared among all those data objects.

"""
import copy
import warnings

import quantities as pq
import numpy as np
from neo.core.baseneo import BaseNeo, _check_annotations


def _normalize_array_annotations(value, length):
    """Check consistency of array annotations

    Recursively check that value is either an array or list containing only "simple" types
    (number, string, date/time) or is a dict of those.

    Args:
        :value: (np.ndarray, list or dict) value to be checked for consistency
        :length: (int) required length of the array annotation

    Returns:
        np.ndarray The array_annotations from value in correct form

    Raises:
        ValueError: In case value is not accepted as array_annotation(s)

    """

    # First stage, resolve dict of annotations into single annotations
    if isinstance(value, dict):
        for key in value.keys():
            if isinstance(value[key], dict):
                raise ValueError("Nested dicts are not allowed as array annotations")
            value[key] = _normalize_array_annotations(value[key], length)

    elif value is None:
        raise ValueError("Array annotations must not be None")
    # If not array annotation, pass on to regular check and make it a list, that is checked again
    # This covers array annotations with length 1
    elif not isinstance(value, (list, np.ndarray)) or (
            isinstance(value, pq.Quantity) and value.shape == ()):
        _check_annotations(value)
        value = _normalize_array_annotations(np.array([value]), length)

    # If array annotation, check for correct length, only single dimension and allowed data
    else:
        # Get length that is required for array annotations, which is equal to the length
        # of the object's data
        own_length = length

        # Escape check if empty array or list and just annotate an empty array (length 0)
        # This enables the user to easily create dummy array annotations that will be filled
        # with data later on
        if len(value) == 0:
            if not isinstance(value, np.ndarray):
                value = np.ndarray((0,))
            val_length = own_length
        else:
            # Note: len(o) also works for np.ndarray, it then uses the first dimension,
            # which is exactly the desired behaviour here
            val_length = len(value)

        if not own_length == val_length:
            raise ValueError(
                "Incorrect length of array annotation: {} != {}".format(val_length, own_length))

        # Local function used to check single elements of a list or an array
        # They must not be lists or arrays and fit the usual annotation data types
        def _check_single_elem(element):
            # Nested array annotations not allowed currently
            # If element is a list or a np.ndarray, it's not conform except if it's a quantity of
            # length 1
            if isinstance(element, list) or (isinstance(element, np.ndarray) and not (
                    isinstance(element, pq.Quantity) and (
                    element.shape == () or element.shape == (1,)))):
                raise ValueError("Array annotations should only be 1-dimensional")
            if isinstance(element, dict):
                raise ValueError("Dictionaries are not supported as array annotations")

            # Perform regular check for elements of array or list
            _check_annotations(element)

        # Arrays only need testing of single element to make sure the others are the same
        if isinstance(value, np.ndarray):
            # Type of first element is representative for all others
            # Thus just performing a check on the first element is enough
            # Even if it's a pq.Quantity, which can be scalar or array, this is still true
            # Because a np.ndarray cannot contain scalars and sequences simultaneously

            # If length of data is 0, then nothing needs to be checked
            if len(value):
                # Perform check on first element
                _check_single_elem(value[0])

            return value

        # In case of list, it needs to be ensured that all data are of the same type
        else:
            # Conversion to numpy array makes all elements same type
            # Converts elements to most general type

            try:
                value = np.array(value)
            # Except when scalar and non-scalar values are mixed, this causes conversion to fail
            except ValueError as e:
                msg = str(e)
                if "setting an array element with a sequence." in msg:
                    raise ValueError("Scalar values and arrays/lists cannot be "
                                     "combined into a single array annotation")
                else:
                    raise e

            # If most specialized data type that possibly fits all elements is object,
            # raise an Error with a telling error message, because this means the elements
            # are not compatible
            if value.dtype == object:
                raise ValueError("Cannot convert list of incompatible types into a single"
                                 " array annotation")

            # Check the first element for correctness
            # If its type is correct for annotations, all others are correct as well
            # Note: Emtpy lists cannot reach this point
            _check_single_elem(value[0])

    return value


class DataObject(BaseNeo, pq.Quantity):
    '''
    This is the base class from which all objects containing data inherit
    It contains common functionality for all those objects and handles array_annotations.

    Common functionality that is not included in BaseNeo includes:
    - duplicating with new data
    - rescaling the object
    - copying the object
    - returning it as pq.Quantity or np.ndarray
    - handling of array_annotations

    Array_annotations are a kind of annotation that contains metadata for every data point,
    i.e. per timestamp (in SpikeTrain, Event and Epoch) or signal channel (in AnalogSignal
    and IrregularlySampledSignal).
    They can contain the same data types as regular annotations, but are always represented
    as numpy arrays of the same length as the number of data points of the annotated neo object.

    Args:
        name (str, optional): Name of the Neo object
        description (str, optional): Human readable string description of the Neo object
        file_origin (str, optional): Origin of the data contained in this Neo object
        array_annotations (dict, optional): Dictionary containing arrays / lists which annotate
            individual data points of the Neo object.
        kwargs: regular annotations stored in a separate annotation dictionary
    '''

    def __init__(self, name=None, description=None, file_origin=None, array_annotations=None,
                 **annotations):
        """
        This method is called by each data object and initializes the newly created object by
        adding array annotations and calling __init__ of the super class, where more annotations
        and attributes are processed.
        """

        if not hasattr(self, 'array_annotations') or not self.array_annotations:
            self.array_annotations = ArrayDict(self._get_arr_ann_length())
        if array_annotations is not None:
            self.array_annotate(**array_annotations)

        BaseNeo.__init__(self, name=name, description=description, file_origin=file_origin,
                         **annotations)

    def array_annotate(self, **array_annotations):
        """
        Add array annotations (annotations for individual data points) as arrays to a Neo data
        object.

        Example:

        >>> obj.array_annotate(code=['a', 'b', 'a'], category=[2, 1, 1])
        >>> obj.array_annotations['code'][1]
        'b'
        """

        self.array_annotations.update(array_annotations)

    def array_annotations_at_index(self, index):
        """
        Return dictionary of array annotations at a given index or list of indices
        :param index: int, list, numpy array: The index (indices) from which the annotations
                      are extracted
        :return: dictionary of values or numpy arrays containing all array annotations
                 for given index/indices

        Example:
        >>> obj.array_annotate(code=['a', 'b', 'a'], category=[2, 1, 1])
        >>> obj.array_annotations_at_index(1)
        {code='b', category=1}
        """

        # Taking only a part of the array annotations
        # Thus not using ArrayDict here, because checks for length are not needed
        index_annotations = {}

        # Use what is given as an index to determine the corresponding annotations,
        # if not possible, numpy raises an Error
        for ann in self.array_annotations.keys():
            # NO deepcopy, because someone might want to alter the actual object using this
            try:
                index_annotations[ann] = self.array_annotations[ann][index]
            except IndexError as e:
                # IndexError caused by 'dummy' array annotations should not result in failure
                # Taking a slice from nothing results in nothing
                if len(self.array_annotations[ann]) == 0 and not self._get_arr_ann_length() == 0:
                    index_annotations[ann] = self.array_annotations[ann]
                else:
                    raise e

        return index_annotations

    def _merge_array_annotations(self, other):
        '''
        Merges array annotations of 2 different objects.
        The merge happens in such a way that the result fits the merged data
        In general this means concatenating the arrays from the 2 objects.
        If an annotation is only present in one of the objects, it will be omitted
        :return Merged array_annotations
        '''

        merged_array_annotations = {}
        omitted_keys_self = []
        # Concatenating arrays for each key
        for key in self.array_annotations:
            try:
                value = copy.deepcopy(self.array_annotations[key])
                other_value = copy.deepcopy(other.array_annotations[key])
                # Quantities need to be rescaled to common unit
                if isinstance(value, pq.Quantity):
                    try:
                        other_value = other_value.rescale(value.units)
                    except ValueError:
                        raise ValueError("Could not merge array annotations "
                                         "due to different units")
                    merged_array_annotations[key] = np.append(value, other_value) * value.units
                else:
                    merged_array_annotations[key] = np.append(value, other_value)

            except KeyError:
                # Save the  omitted keys to be able to print them
                omitted_keys_self.append(key)
                continue
        # Also save omitted keys from 'other'
        omitted_keys_other = [key for key in other.array_annotations if
                              key not in self.array_annotations]

        # Warn if keys were omitted
        if omitted_keys_other or omitted_keys_self:
            warnings.warn("The following array annotations were omitted, because they were only "
                          "present in one of the merged objects: {} from the one that was merged "
                          "into and {} from the one that was merged into the other"
                          "".format(omitted_keys_self, omitted_keys_other), UserWarning)

        # Return the merged array_annotations
        return merged_array_annotations

    def rescale(self, units):
        '''
        Return a copy of the object converted to the specified
        units
        :return: Copy of self with specified units
        '''
        # Use simpler functionality, if nothing will be changed
        dim = pq.quantity.validate_dimensionality(units)
        if self.dimensionality == dim:
            return self.copy()

        # Rescale the object into a new object
        obj = self.duplicate_with_new_data(signal=self.view(pq.Quantity).rescale(dim), units=units)

        # Expected behavior is deepcopy, so deepcopying array_annotations
        obj.array_annotations = copy.deepcopy(self.array_annotations)

        obj.segment = self.segment

        return obj

    # Needed to implement this so array annotations are copied as well, ONLY WHEN copying 1:1
    def copy(self, **kwargs):
        '''
        Returns a copy of the object
        :return: Copy of self
        '''

        obj = super(DataObject, self).copy(**kwargs)
        obj.array_annotations = self.array_annotations
        return obj

    def as_array(self, units=None):
        """
        Return the object's data as a plain NumPy array.

        If `units` is specified, first rescale to those units.
        """
        if units:
            return self.rescale(units).magnitude
        else:
            return self.magnitude

    def as_quantity(self):
        """
        Return the object's data as a quantities array.
        """
        return self.view(pq.Quantity)

    def _get_arr_ann_length(self):
        """
        Return the length of the object's data as required for array annotations
        This is the last dimension of every object.
        :return Required length of array annotations for this object
        """
        # Number of items is last dimension in of data object
        # This method should be overridden in case this changes
        try:
            length = self.shape[-1]
        # Note: This is because __getitem__[int] returns a scalar Epoch/Event/SpikeTrain
        # To be removed if __getitem__[int] is changed
        except IndexError:
            length = 1
        return length

    def duplicate_with_new_array(self, signal, units=None):
        warnings.warn("Use of the `duplicate_with_new_array function is deprecated. "
                      "Please use `duplicate_with_new_data` instead.",
                      DeprecationWarning)
        return self.duplicate_with_new_data(signal, units=units)


class ArrayDict(dict):
    """Dictionary subclass to handle array annotations

       When setting `obj.array_annotations[key]=value`, checks for consistency
       should not be bypassed.
       This class overrides __setitem__ from dict to perform these checks every time.
       The method used for these checks is given as an argument for __init__.
    """

    def __init__(self, length, check_function=_normalize_array_annotations, *args, **kwargs):
        super(ArrayDict, self).__init__(*args, **kwargs)
        self.check_function = check_function
        self.length = length

    def __setitem__(self, key, value):
        # Directly call the defined function
        # Need to wrap key and value in a dict in order to make sure
        # that nested dicts are detected
        value = self.check_function({key: value}, self.length)[key]
        super(ArrayDict, self).__setitem__(key, value)

    # Updating the dict also needs to perform checks, so rerouting this to __setitem__
    def update(self, *args, **kwargs):
        if args:
            if len(args) > 1:
                raise TypeError("update expected at most 1 arguments, "
                                "got %d" % len(args))
            other = dict(args[0])
            for key in other:
                self[key] = other[key]
        for key in kwargs:
            self[key] = kwargs[key]

    def __reduce__(self):
        return super(ArrayDict, self).__reduce__()