Set parent relationship on adding object to list

Note that this removes the need for `create_relationship()` except with deepcopy.

Author: apdavison

doc/source/grouping.rst

@@ -34,7 +34,6 @@ Using :class:`ChannelIndex`::
 
     block = Block()
     segment = Segment()
-    segment.block = block
     block.segments.append(segment)
 
     for i in (0, 1):
@@ -55,7 +54,6 @@ Using array annotations, we annotate the channels of the :class:`AnalogSignal` d
 
     block = Block()
     segment = Segment()
-    segment.block = block
     block.segments.append(segment)
 
     for i in (0, 1):
@@ -77,7 +75,6 @@ Each :class:`ChannelIndex` also contains the list of channels on which that neur
 
     block = Block(name="probe data")
     segment = Segment()
-    segment.block = block
     block.segments.append(segment)
 
     # create 4-channel AnalogSignal with dummy data
@@ -119,7 +116,6 @@ Using :class:`ChannelView` and :class:`Group`::
 
     block = Block(name="probe data")
     segment = Segment()
-    segment.block = block
     block.segments.append(segment)
 
     # create 4-channel AnalogSignal with dummy data

doc/source/io_developers_guide.rst

@@ -38,7 +38,6 @@ Miscellaneous
 =============
 
     * If your IO supports several versions of a format (like ABF1, ABF2), upload to the gin.g-node.org test file repository all file versions possible. (for test coverage).
-    * :py:func:`neo.core.Block.create_relationship` offers a utility to complete the hierarchy when all one-to-many relationships have been created.
     * In the docstring, explain where you obtained the file format specification if it is a closed one.
     * If your IO is based on a database mapper, keep in mind that the returned object MUST be detached,
       because this object can be written to another url for copying.

doc/source/scripts/multi_tetrode_example.py

@@ -35,7 +35,6 @@
 
 # Create dummy data, one segment at a time
 for segment in block.segments:
-    segment.block = block
 
     # create two 4-channel AnalogSignals with dummy data
     signals = {
@@ -46,8 +45,6 @@
     }
     if store_signals:
         segment.analogsignals.extend(signals.values())
-        for signal in signals:
-            signal.segment = segment
 
     # create spike trains with dummy data
     # we will pretend the spikes have been extracted from the dummy signal
@@ -56,7 +53,6 @@
             spiketrain = SpikeTrain(np.random.uniform(0, 100, size=30) * ms, t_stop=100 * ms)
             # assign each spiketrain to the appropriate segment
             segment.spiketrains.append(spiketrain)
-            spiketrain.segment = segment
             # assign each spiketrain to a given neuron
             current_group = next(iter_group)
             current_group.add(spiketrain)

examples/generated_data.py

@@ -56,7 +56,6 @@ def generate_block(n_segments=3, n_channels=4, n_units=3,
                 seg.spiketrains.append(train)
                 u.spiketrains.append(train)
 
-    block.create_relationship()
     return block
 
 

neo/core/block.py

@@ -89,9 +89,9 @@ def __init__(self, name=None, description=None, file_origin=None,
         self.file_datetime = file_datetime
         self.rec_datetime = rec_datetime
         self.index = index
-        self._segments = ObjectList(Segment)
-        self._groups = ObjectList(Group)
-        self._regionsofinterest = ObjectList(RegionOfInterest)
+        self._segments = ObjectList(Segment, parent=self)
+        self._groups = ObjectList(Group, parent=self)
+        self._regionsofinterest = ObjectList(RegionOfInterest, parent=self)
 
     segments = property(
         fget=lambda self: self._get_object_list("_segments"),

neo/core/container.py

@@ -103,9 +103,7 @@ class Container(BaseNeo):
     Each class can define one or more of the following class attributes
     (in  addition to those of BaseNeo):
         :_container_child_objects: Neo container objects that can be children
-                                   of this object. This attribute is used in
-                                   cases where the child can only have one
-                                   parent of this type. An instance attribute
+                                   of this object. An instance attribute
                                    named class.__name__.lower()+'s' will be
                                    automatically defined to hold this child and
                                    will be initialized to an empty list.
@@ -119,8 +117,7 @@ class Container(BaseNeo):
 
     The following helper properties are available
     (in  addition to those of BaseNeo):
-        :_child_objects: All neo container objects that can be children
-                                of this object.
+        :_child_objects: All neo objects that can be children of this object.
                                 :_container_child_objects: +
                                 :_data_child_objects:
         :_container_child_containers: The names of the container attributes
@@ -183,9 +180,9 @@ class Container(BaseNeo):
         2) process its non-universal recommended arguments (in its __new__ or
            __init__ method
     """
-    # Child objects that are a container and have a single parent
+    # Child objects that are a container
     _container_child_objects = ()
-    # Child objects that have data and have a single parent
+    # Child objects that have data
     _data_child_objects = ()
     # Containers that are listed when pretty-printing
     _repr_pretty_containers = ()
@@ -200,13 +197,13 @@ def __init__(self, name=None, description=None, file_origin=None,
 
     def _get_object_list(self, name):
         """
-
+        todo
         """
         return getattr(self, name)
 
     def _set_object_list(self, name, value):
         """
-
+        todo
         """
         assert isinstance(value, list)
         object_list = getattr(self, name)
@@ -397,6 +394,17 @@ def list_children_by_class(self, cls):
             objs.extend(getattr(child, container_name, []))
         return objs
 
+    def check_relationships(self, recursive=True):
+        """
+        Check that the expected child-parent relationships exist.
+        """
+        parent_name = _reference_name(self.__class__.__name__)
+        for child in self._single_children:
+            assert getattr(child, parent_name, None) is self
+        if recursive:
+            for child in self.container_children:
+                child.check_relationships(recursive=True)
+
     def create_relationship(self, force=False, recursive=True):
         """
         For each child of the current object that can only have a single

neo/core/group.py

@@ -59,15 +59,18 @@ def __init__(self, objects=None, name=None, description=None, file_origin=None,
         super().__init__(name=name, description=description,
                          file_origin=file_origin, **annotations)
 
+        # note that we create the ObjectLists here _without_ a parent argument
+        # since objects do not have a reference to the group(s)
+        # they are contained in.
         self._analogsignals = ObjectList(AnalogSignal)
         self._irregularlysampledsignals = ObjectList(IrregularlySampledSignal)
-        self.spiketrains = SpikeTrainList(segment=self)
+        self._spiketrains = SpikeTrainList(parent=self)
         self._events = ObjectList(Event)
         self._epochs = ObjectList(Epoch)
         self._channelviews = ObjectList(ChannelView)
         self._imagesequences = ObjectList(ImageSequence)
-        self.segments = ObjectList(Segment)  # to remove?
-        self.groups = ObjectList(Group)
+        self._segments = ObjectList(Segment)  # to remove?
+        self._groups = ObjectList(Group)
 
         if allowed_types is None:
             self.allowed_types = None
@@ -113,6 +116,23 @@ def __init__(self, objects=None, name=None, description=None, file_origin=None,
         doc="todo"
     )
 
+    spiketrains = property(
+        fget=lambda self: self._get_object_list("_spiketrains"),
+        fset=lambda self, value: self._set_object_list("_spiketrains", value),
+        doc="todo"
+
+    segments = property(
+        fget=lambda self: self._get_object_list("_segments"),
+        fset=lambda self, value: self._set_object_list("_segments", value),
+        doc="list of Segments contained in this group"
+    )
+
+    groups = property(
+        fget=lambda self: self._get_object_list("_groups"),
+        fset=lambda self, value: self._set_object_list("_groups", value),
+        doc="list of Groups contained in this group"
+    )
+
     @property
     def _container_lookup(self):
         return {

neo/core/objectlist.py

@@ -11,7 +11,7 @@ class ObjectList:
     handle relationships within Neo hierarchy
     """
 
-    def __init__(self, allowed_contents):
+    def __init__(self, allowed_contents, parent=None):
         # validate allowed_contents and normalize it to a tuple
         if isinstance(allowed_contents, type) and issubclass(allowed_contents, BaseNeo):
             self.allowed_contents = (allowed_contents,)
@@ -20,6 +20,7 @@ def __init__(self, allowed_contents):
                 assert issubclass(item, BaseNeo)
             self.allowed_contents = tuple(allowed_contents)
         self.contents = []
+        self.parent = parent
 
     def _handle_append(self, obj):
         if not (
@@ -29,6 +30,12 @@ def _handle_append(self, obj):
             )
         ):
             raise TypeError(f"Object is a {type(obj)}. It should be one of {self.allowed_contents}.")
+        # set the child-parent relationship
+        if self.parent:
+            relationship_name = self.parent.__class__.__name__.lower()
+            current_parent = getattr(obj, relationship_name)
+            if current_parent != self.parent:
+                setattr(obj, relationship_name, self.parent)
 
     def __str__(self):
         return str(self.contents)

neo/core/segment.py

@@ -99,13 +99,13 @@ def __init__(self, name=None, description=None, file_origin=None,
         super().__init__(name=name, description=description,
                          file_origin=file_origin, **annotations)
 
-        self._analogsignals = ObjectList(AnalogSignal)
-        self._irregularlysampledsignals = ObjectList(IrregularlySampledSignal)
-        self.spiketrains = SpikeTrainList(segment=self)
-        self._events = ObjectList(Event)
-        self._epochs = ObjectList(Epoch)
-        self._channelviews = ObjectList(ChannelView)
-        self._imagesequences = ObjectList(ImageSequence)
+        self._analogsignals = ObjectList(AnalogSignal, parent=self)
+        self._irregularlysampledsignals = ObjectList(IrregularlySampledSignal, parent=self)
+        self._spiketrains = SpikeTrainList(parent=self)
+        self._events = ObjectList(Event, parent=self)
+        self._epochs = ObjectList(Epoch, parent=self)
+        self._channelviews = ObjectList(ChannelView, parent=self)
+        self._imagesequences = ObjectList(ImageSequence, parent=self)
         self.block = None
 
         self.file_datetime = file_datetime
@@ -148,6 +148,12 @@ def __init__(self, name=None, description=None, file_origin=None,
         doc="todo"
     )
 
+    spiketrains = property(
+        fget=lambda self: self._get_object_list("_spiketrains"),
+        fset=lambda self, value: self._set_object_list("_spiketrains", value),
+        doc="todo"
+    )
+
     # t_start attribute is handled as a property so type checking can be done
     @property
     def t_start(self):
@@ -286,6 +292,6 @@ def time_slice(self, t_start=None, t_stop=None, reset_time=False, **kwargs):
             if len(ep_time_slice):
                 subseg.epochs.append(ep_time_slice)
 
-        subseg.create_relationship()
+        subseg.check_relationships()
 
         return subseg

neo/core/spiketrainlist.py

@@ -75,7 +75,7 @@ class SpikeTrainList(ObjectList):
 
     """
 
-    def __init__(self, items=None, segment=None):
+    def __init__(self, items=None, parent=None):
         """Initialize self"""
         if items is None:
             self._items = items
@@ -89,7 +89,7 @@ def __init__(self, items=None, segment=None):
         self._channel_id_array = None
         self._all_channel_ids = None
         self._spiketrain_metadata = {}
-        self.segment = segment
+        self.segment = parent
 
     def __iter__(self):
         """Implement iter(self)"""
@@ -183,7 +183,7 @@ def __add__(self, other):
             return self._add_spiketrainlists(other)
         elif other and is_spiketrain_or_proxy(other[0]):
             return self._add_spiketrainlists(
-                self.__class__(items=other, segment=self.segment)
+                self.__class__(items=other, parent=self.segment)
             )
         else:
             if self._items is None: