Replace simple lists with a list-like object that can manage relationships

Author: apdavison

neo/core/block.py

@@ -10,6 +10,10 @@
 from datetime import datetime
 
 from neo.core.container import Container, unique_objs
+from neo.core.group import Group
+from neo.core.objectlist import ObjectList
+from neo.core.regionofinterest import RegionOfInterest
+from neo.core.segment import Segment
 
 
 class Block(Container):
@@ -85,11 +89,27 @@ 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 = []
-        self.groups = []
-        self.regionsofinterest = []   # temporary workaround.
-        # the goal is to store all sub-classes of RegionOfInterest in a single list
-        # but this will need substantial changes to container handling
+        self._segments = ObjectList(Segment)
+        self._groups = ObjectList(Group)
+        self._regionsofinterest = ObjectList(RegionOfInterest)
+
+    segments = property(
+        fget=lambda self: self._get_object_list("_segments"),
+        fset=lambda self, value: self._set_object_list("_segments", value),
+        doc="todo"
+    )
+
+    groups = property(
+        fget=lambda self: self._get_object_list("_groups"),
+        fset=lambda self, value: self._set_object_list("_groups", value),
+        doc="todo"
+    )
+
+    regionsofinterest = property(
+        fget=lambda self: self._get_object_list("_regionsofinterest"),
+        fset=lambda self, value: self._set_object_list("_regionsofinterest", value),
+        doc="todo"
+    )
 
     @property
     def data_children_recur(self):

neo/core/container.py

@@ -198,6 +198,22 @@ def __init__(self, name=None, description=None, file_origin=None,
         super().__init__(name=name, description=description,
                          file_origin=file_origin, **annotations)
 
+    def _get_object_list(self, name):
+        """
+
+        """
+        return getattr(self, name)
+
+    def _set_object_list(self, name, value):
+        """
+
+        """
+        assert isinstance(value, list)
+        object_list = getattr(self, name)
+        if len(object_list) > 0:
+            raise Exception("Object list not empty")
+        object_list.extend(value)
+
     @property
     def _child_objects(self):
         """

neo/core/group.py

@@ -8,6 +8,16 @@
 
 from os import close
 from neo.core.container import Container
+from neo.core.analogsignal import AnalogSignal
+from neo.core.container import Container
+from neo.core.objectlist import ObjectList
+from neo.core.epoch import Epoch
+from neo.core.event import Event
+from neo.core.imagesequence import ImageSequence
+from neo.core.irregularlysampledsignal import IrregularlySampledSignal
+from neo.core.segment import Segment
+from neo.core.spiketrainlist import SpikeTrainList
+from neo.core.view import ChannelView
 
 
 class Group(Container):
@@ -49,16 +59,15 @@ def __init__(self, objects=None, name=None, description=None, file_origin=None,
         super().__init__(name=name, description=description,
                          file_origin=file_origin, **annotations)
 
-        self.analogsignals = []
-        self.irregularlysampledsignals = []
-        self.spiketrains = []
-        self.events = []
-        self.epochs = []
-        self.channelviews = []
-        self.imagesequences = []
-        self.segments = []  # to remove?
-        self.groups = []
-        self.block = None
+        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.segments = ObjectList(Segment)  # to remove?
+        self.groups = ObjectList(Group)
 
         if allowed_types is None:
             self.allowed_types = None
@@ -68,6 +77,42 @@ def __init__(self, objects=None, name=None, description=None, file_origin=None,
         if objects:
             self.add(*objects)
 
+    analogsignals = property(
+        fget=lambda self: self._get_object_list("_analogsignals"),
+        fset=lambda self, value: self._set_object_list("_analogsignals", value),
+        doc="todo"
+    )
+
+    irregularlysampledsignals = property(
+        fget=lambda self: self._get_object_list("_irregularlysampledsignals"),
+        fset=lambda self, value: self._set_object_list("_irregularlysampledsignals", value),
+        doc="todo"
+    )
+
+    events = property(
+        fget=lambda self: self._get_object_list("_events"),
+        fset=lambda self, value: self._set_object_list("_events", value),
+        doc="todo"
+    )
+
+    epochs = property(
+        fget=lambda self: self._get_object_list("_epochs"),
+        fset=lambda self, value: self._set_object_list("_epochs", value),
+        doc="todo"
+    )
+
+    channelviews = property(
+        fget=lambda self: self._get_object_list("_channelviews"),
+        fset=lambda self, value: self._set_object_list("_channelviews", value),
+        doc="todo"
+    )
+
+    imagesequences = property(
+        fget=lambda self: self._get_object_list("_imagesequences"),
+        fset=lambda self, value: self._set_object_list("_imagesequences", value),
+        doc="todo"
+    )
+
     @property
     def _container_lookup(self):
         return {

neo/core/objectlist.py

@@ -0,0 +1,109 @@
+"""
+
+
+"""
+
+from neo.core.baseneo import BaseNeo
+
+
+class ObjectList:
+    """
+    handle relationships within Neo hierarchy
+    """
+
+    def __init__(self, allowed_contents):
+        # validate allowed_contents and normalize it to a tuple
+        if isinstance(allowed_contents, type) and issubclass(allowed_contents, BaseNeo):
+            self.allowed_contents = (allowed_contents,)
+        else:
+            for item in allowed_contents:
+                assert issubclass(item, BaseNeo)
+            self.allowed_contents = tuple(allowed_contents)
+        self.contents = []
+
+    def _handle_append(self, obj):
+        if not (
+            isinstance(obj, self.allowed_contents)
+            or (  # also allow proxy objects of the correct type
+                hasattr(obj, "proxy_for") and obj.proxy_for in self.allowed_contents
+            )
+        ):
+            raise TypeError(f"Object is a {type(obj)}. It should be one of {self.allowed_contents}.")
+
+    def __str__(self):
+        return str(self.contents)
+
+    def __repr__(self):
+        return repr(self.contents)
+
+    def __add__(self, objects):
+        # todo: decision: return a list, or a new DataObjectList?
+        if isinstance(objects, ObjectList):
+            return self.contents + objects.contents
+        else:
+            return self.contents + objects
+
+    def __radd__(self, objects):
+        if isinstance(objects, ObjectList):
+            return objects.contents + self.contents
+        else:
+            return objects + self.contents
+
+    def __contains__(self, key):
+        return key in self.contents
+
+    def __iadd__(self, objects):
+        for obj in objects:
+            self._handle_append(obj)
+        self.contents.extend(objects)
+
+    def __iter__(self):
+        return iter(self.contents)
+
+    def __getitem__(self, i):
+        return self.contents[i]
+
+    def __len__(self):
+        return len(self.contents)
+
+    def __reversed__(self):
+        raise NotImplementedError
+
+    def __setitem__(self, i):
+        raise NotImplementedError
+
+    def append(self, obj):
+        self._handle_append(obj)
+        self.contents.append(obj)
+
+    def extend(self, objects):
+        for obj in objects:
+            self._handle_append(obj)
+        self.contents.extend(objects)
+
+    def clear(self):
+        raise NotImplementedError
+
+    def copy(self):
+         raise NotImplementedError
+
+    def count(self):
+        raise NotImplementedError
+
+    def index(self):
+        raise NotImplementedError
+
+    def insert(self):
+        raise NotImplementedError
+
+    def pop(self):
+        raise NotImplementedError
+
+    def remove(self):
+        raise NotImplementedError
+
+    def reverse(self):
+        raise NotImplementedError
+
+    def sort(self):
+        raise NotImplementedError

neo/core/regionofinterest.py

@@ -1,7 +1,9 @@
 from math import floor, ceil
 
+from neo.core.baseneo import BaseNeo
 
-class RegionOfInterest:
+
+class RegionOfInterest(BaseNeo):
     """Abstract base class"""
     pass
 

neo/core/segment.py

@@ -7,13 +7,20 @@
 '''
 
 from datetime import datetime
+from copy import deepcopy
 
 import numpy as np
 
-from copy import deepcopy
 
+from neo.core.analogsignal import AnalogSignal
 from neo.core.container import Container
+from neo.core.objectlist import ObjectList
+from neo.core.epoch import Epoch
+from neo.core.event import Event
+from neo.core.imagesequence import ImageSequence
+from neo.core.irregularlysampledsignal import IrregularlySampledSignal
 from neo.core.spiketrainlist import SpikeTrainList
+from neo.core.view import ChannelView
 
 
 class Segment(Container):
@@ -92,19 +99,55 @@ def __init__(self, name=None, description=None, file_origin=None,
         super().__init__(name=name, description=description,
                          file_origin=file_origin, **annotations)
 
-        self.analogsignals = []
-        self.irregularlysampledsignals = []
+        self._analogsignals = ObjectList(AnalogSignal)
+        self._irregularlysampledsignals = ObjectList(IrregularlySampledSignal)
         self.spiketrains = SpikeTrainList(segment=self)
-        self.events = []
-        self.epochs = []
-        self.channelviews = []
-        self.imagesequences = []
+        self._events = ObjectList(Event)
+        self._epochs = ObjectList(Epoch)
+        self._channelviews = ObjectList(ChannelView)
+        self._imagesequences = ObjectList(ImageSequence)
         self.block = None
 
         self.file_datetime = file_datetime
         self.rec_datetime = rec_datetime
         self.index = index
 
+    analogsignals = property(
+        fget=lambda self: self._get_object_list("_analogsignals"),
+        fset=lambda self, value: self._set_object_list("_analogsignals", value),
+        doc="todo"
+    )
+
+    irregularlysampledsignals = property(
+        fget=lambda self: self._get_object_list("_irregularlysampledsignals"),
+        fset=lambda self, value: self._set_object_list("_irregularlysampledsignals", value),
+        doc="todo"
+    )
+
+    events = property(
+        fget=lambda self: self._get_object_list("_events"),
+        fset=lambda self, value: self._set_object_list("_events", value),
+        doc="todo"
+    )
+
+    epochs = property(
+        fget=lambda self: self._get_object_list("_epochs"),
+        fset=lambda self, value: self._set_object_list("_epochs", value),
+        doc="todo"
+    )
+
+    channelviews = property(
+        fget=lambda self: self._get_object_list("_channelviews"),
+        fset=lambda self, value: self._set_object_list("_channelviews", value),
+        doc="todo"
+    )
+
+    imagesequences = property(
+        fget=lambda self: self._get_object_list("_imagesequences"),
+        fset=lambda self, value: self._set_object_list("_imagesequences", value),
+        doc="todo"
+    )
+
     # t_start attribute is handled as a property so type checking can be done
     @property
     def t_start(self):

neo/core/spiketrainlist.py

@@ -10,6 +10,7 @@
 import numpy as np
 import quantities as pq
 from .spiketrain import SpikeTrain, normalize_times_array
+from .objectlist import ObjectList
 
 
 def is_spiketrain_or_proxy(obj):
@@ -32,7 +33,7 @@ def unique(quantities):
 
 
 
-class SpikeTrainList(object):
+class SpikeTrainList(ObjectList):
     """
     This class contains multiple spike trains, and can represent them
     either as a list of SpikeTrain objects or as a pair of arrays