Merge pull request #1266 from apdavison/autorel3

Automatic handling of relationships between objects

Author: JuliaSprenger

doc/old_stuffs/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/old_stuffs/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_many_to_one_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/images/generate_diagram.py

@@ -28,7 +28,6 @@ def get_rect_height(name, obj):
     nlines = 1.5
     nlines += len(getattr(obj, '_all_attrs', []))
     nlines += len(getattr(obj, '_single_child_objects', []))
-    nlines += len(getattr(obj, '_multi_child_objects', []))
     return nlines * line_heigth
 
 
@@ -74,9 +73,7 @@ def generate_diagram(rect_pos, rect_width, figsize):
     alpha = [1., 1., 0.3]
     for name, pos in rect_pos.items():
         obj = objs[name]
-        relationships = [getattr(obj, '_single_child_objects', []),
-                         getattr(obj, '_multi_child_objects', []),
-                         getattr(obj, '_child_properties', [])]
+        relationships = [getattr(obj, '_single_child_objects', [])]
 
         for r in range(3):
             for ch_name in relationships[r]:
@@ -122,16 +119,6 @@ def generate_diagram(rect_pos, rect_width, figsize):
                          facecolor='c', edgecolor='k', alpha=.5)
         ax.add_patch(rect)
 
-        # multi relationship
-        relationship = list(getattr(obj, '_multi_child_objects', []))
-        pos2 = (pos[1] + htotal - line_heigth * (1.5 + len(relationship))
-                - rect_height)
-        rect_height = len(relationship) * line_heigth
-
-        rect = Rectangle((pos[0], pos2), rect_width, rect_height,
-                         facecolor='m', edgecolor='k', alpha=.5)
-        ax.add_patch(rect)
-
         # necessary attr
         pos2 = (pos[1] + htotal
                 - line_heigth * (1.5 + len(allrelationship) + len(obj._necessary_attrs)))

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

@@ -58,7 +58,6 @@ def generate_block(n_segments=3, n_channels=4, n_units=3,
                 seg.spiketrains.append(train)
                 u.spiketrains.append(train)
 
-    block.create_many_to_one_relationship()
     return block
 
 

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):
@@ -64,7 +68,6 @@ class Block(Container):
     '''
 
     _container_child_objects = ('Segment', 'Group')
-    _child_properties = ()
     _recommended_attrs = ((('file_datetime', datetime),
                            ('rec_datetime', datetime),
                            ('index', int)) +
@@ -86,9 +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.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, parent=self)
+        self._groups = ObjectList(Group, parent=self)
+        self._regionsofinterest = ObjectList(RegionOfInterest, parent=self)
+
+    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 block"
+    )
+
+    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 block"
+    )
+
+    regionsofinterest = property(
+        fget=lambda self: self._get_object_list("_regionsofinterest"),
+        fset=lambda self, value: self._set_object_list("_regionsofinterest", value),
+        doc="list of RegionOfInterest objects contained in this block"
+    )
 
     @property
     def data_children_recur(self):