Merge pull request #1386 from apdavison/matlabio

Improved support for saving/loading Groups in NeoMatlabIO

Author: alejoe91

neo/core/baseneo.py

@@ -180,7 +180,7 @@ class BaseNeo:
                            class must have. The tuple can have 2-4 elements.
                            The first element is the attribute name.
                            The second element is the attribute type.
-                           The third element is the number of  dimensions
+                           The third element is the number of dimensions
                            (only for numpy arrays and quantities).
                            The fourth element is the dtype of array
                            (only for numpy arrays and quantities).
@@ -253,6 +253,8 @@ class attributes. :_recommended_attrs: should append
     # Attributes that are used for pretty-printing
     _repr_pretty_attrs_keys_ = ("name", "description", "annotations")
 
+    is_view = False
+
     def __init__(self, name=None, description=None, file_origin=None,
                  **annotations):
         """

neo/core/container.py

@@ -251,16 +251,19 @@ def _data_child_containers(self):
         """
         Containers for child objects that have data and have a single parent.
         """
-        return tuple([_container_name(child) for child in
-                      self._data_child_objects])
+        # the following construction removes the duplicate 'regionsofinterest'
+        # while preserving the child order (which `set()` would not do)
+        # I don't know if preserving the order is important, but I'm playing it safe
+        return tuple({_container_name(child): None for child in
+                      self._data_child_objects}.keys())
 
     @property
     def _child_containers(self):
         """
         Containers for child objects with a single parent.
         """
-        return tuple([_container_name(child) for child in
-                      self._child_objects])
+        return tuple({_container_name(child): None for child in
+                      self._child_objects}.keys())
 
     @property
     def _single_children(self):

neo/core/regionofinterest.py

@@ -10,8 +10,9 @@ class RegionOfInterest(BaseNeo):
     _parent_objects = ('Group',)
     _parent_attrs = ('group',)
     _necessary_attrs = (
-        ('obj', ('ImageSequence', ), 1),
+        ('image_sequence', ('ImageSequence', ), 1),
     )
+    is_view = True
 
     def __init__(self, image_sequence, name=None, description=None, file_origin=None, **annotations):
         super().__init__(name=name, description=description,
@@ -22,6 +23,17 @@ def __init__(self, image_sequence, name=None, description=None, file_origin=None
             raise ValueError("Can only take a RegionOfInterest of an ImageSequence")
         self.image_sequence = image_sequence
 
+    def _get_obj(self):
+        # for consistency with ChannelView
+        return self.image_sequence
+
+    def _set_obj(self, value):
+        if not isinstance(value, ImageSequence):
+            raise TypeError(f"Value must be ImageSequence, not of type: {type(value)}")
+        self.image_sequence = value
+
+    obj = property(fget=_get_obj, fset=_set_obj)
+
     def resolve(self):
         """
         Return a signal from within this region of the underlying ImageSequence.
@@ -44,6 +56,13 @@ class CircularRegionOfInterest(RegionOfInterest):
             Radius of the ROI in pixels
     """
 
+    _necessary_attrs = (
+        ('image_sequence', ('ImageSequence', ), 1),
+        ('x', int),
+        ('y', int),
+        ('radius', int)
+    )
+
     def __init__(self, image_sequence, x, y, radius, name=None, description=None,
                  file_origin=None, **annotations):
         super().__init__(image_sequence, name, description, file_origin, **annotations)
@@ -94,6 +113,14 @@ class RectangularRegionOfInterest(RegionOfInterest):
             Height (y-direction) of the ROI in pixels
     """
 
+    _necessary_attrs = (
+        ('image_sequence', ('ImageSequence', ), 1),
+        ('x', int),
+        ('y', int),
+        ('width', int),
+        ('height', int)
+    )
+
     def __init__(self, image_sequence, x, y, width, height, name=None, description=None,
                  file_origin=None, **annotations):
         super().__init__(image_sequence, name, description, file_origin, **annotations)
@@ -139,6 +166,11 @@ class PolygonRegionOfInterest(RegionOfInterest):
             of the vertices of the polygon
     """
 
+    _necessary_attrs = (
+        ('image_sequence', ('ImageSequence', ), 1),
+        ('vertices', list),
+    )
+
     def __init__(self, image_sequence, *vertices, name=None, description=None,
                  file_origin=None, **annotations):
         super().__init__(image_sequence, name, description, file_origin, **annotations)

neo/core/spiketrainlist.py

@@ -115,6 +115,11 @@ def __getitem__(self, i):
         else:
             return SpikeTrainList(items=items)
 
+    def __setitem__(self, i, value):
+        if self._items is None:
+            self._spiketrains_from_array()
+        self._items[i] = value
+
     def __str__(self):
         """Return str(self)"""
         if self._items is None:

neo/core/view.py

@@ -30,12 +30,14 @@ class ChannelView(BaseNeo):
     Note: Any other additional arguments are assumed to be user-specific
             metadata and stored in :attr:`annotations`.
     """
-    _parent_objects = ('Segment',)
-    _parent_attrs = ('segment',)
+    _parent_objects = ('Group',)
+    _parent_attrs = ('group',)
     _necessary_attrs = (
+        ('obj', ('AnalogSignal', 'IrregularlySampledSignal'), 1),
         ('index', np.ndarray, 1, np.dtype('i')),
-        ('obj', ('AnalogSignal', 'IrregularlySampledSignal'), 1)
     )
+    is_view = True
+
     # "mask" would be an alternative name, proposing "index" for
     # backwards-compatibility with ChannelIndex
 
@@ -73,7 +75,7 @@ def shape(self):
         return (self.obj.shape[0], self.index.size)
 
     def _get_arr_ann_length(self):
-        return self.shape[-1]
+        return self.index.size
 
     def array_annotate(self, **array_annotations):
         self.array_annotations.update(array_annotations)