Merge pull request #1313 from apdavison/fix-regionsofinterest

make the handling of RegionOfInterest subclasses consistent with ChannelView

neo/core/baseneo.py

@@ -154,7 +154,11 @@ def _container_name(class_name):
     referenced by `block.segments`. The attribute name `segments` is
     obtained by calling `_container_name_plural("Segment")`.
     """
-    return _reference_name(class_name) + 's'
+    if "RegionOfInterest" in class_name:
+        # this is a hack, pending a more principled way to handle this
+        return "regionsofinterest"
+    else:
+        return _reference_name(class_name) + 's'
 
 
 class BaseNeo:

neo/core/block.py

@@ -12,7 +12,6 @@
 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
 
 
@@ -91,7 +90,6 @@ def __init__(self, name=None, description=None, file_origin=None,
         self.index = index
         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"),
@@ -105,12 +103,6 @@ def __init__(self, name=None, description=None, file_origin=None,
         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):
         '''

neo/core/group.py

@@ -18,6 +18,7 @@
 from neo.core.segment import Segment
 from neo.core.spiketrainlist import SpikeTrainList
 from neo.core.view import ChannelView
+from neo.core.regionofinterest import RegionOfInterest
 
 
 class Group(Container):
@@ -49,7 +50,8 @@ class Group(Container):
     """
     _data_child_objects = (
         'AnalogSignal', 'IrregularlySampledSignal', 'SpikeTrain',
-        'Event', 'Epoch', 'ChannelView', 'ImageSequence'
+        'Event', 'Epoch', 'ChannelView', 'ImageSequence', 'CircularRegionOfInterest',
+        'RectangularRegionOfInterest', 'PolygonRegionOfInterest'
     )
     _container_child_objects = ('Group',)
     _parent_objects = ('Block',)
@@ -69,6 +71,7 @@ def __init__(self, objects=None, name=None, description=None, file_origin=None,
         self._epochs = ObjectList(Epoch)
         self._channelviews = ObjectList(ChannelView)
         self._imagesequences = ObjectList(ImageSequence)
+        self._regionsofinterest = ObjectList(RegionOfInterest)
         self._segments = ObjectList(Segment)  # to remove?
         self._groups = ObjectList(Group)
 
@@ -119,6 +122,12 @@ def __init__(self, objects=None, name=None, description=None, file_origin=None,
         doc="list of ImageSequences contained in this group"
     )
 
+    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 group"
+    )
+
     spiketrains = property(
         fget=lambda self: self._get_object_list("_spiketrains"),
         fset=lambda self, value: self._set_object_list("_spiketrains", value),

neo/core/imagesequence.py

@@ -97,7 +97,7 @@ class ImageSequence(BaseSignal):
     )
     _recommended_attrs = BaseNeo._recommended_attrs
 
-    def __new__(cls, image_data, units=None, dtype=None, copy=True, t_start=0 * pq.s,
+    def __new__(cls, image_data, units=pq.dimensionless, dtype=None, copy=True, t_start=0 * pq.s,
                 spatial_scale=None, frame_duration=None,
                 sampling_rate=None, name=None, description=None, file_origin=None,
                 **annotations):
@@ -127,7 +127,7 @@ def __new__(cls, image_data, units=None, dtype=None, copy=True, t_start=0 * pq.s
 
         return obj
 
-    def __init__(self, image_data, units=None, dtype=None, copy=True, t_start=0 * pq.s,
+    def __init__(self, image_data, units=pq.dimensionless, dtype=None, copy=True, t_start=0 * pq.s,
                  spatial_scale=None, frame_duration=None,
                  sampling_rate=None, name=None, description=None, file_origin=None,
                  **annotations):
@@ -142,7 +142,7 @@ def __array_finalize__spec(self, obj):
 
         self.sampling_rate = getattr(obj, "sampling_rate", None)
         self.spatial_scale = getattr(obj, "spatial_scale", None)
-        self.units = getattr(obj, "units", None)
+        self.units = getattr(obj, "units", pq.dimensionless)
         self._t_start = getattr(obj, "_t_start", 0 * pq.s)
 
         return obj

neo/core/regionofinterest.py

@@ -1,11 +1,32 @@
 from math import floor, ceil
 
 from neo.core.baseneo import BaseNeo
+from neo.core.imagesequence import ImageSequence
 
 
 class RegionOfInterest(BaseNeo):
     """Abstract base class"""
-    pass
+
+    _parent_objects = ('Group',)
+    _parent_attrs = ('group',)
+    _necessary_attrs = (
+        ('obj', ('ImageSequence', ), 1),
+    )
+
+    def __init__(self, image_sequence, name=None, description=None, file_origin=None, **annotations):
+        super().__init__(name=name, description=description,
+                        file_origin=file_origin, **annotations)
+
+        if not (isinstance(image_sequence, ImageSequence) or (
+                hasattr(image_sequence, "proxy_for") and issubclass(image_sequence.proxy_for, ImageSequence))):
+            raise ValueError("Can only take a RegionOfInterest of an ImageSequence")
+        self.image_sequence = image_sequence
+
+    def resolve(self):
+        """
+        Return a signal from within this region of the underlying ImageSequence.
+        """
+        return self.image_sequence.signal_from_region(self)
 
 
 class CircularRegionOfInterest(RegionOfInterest):
@@ -23,8 +44,9 @@ class CircularRegionOfInterest(RegionOfInterest):
             Radius of the ROI in pixels
     """
 
-    def __init__(self, x, y, radius):
-
+    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)
         self.y = y
         self.x = x
         self.radius = radius
@@ -72,7 +94,9 @@ class RectangularRegionOfInterest(RegionOfInterest):
             Height (y-direction) of the ROI in pixels
     """
 
-    def __init__(self, x, y, width, height):
+    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)
         self.x = x
         self.y = y
         self.width = width
@@ -115,7 +139,9 @@ class PolygonRegionOfInterest(RegionOfInterest):
             of the vertices of the polygon
     """
 
-    def __init__(self, *vertices):
+    def __init__(self, image_sequence, *vertices, name=None, description=None,
+                 file_origin=None, **annotations):
+        super().__init__(image_sequence, name, description, file_origin, **annotations)
         self.vertices = vertices
 
     def polygon_ray_casting(self, bounding_points, bounding_box_positions):

neo/test/coretest/test_group.py

@@ -16,13 +16,16 @@
 from neo.core.view import ChannelView
 from neo.core.group import Group
 from neo.core.block import Block
+from neo.core.imagesequence import ImageSequence
+from neo.core.regionofinterest import CircularRegionOfInterest
 
 
 class TestGroup(unittest.TestCase):
 
     def setUp(self):
         test_data = np.random.rand(100, 8) * pq.mV
         channel_names = np.array(["a", "b", "c", "d", "e", "f", "g", "h"])
+        test_image_data = np.random.rand(640).reshape(10, 8, 8)
         self.test_signal = AnalogSignal(test_data,
                                         sampling_period=0.1 * pq.ms,
                                         name="test signal",
@@ -34,21 +37,28 @@ def setUp(self):
                               description="this is a view of a test signal",
                               array_annotations={"something": np.array(["A", "B", "C", "D"])},
                               sLaTfat="fish")
+        self.test_image_seq = ImageSequence(test_image_data,
+                                            frame_duration=20 * pq.ms,
+                                            spatial_scale=1 * pq.um)
+        self.roi = CircularRegionOfInterest(self.test_image_seq, 0, 0, 3)
         self.test_spiketrains = [SpikeTrain(np.arange(100.0), units="ms", t_stop=200),
                                  SpikeTrain(np.arange(0.5, 100.5), units="ms", t_stop=200)]
         self.test_segment = Segment()
         self.test_segment.analogsignals.append(self.test_signal)
         self.test_segment.spiketrains.extend(self.test_spiketrains)
+        self.test_segment.imagesequences.append(self.test_image_seq)
 
     def test_create_group(self):
-        objects = [self.test_view, self.test_signal]
+        objects = [self.test_view, self.test_signal, self.test_image_seq, self.roi]
         objects.extend(self.test_spiketrains)
         group = Group(objects)
 
         assert group.analogsignals[0] is self.test_signal
         assert group.spiketrains[0] is self.test_spiketrains[0]
         assert group.spiketrains[1] is self.test_spiketrains[1]
         assert group.channelviews[0] is self.test_view
+        assert group.imagesequences[0] is self.test_image_seq
+        assert group.regionsofinterest[0] is self.roi
         assert len(group.irregularlysampledsignals) == 0
 
     def test_create_empty_group(self):

neo/test/coretest/test_imagesequence.py

@@ -39,7 +39,7 @@ def test_error_spatial_scale(self):
 
     def test_units(self):
         with self.assertRaises(TypeError):
-            ImageSequence(self.data, sampling_rate=500 * pq.Hz, spatial_scale=1 * pq.um)
+            ImageSequence(self.data, units=None, sampling_rate=500 * pq.Hz, spatial_scale=1 * pq.um)
 
     def test_wrong_dimensions(self):
         seq = ImageSequence(self.data, sampling_rate=500 * pq.Hz,
@@ -71,36 +71,37 @@ def test_t_start(self):
 
 
 class TestMethodImageSequence(unittest.TestCase):
-    def fake_region_of_interest(self):
-        self.rect_ROI = RectangularRegionOfInterest(2, 2, 2, 2)
+    def _create_test_objects(self):
         self.data = []
         for frame in range(25):
             self.data.append([])
             for y in range(5):
                 self.data[frame].append([])
                 for x in range(5):
                     self.data[frame][y].append(x)
-
-    def test_signal_from_region(self):
-        self.fake_region_of_interest()
-        seq = ImageSequence(
+        self.seq = ImageSequence(
             self.data,
             units="V",
             sampling_rate=500 * pq.Hz,
             t_start=250 * pq.ms,
             spatial_scale=1 * pq.um,
         )
-        signals = seq.signal_from_region(self.rect_ROI)
+        self.rect_ROI = RectangularRegionOfInterest(self.seq, 2, 2, 2, 2)
+
+    def test_signal_from_region(self):
+        self._create_test_objects()
+        signals = self.seq.signal_from_region(self.rect_ROI)
         self.assertIsInstance(signals, list)
         self.assertEqual(len(signals), 1)
         for signal in signals:
             self.assertIsInstance(signal, AnalogSignal)
-            self.assertEqual(signal.t_start, seq.t_start)
-            self.assertEqual(signal.sampling_period, seq.frame_duration)
+            self.assertEqual(signal.t_start, self.seq.t_start)
+            self.assertEqual(signal.sampling_period, self.seq.frame_duration)
         with self.assertRaises(ValueError):  # no pixels in region
+            zero_size_roi = RectangularRegionOfInterest(self.seq, 1, 1, 0, 0)
             ImageSequence(
                 self.data, units="V", sampling_rate=500 * pq.Hz, spatial_scale=1 * pq.um
-            ).signal_from_region(RectangularRegionOfInterest(1, 1, 0, 0))
+            ).signal_from_region(zero_size_roi)
         with self.assertRaises(ValueError):
             ImageSequence(
                 self.data, units="V", sampling_rate=500 * pq.Hz, spatial_scale=1 * pq.um

neo/test/coretest/test_regionofinterest.py

@@ -1,31 +1,37 @@
-from neo.core.regionofinterest import RectangularRegionOfInterest, \
-    CircularRegionOfInterest,\
+import quantities as pq
+from neo.core.regionofinterest import (
+    RectangularRegionOfInterest,
+    CircularRegionOfInterest,
     PolygonRegionOfInterest
+)
+from neo.core.imagesequence import ImageSequence
 import unittest
 
 
 class Test_CircularRegionOfInterest(unittest.TestCase):
 
     def test_result(self):
-
-        self.assertEqual((CircularRegionOfInterest(6, 6, 1).pixels_in_region()),
+        seq = ImageSequence([[[]]], spatial_scale=1, frame_duration=20 * pq.ms)
+        self.assertEqual((CircularRegionOfInterest(seq, 6, 6, 1).pixels_in_region()),
                          [[6, 5], [5, 6], [6, 6]])
-        self.assertEqual((CircularRegionOfInterest(6, 6, 1.01).pixels_in_region()),
+        self.assertEqual((CircularRegionOfInterest(seq, 6, 6, 1.01).pixels_in_region()),
                          [[6, 5], [5, 6], [6, 6], [7, 6], [6, 7]])
 
 
 class Test_RectangularRegionOfInterest(unittest.TestCase):
 
     def test_result(self):
-        self.assertEqual(RectangularRegionOfInterest(5, 5, 2, 2).pixels_in_region(),
+        seq = ImageSequence([[[]]], spatial_scale=1, frame_duration=20 * pq.ms)
+        self.assertEqual(RectangularRegionOfInterest(seq, 5, 5, 2, 2).pixels_in_region(),
                          [[4, 4], [5, 4], [4, 5], [5, 5]])
 
 
 class Test_PolygonRegionOfInterest(unittest.TestCase):
 
     def test_result(self):
+        seq = ImageSequence([[[]]], spatial_scale=1, frame_duration=20 * pq.ms)
         self.assertEqual(
-            PolygonRegionOfInterest((3, 3), (2, 5), (5, 5), (5, 1), (1, 1)).pixels_in_region(),
+            PolygonRegionOfInterest(seq, (3, 3), (2, 5), (5, 5), (5, 1), (1, 1)).pixels_in_region(),
             [(1, 1), (2, 1), (3, 1), (4, 1), (2, 2), (3, 2),
              (4, 2), (3, 3), (4, 3), (3, 4), (4, 4)]
         )