Merge branch 'master' into black-formatting-action

.github/workflows/publish-to-pypi-test.yml

@@ -20,14 +20,19 @@ jobs:
         python -m pip install --upgrade pip
         pip install setuptools wheel twine build
         pip install .
+    - name: Get the tag version
+      id: get-version
+      run: |
+        echo ${GITHUB_REF#refs/tags/}
+        echo "TAG::${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
     - name: Test version/tag correspondence
       id: version-check
       run: |
         neo_version=$(python -c "import neo; print(neo.__version__)")
+        tag_version=${{ steps.get-version.outputs.TAG }}
         echo $neo_version
-        TAG=${{ github.event.release.tag_name }}
-        echo $TAG
-        if [[ $TAG == $neo_version ]]; then
+        echo $tag_version
+        if [[ $tag_version == $neo_version ]]; then
             echo "VERSION_TAG_MATCH=true" >> $GITHUB_OUTPUT
             echo "Version matches tag, proceeding with release to Test PyPI"
         else

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/io/baseio.py

@@ -10,6 +10,8 @@
 
 If you want a model for developing a new IO start from exampleIO.
 """
+from __future__ import annotations
+from pathlib import Path
 
 try:
     from collections.abc import Sequence
@@ -96,7 +98,7 @@ class BaseIO:
 
     mode = 'file'  # or 'fake' or 'dir' or 'database'
 
-    def __init__(self, filename=None, **kargs):
+    def __init__(self, filename: str | Path = None, **kargs):
         self.filename = str(filename)
         # create a logger for the IO class
         fullname = self.__class__.__module__ + '.' + self.__class__.__name__
@@ -111,7 +113,7 @@ def __init__(self, filename=None, **kargs):
             corelogger.addHandler(logging_handler)
 
     ######## General read/write methods #######################
-    def read(self, lazy=False, **kargs):
+    def read(self, lazy: bool = False, **kargs):
         """
         Return all data from the file as a list of Blocks
         """