Merge branch '0.6.0dev' into 0.6.0

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ### Features
 * Added a seed to dummy generators [#361](https://github.com/catalystneuro/roiextractors/pull/361)
+* Added depth_slice for VolumetricImagingExtractors [PR #363](https://github.com/catalystneuro/roiextractors/pull/363)
 
 ### Fixes
 * Added specific error message for single-frame scanimage data [PR #360](https://github.com/catalystneuro/roiextractors/pull/360)

old_tests/test_volumetricimagingextractor.py

@@ -119,3 +119,47 @@ def test_get_dtype(dtype):
     imaging_extractors = [generate_dummy_imaging_extractor(dtype=dtype)]
     volumetric_imaging_extractor = VolumetricImagingExtractor(imaging_extractors=imaging_extractors)
     assert volumetric_imaging_extractor.get_dtype() == dtype
+
+
+@pytest.mark.parametrize("start_plane, end_plane", [(None, None), (0, 1), (1, 2)])
+def test_depth_slice(volumetric_imaging_extractor, start_plane, end_plane):
+    start_plane = start_plane or 0
+    end_plane = end_plane or volumetric_imaging_extractor.get_num_planes()
+    sliced_extractor = volumetric_imaging_extractor.depth_slice(start_plane=start_plane, end_plane=end_plane)
+
+    assert sliced_extractor.get_num_planes() == end_plane - start_plane
+    assert sliced_extractor.get_image_size() == (
+        *volumetric_imaging_extractor.get_image_size()[:2],
+        end_plane - start_plane,
+    )
+    video = volumetric_imaging_extractor.get_video()
+    sliced_video = sliced_extractor.get_video()
+    assert np.all(video[..., start_plane:end_plane] == sliced_video)
+    frames = volumetric_imaging_extractor.get_frames(frame_idxs=[0, 1, 2])
+    sliced_frames = sliced_extractor.get_frames(frame_idxs=[0, 1, 2])
+    assert np.all(frames[..., start_plane:end_plane] == sliced_frames)
+
+
+@pytest.mark.parametrize("start_plane, end_plane", [(0, -1), (1, 0), (0, 4)])
+def test_depth_slice_invalid(volumetric_imaging_extractor, start_plane, end_plane):
+    with pytest.raises(AssertionError):
+        volumetric_imaging_extractor.depth_slice(start_plane=start_plane, end_plane=end_plane)
+
+
+def test_depth_slice_twice(volumetric_imaging_extractor):
+    sliced_extractor = volumetric_imaging_extractor.depth_slice(start_plane=0, end_plane=2)
+    twice_sliced_extractor = sliced_extractor.depth_slice(start_plane=0, end_plane=1)
+
+    assert twice_sliced_extractor.get_num_planes() == 1
+    assert twice_sliced_extractor.get_image_size() == (*volumetric_imaging_extractor.get_image_size()[:2], 1)
+    video = volumetric_imaging_extractor.get_video()
+    sliced_video = twice_sliced_extractor.get_video()
+    assert np.all(video[..., :1] == sliced_video)
+    frames = volumetric_imaging_extractor.get_frames(frame_idxs=[0, 1, 2])
+    sliced_frames = twice_sliced_extractor.get_frames(frame_idxs=[0, 1, 2])
+    assert np.all(frames[..., :1] == sliced_frames)
+
+
+def test_frame_slice(volumetric_imaging_extractor):
+    with pytest.raises(NotImplementedError):
+        volumetric_imaging_extractor.frame_slice(start_frame=0, end_frame=1)

src/roiextractors/volumetricimagingextractor.py

@@ -168,3 +168,59 @@ def get_num_channels(self) -> int:
 
     def get_dtype(self) -> DtypeType:
         return self._imaging_extractors[0].get_dtype()
+
+    def depth_slice(self, start_plane: Optional[int] = None, end_plane: Optional[int] = None):
+        """Return a new VolumetricImagingExtractor ranging from the start_plane to the end_plane."""
+        start_plane = start_plane if start_plane is not None else 0
+        end_plane = end_plane if end_plane is not None else self._num_planes
+        assert (
+            0 <= start_plane < self._num_planes
+        ), f"'start_plane' ({start_plane}) must be greater than 0 and smaller than the number of planes ({self._num_planes})."
+        assert (
+            start_plane < end_plane <= self._num_planes
+        ), f"'end_plane' ({end_plane}) must be greater than 'start_plane' ({start_plane}) and smaller than or equal to the number of planes ({self._num_planes})."
+
+        return DepthSliceVolumetricImagingExtractor(parent_extractor=self, start_plane=start_plane, end_plane=end_plane)
+
+    def frame_slice(self, start_frame: Optional[int] = None, end_frame: Optional[int] = None):
+        """Return a new VolumetricImagingExtractor with a subset of frames."""
+        raise NotImplementedError(
+            "frame_slice is not implemented for VolumetricImagingExtractor due to conflicts with get_video()."
+        )
+
+
+class DepthSliceVolumetricImagingExtractor(VolumetricImagingExtractor):
+    """Class to get a lazy depth slice.
+
+    This class can only be used for volumetric imaging data.
+    Do not use this class directly but use `.depth_slice(...)` on a VolumetricImagingExtractor object.
+    """
+
+    extractor_name = "DepthSliceVolumetricImagingExtractor"
+    installed = True
+    is_writable = True
+    installation_mesg = ""
+
+    def __init__(
+        self,
+        parent_extractor: VolumetricImagingExtractor,
+        start_plane: Optional[int] = None,
+        end_plane: Optional[int] = None,
+    ):
+        """Initialize a VolumetricImagingExtractor whose plane(s) subset the parent.
+
+        Subset is exclusive on the right bound, that is, the plane indices of this VolumetricImagingExtractor range over
+        [0, ..., end_plane-start_plane-1].
+
+        Parameters
+        ----------
+        parent_extractor : VolumetricImagingExtractor
+            The VolumetricImagingExtractor object to subset the planes of.
+        start_plane : int, optional
+            The left bound of the depth to subset.
+            The default is the first plane of the parent.
+        end_plane : int, optional
+            The right bound of the depth, exclusively, to subset.
+            The default is the last plane of the parent.
+        """
+        super().__init__(imaging_extractors=parent_extractor._imaging_extractors[start_plane:end_plane])