Deprecate ImageMaskSeries

NeurodataWithoutBorders · Jul 23, 2024 · f0b3f08 · f0b3f08
1 parent fcd7008
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Showing 4 changed files with 11 additions and 14 deletions.
diff --git a/docs/gallery/general/plot_file.py b/docs/gallery/general/plot_file.py
@@ -55,7 +55,6 @@
 
     * **Optical physiology and imaging:** :py:class:`~pynwb.image.ImageSeries` is the base type
       for image recordings and is further refined by the
-      :py:class:`~pynwb.image.ImageMaskSeries`,
       :py:class:`~pynwb.image.OpticalSeries`,
       :py:class:`~pynwb.ophys.OnePhotonSeries`, and
       :py:class:`~pynwb.ophys.TwoPhotonSeries` types.

diff --git a/src/pynwb/image.py b/src/pynwb/image.py
@@ -280,7 +280,7 @@ def __init__(self, **kwargs):
 @register_class('ImageMaskSeries', CORE_NAMESPACE)
 class ImageMaskSeries(ImageSeries):
     '''
-    An alpha mask that is applied to a presented visual stimulus. The data[] array contains an array
+    DEPRECATED. An alpha mask that is applied to a presented visual stimulus. The data[] array contains an array
     of mask values that are applied to the displayed image. Mask values are stored as RGBA. Mask
     can vary with time. The timestamps array indicates the starting time of a mask, and that mask
     pattern continues until it's explicitly changed.
@@ -299,9 +299,13 @@ class ImageMaskSeries(ImageSeries):
                      'The device used to capture the masked ImageSeries data should be stored in the ImageSeries.'),
              'default': None},)
     def __init__(self, **kwargs):
-        masked_imageseries = popargs('masked_imageseries', kwargs)
-        super().__init__(**kwargs)
-        self.masked_imageseries = masked_imageseries
+        raise ValueError(
+            "This neurodata type is deprecated. If you are interested in using it, "
+            "please create an issue on https://github.com/NeurodataWithoutBorders/nwb-schema/issues."
+        )
+        # masked_imageseries = popargs('masked_imageseries', kwargs)
+        # super().__init__(**kwargs)
+        # self.masked_imageseries = masked_imageseries
 
 
 @register_class('OpticalSeries', CORE_NAMESPACE)

diff --git a/src/pynwb/nwb-schema b/src/pynwb/nwb-schema
diff --git a/tests/unit/test_image.py b/tests/unit/test_image.py
@@ -375,16 +375,10 @@ def test_init(self):
                          external_file=['external_file'], starting_frame=[0], format='external',
                          timestamps=[1., .2])
 
-        ims = ImageMaskSeries(name='test_ims', unit='unit',
+        with self.assertRaises(ValueError):
+            ImageMaskSeries(name='test_ims', unit='unit',
                               masked_imageseries=iS, external_file=['external_file'], starting_frame=[0],
                               format='external', timestamps=[1., 2.])
-        self.assertEqual(ims.name, 'test_ims')
-        self.assertEqual(ims.unit, 'unit')
-        self.assertIs(ims.masked_imageseries, iS)
-        self.assertEqual(ims.external_file, ['external_file'])
-        self.assertEqual(ims.starting_frame, [0])
-        self.assertEqual(ims.format, 'external')
-
 
 class OpticalSeriesConstructor(TestCase):
+2 −0		.github/PULL_REQUEST_TEMPLATE.md
+18 −0		core/nwb.behavior.yaml
+1 −1		core/nwb.file.yaml
+1 −1		core/nwb.image.yaml
+27 −5		core/nwb.misc.yaml
+1 −1		core/nwb.namespace.yaml
+2 −2		docs/format/source/conf.py
+12 −0		docs/format/source/format_release_notes.rst