Fix bad validation check for postion in ElectrodeGroup.__init__ (#1770)

Co-authored-by: Cody Baker <[email protected]>
Co-authored-by: Steph Prince <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>

Author: 4 people

CHANGELOG.md

@@ -5,6 +5,9 @@
 ### Performance
 - Cache global type map to speed import 3X. @sneakers-the-rat [#1931](https://github.com/NeurodataWithoutBorders/pynwb/pull/1931)
 
+### Bug fixes
+- Fixed bug in how `ElectrodeGroup.__init__` validates its `position` argument. @oruebel [#1770](https://github.com/NeurodataWithoutBorders/pynwb/pull/1770)
+
 ## PyNWB 2.8.2 (September 9, 2024)
 
 ### Enhancements and minor changes

docs/source/conf.py

@@ -244,7 +244,6 @@ def __call__(self, filename):
 # html_theme = 'default'
 # html_theme = "sphinxdoc"
 html_theme = "sphinx_rtd_theme"
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -260,9 +259,6 @@ def __call__(self, filename):
     'css/custom.css',
 ]
 
-# Add any paths that contain custom themes here, relative to this directory.
-# html_theme_path = []
-
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
 # html_title = None

pyproject.toml

@@ -34,7 +34,7 @@ classifiers = [
 ]
 dependencies = [
     "h5py>=2.10",
-    "hdmf>=3.14.3",
+    "hdmf>=3.14.5",
     "numpy>=1.18",
     "pandas>=1.1.5",
     "python-dateutil>=2.7.3",

requirements-min.txt

@@ -1,6 +1,6 @@
 # minimum versions of package dependencies for installing PyNWB
 h5py==2.10  # support for selection of datasets with list of indices added in 2.10
-hdmf==3.14.3
+hdmf==3.14.5
 numpy==1.18
 pandas==1.1.5
 python-dateutil==2.7.3

requirements.txt

@@ -1,6 +1,6 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB
 h5py==3.11.0
-hdmf==3.14.3
+hdmf==3.14.5
 numpy==2.1.1; python_version > "3.9"  # numpy 2.1+ is not compatible with py3.9
 numpy==2.0.2; python_version == "3.9"
 pandas==2.2.2

src/pynwb/ecephys.py

@@ -1,4 +1,5 @@
 import warnings
+import numpy as np
 from collections.abc import Iterable
 
 from hdmf.common import DynamicTableRegion
@@ -26,13 +27,31 @@ class ElectrodeGroup(NWBContainer):
             {'name': 'location', 'type': str, 'doc': 'description of location of this electrode group'},
             {'name': 'device', 'type': Device, 'doc': 'the device that was used to record from this electrode group'},
             {'name': 'position', 'type': 'array_data',
-             'doc': 'stereotaxic position of this electrode group (x, y, z)', 'default': None})
+             'doc': 'Compound dataset with stereotaxic position of this electrode group (x, y, z). '
+                    'The data array must have three elements or the dtype of the '
+                    'array must be ``(float, float, float)``', 'default': None})
     def __init__(self, **kwargs):
         args_to_set = popargs_to_dict(('description', 'location', 'device', 'position'), kwargs)
         super().__init__(**kwargs)
-        if args_to_set['position'] and len(args_to_set['position']) != 3:
-            raise ValueError('ElectrodeGroup position argument must have three elements: x, y, z, but received: %s'
-                             % str(args_to_set['position']))
+
+        # position is a compound dataset, i.e., this must be a scalar with a
+        # compound data type of three floats or a list/tuple of three entries
+        position = args_to_set['position']
+        if position:
+            # check position argument is valid
+            position_dtype_invalid = (
+                (hasattr(position, 'dtype') and len(position.dtype) != 3) or
+                (not hasattr(position, 'dtype') and len(position) != 3) or
+                (len(np.shape(position)) > 1)
+            )
+            if position_dtype_invalid:
+                raise ValueError(f"ElectrodeGroup position argument must have three elements: x, y, z,"
+                                 f"but received: {position}")
+
+            # convert position to scalar with compound data type if needed
+            if not hasattr(position, 'dtype'):
+                args_to_set['position'] = np.array(tuple(position), dtype=[('x', float), ('y', float), ('z', float)])
+
         for key, val in args_to_set.items():
             setattr(self, key, val)
 

tests/integration/hdf5/test_ecephys.py

@@ -26,7 +26,8 @@ def setUpContainer(self):
         eg = ElectrodeGroup(name='elec1',
                             description='a test ElectrodeGroup',
                             location='a nonexistent place',
-                            device=self.dev1)
+                            device=self.dev1,
+                            position=(1., 2., 3.))
         return eg
 
     def addContainer(self, nwbfile):

tests/unit/test_ecephys.py

@@ -178,16 +178,34 @@ class ElectrodeGroupConstructor(TestCase):
 
     def test_init(self):
         dev1 = Device('dev1')
-        group = ElectrodeGroup('elec1', 'electrode description', 'electrode location', dev1, (1, 2, 3))
+        group = ElectrodeGroup(name='elec1',
+                               description='electrode description',
+                               location='electrode location',
+                               device=dev1,
+                               position=(1, 2, 3))
         self.assertEqual(group.name, 'elec1')
         self.assertEqual(group.description, 'electrode description')
         self.assertEqual(group.location, 'electrode location')
         self.assertEqual(group.device, dev1)
-        self.assertEqual(group.position, (1, 2, 3))
+        self.assertEqual(group.position.tolist(), (1, 2, 3))
+
+    def test_init_position_array(self):
+        position = np.array((1, 2, 3), dtype=np.dtype([('x', float), ('y', float), ('z', float)]))
+        dev1 = Device('dev1')
+        group = ElectrodeGroup('elec1', 'electrode description', 'electrode location', dev1,
+                               position)
+        self.assertEqual(group.name, 'elec1')
+        self.assertEqual(group.description, 'electrode description')
+        self.assertEqual(group.location, 'electrode location')
+        self.assertEqual(group.device, dev1)
+        self.assertEqual(group.position, position)
 
     def test_init_position_none(self):
         dev1 = Device('dev1')
-        group = ElectrodeGroup('elec1', 'electrode description', 'electrode location', dev1)
+        group = ElectrodeGroup(name='elec1',
+                               description='electrode description',
+                               location='electrode location',
+                               device=dev1)
         self.assertEqual(group.name, 'elec1')
         self.assertEqual(group.description, 'electrode description')
         self.assertEqual(group.location, 'electrode location')
@@ -197,7 +215,29 @@ def test_init_position_none(self):
     def test_init_position_bad(self):
         dev1 = Device('dev1')
         with self.assertRaises(ValueError):
-            ElectrodeGroup('elec1', 'electrode description', 'electrode location', dev1, (1, 2))
+            ElectrodeGroup(name='elec1',
+                           description='electrode description',
+                           location='electrode location',
+                           device=dev1,
+                           position=(1, 2))
+        with self.assertRaises(ValueError):
+            ElectrodeGroup(name='elec1',
+                           description='electrode description',
+                           location='electrode location',
+                           device=dev1,
+                           position=[(1, 2), ])
+        with self.assertRaises(ValueError):
+            ElectrodeGroup(name='elec1',
+                           description='electrode description',
+                           location='electrode location',
+                           device=dev1,
+                           position=np.array([(1., 2.)], dtype=np.dtype([('x', float), ('y', float)])))
+        with self.assertRaises(ValueError):
+            ElectrodeGroup(name='elec1',
+                           description='electrode description',
+                           location='electrode location',
+                           device=dev1,
+                           position=[(1, 2, 3), (4, 5, 6), (7, 8, 9)])
 
 
 class EventDetectionConstructor(TestCase):