Merge branch 'dev' into conda-release-docs-improvements

Author: bendichter

docs/gallery/domain/ecephys.py

@@ -45,7 +45,7 @@
 device = nwbfile.create_device(name='trodes_rig123', source="a source")
 
 #######################
-# Once you have created the :py:class:`~pynwb.ecephys.Device`, you can create an
+# Once you have created the :py:class:`~pynwb.device.Device`, you can create an
 # :py:class:`~pynwb.ecephys.ElectrodeGroup`.
 
 electrode_name = 'tetrode1'

docs/gallery/domain/icephys.py

@@ -31,8 +31,8 @@
 # Device metadata
 # ^^^^^^^^^^^^^^^
 #
-# Device metadata is represented by :py:class:`~pynwb.ecephys.Device` objects.
-# To create a device, you can use the :py:class:`~pynwb.ecephys.Device` instance method
+# Device metadata is represented by :py:class:`~pynwb.device.Device` objects.
+# To create a device, you can use the :py:class:`~pynwb.device.Device` instance method
 # :py:meth:`~pynwb.file.NWBFile.create_device`.
 
 device = nwbfile.create_device(name='Heka ITC-1600', source='a source')
@@ -74,6 +74,7 @@
 
 nwbfile.add_stimulus(ccss)
 
+#######################
 # Here, we will use :py:class:`~pynwb.icephys.VoltageClampSeries` to store voltage clamp
 # data and then add it to our NWBFile as acquired data using the :py:class:`~pynwb.file.NWBFile` method
 # :py:meth:`~pynwb.file.NWBFile.add_acquisition`.
@@ -124,6 +125,7 @@
 
 ccss = nwbfile.get_stimulus('ccss')
 
+####################
 # Grabbing acquisition data an be done via :py:meth:`~pynwb.file.NWBFile.get_acquisition`
 
 vcs = nwbfile.get_acquisition('vcs')

src/pynwb/__init__.py

@@ -232,6 +232,7 @@ def __init__(self, **kwargs):
 from .file import NWBFile  # noqa: E402, F401
 
 from . import behavior  # noqa: F401,E402
+from . import device  # noqa: F401,E402
 from . import ecephys  # noqa: F401,E402
 from . import epoch  # noqa: F401,E402
 from . import icephys  # noqa: F401,E402

src/pynwb/device.py

@@ -0,0 +1,18 @@
+from .form.utils import docval, call_docval_func
+from . import register_class, CORE_NAMESPACE
+from .core import NWBContainer
+
+
+@register_class('Device', CORE_NAMESPACE)
+class Device(NWBContainer):
+    """
+    """
+
+    __nwbfields__ = ('name',)
+
+    @docval({'name': 'name', 'type': str, 'doc': 'the name of this device'},
+            {'name': 'source', 'type': str, 'doc': 'the source of the data'},
+            {'name': 'parent', 'type': 'NWBContainer',
+             'doc': 'The parent NWBContainer for this NWBContainer', 'default': None})
+    def __init__(self, **kwargs):
+        call_docval_func(super(Device, self).__init__, kwargs)

src/pynwb/ecephys.py

@@ -8,21 +8,7 @@
 from . import register_class, CORE_NAMESPACE
 from .base import TimeSeries, _default_resolution, _default_conversion
 from .core import NWBContainer, NWBTable, NWBTableRegion, NWBDataInterface, MultiContainerInterface
-
-
-@register_class('Device', CORE_NAMESPACE)
-class Device(NWBContainer):
-    """
-    """
-
-    __nwbfields__ = ('name',)
-
-    @docval({'name': 'name', 'type': str, 'doc': 'the name of this device'},
-            {'name': 'source', 'type': str, 'doc': 'the source of the data'},
-            {'name': 'parent', 'type': 'NWBContainer',
-             'doc': 'The parent NWBContainer for this NWBContainer', 'default': None})
-    def __init__(self, **kwargs):
-        call_docval_func(super(Device, self).__init__, kwargs)
+from .device import Device
 
 
 @register_class('ElectrodeGroup', CORE_NAMESPACE)

src/pynwb/file.py

@@ -341,6 +341,11 @@ def create_electrode_table_region(self, **kwargs):
             msg = "no electrodes available. add electrodes before creating a region"
             raise RuntimeError(msg)
         region = getargs('region', kwargs)
+        for idx in region:
+            if idx < 0 or idx >= len(self.ec_electrodes):
+                raise IndexError('The index ' + str(idx) +
+                                 ' is out of range for the ElectrodeTable of length '
+                                 + str(len(self.ec_electrodes)))
         desc = getargs('description', kwargs)
         name = getargs('name', kwargs)
         return ElectrodeTableRegion(self.ec_electrodes, region, desc, name)

tests/unit/pynwb_tests/test_file.py

@@ -60,6 +60,21 @@ def test_create_electrode_group(self):
         self.assertEqual(elecgrp.location, loc)
         self.assertIs(elecgrp.device, d)
 
+    def test_create_electrode_group_invalid_index(self):
+        """
+        Test the case where the user creates an electrode table region with
+        indexes that are out of range of the amount of electrodes added.
+        """
+        nwbfile = NWBFile('a', 'b', 'c', datetime.now())
+        device = nwbfile.create_device('a', 'b')
+        elecgrp = nwbfile.create_electrode_group('a', 'b', 'c', device=device, location='a')
+        for i in range(4):
+            nwbfile.add_electrode(i, np.nan, np.nan, np.nan, np.nan, group=elecgrp,
+                                  location='a', filtering='a', description='a')
+        with self.assertRaises(IndexError) as err:
+            nwbfile.create_electrode_table_region(list(range(6)), 'test')
+        self.assertTrue('out of range' in str(err.exception))
+
     def test_epoch_tags(self):
         tags1 = ['t1', 't2']
         tags2 = ['t3', 't4']