checkpoint

src/pynwb/__init__.py

@@ -3,7 +3,7 @@
 '''
 import os.path
 from pathlib import Path
-from copy import deepcopy
+from copy import deepcopy, copy
 import h5py
 
 from hdmf.spec import NamespaceCatalog
@@ -46,11 +46,34 @@ def _get_resources():
 
 __NS_CATALOG = NamespaceCatalog(NWBGroupSpec, NWBDatasetSpec, NWBNamespace)
 
+class NWBTypeMap(TypeMap):
+    def __init__(self, **kwargs):
+        super().__init__(**kwargs)
+
+    def __copy__(self):
+        ret = NWBTypeMap(namespaces=copy(self._TypeMap__ns_catalog),
+                         mapper_cls=self._TypeMap__default_mapper_cls,
+                         type_config=self.type_config)
+        ret.merge(self)
+        return ret
+
+    def modify_builder(self, builder):
+        try:
+            ndtype = builder['neurodata_type']
+        except KeyError:
+            ndtype = 'Not Group'
+        # remap ElectrodesTable from a DynamicTable named electrodes
+        if ndtype == 'DynamicTable' and builder.name == 'electrodes':
+            builder.set_attribute(name='namespace', value='core')
+            builder.set_attribute(name='neurodata_type', value='ElectrodesTable')
+            return builder
+        else:
+            return None
+
 hdmf_typemap = hdmf.common.get_type_map()
-__TYPE_MAP = TypeMap(__NS_CATALOG)
+__TYPE_MAP = NWBTypeMap(namespaces=__NS_CATALOG)
 __TYPE_MAP.merge(hdmf_typemap, ns_catalog=True)
 
-
 @docval({'name': 'extensions', 'type': (str, TypeMap, list),
          'doc': 'a path to a namespace, a TypeMap, or a list consisting of paths to namespaces and TypeMaps',
          'default': None},

src/pynwb/file.py

@@ -820,7 +820,7 @@ def add_invalid_time_interval(self, **kwargs):
         self.__check_invalid_times()
         self.invalid_times.add_interval(**kwargs)
 
-    @docval({'name': 'electrode_table', 'type': DynamicTable, 'doc': 'the ElectrodesTable for this file'})
+    @docval({'name': 'electrode_table', 'type': ElectrodesTable, 'doc': 'the ElectrodesTable for this file'})
     def set_electrode_table(self, **kwargs):
         """
         Set the electrode table of this NWBFile to an existing ElectrodesTable

src/pynwb/testing/mock/ecephys.py

@@ -5,8 +5,8 @@
 from hdmf.common.table import DynamicTableRegion, DynamicTable
 
 from ...device import Device
-from ...file import ElectrodeTable, NWBFile
-from ...ecephys import ElectricalSeries, ElectrodeGroup, SpikeEventSeries
+from ...file import NWBFile
+from ...ecephys import ElectricalSeries, ElectrodeGroup, SpikeEventSeries, ElectrodesTable
 from .device import mock_Device
 from .utils import name_generator
 from ...misc import Units

tests/integration/hdf5/test_ecephys.py

@@ -14,7 +14,7 @@
     FeatureExtraction,
 )
 from pynwb.device import Device
-from pynwb.file import ElectrodeTable as get_electrode_table
+from pynwb.ecephys import ElectrodesTable as get_electrode_table
 from pynwb.testing import NWBH5IOMixin, AcquisitionH5IOMixin, NWBH5IOFlexMixin, TestCase
 
 

tests/integration/hdf5/test_misc.py

@@ -6,7 +6,7 @@
 from pynwb.testing import NWBH5IOMixin, AcquisitionH5IOMixin, TestCase
 from pynwb.ecephys import ElectrodeGroup
 from pynwb.device import Device
-from pynwb.file import ElectrodeTable as get_electrode_table
+from pynwb.ecephys import ElectrodesTable as get_electrode_table
 
 
 class TestUnitsIO(AcquisitionH5IOMixin, TestCase):

tests/unit/foo.py

@@ -62,6 +62,9 @@
 # breakpoint()
 # with NWBHDF5IO("ecephys_tutorial.nwb", "w") as io:
 #     io.write(nwbfile)
+# new='/Users/mavaylon/Research/NWB/pynwb/ecephys_tutorial.nwb'
 io= NWBHDF5IO("/Users/mavaylon/Research/NWB/pynwb/tests/back_compat/2.6.0_DynamicTableElectrodes.nwb", "r")
+# io= NWBHDF5IO(new, 'r')
 read_nwbfile = io.read()
+
 breakpoint()

tests/unit/test_ecephys.py

@@ -14,9 +14,9 @@
     FilteredEphys,
     FeatureExtraction,
     ElectrodeGroup,
+    ElectrodesTable
 )
 from pynwb.device import Device
-from pynwb.file import ElectrodeTable
 from pynwb.testing import TestCase
 from pynwb.testing.mock.ecephys import mock_ElectricalSeries
 

tests/unit/test_file.py

@@ -9,9 +9,9 @@
 from hdmf.utils import docval, get_docval, popargs
 from pynwb import NWBFile, TimeSeries, NWBHDF5IO
 from pynwb.base import Image, Images
-from pynwb.file import Subject, ElectrodeTable, _add_missing_timezone
+from pynwb.file import Subject, _add_missing_timezone
 from pynwb.epoch import TimeIntervals
-from pynwb.ecephys import ElectricalSeries
+from pynwb.ecephys import ElectricalSeries, ElectrodesTable
 from pynwb.testing import TestCase, remove_test_file
 
 

tests/unit/test_misc.py

@@ -3,9 +3,9 @@
 from hdmf.common import DynamicTable, VectorData, DynamicTableRegion
 
 from pynwb.misc import AnnotationSeries, AbstractFeatureSeries, IntervalSeries, Units, DecompositionSeries
-from pynwb.file import TimeSeries, ElectrodeTable as get_electrode_table
+from pynwb.file import TimeSeries
 from pynwb.device import Device
-from pynwb.ecephys import ElectrodeGroup
+from pynwb.ecephys import ElectrodeGroup, ElectrodesTable as get_electrode_table
 from pynwb.testing import TestCase