Update tables to ElectrodesTable/FrequencyBandsTable earlier

CHANGELOG.md

@@ -1,11 +1,12 @@
 # PyNWB Changelog
 
-## PyNWB 3.1.1 (July 14, 2025)
+## PyNWB 3.1.1 (July 16, 2025)
 
 ### Bug fixes
-
+- Fixed reading and exporting of files written with NWB Schema < 2.9.0 that contained a reference to the electrodes table. @rly [#2112](https://github.com/NeurodataWithoutBorders/pynwb/pull/2112)
 - Skip streaming tests gracefully if offline. @rly [#2113](https://github.com/NeurodataWithoutBorders/pynwb/pull/2113)
 
+
 ## PyNWB 3.1.0 (July 8, 2025)
 
 ### Breaking changes
@@ -41,7 +42,7 @@
 - Fixed caching of the type map when using HDMF 4.1.0. @rly [#2087](https://github.com/NeurodataWithoutBorders/pynwb/pull/2087)
 - Removed use of complex numbers in scratch tutorial because of incompatibilities with HDMF 4.1.0. @stephprince [#2090](https://github.com/NeurodataWithoutBorders/pynwb/pull/2090/)
 - Made `ImagingPlane.description` optional to conform with the NWB Schema. @rly [#2051](https://github.com/NeurodataWithoutBorders/pynwb/pull/2051)
-  
+
 ### Documentation and tutorial enhancements
 - Added NWB AI assistant to the home page of the documentation. @magland [#2076](https://github.com/NeurodataWithoutBorders/pynwb/pull/2076)
 

src/pynwb/io/epoch.py

@@ -14,6 +14,9 @@ class TimeIntervalsMap(DynamicTableMap):
     def columns_carg(self, builder, manager):
         # handle the case when a TimeIntervals is read with a non-TimeSeriesReferenceVectorData "timeseries" column
         # this is the case for NWB schema v2.4 and earlier, where the timeseries column was a regular VectorData.
+        # NOTE: the below machinery might be movable into the NWBFileMap.construct override which might better
+        # handle the rare edge case where the "timeseries" column is referenced in another field elsewhere in the file.
+
         timeseries_builder = builder.get('timeseries')
 
         # handle the case when the TimeIntervals has a "timeseries" column that is a link (e.g., it exists in

src/pynwb/io/file.py

@@ -1,6 +1,8 @@
 from dateutil.parser import parse as dateutil_parse
+import typing
 
-from hdmf.build import ObjectMapper
+from hdmf.build import ObjectMapper, Builder, GroupBuilder
+from hdmf.utils import docval, get_docval
 
 from .. import register_map
 from ..file import NWBFile, Subject
@@ -130,6 +132,34 @@ def __init__(self, spec):
         self.map_spec('scratch_containers', scratch_spec.get_neurodata_type('NWBContainer'))
         self.map_spec('scratch_containers', scratch_spec.get_neurodata_type('DynamicTable'))
 
+    @docval(*get_docval(ObjectMapper.construct))
+    def construct(self, **kwargs):
+        nwbfile_builder = kwargs["builder"]
+        electrodes_builder = nwbfile_builder.get("general", dict()).get("extracellular_ephys", dict()).get("electrodes")
+        if (electrodes_builder is not None and electrodes_builder.attributes['neurodata_type'] != 'ElectrodesTable'):
+            electrodes_builder.attributes['neurodata_type'] = 'ElectrodesTable'
+            electrodes_builder.attributes['namespace'] = 'core'
+
+        def apply_to_child_builders(builder: Builder, funcs: list[typing.Callable]):
+            # iterate recursively through each builder (which is just a dict of dicts) and make migration changes
+            for bchild_value in builder.values():
+                if isinstance(bchild_value, Builder):
+                    for func in funcs:
+                        func(bchild_value)
+                    apply_to_child_builders(bchild_value, funcs)
+
+        def update_builder_frequency_bands_table(builder: Builder):
+            if (isinstance(builder, GroupBuilder) and
+                builder.attributes.get('namespace') == 'core' and
+                builder.attributes.get('neurodata_type') == 'DecompositionSeries' and
+                builder.groups['bands'].attributes['neurodata_type'] == 'DynamicTable'):
+                builder.groups['bands'].attributes['neurodata_type'] = 'FrequencyBandsTable'
+                builder.groups['bands'].attributes['namespace'] = 'core'
+
+        apply_to_child_builders(nwbfile_builder, [update_builder_frequency_bands_table])
+
+        return super().construct(**kwargs)
+
     @ObjectMapper.object_attr('scratch_datas')
     def scratch_datas(self, container, manager):
         """Set the value for the 'scratch_datas' spec on NWBFile to a list of ScratchData objects.
@@ -185,24 +215,6 @@ def scratch(self, builder, manager):
                 ret.append(manager.construct(d))
         return tuple(ret) if len(ret) > 0 else None
 
-    @ObjectMapper.constructor_arg('electrodes')
-    def electrodes(self, builder, manager):
-        try:
-            electrodes_builder = builder['general']['extracellular_ephys']['electrodes']
-        except KeyError:
-            # Note: This is here because the ObjectMapper pulls argname from docval and checks to see
-            # if there is an override even if the file doesn't have what is looking for. In this case,
-            # electrodes for NWBFile.
-            electrodes_builder = None
-        if (electrodes_builder is not None and electrodes_builder.attributes['neurodata_type'] != 'ElectrodesTable'):
-            electrodes_builder.attributes['neurodata_type'] = 'ElectrodesTable'
-            electrodes_builder.attributes['namespace'] = 'core'
-            manager.clear_cache()
-            new_container =  manager.construct(electrodes_builder)
-            return new_container
-        else:
-            return None
-
     @ObjectMapper.constructor_arg('session_start_time')
     def dateconversion(self, builder, manager):
         """Set the constructor arg for 'session_start_time' to a datetime object.

src/pynwb/io/misc.py

@@ -1,21 +1,7 @@
 from hdmf.common.io.table import DynamicTableMap
-from .base import TimeSeriesMap
 
 from .. import register_map
-from pynwb.misc import Units, DecompositionSeries
-
-
-@register_map(DecompositionSeries)
-class DecompositionSeriesMap(TimeSeriesMap):
-
-    @TimeSeriesMap.constructor_arg('bands')
-    def bands(self, builder, manager):
-        if builder.groups['bands'].attributes['neurodata_type'] != 'FrequencyBandsTable':
-            builder.groups['bands'].attributes['neurodata_type'] = 'FrequencyBandsTable'
-            builder.groups['bands'].attributes['namespace'] = 'core'
-        manager.clear_cache()
-        new_container =  manager.construct(builder.groups['bands'])
-        return new_container
+from pynwb.misc import Units
 
 
 @register_map(Units)

src/pynwb/testing/make_test_files.py

@@ -2,6 +2,7 @@
 import numpy as np
 from pathlib import Path
 from pynwb import NWBFile, NWBHDF5IO, __version__, TimeSeries, get_class, load_namespaces
+from pynwb.ecephys import ElectricalSeries
 from pynwb.file import Subject
 from pynwb.image import ImageSeries
 from pynwb.misc import DecompositionSeries
@@ -237,6 +238,20 @@ def _make_electrodes_dynamic_table():
                 label=f"shank{i}electrode{j}",
             )
 
+    nwbfile.add_unit(
+        spike_times=[0.1, 0.2, 0.3],
+        electrodes=[0, 1],
+    )
+
+    eseries = ElectricalSeries(
+        name="ElectricalSeries",
+        description="Test electrodes reference",
+        data=[[0.1, 0.2], [0.3, 0.4], [0.5, 0.6]],
+        timestamps=[0.1, 0.2, 0.3],
+        electrodes=nwbfile.create_electrode_table_region(region=[2, 3], description="electrodes table indices 2 and 3"),
+    )
+    nwbfile.add_acquisition(eseries)
+
     test_name = 'electrodes_dynamic_table'
     _write(test_name, nwbfile)
 

tests/back_compat/test_read.py

@@ -1,5 +1,6 @@
 import numpy as np
 from pathlib import Path
+import tempfile
 import warnings
 
 from pynwb import NWBHDF5IO, validate, TimeSeries
@@ -140,6 +141,26 @@ def test_read_electrodes_table_as_neurodata_type(self):
             read_nwbfile = io.read()
             assert isinstance(read_nwbfile.electrodes, ElectrodesTable)
 
+            # test that references to the electrodes table are also ElectrodesTable
+            assert read_nwbfile.units.electrodes.table is read_nwbfile.electrodes
+            assert read_nwbfile.acquisition["ElectricalSeries"].electrodes.table is read_nwbfile.electrodes
+
+            # test that export writes the correct builders
+            temp_dir = tempfile.TemporaryDirectory()
+            export_file = Path(temp_dir.name) / "3.0.0_electrodes_dynamic_table_export.nwb"
+            with NWBHDF5IO(export_file, 'w') as export_io:
+                export_io.export(io)
+
+            with self.get_io(export_file) as read_export_io:
+                read_export_nwbfile = read_export_io.read()
+                assert isinstance(read_export_nwbfile.electrodes, ElectrodesTable)
+
+                # test that references to the electrodes table are also ElectrodesTable
+                units_table_ref = read_export_nwbfile.units.electrodes.table
+                assert units_table_ref is read_export_nwbfile.electrodes
+                eseries_table_ref = read_export_nwbfile.acquisition["ElectricalSeries"].electrodes.table
+                assert eseries_table_ref is read_export_nwbfile.electrodes
+
     def test_read_bands_table_as_neurodata_type(self):
         """Test that a "bands" table written as a DynamicTable is read as an FrequencyBandsTable"""
         f = Path(__file__).parent / '3.0.0_decompositionseries_bands_dynamic_table.nwb'