Merge branch 'dev' into nwb_schema_2.8.0

Author: rly

CHANGELOG.md

@@ -10,26 +10,23 @@
   - Deprecated `EventWaveform` neurodata type. @rly [#1940](https://github.com/NeurodataWithoutBorders/pynwb/pull/1940)
   - Deprecated `ImageMaskSeries` neurodata type. @rly [#1941](https://github.com/NeurodataWithoutBorders/pynwb/pull/1941)
 
-## PyNWB 2.8.3 (Upcoming)
+## PyNWB 2.8.3 (November 19, 2024)
 
 ### Enhancements and minor changes
-* Added `NWBHDF5IO.read_nwb` convenience method to simplify reading an NWB file. @h-mayorquin [#1979](https://github.com/NeurodataWithoutBorders/pynwb/pull/1979)
-* Removed unused references to region references and builders in preparation for changes in HDMF 4.0. @rly [#1991](https://github.com/NeurodataWithoutBorders/pynwb/pull/1991)
-
-### Documentation and tutorial enhancements
-- Added documentation example for `SpikeEventSeries`. @stephprince [#1983](https://github.com/NeurodataWithoutBorders/pynwb/pull/1983)
-- Added documentation example for `AnnotationSeries`. @stephprince [#1989](https://github.com/NeurodataWithoutBorders/pynwb/pull/1989)
-
-### Performance
+- Added `NWBHDF5IO.read_nwb` convenience method to simplify reading an NWB file. @h-mayorquin [#1979](https://github.com/NeurodataWithoutBorders/pynwb/pull/1979)
+- Removed unused references to region references and builders in preparation for changes in HDMF 4.0. @rly [#1991](https://github.com/NeurodataWithoutBorders/pynwb/pull/1991)
+- Made gain an optional argument for PatchClampSeries to match the schema. @stephprince [#1975](https://github.com/NeurodataWithoutBorders/pynwb/pull/1975)
+- Added warning when writing files with `NWBHDF5IO` without the `.nwb` extension. @stephprince [#1978](https://github.com/NeurodataWithoutBorders/pynwb/pull/1978)
 - 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)
 - Changed `SpatialSeries.reference_frame` from required to optional as specified in the schema. @rly [#1986](https://github.com/NeurodataWithoutBorders/pynwb/pull/1986)
 
-### Enhancements and minor changes
-- Made gain an optional argument for PatchClampSeries to match the schema. @stephprince [#1975](https://github.com/NeurodataWithoutBorders/pynwb/pull/1975)
-- Added warning when writing files with `NWBHDF5IO` without the `.nwb` extension. @stephprince [#1978](https://github.com/NeurodataWithoutBorders/pynwb/pull/1978)
+### Documentation and tutorial enhancements
+- Added documentation example for `SpikeEventSeries`. @stephprince [#1983](https://github.com/NeurodataWithoutBorders/pynwb/pull/1983)
+- Added documentation example for `AnnotationSeries`. @stephprince [#1989](https://github.com/NeurodataWithoutBorders/pynwb/pull/1989)
+- Added documentation example for `DecompositionSeries`. @stephprince [#1981](https://github.com/NeurodataWithoutBorders/pynwb/pull/1981)
 
 ## PyNWB 2.8.2 (September 9, 2024)
 

docs/gallery/domain/ecephys.py

@@ -31,7 +31,9 @@
 from dateutil.tz import tzlocal
 
 from pynwb import NWBHDF5IO, NWBFile
+
 from pynwb.ecephys import LFP, ElectricalSeries, SpikeEventSeries
+from pynwb.misc import DecompositionSeries
 
 #######################
 # Creating and Writing NWB files
@@ -247,6 +249,41 @@
 )
 ecephys_module.add(lfp)
 
+####################
+# In some cases, you may want to further process the LFP data and decompose the signal into different frequency bands 
+# to use for other downstream analyses. You can store the processed data from these spectral analyses using a
+# :py:class:`~pynwb.misc.DecompositionSeries` object. This object allows you to include metadata about the frequency
+# bands and metric used (e.g., power, phase, amplitude), as well as link the decomposed data to the original 
+# :py:class:`~pynwb.base.TimeSeries` signal the data was derived from.
+
+#######################
+# .. note:: When adding data to :py:class:`~pynwb.misc.DecompositionSeries`, the ``data`` argument is assumed to be 
+#           3D where the first dimension is time, the second dimension is channels, and the third dimension is bands.
+
+
+bands = dict(theta=(4.0, 12.0), 
+             beta=(12.0, 30.0), 
+             gamma=(30.0, 80.0))  # in Hz
+phase_data = np.random.randn(50, 12, len(bands))  # 50 samples, 12 channels, 3 frequency bands  
+
+decomp_series = DecompositionSeries(name="theta",
+                                    description="phase of bandpass filtered LFP data",
+                                    data=phase_data,
+                                    metric='phase',
+                                    rate=200.0,
+                                    source_channels=all_table_region,
+                                    source_timeseries=lfp_electrical_series)
+
+for band_name, band_limits in bands.items():
+    decomp_series.add_band(band_name=band_name, band_limits=band_limits, band_mean=np.nan, band_stdev=np.nan)
+
+ecephys_module.add(decomp_series)
+
+#######################
+# The frequency band information can also be viewed as a pandas DataFrame.
+
+decomp_series.bands.to_dataframe()
+
 ####################
 # .. _units_electrode:
 #

docs/source/conf.py

@@ -168,6 +168,10 @@ def __call__(self, filename):
 nitpick_ignore = [('py:class', 'Intracomm'),
                   ('py:class', 'BaseStorageSpec')]
 
+linkcheck_ignore = [
+    r'https://training.incf.org/*'  # temporary ignore until SSL certificate issue is resolved
+]
+
 suppress_warnings = ["config.cache"]
 
 # Add any paths that contain templates here, relative to this directory.