Add support for NWB schema 2.7.0

CHANGELOG.md

@@ -3,6 +3,11 @@
 ## PyNWB 2.7.0 (Upcoming)
 
 ### Enhancements and minor changes
+- Added support for NWB schema 2.7.0. See [2.7.0 release notes](https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html) for details
+  - Deprecated `ImagingRetinotopy` neurodata type. @rly [#1813](https://github.com/NeurodataWithoutBorders/pynwb/pull/1813)
+  - Modified `OptogeneticSeries` to allow 2D data, primarily in extensions of `OptogeneticSeries`. @rly [#1812](https://github.com/NeurodataWithoutBorders/pynwb/pull/1812)
+  - Support `stimulus_template` as optional predefined column in `IntracellularStimuliTable`. @stephprince [#1815](https://github.com/NeurodataWithoutBorders/pynwb/pull/1815)
+  - Support `NWBDataInterface` and `DynamicTable` in `NWBFile.stimulus`. @rly [#1842](https://github.com/NeurodataWithoutBorders/pynwb/pull/1842)
 - Added support for python 3.12 and upgraded dependency versions. This also includes infrastructure updates for developers. @mavaylon1 [#1853](https://github.com/NeurodataWithoutBorders/pynwb/pull/1853)
 
 ### Bug fixes

docs/gallery/domain/images.py

@@ -106,7 +106,7 @@
     description="The images presented to the subject as stimuli",
 )
 
-nwbfile.add_stimulus(timeseries=optical_series)
+nwbfile.add_stimulus(stimulus=optical_series)
 
 ####################
 # ImageSeries: Storing series of images as acquisition

docs/gallery/domain/plot_icephys.py

@@ -97,6 +97,7 @@
 
 # Import additional core datatypes used in the example
 from pynwb.core import DynamicTable, VectorData
+from pynwb.base import TimeSeriesReference, TimeSeriesReferenceVectorData
 
 # Import icephys TimeSeries types used
 from pynwb.icephys import VoltageClampSeries, VoltageClampStimulusSeries
@@ -457,6 +458,59 @@
     category="electrodes",
 )
 
+#####################################################################
+# Adding stimulus templates
+# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+# One predefined subcategory column is the ``stimulus_template`` column in the stimuli table. This column is
+# used to store template waveforms of stimuli in addition to the actual recorded stimulus that is stored in the
+# ``stimulus`` column. The ``stimulus_template`` column contains an idealized version of the template waveform used as
+# the stimulus. This can be useful as a noiseless version of the stimulus for data analysis or to validate that the
+# recorded stimulus matches the expected waveform of the template. Similar to the ``stimulus`` and ``response``
+# columns, we can specify a relevant time range.
+
+stimulus_template = VoltageClampStimulusSeries(
+    name="ccst",
+    data=[0, 1, 2, 3, 4],
+    starting_time=0.0,
+    rate=10e3,
+    electrode=electrode,
+    gain=0.02,
+)
+nwbfile.add_stimulus_template(stimulus_template)
+
+nwbfile.intracellular_recordings.add_column(
+    name="stimulus_template",
+    data=[TimeSeriesReference(0, 5, stimulus_template),  # (start_index, index_count, stimulus_template)
+          TimeSeriesReference(1, 3, stimulus_template),
+          TimeSeriesReference.empty(stimulus_template)],  # if there was no data for that recording, use empty reference
+    description="Column storing the reference to the stimulus template for the recording (rows).",
+    category="stimuli",
+    col_cls=TimeSeriesReferenceVectorData
+)
+
+# we can also add stimulus template data as follows
+rowindex = nwbfile.add_intracellular_recording(
+    electrode=electrode,
+    stimulus=stimulus,
+    stimulus_template=stimulus_template,  # the full time range of the stimulus template will be used unless specified
+    recording_tag='A4',
+    recording_lab_data={'location': 'Isengard'},
+    electrode_metadata={'voltage_threshold': 0.14},
+    id=13,
+)
+
+#####################################################################
+# .. note:: If a stimulus template column exists but there is no stimulus template data for that recording, then
+#           :py:meth:`~pynwb.file.NWBFile.add_intracellular_recording` will internally set the stimulus template to the
+#           provided stimulus or response TimeSeries and the start_index and index_count for the missing parameter are
+#           set to -1. The missing values will be represented via masked numpy arrays.
+
+#####################################################################
+# .. note:: Since stimulus templates are often reused across many recordings, the timestamps in the templates are not
+#           usually aligned with the recording nor with the reference time of the file. The timestamps often start
+#           at 0 and are relative to the time of the application of the stimulus.
+
 #####################################################################
 # Add a simultaneous recording
 # ---------------------------------

docs/gallery/general/plot_file.py

@@ -108,8 +108,7 @@
       :py:class:`~pynwb.ophys.ImageSegmentation`,
       :py:class:`~pynwb.ophys.MotionCorrection`.
 
-    * **Others:** :py:class:`~pynwb.retinotopy.ImagingRetinotopy`,
-      :py:class:`~pynwb.base.Images`.
+    * **Others:** :py:class:`~pynwb.base.Images`.
 
     * **TimeSeries:** Any :ref:`timeseries_overview` is also a subclass of :py:class:`~pynwb.core.NWBDataInterface`
       and can be used anywhere :py:class:`~pynwb.core.NWBDataInterface` is allowed.
@@ -372,7 +371,7 @@
 # Processing modules can be thought of as folders within the file for storing the related processed data.
 #
 # .. tip:: Use the NWB schema module names as processing module names where appropriate.
-#    These are: ``"behavior"``, ``"ecephys"``, ``"icephys"``, ``"ophys"``, ``"ogen"``, ``"retinotopy"``, and ``"misc"``.
+#    These are: ``"behavior"``, ``"ecephys"``, ``"icephys"``, ``"ophys"``, ``"ogen"``, and ``"misc"``.
 #
 # Let's assume that the subject's position was computed from a video tracking algorithm,
 # so it would be classified as processed data.

docs/gallery/general/plot_read_basics.py

@@ -283,3 +283,10 @@
 # object and accessing its attributes, but it may be useful to explore the data in a
 # more interactive, visual way. See :ref:`analysistools-explore` for an updated list of programs for
 # exploring NWB files.
+
+####################
+# Close the open NWB file
+# -----------------------
+# It is good practice, especially on Windows, to close any files that you have opened.
+
+io.close()

docs/source/api_docs.rst

@@ -13,7 +13,6 @@ API Documentation
    Intracellular Electrophysiology <pynwb.icephys>
    Optophysiology <pynwb.ophys>
    Optogenetics <pynwb.ogen>
-   Retinotopy <pynwb.retinotopy>
    General Imaging <pynwb.image>
    Behavior <pynwb.behavior>
    NWB Base Classes <pynwb.base>

docs/source/conf.py

@@ -208,6 +208,12 @@ def __call__(self, filename):
 # directories to ignore when looking for source files.
 exclude_patterns = ['_build', 'test.py']
 
+# List of patterns, relative to source directory, of modules to be
+# excluded by apidoc when generating rst files.
+apidoc_exclude = [
+    "../../src/pynwb/retinotopy.py",
+]
+
 # The reST default role (used for this markup: `text`) to use for all documents.
 # default_role = None
 
@@ -410,7 +416,8 @@ def run_apidoc(_):
     out_dir = os.path.dirname(__file__)
     src_dir = os.path.join(out_dir, '../../src')
     sys.path.append(src_dir)
-    apidoc_main(['-f', '-e', '--no-toc', '-o', out_dir, src_dir])
+    apidoc_exclude_abs = [os.path.join(out_dir, f) for f in apidoc_exclude]
+    apidoc_main(['-f', '-e', '--no-toc', '-o', out_dir, src_dir, *apidoc_exclude_abs])
 
 
 from abc import abstractproperty

src/pynwb/__init__.py

@@ -386,7 +386,6 @@ def export(self, **kwargs):
 from . import misc  # noqa: F401,E402
 from . import ogen  # noqa: F401,E402
 from . import ophys  # noqa: F401,E402
-from . import retinotopy  # noqa: F401,E402
 from . import legacy  # noqa: F401,E402
 from hdmf.data_utils import DataChunkIterator  # noqa: F401,E402
 from hdmf.backends.hdf5 import H5DataIO  # noqa: F401,E402

src/pynwb/base.py

@@ -533,6 +533,26 @@ def data(self):
         # load the data from the timeseries
         return self.timeseries.data[self.idx_start: (self.idx_start + self.count)]
 
+    @classmethod
+    @docval({'name': 'timeseries', 'type': TimeSeries, 'doc': 'the timeseries object to reference.'})
+    def empty(cls, timeseries):
+        """
+        Creates an empty TimeSeriesReference object to represent missing data.
+
+        When missing data needs to be represented, NWB defines ``None`` for the complex data type ``(idx_start,
+        count, TimeSeries)`` as (-1, -1, TimeSeries) for storage. The exact timeseries object will technically not
+        matter since the empty reference is a way of indicating a NaN value in a
+        :py:class:`~pynwb.base.TimeSeriesReferenceVectorData` column.
+
+        An example where this functionality is used is :py:class:`~pynwb.icephys.IntracellularRecordingsTable`
+        where only one of stimulus or response data was recorded. In such cases, the timeseries object for the
+        empty stimulus :py:class:`~pynwb.base.TimeSeriesReference` could be set to the response series, or vice versa.
+
+        :returns: Returns :py:class:`~pynwb.base.TimeSeriesReference`
+        """
+
+        return cls(-1, -1, timeseries)
+
 
 @register_class('TimeSeriesReferenceVectorData', CORE_NAMESPACE)
 class TimeSeriesReferenceVectorData(VectorData):

src/pynwb/file.py

@@ -177,7 +177,7 @@ class NWBFile(MultiContainerInterface, HERDManager):
         {
             'attr': 'stimulus',
             'add': '_add_stimulus_internal',
-            'type': TimeSeries,
+            'type': (NWBDataInterface, DynamicTable),
             'get': 'get_stimulus'
         },
         {
@@ -356,7 +356,8 @@ class NWBFile(MultiContainerInterface, HERDManager):
             {'name': 'analysis', 'type': (list, tuple),
              'doc': 'result of analysis', 'default': None},
             {'name': 'stimulus', 'type': (list, tuple),
-             'doc': 'Stimulus TimeSeries objects belonging to this NWBFile', 'default': None},
+             'doc': 'Stimulus TimeSeries, DynamicTable, or NWBDataInterface objects belonging to this NWBFile',
+             'default': None},
             {'name': 'stimulus_template', 'type': (list, tuple),
              'doc': 'Stimulus template TimeSeries objects belonging to this NWBFile', 'default': None},
             {'name': 'epochs', 'type': TimeIntervals,
@@ -856,14 +857,29 @@ def add_acquisition(self, **kwargs):
         if use_sweep_table:
             self._update_sweep_table(nwbdata)
 
-    @docval({'name': 'timeseries', 'type': TimeSeries},
-            {'name': 'use_sweep_table', 'type': bool, 'default': False, 'doc': 'Use the deprecated SweepTable'})
+    @docval({'name': 'stimulus', 'type': (TimeSeries, DynamicTable, NWBDataInterface), 'default': None,
+             'doc': 'The stimulus presentation data to add to this NWBFile.'},
+            {'name': 'use_sweep_table', 'type': bool, 'default': False, 'doc': 'Use the deprecated SweepTable'},
+            {'name': 'timeseries', 'type': TimeSeries, 'default': None,
+             'doc': 'The "timeseries" keyword argument is deprecated. Use the "nwbdata" argument instead.'},)
     def add_stimulus(self, **kwargs):
-        timeseries = popargs('timeseries', kwargs)
-        self._add_stimulus_internal(timeseries)
+        stimulus, timeseries = popargs('stimulus', 'timeseries', kwargs)
+        if stimulus is None and timeseries is None:
+            raise ValueError(
+                "The 'stimulus' keyword argument is required. The 'timeseries' keyword argument can be "
+                "provided for backwards compatibility but is deprecated in favor of 'stimulus' and will be "
+                "removed in PyNWB 3.0."
+            )
+        # TODO remove this support in PyNWB 3.0
+        if timeseries is not None:
+            warn("The 'timeseries' keyword argument is deprecated and will be removed in PyNWB 3.0. "
+                 "Use the 'stimulus' argument instead.", DeprecationWarning)
+            if stimulus is None:
+                stimulus = timeseries
+        self._add_stimulus_internal(stimulus)
         use_sweep_table = popargs('use_sweep_table', kwargs)
         if use_sweep_table:
-            self._update_sweep_table(timeseries)
+            self._update_sweep_table(stimulus)
 
     @docval({'name': 'timeseries', 'type': (TimeSeries, Images)},
             {'name': 'use_sweep_table', 'type': bool, 'default': False, 'doc': 'Use the deprecated SweepTable'})

src/pynwb/icephys.py

@@ -415,6 +415,12 @@ class IntracellularStimuliTable(DynamicTable):
          'index': False,
          'table': False,
          'class': TimeSeriesReferenceVectorData},
+        {'name': 'stimulus_template',
+         'description': 'Column storing the reference to the stimulus template for the recording (rows)',
+         'required': False,
+         'index': False,
+         'table': False,
+         'class': TimeSeriesReferenceVectorData},
     )
 
     @docval(*get_docval(DynamicTable.__init__, 'id', 'columns', 'colnames'))
@@ -518,6 +524,13 @@ def __init__(self, **kwargs):
         {'name': 'stimulus', 'type': TimeSeries,
          'doc': 'The TimeSeries (usually a PatchClampSeries) with the stimulus',
          'default': None},
+        {'name': 'stimulus_template_start_index', 'type': int, 'doc': 'Start index of the stimulus template',
+         'default': None},
+        {'name': 'stimulus_template_index_count', 'type': int, 'doc': 'Stop index of the stimulus template',
+         'default': None},
+        {'name': 'stimulus_template', 'type': TimeSeries,
+         'doc': 'The TimeSeries (usually a PatchClampSeries) with the stimulus template waveforms',
+         'default': None},
         {'name': 'response_start_index', 'type': int, 'doc': 'Start index of the response', 'default': None},
         {'name': 'response_index_count', 'type': int, 'doc': 'Stop index of the response', 'default': None},
         {'name': 'response', 'type': TimeSeries,
@@ -553,6 +566,11 @@ def add_recording(self, **kwargs):
                                                                        'response',
                                                                        kwargs)
         electrode = popargs('electrode', kwargs)
+        stimulus_template_start_index, stimulus_template_index_count, stimulus_template = popargs(
+            'stimulus_template_start_index',
+            'stimulus_template_index_count',
+            'stimulus_template',
+            kwargs)
 
         # if electrode is not provided, take from stimulus or response object
         if electrode is None:
@@ -572,6 +590,15 @@ def add_recording(self, **kwargs):
         response_start_index, response_index_count = self.__compute_index(response_start_index,
                                                                           response_index_count,
                                                                           response, 'response')
+        stimulus_template_start_index, stimulus_template_index_count = self.__compute_index(
+            stimulus_template_start_index,
+            stimulus_template_index_count,
+            stimulus_template, 'stimulus_template')
+
+        # if stimulus template is already a column in the stimuli table, but stimulus_template was None
+        if 'stimulus_template' in self.category_tables['stimuli'].colnames and stimulus_template is None:
+            stimulus_template = stimulus if stimulus is not None else response  # set to stimulus if it was provided
+
         # If either stimulus or response are None, then set them to the same TimeSeries to keep the I/O happy
         response = response if response is not None else stimulus
         stimulus_provided_is_not_none = stimulus is not None  # Store if stimulus is None for error checks later
@@ -612,6 +639,9 @@ def add_recording(self, **kwargs):
             stimuli = {}
         stimuli['stimulus'] = TimeSeriesReferenceVectorData.TIME_SERIES_REFERENCE_TUPLE(
             stimulus_start_index, stimulus_index_count, stimulus)
+        if stimulus_template is not None:
+            stimuli['stimulus_template'] = TimeSeriesReferenceVectorData.TIME_SERIES_REFERENCE_TUPLE(
+                stimulus_template_start_index, stimulus_template_index_count, stimulus_template)
 
         # Compile the responses table data
         responses = copy(popargs('response_metadata', kwargs))

src/pynwb/io/__init__.py

@@ -9,4 +9,3 @@
 from . import misc as __misc
 from . import ogen as __ogen
 from . import ophys as __ophys
-from . import retinotopy as __retinotopy

src/pynwb/io/file.py

@@ -31,7 +31,11 @@ def __init__(self, spec):
         self.unmap(stimulus_spec)
         self.unmap(stimulus_spec.get_group('presentation'))
         self.unmap(stimulus_spec.get_group('templates'))
-        self.map_spec('stimulus', stimulus_spec.get_group('presentation').get_neurodata_type('TimeSeries'))
+        # map "stimulus" to NWBDataInterface and DynamicTable and unmap the spec for TimeSeries because it is
+        # included in the mapping to NWBDataInterface
+        self.unmap(stimulus_spec.get_group('presentation').get_neurodata_type('TimeSeries'))
+        self.map_spec('stimulus', stimulus_spec.get_group('presentation').get_neurodata_type('NWBDataInterface'))
+        self.map_spec('stimulus', stimulus_spec.get_group('presentation').get_neurodata_type('DynamicTable'))
         self.map_spec('stimulus_template', stimulus_spec.get_group('templates').get_neurodata_type('TimeSeries'))
         self.map_spec('stimulus_template', stimulus_spec.get_group('templates').get_neurodata_type('Images'))
 

src/pynwb/legacy/io/__init__.py

@@ -8,4 +8,3 @@
 from . import misc as __misc
 from . import ogen as __ogen
 from . import ophys as __ophys
-from . import retinotopy as __retinotopy

src/pynwb/ogen.py

@@ -37,8 +37,9 @@ class OptogeneticSeries(TimeSeries):
     __nwbfields__ = ('site',)
 
     @docval(*get_docval(TimeSeries.__init__, 'name'),  # required
-            {'name': 'data', 'type': ('array_data', 'data', TimeSeries), 'shape': (None, ),  # required
-             'doc': 'The data values over time. Must be 1D.'},
+            {'name': 'data', 'type': ('array_data', 'data', TimeSeries),  # required
+             'shape': [(None, ), (None, None)],
+             'doc': 'The data values over time.'},
             {'name': 'site', 'type': OptogeneticStimulusSite,  # required
              'doc': 'The site to which this stimulus was applied.'},
             *get_docval(TimeSeries.__init__, 'resolution', 'conversion', 'timestamps', 'starting_time', 'rate',