add mock neurodata objects

CHANGELOG.md

@@ -34,6 +34,8 @@
   [#1550](https://github.com/NeurodataWithoutBorders/pynwb/pull/1550)
 - Enhanced docs for ``LabMetaData`` to clarify its usage. @oruebel 
   [#1546](https://github.com/NeurodataWithoutBorders/pynwb/pull/1546)
+- Add testing/mock, which provides mock neurodata objects for testing. @bendichter
+  [#1454](https://github.com/NeurodataWithoutBorders/pynwb/pull/1454)
 
 ## PyNWB 2.1.0 (July 6, 2022)
 

src/pynwb/testing/mock/__init__.py

@@ -0,0 +1,9 @@
+"""
+The mock module provides mock instances of common neurodata types which can be used to write
+tests for downstream libraries. For instance, to write an RoiResponseSeries, you need a
+PlaneSegmentation, which requires an ImagingPlane, which in turn requires an
+OpticalChannel and a Device, all of which need to be populated with reasonable mock
+data. This library streamlines the process of creating mock objects by generating the
+required prerequisites for this object on-the-fly and automatically using reasonable
+defaults. Any of these default objects and parameters can be overridden.
+"""

src/pynwb/testing/mock/base.py

@@ -0,0 +1,36 @@
+import numpy as np
+
+from ...base import TimeSeries
+from .utils import name_generator
+
+
+def mock_TimeSeries(
+    name=None,
+    data=None,
+    unit="volts",
+    resolution=-1.0,
+    conversion=1.0,
+    timestamps=None,
+    starting_time=None,
+    rate=10.0,
+    comments="no comments",
+    description="no description",
+    control=None,
+    control_description=None,
+    continuity=None,
+):
+    return TimeSeries(
+        name=name or name_generator("TimeSeries"),
+        data=data if data is not None else np.array([1, 2, 3, 4]),
+        unit=unit,
+        resolution=resolution,
+        conversion=conversion,
+        timestamps=timestamps,
+        starting_time=starting_time,
+        rate=rate,
+        comments=comments,
+        description=description,
+        control=control,
+        control_description=control_description,
+        continuity=continuity,
+    )

src/pynwb/testing/mock/behavior.py

@@ -0,0 +1,61 @@
+import numpy as np
+
+from ...behavior import (
+    PupilTracking,
+    Position,
+    SpatialSeries,
+    CompassDirection,
+)
+from .utils import name_generator
+from .base import mock_TimeSeries
+
+
+def mock_SpatialSeries(
+    name=None,
+    data=None,
+    reference_frame="lower left is (0, 0)",
+    unit="meters",
+    conversion=1.0,
+    resolution=-1.0,
+    timestamps=None,
+    starting_time=None,
+    rate=10.0,
+    comments="no comments",
+    description="no description",
+    control=None,
+    control_description=None,
+):
+    return SpatialSeries(
+        name=name or name_generator("SpatialSeries"),
+        data=data if data is not None else np.array([1, 2, 3, 4]),
+        reference_frame=reference_frame,
+        unit=unit,
+        conversion=conversion,
+        resolution=resolution,
+        timestamps=timestamps,
+        starting_time=starting_time,
+        rate=rate,
+        comments=comments,
+        description=description,
+        control=control,
+        control_description=control_description,
+    )
+
+
+def mock_Position(
+    name=None, spatial_series=None,
+):
+    return Position(name=name or name_generator("Position"), spatial_series=spatial_series or [mock_SpatialSeries()])
+
+
+def mock_PupilTracking(
+    name=None, time_series=None,
+):
+    return PupilTracking(name=name or name_generator("PupilTracking"), time_series=time_series or [mock_TimeSeries()])
+
+
+def mock_CompassDirection(name=None, spatial_series=None):
+    return CompassDirection(
+        name=name or name_generator("CompassDirection"),
+        spatial_series=spatial_series or [mock_SpatialSeries(unit="radians")],
+    )

src/pynwb/testing/mock/device.py

@@ -0,0 +1,15 @@
+from ...device import Device
+
+from .utils import name_generator
+
+
+def mock_Device(
+    name=None,
+    description="description",
+    manufacturer=None,
+):
+    return Device(
+        name=name or name_generator("Device"),
+        description=description,
+        manufacturer=manufacturer,
+    )

src/pynwb/testing/mock/ecephys.py

@@ -0,0 +1,78 @@
+import numpy as np
+
+from hdmf.common.table import DynamicTableRegion
+
+from ...file import ElectrodeTable
+from ...ecephys import ElectricalSeries, ElectrodeGroup, SpikeEventSeries
+from .device import mock_Device
+from .utils import name_generator
+
+
+def mock_ElectrodeGroup(
+    name=None,
+    description="description",
+    location="location",
+    device=None,
+    position=None,
+):
+    return ElectrodeGroup(
+        name=name or name_generator("ElectrodeGroup"),
+        description=description,
+        location=location,
+        device=device or mock_Device(),
+        position=position,
+    )
+
+
+def mock_ElectrodeTable(n_rows=5, group=None):
+    table = ElectrodeTable()
+    group = group if group is not None else mock_ElectrodeGroup()
+    for i in range(n_rows):
+        table.add_row(
+            location="CA1",
+            group=group,
+            group_name=group.name,
+        )
+    return table
+
+
+def mock_electrodes(n_electrodes=5, table=mock_ElectrodeTable(n_rows=5)):
+    return DynamicTableRegion(
+        "electrodes", list(range(n_electrodes)), "the first and third electrodes", table
+    )
+
+
+def mock_ElectricalSeries(
+    name=None,
+    description="description",
+    data=None,
+    rate=30000.0,
+    timestamps=None,
+    electrodes=None,
+    filtering="filtering",
+):
+    return ElectricalSeries(
+        name=name or name_generator("ElectricalSeries"),
+        description=description,
+        data=data if data is not None else np.ones((10, 5)),
+        rate=rate,
+        timestamps=timestamps,
+        electrodes=electrodes or mock_electrodes(),
+        filtering=filtering,
+    )
+
+
+def mock_SpikeEventSeries(
+    name=None,
+    description="description",
+    data=None,
+    timestamps=np.arange(10).astype(float),
+    electrodes=None,
+):
+    return SpikeEventSeries(
+        name=name or name_generator("SpikeEventSeries"),
+        description=description,
+        data=data if data is not None else np.ones((10, 5)),
+        timestamps=timestamps if timestamps is not None else np.arange(10).astype(float),
+        electrodes=electrodes if electrodes is not None else mock_electrodes(),
+    )

src/pynwb/testing/mock/file.py

@@ -0,0 +1,36 @@
+from uuid import uuid4
+from datetime import datetime
+
+from ...file import NWBFile, Subject
+from .utils import name_generator
+
+
+def mock_NWBFile(
+    session_description='session_description',
+    identifier=None,
+    session_start_time=datetime(1970, 1, 1),
+    subject=None,
+    **kwargs
+):
+    return NWBFile(
+        session_description=session_description,
+        identifier=identifier or uuid4(),
+        session_start_time=session_start_time,
+        subject=subject or mock_Subject(),
+        **kwargs
+    )
+
+
+def mock_Subject(
+    age="P50D",
+    description="this is a mock mouse.",
+    sex="F",
+    subject_id=None,
+):
+
+    return Subject(
+        age=age,
+        description=description,
+        sex=sex,
+        subject_id=subject_id or name_generator("subject"),
+    )

src/pynwb/testing/mock/ogen.py

@@ -0,0 +1,52 @@
+import numpy as np
+
+from ...ogen import OptogeneticStimulusSite, OptogeneticSeries
+
+from .device import mock_Device
+from .utils import name_generator
+
+
+def mock_OptogeneticStimulusSite(
+    name=None,
+    device=None,
+    description="optogenetic stimulus site",
+    excitation_lambda=500.,
+    location="part of the brain",
+):
+    return OptogeneticStimulusSite(
+        name=name or name_generator("OptogeneticStimulusSite"),
+        device=device or mock_Device(),
+        description=description,
+        excitation_lambda=excitation_lambda,
+        location=location
+    )
+
+
+def mock_OptogeneticSeries(
+    name=None,
+    data=None,
+    site=None,
+    resolution=-1.0,
+    conversion=1.0,
+    timestamps=None,
+    starting_time=None,
+    rate=10.0,
+    comments="no comments",
+    description="no description",
+    control=None,
+    control_description=None,
+):
+    return OptogeneticSeries(
+        name=name or name_generator("OptogeneticSeries"),
+        data=data if data is not None else np.array([1, 2, 3, 4]),
+        site=site or mock_OptogeneticStimulusSite(),
+        resolution=resolution,
+        conversion=conversion,
+        timestamps=timestamps,
+        starting_time=starting_time,
+        rate=rate,
+        comments=comments,
+        description=description,
+        control=control,
+        control_description=control_description,
+    )