Add asserts to test all

src/pynwb/tests/test_example_usage_all.py

@@ -14,149 +14,228 @@
 )
 
 
-# initialize an NWBFile object
-nwbfile = NWBFile(
-    session_description="A description of my session",
-    identifier=str(uuid.uuid4()),
-    session_start_time=datetime.datetime.now(datetime.timezone.utc),
-)
-
-contacts_table = ContactsTable(
-    description="Test contacts table",
-)
-# for demonstration, mix and match different shapes. np.nan means the radius/width/height does not apply
-contacts_table.add_row(
-    relative_position_in_mm=[10.0, 10.0],
-    shape="circle",
-    contact_id="C1",
-    shank_id="shank0",
-    plane_axes=[[0.0, 1.0], [1.0, 0.0]],  # TODO make realistic
-    radius_in_um=10.0,
-    width_in_um=np.nan,
-    height_in_um=np.nan,
-    device_channel=1,
-)
-contacts_table.add_row(
-    relative_position_in_mm=[20.0, 10.0],
-    shape="square",
-    contact_id="C2",
-    shank_id="shank0",
-    plane_axes=[[0.0, 1.0], [1.0, 0.0]],  # TODO make realistic
-    radius_in_um=np.nan,
-    width_in_um=10.0,
-    height_in_um=10.0,
-    device_channel=2,
-)
-
-# add the object into nwbfile.acquisition for testing
-# TODO after integration, put this into /general/extracellular_ephys
-nwbfile.add_acquisition(contacts_table)
-
-pm = ProbeModel(
-    name="Neuropixels 1.0",
-    description="A neuropixels probe",
-    model="neuropixels 1.0",
-    manufacturer="IMEC",
-    planar_contour_in_um=[[-10.0, -10.0], [10.0, -10.0], [10.0, 10.0], [-10.0, 10.0]],
-    contacts_table=contacts_table,
-)
-# TODO put this into /general/device_models
-nwbfile.add_device(pm)
-
-probe = Probe(
-    name="Neuropixels Probe 1",
-    identifier="28948291",
-    probe_model=pm,
-)
-nwbfile.add_device(probe)
-
-pi = ProbeInsertion(
-    position_reference="(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
-    hemisphere="left",
-    depth_in_mm=10.0,
-    insertion_position_ap_in_mm=2.0,
-    insertion_position_ml_in_mm=-4.0,
-    insertion_angle_roll_in_deg=-10.0,
-    insertion_angle_pitch_in_deg=0.0,
-    insertion_angle_yaw_in_deg=0.0,
-)
-
-channels_table = ChannelsTable(
-    name="Neuropixels1ChannelsTable",  # test custom name
-    description="Test channels table",
-    reference_mode="Referenced to channel 2.",
-    position_reference="(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
-    position_confirmation_method="Histology",
-    probe=probe,
-    probe_insertion=pi,
-    target_tables={
-        "contact": probe.probe_model.contacts_table,
-        "reference_contact": probe.probe_model.contacts_table,
-    },
-    # TODO should not need to specify the above
-)
-
-# all of the keyword arguments in add_row are optional
-channels_table.add_row(
-    contact=0,
-    reference_contact=2,
-    filter="High-pass at 300 Hz",
-    estimated_position_ap_in_mm=2.0,
-    estimated_position_ml_in_mm=-5.0,
-    estimated_position_dv_in_mm=-9.5,
-    estimated_brain_area="CA3",
-    confirmed_position_ap_in_mm=2.0,
-    confirmed_position_ml_in_mm=-4.9,
-    confirmed_position_dv_in_mm=-9.5,
-    confirmed_brain_area="CA3",
-)
-channels_table.add_row(
-    contact=1,
-    reference_contact=2,
-    filter="High-pass at 300 Hz",
-    estimated_position_ap_in_mm=2.0,
-    estimated_position_ml_in_mm=-4.9,
-    estimated_position_dv_in_mm=-9.3,
-    estimated_brain_area="CA3",
-    confirmed_position_ap_in_mm=2.0,
-    confirmed_position_ml_in_mm=-4.8,
-    confirmed_position_dv_in_mm=-9.3,
-    confirmed_brain_area="CA3",
-)
-
-# put this in nwbfile.acquisition for testing
-nwbfile.add_acquisition(channels_table)
-
-channels = DynamicTableRegion(
-    name="channels",  # NOTE: this must be named "channels" when used in ExtracellularSeries
-    data=[0, 1, 2],
-    description="All of the channels",
-    table=channels_table,
-)
-
-es = ExtracellularSeries(
-    name="ExtracellularSeries",
-    data=[0.0, 1.0, 2.0],
-    timestamps=[0.0, 0.001, 0.0002],
-    channels=channels,
-    channel_conversion=[1.0, 1.1, 1.2],
-    conversion=1e5,
-    offset=0.001,
-    unit="volts",  # TODO should not have to specify this in init
-)
-
-nwbfile.add_acquisition(es)
-
-# write the NWBFile to disk
-path = "test_extracellular_channels.nwb"
-with NWBHDF5IO(path, mode="w") as io:
-    io.write(nwbfile)
-
-# read the NWBFile from disk
-with NWBHDF5IO(path, mode="r") as io:
-    read_nwbfile = io.read()
-    print(read_nwbfile.acquisition["ExtracellularSeries"])
-    print(read_nwbfile.acquisition["Neuropixels1ChannelsTable"])
-    print(read_nwbfile.devices["Neuropixels Probe 1"])
-    print(read_nwbfile.devices["Neuropixels 1.0"])
-    print(read_nwbfile.acquisition["contacts_table"])
+def test_all_classes():
+
+    # initialize an NWBFile object
+    nwbfile = NWBFile(
+        session_description="A description of my session",
+        identifier=str(uuid.uuid4()),
+        session_start_time=datetime.datetime.now(datetime.timezone.utc),
+    )
+
+    contacts_table = ContactsTable(
+        description="Test contacts table",
+    )
+    # for demonstration, mix and match different shapes. np.nan means the radius/width/height does not apply
+    contacts_table.add_row(
+        relative_position_in_mm=[10.0, 10.0],
+        contact_id="C1",
+        device_channel=1,
+        shank_id="shank0",
+        plane_axes=[[0.0, 1.0], [1.0, 0.0]],  # TODO make realistic
+        shape="circle",
+        radius_in_um=10.0,
+        width_in_um=np.nan,
+        height_in_um=np.nan,
+    )
+    contacts_table.add_row(
+        relative_position_in_mm=[20.0, 10.0],
+        contact_id="C2",
+        device_channel=2,
+        shank_id="shank0",
+        plane_axes=[[0.0, 1.0], [1.0, 0.0]],  # TODO make realistic
+        shape="square",
+        radius_in_um=np.nan,
+        width_in_um=10.0,
+        height_in_um=10.0,
+    )
+
+    # add the object into nwbfile.acquisition for testing
+    # TODO after integration, put this into /general/extracellular_ephys
+    nwbfile.add_acquisition(contacts_table)
+
+    pm = ProbeModel(
+        name="Neuropixels 1.0",
+        description="A neuropixels probe",
+        model="Neuropixels 1.0",
+        manufacturer="IMEC",
+        planar_contour_in_um=[[-10.0, -10.0], [10.0, -10.0], [10.0, 10.0], [-10.0, 10.0]],
+        contacts_table=contacts_table,
+    )
+    # TODO put this into /general/device_models
+    nwbfile.add_device(pm)
+
+    probe = Probe(
+        name="Neuropixels Probe 1",
+        identifier="28948291",
+        probe_model=pm,
+    )
+    nwbfile.add_device(probe)
+
+    pi = ProbeInsertion(
+        position_reference="(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
+        hemisphere="left",
+        depth_in_mm=10.0,
+        insertion_position_ap_in_mm=2.0,
+        insertion_position_ml_in_mm=-4.0,
+        insertion_angle_roll_in_deg=-10.0,
+        insertion_angle_pitch_in_deg=0.0,
+        insertion_angle_yaw_in_deg=0.0,
+    )
+
+    channels_table = ChannelsTable(
+        name="Neuropixels1ChannelsTable",  # test custom name
+        description="Test channels table",
+        reference_mode="Referenced to channel 2.",
+        position_reference="(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
+        position_confirmation_method="Histology",
+        probe=probe,
+        probe_insertion=pi,
+        target_tables={
+            "contact": probe.probe_model.contacts_table,
+            "reference_contact": probe.probe_model.contacts_table,
+        },
+        # TODO should not need to specify the above
+    )
+
+    # all of the keyword arguments in add_row are optional
+    channels_table.add_row(
+        contact=0,
+        reference_contact=2,
+        filter="High-pass at 300 Hz",
+        estimated_position_ap_in_mm=2.0,
+        estimated_position_ml_in_mm=-5.0,
+        estimated_position_dv_in_mm=-9.5,
+        estimated_brain_area="CA3",
+        confirmed_position_ap_in_mm=2.0,
+        confirmed_position_ml_in_mm=-4.9,
+        confirmed_position_dv_in_mm=-9.5,
+        confirmed_brain_area="CA3",
+    )
+    channels_table.add_row(
+        contact=1,
+        reference_contact=2,
+        filter="High-pass at 300 Hz",
+        estimated_position_ap_in_mm=2.0,
+        estimated_position_ml_in_mm=-4.9,
+        estimated_position_dv_in_mm=-9.3,
+        estimated_brain_area="CA3",
+        confirmed_position_ap_in_mm=2.0,
+        confirmed_position_ml_in_mm=-4.8,
+        confirmed_position_dv_in_mm=-9.3,
+        confirmed_brain_area="CA3",
+    )
+
+    # put this in nwbfile.acquisition for testing
+    nwbfile.add_acquisition(channels_table)
+
+    channels = DynamicTableRegion(
+        name="channels",  # NOTE: this must be named "channels" when used in ExtracellularSeries
+        data=[0, 1, 2],
+        description="All of the channels",
+        table=channels_table,
+    )
+
+    es = ExtracellularSeries(
+        name="ExtracellularSeries",
+        data=[0.0, 1.0, 2.0],
+        timestamps=[0.0, 0.001, 0.0002],
+        channels=channels,
+        channel_conversion=[1.0, 1.1, 1.2],
+        conversion=1e5,
+        offset=0.001,
+        unit="volts",  # TODO should not have to specify this in init
+    )
+
+    nwbfile.add_acquisition(es)
+
+    # write the NWBFile to disk
+    path = "test_extracellular_channels.nwb"
+    with NWBHDF5IO(path, mode="w") as io:
+        io.write(nwbfile)
+
+    # read the NWBFile from disk
+    with NWBHDF5IO(path, mode="r") as io:
+        read_nwbfile = io.read()
+
+        read_eseries = read_nwbfile.acquisition["ExtracellularSeries"]
+        read_channels_table = read_nwbfile.acquisition["Neuropixels1ChannelsTable"]
+        read_contacts_table = read_nwbfile.acquisition["contacts_table"]
+
+        np.testing.assert_array_equal(read_eseries.data[:], [0.0, 1.0, 2.0])
+        np.testing.assert_array_equal(read_eseries.timestamps[:], [0.0, 0.001, 0.0002])
+        np.testing.assert_array_equal(read_eseries.channels.data[:], [0, 1, 2])
+        assert read_eseries.channels.description == "All of the channels"
+        assert read_eseries.channels.table is read_channels_table
+        np.testing.assert_array_equal(read_eseries.channel_conversion[:], [1.0, 1.1, 1.2])
+        assert read_eseries.conversion == 1e5
+        assert read_eseries.offset == 0.001
+        assert read_eseries.unit == "volts"
+
+        assert read_channels_table.name == "Neuropixels1ChannelsTable"
+        assert read_channels_table.description == "Test channels table"
+        assert read_channels_table.reference_mode == "Referenced to channel 2."
+        assert (
+            read_channels_table.position_reference
+            == "(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface."
+        )
+        assert read_channels_table.position_confirmation_method == "Histology"
+        assert read_channels_table.probe is read_nwbfile.devices["Neuropixels Probe 1"]
+        assert len(read_channels_table) == 2
+        assert read_channels_table["contact"].table is read_contacts_table
+        np.testing.assert_array_equal(read_channels_table["contact"].data[:], [0, 1])
+        assert read_channels_table["reference_contact"].table is read_contacts_table
+        np.testing.assert_array_equal(read_channels_table["reference_contact"].data[:], [2, 2])
+        np.testing.assert_array_equal(
+            read_channels_table["filter"].data[:], ["High-pass at 300 Hz", "High-pass at 300 Hz"]
+        )
+        np.testing.assert_array_equal(read_channels_table["estimated_position_ap_in_mm"].data[:], [2.0, 2.0])
+        np.testing.assert_array_equal(read_channels_table["estimated_position_ml_in_mm"].data[:], [-5.0, -4.9])
+        np.testing.assert_array_equal(read_channels_table["estimated_position_dv_in_mm"].data[:], [-9.5, -9.3])
+        np.testing.assert_array_equal(read_channels_table["estimated_brain_area"].data[:], ["CA3", "CA3"])
+        np.testing.assert_array_equal(read_channels_table["confirmed_position_ap_in_mm"].data[:], [2.0, 2.0])
+        np.testing.assert_array_equal(read_channels_table["confirmed_position_ml_in_mm"].data[:], [-4.9, -4.8])
+        np.testing.assert_array_equal(read_channels_table["confirmed_position_dv_in_mm"].data[:], [-9.5, -9.3])
+        np.testing.assert_array_equal(read_channels_table["confirmed_brain_area"].data[:], ["CA3", "CA3"])
+
+        assert (
+            read_channels_table.probe_insertion.position_reference
+            == "(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface."
+        )
+        assert read_channels_table.probe_insertion.hemisphere == "left"
+        assert read_channels_table.probe_insertion.depth_in_mm == 10.0
+        assert read_channels_table.probe_insertion.insertion_position_ap_in_mm == 2.0
+        assert read_channels_table.probe_insertion.insertion_position_ml_in_mm == -4.0
+        assert read_channels_table.probe_insertion.insertion_angle_roll_in_deg == -10.0
+        assert read_channels_table.probe_insertion.insertion_angle_pitch_in_deg == 0.0
+        assert read_channels_table.probe_insertion.insertion_angle_yaw_in_deg == 0.0
+
+        assert read_nwbfile.devices["Neuropixels Probe 1"].name == "Neuropixels Probe 1"
+        assert read_nwbfile.devices["Neuropixels Probe 1"].identifier == "28948291"
+        assert read_nwbfile.devices["Neuropixels Probe 1"].probe_model is read_nwbfile.devices["Neuropixels 1.0"]
+
+        assert read_nwbfile.devices["Neuropixels 1.0"].name == "Neuropixels 1.0"
+        assert read_nwbfile.devices["Neuropixels 1.0"].description == "A neuropixels probe"
+        assert read_nwbfile.devices["Neuropixels 1.0"].model == "Neuropixels 1.0"
+        assert read_nwbfile.devices["Neuropixels 1.0"].manufacturer == "IMEC"
+        np.testing.assert_array_equal(
+            read_nwbfile.devices["Neuropixels 1.0"].planar_contour_in_um,
+            [[-10.0, -10.0], [10.0, -10.0], [10.0, 10.0], [-10.0, 10.0]],
+        )
+        assert read_nwbfile.devices["Neuropixels 1.0"].contacts_table is read_contacts_table
+
+        assert read_contacts_table.name == "contacts_table"
+        assert read_contacts_table.description == "Test contacts table"
+        np.testing.assert_array_equal(
+            read_contacts_table["relative_position_in_mm"].data[:], [[10.0, 10.0], [20.0, 10.0]]
+        )
+        np.testing.assert_array_equal(read_contacts_table["shape"].data[:], ["circle", "square"])
+        np.testing.assert_array_equal(read_contacts_table["contact_id"].data[:], ["C1", "C2"])
+        np.testing.assert_array_equal(read_contacts_table["shank_id"].data[:], ["shank0", "shank0"])
+        np.testing.assert_array_equal(
+            read_contacts_table["plane_axes"].data[:], [[[0.0, 1.0], [1.0, 0.0]], [[0.0, 1.0], [1.0, 0.0]]]
+        )
+        np.testing.assert_array_equal(read_contacts_table["radius_in_um"].data[:], [10.0, np.nan])
+        np.testing.assert_array_equal(read_contacts_table["width_in_um"].data[:], [np.nan, 10.0])
+        np.testing.assert_array_equal(read_contacts_table["height_in_um"].data[:], [np.nan, 10.0])
+        np.testing.assert_array_equal(read_contacts_table["device_channel"].data[:], [1, 2])