[Bug] Pass customized backend to run_conversion (#885)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

CHANGELOG.md

@@ -35,6 +35,7 @@
 * Fixed a bug when adding ragged arrays to the electrode and units table. [PR #870](https://github.com/catalystneuro/neuroconv/pull/870)
 * Fixed a bug where `write_recording` will call an empty nwbfile when passing a path. [PR #877](https://github.com/catalystneuro/neuroconv/pull/877)
 * Fixed a bug that failed to properly include time alignment information in the output NWB file for objects added from any `RecordingInterface` in combination with `stub_test=True`. [PR #884](https://github.com/catalystneuro/neuroconv/pull/884)
+* Fixed a bug that prevented passing `nwbfile=None` and a `backend_configuration` to `NWBConverter.run_conversion`. [PR #885](https://github.com/catalystneuro/neuroconv/pull/885)
 
 ### Improvements
 * Fixed docstrings related to backend configurations for various methods. [PR #822](https://github.com/catalystneuro/neuroconv/pull/822)

src/neuroconv/basedatainterface.py

@@ -153,6 +153,7 @@ def run_conversion(
                 " use DataInterface.add_to_nwbfile."
             )
         backend = _resolve_backend(backend, backend_configuration)
+        no_nwbfile_provided = nwbfile is None  # Otherwise, variable reference may mutate later on inside the context
 
         if metadata is None:
             metadata = self.get_metadata()
@@ -165,10 +166,10 @@ def run_conversion(
             backend=backend,
             verbose=getattr(self, "verbose", False),
         ) as nwbfile_out:
-            if backend_configuration is None:
-                # In this case, assume the relevant data has not been added to the NWBFile
+            if no_nwbfile_provided:
                 self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, **conversion_options)
 
+            if backend_configuration is None:
                 backend_configuration = self.get_default_backend_configuration(nwbfile=nwbfile_out, backend=backend)
 
             configure_backend(nwbfile=nwbfile_out, backend_configuration=backend_configuration)

src/neuroconv/nwbconverter.py

@@ -203,6 +203,7 @@ def run_conversion(
             conversion specification is requested.
         """
         backend = _resolve_backend(backend, backend_configuration)
+        no_nwbfile_provided = nwbfile is None  # Otherwise, variable reference may mutate later on inside the context
 
         if metadata is None:
             metadata = self.get_metadata()
@@ -220,10 +221,10 @@ def run_conversion(
             backend=backend,
             verbose=getattr(self, "verbose", False),
         ) as nwbfile_out:
-            if backend_configuration is None:
-                # Otherwise assume the data has already been added to the NWBFile
-                self.add_to_nwbfile(nwbfile_out, metadata=metadata, conversion_options=conversion_options)
+            if no_nwbfile_provided:
+                self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, conversion_options=conversion_options)
 
+            if backend_configuration is None:
                 backend_configuration = self.get_default_backend_configuration(nwbfile=nwbfile_out, backend=backend)
 
             configure_backend(nwbfile=nwbfile_out, backend_configuration=backend_configuration)

tests/test_ecephys/test_mock_nidq_interface.py

@@ -1,88 +1,96 @@
+import pathlib
 from datetime import datetime
 
 from hdmf.testing import TestCase
 from numpy.testing import assert_array_almost_equal
+from pynwb import NWBHDF5IO
 from pynwb.testing.mock.file import mock_NWBFile
 
 from neuroconv.tools.testing import MockSpikeGLXNIDQInterface
 
 
-class TestMockSpikeGLXNIDQInterface(TestCase):
-    maxDiff = None
-
-    def test_current_default_inferred_ttl_times(self):
-        interface = MockSpikeGLXNIDQInterface()
-
-        channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3", "nidq#XA4", "nidq#XA5", "nidq#XA6", "nidq#XA7"]
-        inferred_starting_times = list()
-        for channel_index, channel_name in enumerate(channel_names):
-            inferred_starting_times.append(interface.get_event_times_from_ttl(channel_name=channel_name))
-
-        expected_ttl_times = [[1.0 * (1 + 2 * period) + 0.1 * channel for period in range(3)] for channel in range(8)]
-        for channel_index, channel_name in enumerate(channel_names):
-            inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
-            assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
-
-    def test_explicit_original_default_inferred_ttl_times(self):
-        interface = MockSpikeGLXNIDQInterface(signal_duration=7.0, ttl_times=None, ttl_duration=1.0)
-
-        channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3", "nidq#XA4", "nidq#XA5", "nidq#XA6", "nidq#XA7"]
-        expected_ttl_times = [[1.0 * (1 + 2 * period) + 0.1 * channel for period in range(3)] for channel in range(8)]
-        for channel_index, channel_name in enumerate(channel_names):
-            inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
-            assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
-
-    def test_custom_inferred_ttl_times(self):
-        custom_ttl_times = [[1.2], [3.6], [0.7, 4.5], [5.1]]
-        interface = MockSpikeGLXNIDQInterface(ttl_times=custom_ttl_times)
-
-        channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3"]
-        for channel_index, channel_name in enumerate(channel_names):
-            inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
-            assert_array_almost_equal(x=inferred_ttl_times, y=custom_ttl_times[channel_index], decimal=4)
-
-    def test_mock_metadata(self):
-        interface = MockSpikeGLXNIDQInterface()
-
-        metadata = interface.get_metadata()
-
-        expected_ecephys_metadata = {
-            "Ecephys": {
-                "Device": [
-                    {"description": "no description", "manufacturer": "Imec", "name": "Neuropixel-Imec"},
-                ],
-                "ElectrodeGroup": [
-                    {
-                        "name": "NIDQChannelGroup",
-                        "description": "A group representing the NIDQ channels.",
-                        "device": "Neuropixel-Imec",
-                        "location": "unknown",
-                    },
-                ],
-                "Electrodes": [
-                    {"name": "group_name", "description": "Name of the ElectrodeGroup this electrode is a part of."}
-                ],
-                "ElectricalSeriesNIDQ": {
-                    "name": "ElectricalSeriesNIDQ",
-                    "description": "Raw acquisition traces from the NIDQ (.nidq.bin) channels.",
+def test_current_default_inferred_ttl_times():
+    interface = MockSpikeGLXNIDQInterface()
+
+    channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3", "nidq#XA4", "nidq#XA5", "nidq#XA6", "nidq#XA7"]
+    inferred_starting_times = list()
+    for channel_index, channel_name in enumerate(channel_names):
+        inferred_starting_times.append(interface.get_event_times_from_ttl(channel_name=channel_name))
+
+    expected_ttl_times = [[1.0 * (1 + 2 * period) + 0.1 * channel for period in range(3)] for channel in range(8)]
+    for channel_index, channel_name in enumerate(channel_names):
+        inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
+        assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
+
+
+def test_explicit_original_default_inferred_ttl_times():
+    interface = MockSpikeGLXNIDQInterface(signal_duration=7.0, ttl_times=None, ttl_duration=1.0)
+
+    channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3", "nidq#XA4", "nidq#XA5", "nidq#XA6", "nidq#XA7"]
+    expected_ttl_times = [[1.0 * (1 + 2 * period) + 0.1 * channel for period in range(3)] for channel in range(8)]
+    for channel_index, channel_name in enumerate(channel_names):
+        inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
+        assert_array_almost_equal(x=inferred_ttl_times, y=expected_ttl_times[channel_index], decimal=4)
+
+
+def test_custom_inferred_ttl_times():
+    custom_ttl_times = [[1.2], [3.6], [0.7, 4.5], [5.1]]
+    interface = MockSpikeGLXNIDQInterface(ttl_times=custom_ttl_times)
+
+    channel_names = ["nidq#XA0", "nidq#XA1", "nidq#XA2", "nidq#XA3"]
+    for channel_index, channel_name in enumerate(channel_names):
+        inferred_ttl_times = interface.get_event_times_from_ttl(channel_name=channel_name)
+        assert_array_almost_equal(x=inferred_ttl_times, y=custom_ttl_times[channel_index], decimal=4)
+
+
+def test_mock_metadata():
+    interface = MockSpikeGLXNIDQInterface()
+
+    metadata = interface.get_metadata()
+
+    expected_ecephys_metadata = {
+        "Ecephys": {
+            "Device": [
+                {"description": "no description", "manufacturer": "Imec", "name": "Neuropixel-Imec"},
+            ],
+            "ElectrodeGroup": [
+                {
+                    "name": "NIDQChannelGroup",
+                    "description": "A group representing the NIDQ channels.",
+                    "device": "Neuropixel-Imec",
+                    "location": "unknown",
                 },
-            }
+            ],
+            "Electrodes": [
+                {"name": "group_name", "description": "Name of the ElectrodeGroup this electrode is a part of."}
+            ],
+            "ElectricalSeriesNIDQ": {
+                "name": "ElectricalSeriesNIDQ",
+                "description": "Raw acquisition traces from the NIDQ (.nidq.bin) channels.",
+            },
         }
-        print(metadata["Ecephys"])
-        self.assertDictEqual(d1=metadata["Ecephys"], d2=expected_ecephys_metadata["Ecephys"])
+    }
+    print(metadata["Ecephys"])
+    assert metadata["Ecephys"] == expected_ecephys_metadata["Ecephys"]
+
+    expected_start_time = datetime(2020, 11, 3, 10, 35, 10)
+    assert metadata["NWBFile"]["session_start_time"] == expected_start_time
+
 
-        expected_start_time = datetime(2020, 11, 3, 10, 35, 10)
-        assert metadata["NWBFile"]["session_start_time"] == expected_start_time
+def test_mock_run_conversion(tmpdir: pathlib.Path):
+    interface = MockSpikeGLXNIDQInterface()
 
-    def test_mock_run_conversion(self):
-        interface = MockSpikeGLXNIDQInterface()
+    metadata = interface.get_metadata()
 
-        metadata = interface.get_metadata()
+    test_directory = pathlib.Path(tmpdir) / "TestMockSpikeGLXNIDQInterface"
+    test_directory.mkdir(exist_ok=True)
+    nwbfile_path = test_directory / "test_mock_run_conversion.nwb"
+    interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True)
 
-        nwbfile = mock_NWBFile()
-        interface.run_conversion(nwbfile=nwbfile, metadata=metadata)
+    with NWBHDF5IO(path=nwbfile_path, mode="r") as io:
+        nwbfile = io.read()
 
         assert "Neuropixel-Imec" in nwbfile.devices
         assert "NIDQChannelGroup" in nwbfile.electrode_groups
-        assert nwbfile.electrodes.id[:] == [0, 1, 2, 3, 4, 5, 6, 7]
+        assert list(nwbfile.electrodes.id[:]) == [0, 1, 2, 3, 4, 5, 6, 7]
         assert "ElectricalSeriesNIDQ" in nwbfile.acquisition