Add plexon 2 support (#918)

Co-authored-by: Ben Dichter <[email protected]>
Co-authored-by: Cody Baker <[email protected]>

.github/actions/install-wine/action.yml

@@ -0,0 +1,30 @@
+name: Install packages
+description: This action installs the package and its dependencies for testing
+
+inputs:
+  os:
+    description: 'Operating system to set up'
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install wine on Linux
+      if: runner.os == 'Linux'
+      run: |
+        sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
+        sudo dpkg --add-architecture i386
+        sudo apt-get update -qq
+        sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
+      shell: bash
+    - name: Install wine on macOS
+      if: runner.os == 'macOS'
+      run: |
+        brew install --cask xquartz
+        brew install --cask wine-stable
+      shell: bash
+
+    - name: Skip installation on Windows
+      if: ${{ inputs.os == 'Windows' }}
+      run: echo "Skipping Wine installation on Windows. Not necessary."
+      shell: bash

.github/workflows/dev-testing.yml

@@ -38,6 +38,11 @@ jobs:
           git config --global user.email "[email protected]"
           git config --global user.name "CI Almighty"
 
+      - name: Install Wine (For Plexon2 Tests)
+        uses: ./.github/actions/install-wine
+        with:
+          os: ${{ runner.os }}
+
       - name: Install full requirements
         run: pip install --no-cache-dir .[full,test]
 
@@ -70,7 +75,7 @@ jobs:
         id: cache-ephys-datasets
         with:
           path: ./ephy_testing_data
-          key: ephys-datasets-2024-03-27-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
+          key: ephys-datasets-2024-06-21-ubuntu-latest-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
       - name: Get ophys_testing_data current head hash
         id: ophys
         run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"
@@ -79,7 +84,7 @@ jobs:
         id: cache-ophys-datasets
         with:
           path: ./ophys_testing_data
-          key: ophys-datasets-2022-08-18-${{ matrix.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
+          key: ophys-datasets-2022-08-18-ubuntu-latest-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
       - name: Get behavior_testing_data current head hash
         id: behavior
         run: echo "::set-output name=HASH_BEHAVIOR_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/behavior_testing_data.git HEAD | cut -f1)"
@@ -88,7 +93,7 @@ jobs:
         id: cache-behavior-datasets
         with:
           path: ./behavior_testing_data
-          key: behavior-datasets-2023-07-26-${{ matrix.os }}-${{ steps.behavior.outputs.HASH_behavior_DATASET }}
+          key: behavior-datasets-2023-07-26-ubuntu-latest-${{ steps.behavior.outputs.HASH_behavior_DATASET }}
 
 
 

.github/workflows/doctests.yml

@@ -29,7 +29,10 @@ jobs:
       - name: Install neuroconv with minimal requirements
         run: pip install .[full,test]
 
-
+      - name: Install Wine (For Plexon2 Tests)
+        uses: ./.github/actions/install-wine
+        with:
+          os: ${{ runner.os }}
 
       - name: Get ephy_testing_data current head hash
         id: ephys
@@ -39,7 +42,7 @@ jobs:
         id: cache-ephys-datasets
         with:
           path: ./ephy_testing_data
-          key: ephys-datasets-2024-03-27-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
+          key: ephys-datasets-2024-08-07-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
       - name: Get ophys_testing_data current head hash
         id: ophys
         run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"

.github/workflows/formatwise-installation-testing.yml

@@ -44,7 +44,7 @@ jobs:
         id: cache-ephys-datasets
         with:
           path: ./ephy_testing_data
-          key: ephys-datasets-2024-03-27-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
+          key: ephys-datasets-2024-08-27-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
       - name: Get ophys_testing_data current head hash
         id: ophys
         run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"

.github/workflows/testing.yml

@@ -38,7 +38,10 @@ jobs:
         run: pip install .
       - name: Test initial import of all non-lazy dependencies
         run: python -c "import neuroconv"
-
+      - name: Install Wine (For Plexon2 Tests)
+        uses: ./.github/actions/install-wine
+        with:
+          os: ${{ runner.os }}
       - name: Install NeuroConv with testing requirements
         run: pip install .[test]
       - name: Run import tests
@@ -88,7 +91,7 @@ jobs:
         id: cache-ephys-datasets
         with:
           path: ./ephy_testing_data
-          key: ephys-datasets-2024-03-27-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
+          key: ephys-datasets-2024-08-07-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
       - name: Get ophys_testing_data current head hash
         id: ophys
         run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"

CHANGELOG.md

@@ -6,6 +6,8 @@
 
 ### Features
 * Support `SortingAnalyzer` in the `SpikeGLXConverterPipe`. [PR #821](https://github.com/catalystneuro/neuroconv/pull/821)
+* Add Plexon2 support [PR #918](https://github.com/catalystneuro/neuroconv/pull/918)
+* Converter working with multiple VideoInterface instances [PR 914](https://github.com/catalystneuro/neuroconv/pull/914)
 
 ### Bug fixes
 * Fixed the default naming of multiple electrical series in the `SpikeGLXConverterPipe`. [PR #957](https://github.com/catalystneuro/neuroconv/pull/957)
@@ -58,7 +60,7 @@
 
 ### Improvements
 * Propagated `photon_series_type` to `BaseImagingExtractorInterface` init instead of passing it as an argument of `get_metadata()` and `get_metadata_schema()`. [PR #847](https://github.com/catalystneuro/neuroconv/pull/847)
-* Converter working with multiple VideoInterface instances [PR 914](https://github.com/catalystneuro/neuroconv/pull/914)
+
 
 
 

docs/conversion_examples_gallery/index.rst

@@ -28,6 +28,7 @@ Recording
     NeuroScope <recording/neuroscope>
     OpenEphys <recording/openephys>
     Plexon <recording/plexon>
+    Plexon2 <recording/plexon2>
     Spike2 <recording/spike2>
     Spikegadgets <recording/spikegadgets>
     SpikeGLX <recording/spikeglx>

docs/conversion_examples_gallery/recording/plexon2.rst

@@ -0,0 +1,35 @@
+Plexon2 Recording Conversion
+----------------------------
+
+Install NeuroConv with the additional dependencies necessary for reading Plexon acquisition data.
+
+.. code-block:: bash
+
+    pip install neuroconv[plexon]
+
+.. warning::
+    When running plexon2 conversion on platforms other than Windows, you also need to install `wine <https://www.winehq.org/>`_.
+
+Convert Plexon2 recording data to NWB using :py:class:`~neuroconv.datainterfaces.ecephys.plexon.plexondatainterface.Plexon2RecordingInterface`.
+
+.. code-block:: python
+
+    >>> from datetime import datetime
+    >>> from zoneinfo import ZoneInfo
+    >>> from pathlib import Path
+    >>> from neuroconv.datainterfaces import Plexon2RecordingInterface
+    >>>
+    >>> file_path = f"{ECEPHY_DATA_PATH}/plexon/4chDemoPL2.pl2"
+    >>> # Change the file_path to the location in your system
+    >>> interface = Plexon2RecordingInterface(file_path=file_path, verbose=False)
+    >>>
+    >>> # Extract what metadata we can from the source files
+    >>> metadata = interface.get_metadata()
+    >>> # For data provenance we add the time zone information to the conversion
+    >>> tzinfo = ZoneInfo("US/Pacific")
+    >>> session_start_time = metadata["NWBFile"]["session_start_time"]
+    >>> metadata["NWBFile"].update(session_start_time=session_start_time.replace(tzinfo=tzinfo))
+    >>>
+    >>> # Choose a path for saving the nwb file and run the conversion
+    >>> nwbfile_path = f"{path_to_save_nwbfile}"
+    >>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)

src/neuroconv/datainterfaces/__init__.py

@@ -54,6 +54,7 @@
 from .ecephys.openephys.openephyssortingdatainterface import OpenEphysSortingInterface
 from .ecephys.phy.phydatainterface import PhySortingInterface
 from .ecephys.plexon.plexondatainterface import (
+    Plexon2RecordingInterface,
     PlexonRecordingInterface,
     PlexonSortingInterface,
 )
@@ -124,6 +125,7 @@
     EDFRecordingInterface,
     TdtRecordingInterface,
     PlexonRecordingInterface,
+    Plexon2RecordingInterface,
     PlexonSortingInterface,
     BiocamRecordingInterface,
     AlphaOmegaRecordingInterface,

src/neuroconv/datainterfaces/ecephys/plexon/plexondatainterface.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 from ..baserecordingextractorinterface import BaseRecordingExtractorInterface
 from ..basesortingextractorinterface import BaseSortingExtractorInterface
 from ....utils import DeepDict
@@ -48,6 +50,57 @@ def get_metadata(self) -> DeepDict:
         return metadata
 
 
+class Plexon2RecordingInterface(BaseRecordingExtractorInterface):
+    """
+    Primary data interface class for converting Plexon2 data.
+
+    Uses the :py:class:`~spikeinterface.extractors.Plexon2RecordingExtractor`.
+    """
+
+    display_name = "Plexon2 Recording"
+    associated_suffixes = (".pl2",)
+    info = "Interface for Plexon2 recording data."
+
+    @classmethod
+    def get_source_schema(cls) -> dict:
+        source_schema = super().get_source_schema()
+        source_schema["properties"]["file_path"]["description"] = "Path to the .pl2 file."
+        return source_schema
+
+    def __init__(self, file_path: FilePathType, verbose: bool = True, es_key: str = "ElectricalSeries"):
+        """
+        Load and prepare data for Plexon.
+
+        Parameters
+        ----------
+        file_path : str or Path
+            Path to the .plx file.
+        verbose : bool, default: True
+            Allows verbosity.
+        es_key : str, default: "ElectricalSeries"
+        """
+        stream_id = "3"
+        assert Path(file_path).is_file(), f"Plexon file not found in: {file_path}"
+        super().__init__(
+            file_path=file_path,
+            verbose=verbose,
+            es_key=es_key,
+            stream_id=stream_id,
+            all_annotations=True,
+        )
+
+    def get_metadata(self) -> DeepDict:
+        metadata = super().get_metadata()
+
+        neo_reader = self.recording_extractor.neo_reader
+
+        block_ind = self.recording_extractor.block_index
+        neo_metadata = neo_reader.raw_annotations["blocks"][block_ind]
+        metadata["NWBFile"].update(session_start_time=neo_metadata["m_CreatorDateTime"])
+
+        return metadata
+
+
 class PlexonSortingInterface(BaseSortingExtractorInterface):
     """
     Primary data interface class for converting Plexon spiking data.

src/neuroconv/datainterfaces/ecephys/plexon/requirements.txt

@@ -0,0 +1 @@
+zugbruecke >= 0.2.1; platform_system != "Windows"

src/neuroconv/datainterfaces/ecephys/requirements.txt

@@ -1,2 +1,2 @@
 spikeinterface>=0.101.0
-neo>=0.13.1
+neo>=0.13.2

src/neuroconv/datainterfaces/icephys/requirements.txt

@@ -1 +1 @@
-neo>=0.9.0
+neo>=0.13.2

tests/test_on_data/test_gin_ecephys/test_raw_recordings.py

@@ -26,6 +26,7 @@
     NeuroScopeRecordingInterface,
     OpenEphysBinaryRecordingInterface,
     OpenEphysLegacyRecordingInterface,
+    Plexon2RecordingInterface,
     PlexonRecordingInterface,
     SpikeGadgetsRecordingInterface,
     SpikeGLXRecordingInterface,
@@ -95,6 +96,12 @@ class TestEcephysRawRecordingsNwbConversions(unittest.TestCase):
             ),
             case_name="plexon_recording",
         ),
+        param(
+            data_interface=Plexon2RecordingInterface,
+            interface_kwargs=dict(
+                file_path=str(DATA_PATH / "plexon" / "4chDemoPL2.pl2"),
+            ),
+        ),
         param(
             data_interface=BiocamRecordingInterface,
             interface_kwargs=dict(file_path=str(DATA_PATH / "biocam" / "biocam_hw3.0_fw1.6.brw")),

tests/test_on_data/test_metadata/test_plexon_metadata.py

@@ -0,0 +1,14 @@
+import datetime
+
+from neuroconv.datainterfaces import Plexon2RecordingInterface
+
+from ..setup_paths import ECEPHY_DATA_PATH
+
+
+def test_session_start_time():
+    file_path = f"{ECEPHY_DATA_PATH}/plexon/4chDemoPL2.pl2"
+    interface = Plexon2RecordingInterface(file_path=file_path)
+    metadata = interface.get_metadata()
+    session_start_time = metadata["NWBFile"]["session_start_time"]
+
+    assert session_start_time == datetime.datetime(2013, 11, 20, 15, 59, 39)