Fix stream in Plexon 1 interface (#1013)

catalystneuro · Sep 17, 2024 · 36464df · 36464df
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Showing 10 changed files with 25 additions and 12 deletions.
diff --git a/.github/workflows/dev-testing.yml b/.github/workflows/dev-testing.yml
@@ -74,7 +74,7 @@ jobs:
         id: cache-ephys-datasets
         with:
           path: ./ephy_testing_data
-          key: ephys-datasets-2024-06-21-ubuntu-latest-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
+          key: ephys-datasets-2024-08-30-ubuntu-latest-${{ 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)"

diff --git a/.github/workflows/doctests.yml b/.github/workflows/doctests.yml
@@ -42,7 +42,7 @@ jobs:
         id: cache-ephys-datasets
         with:
           path: ./ephy_testing_data
-          key: ephys-datasets-2024-08-07-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
+          key: ephys-datasets-2024-08-30-${{ matrix.os }}-${{ 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)"

diff --git a/.github/workflows/formatwise-installation-testing.yml b/.github/workflows/formatwise-installation-testing.yml
@@ -44,7 +44,7 @@ jobs:
         id: cache-ephys-datasets
         with:
           path: ./ephy_testing_data
-          key: ephys-datasets-2024-08-27-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
+          key: ephys-datasets-2024-08-30-${{ matrix.os }}-${{ 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)"

diff --git a/.github/workflows/neuroconv_docker_testing.yml b/.github/workflows/neuroconv_docker_testing.yml
@@ -43,7 +43,7 @@ jobs:
         id: cache-ephys-datasets
         with:
           path: ./ephy_testing_data
-          key: ephys-datasets-2023-06-26-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
+          key: ephys-datasets-2024-08-30-${{ matrix.os }}-${{ 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)"

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -94,7 +94,7 @@ jobs:
         id: cache-ephys-datasets
         with:
           path: ./ephy_testing_data
-          key: ephys-datasets-2024-08-07-${{ matrix.os }}-${{ steps.ephys.outputs.HASH_EPHY_DATASET }}
+          key: ephys-datasets-2024-08-30-${{ matrix.os }}-${{ 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)"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ## Bug Fixes
 * Fixed a setup bug introduced in `v0.6.2` where installation process created a directory instead of a file for test configuration file  [PR #1070](https://github.com/catalystneuro/neuroconv/pull/1070)
 * The method `get_extractor` now works for `MockImagingInterface`  [PR #1076](https://github.com/catalystneuro/neuroconv/pull/1076)
+* Solved a bug of `PlexonRecordingInterface` where data with multiple streams could not be opened [PR #989](https://github.com/catalystneuro/neuroconv/pull/989)
 
 ## Deprecations
 

diff --git a/docs/conversion_examples_gallery/recording/plexon.rst b/docs/conversion_examples_gallery/recording/plexon.rst
@@ -16,7 +16,7 @@ Convert Plexon recording data to NWB using :py:class:`~neuroconv.datainterfaces.
     >>> from pathlib import Path
     >>> from neuroconv.datainterfaces import PlexonRecordingInterface
     >>>
-    >>> file_path = f"{ECEPHY_DATA_PATH}/plexon/File_plexon_3.plx"
+    >>> file_path = f"{ECEPHY_DATA_PATH}/plexon/4chDemoPLX.plx"
     >>> # Change the file_path to the location in your system
     >>> interface = PlexonRecordingInterface(file_path=file_path, verbose=False)
     >>>

diff --git a/src/neuroconv/datainterfaces/ecephys/plexon/plexondatainterface.py b/src/neuroconv/datainterfaces/ecephys/plexon/plexondatainterface.py
@@ -25,7 +25,13 @@ def get_source_schema(cls) -> dict:
         return source_schema
 
     @validate_call
-    def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"):
+    def __init__(
+        self,
+        file_path: FilePath,
+        verbose: bool = True,
+        es_key: str = "ElectricalSeries",
+        stream_name: str = "WB-Wideband",
+    ):
         """
         Load and prepare data for Plexon.
 
@@ -36,8 +42,15 @@ def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "Ele
         verbose : bool, default: True
             Allows verbosity.
         es_key : str, default: "ElectricalSeries"
+        stream_name: str, optional
+            Only pass a stream if you modified the channel prefixes in the Plexon file and you know the prefix of
+            the wideband data.
         """
-        super().__init__(file_path=file_path, verbose=verbose, es_key=es_key)
+
+        invalid_stream_names = ["FPl-Low Pass Filtered", "SPKC-High Pass Filtered", "AI-Auxiliary Input"]
+        assert stream_name not in invalid_stream_names, f"Invalid stream name: {stream_name}"
+
+        super().__init__(file_path=file_path, verbose=verbose, es_key=es_key, stream_name=stream_name)
 
     def get_metadata(self) -> DeepDict:
         metadata = super().get_metadata()

diff --git a/src/neuroconv/datainterfaces/ecephys/requirements.txt b/src/neuroconv/datainterfaces/ecephys/requirements.txt
@@ -1,2 +1,2 @@
 spikeinterface>=0.101.0
-neo>=0.13.2
+neo>=0.13.3
diff --git a/tests/test_on_data/ecephys/test_recording_interfaces.py b/tests/test_on_data/ecephys/test_recording_interfaces.py
@@ -693,10 +693,9 @@ def check_read_nwb(self, nwbfile_path: str):
 class TestPlexonRecordingInterface(RecordingExtractorInterfaceTestMixin):
     data_interface_cls = PlexonRecordingInterface
     interface_kwargs = dict(
-        # Only File_plexon_3.plx has an ecephys recording stream
-        file_path=str(ECEPHY_DATA_PATH / "plexon" / "File_plexon_3.plx"),
+        file_path=str(ECEPHY_DATA_PATH / "plexon" / "4chDemoPLX.plx"),
     )
     save_directory = OUTPUT_PATH
 
     def check_extracted_metadata(self, metadata: dict):
-        assert metadata["NWBFile"]["session_start_time"] == datetime(2010, 2, 22, 20, 0, 57)
+        assert metadata["NWBFile"]["session_start_time"] == datetime(2013, 11, 19, 13, 48, 13)