Merge pull request #338 from catalystneuro/spike2

change ced to spike2
catalystneuro · Feb 26, 2023 · dea9a25 · dea9a25
2 parents dc517e2 + 9aaa91f
commit dea9a25
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,7 +29,10 @@
 * Moved NeuroConv catalogue from ReadMe.md to ReadTheDocs.
   [PR #322](https://github.com/catalystneuro/neuroconv/pull/322)
 * Moved instructions to build the documentation from README.md to ReadTheDocs. [PR #323](https://github.com/catalystneuro/neuroconv/pull/323)
+* Add `Spike2RecordingInterface` to conversion gallery. [PR #338](https://github.com/catalystneuro/neuroconv/pull/338)
 
+### Pending deprecation
+* Change name from `CedRecordingInterface` to `Spike2RecordingInterface`. [PR #338](https://github.com/catalystneuro/neuroconv/pull/338)
 
 
 # v0.2.4

diff --git a/README.md b/README.md
@@ -24,7 +24,7 @@ NeuroConv is a Python package for converting neurophysiology data in a variety o
 
 Features:
 
-* Reads data from 36 popular neurophysiology data formats and writes to NWB using best practices.
+* Reads data from 38 popular neurophysiology data formats and writes to NWB using best practices.
 * Extracts relevant metadata from each format.
 * Handles large data volume by reading datasets piece-wise.
 * Minimizes the size of the NWB files by automatically applying chunking and lossless compression.

diff --git a/docs/api/interfaces.ecephys.rst b/docs/api/interfaces.ecephys.rst
@@ -17,10 +17,6 @@ Blackrock Recording
 -------------------
 .. automodule:: neuroconv.datainterfaces.ecephys.blackrock.blackrockdatainterface
 
-Cambridge Electronic Design (CED) Recording
--------------------------------------------
-.. automodule:: neuroconv.datainterfaces.ecephys.ced.ceddatainterface
-
 CellExplorer Sorting
 --------------------
 .. automodule:: neuroconv.datainterfaces.ecephys.cellexplorer.cellexplorerdatainterface
@@ -53,6 +49,10 @@ Phy Sorting
 -----------
 .. automodule:: neuroconv.datainterfaces.ecephys.phy.phydatainterface
 
+Spike2
+------
+.. automodule:: neuroconv.datainterfaces.ecephys.spike2.spike2datainterface
+
 Spikegadgets Recording
 ----------------------
 .. automodule:: neuroconv.datainterfaces.ecephys.spikegadgets.spikegadgetsdatainterface

diff --git a/docs/conversion_examples_gallery/conversion_example_gallery.rst b/docs/conversion_examples_gallery/conversion_example_gallery.rst
@@ -3,8 +3,8 @@
 Conversion Gallery
 ==================
 
-The examples here are guaranteed to be running correctly with our testing suite.
-Their aim is to be a showcase of the library capabilities and to get you to hit the ground running with your own conversion.
+The examples here are guaranteed to be running correctly with our testing suite. Their aim is to be a showcase of the
+library capabilities and to get you to hit the ground running with your own conversion.
 
 Extracellular electrophysiology
 -------------------------------
@@ -19,16 +19,17 @@ Recording
     Axona <recording/axona>
     Biocam <recording/biocam>
     Blackrock <recording/blackrock>
+    European Data Format (EDF) <recording/edf>
     Intan <recording/intan>
-    MEArec <recording/mearec>
     MCSRaw <recording/mcsraw>
+    MEArec <recording/mearec>
     Neuralynx <recording/neuralynx>
     NeuroScope <recording/neuroscope>
     OpenEphys <recording/openephys>
     Plexon <recording/plexon>
+    Spike2 <recording/spike2>
     Spikegadgets <recording/spikegadgets>
     SpikeGLX <recording/spikeglx>
-    European Data Format (EDF) <recording/edf>
     Tucker-Davis Technologies (TDT) <recording/tdt>
 
 Sorting
@@ -73,21 +74,22 @@ Segmentation
 .. toctree::
     :maxdepth: 1
 
-    Suite2P <segmentation/suite2p>
     Caiman <segmentation/caiman>
-    EXTRACT <segmentation/extract>
     CNMFE <segmentation/cnmfe>
+    EXTRACT <segmentation/extract>
+    Suite2P <segmentation/suite2p>
 
 Behavior
 --------
 
 .. toctree::
     :maxdepth: 1
 
+    Audio <behavior/audio>
     DeepLabCut <behavior/deeplabcut>
     SLEAP <behavior/sleap>
     Videos <behavior/video>
-    Audio <behavior/audio>
+
 
 Text
 ----

diff --git a/docs/conversion_examples_gallery/recording/spike2.rst b/docs/conversion_examples_gallery/recording/spike2.rst
@@ -0,0 +1,33 @@
+Spike2 data conversion
+----------------------
+
+Install NeuroConv with the additional dependencies necessary for reading Spike2 data by CED.
+
+.. code-block:: bash
+
+    pip install neuroconv[spike2]
+
+Convert Spike2 data to NWB using
+:py:class:`~neuroconv.datainterfaces.ecephys.spike2.spike2datainterface.Spike2RecordingInterface`.
+
+.. code-block:: python
+
+    from datetime import datetime
+    from dateutil import tz
+    from pathlib import Path
+    from neuroconv.datainterfaces import Spike2RecordingInterface
+
+    # For this interface we need to pass the specific path to the files.
+    file_path = f"{ECEPHY_DATA_PATH}/spike2/m365_1sec.smrx"
+    # Change the file_path to the location in your system
+    interface = Spike2RecordingInterface(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
+    session_start_time = datetime(2020, 1, 1, 12, 30, 0, tzinfo=tz.gettz("US/Pacific"))
+    metadata["NWBFile"].update(session_start_time=session_start_time)
+
+    # 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)
diff --git a/docs/index.rst b/docs/index.rst
@@ -10,7 +10,7 @@ of proprietary formats to the Neurodata Without Borders (NWB) standard.
 
 Features:
 
-* Reads data from 37 popular neurophysiology data formats and writes to NWB using best practices.
+* Reads data from 38 popular neurophysiology data formats and writes to NWB using best practices.
 * Extracts relevant metadata from each format.
 * Handles large data volume by reading datasets piece-wise.
 * Minimizes the size of the NWB files by automatically applying chunking and lossless compression.

diff --git a/src/neuroconv/datainterfaces/__init__.py b/src/neuroconv/datainterfaces/__init__.py
@@ -8,7 +8,8 @@
 from .ecephys.spikeglx.spikeglxnidqinterface import SpikeGLXNIDQInterface
 from .ecephys.spikegadgets.spikegadgetsdatainterface import SpikeGadgetsRecordingInterface
 from .ecephys.intan.intandatainterface import IntanRecordingInterface
-from .ecephys.ced.ceddatainterface import CEDRecordingInterface
+from .ecephys.spike2.spike2datainterface import Spike2RecordingInterface
+from .ecephys.spike2.spike2datainterface import CEDRecordingInterface
 from .ecephys.cellexplorer.cellexplorerdatainterface import CellExplorerSortingInterface
 from .ecephys.blackrock.blackrockdatainterface import (
     BlackrockRecordingInterface,
@@ -66,6 +67,7 @@
     NeuroScopeRecordingInterface,
     NeuroScopeSortingInterface,
     NeuroScopeLFPInterface,
+    Spike2RecordingInterface,
     SpikeGLXRecordingInterface,
     SpikeGLXLFPInterface,
     SpikeGLXNIDQInterface,

diff --git a/...nv/datainterfaces/ecephys/ced/__init__.py → ...datainterfaces/ecephys/spike2/__init__.py b/...nv/datainterfaces/ecephys/ced/__init__.py → ...datainterfaces/ecephys/spike2/__init__.py
diff --git a/...tainterfaces/ecephys/ced/requirements.txt → ...nterfaces/ecephys/spike2/requirements.txt b/...tainterfaces/ecephys/ced/requirements.txt → ...nterfaces/ecephys/spike2/requirements.txt
diff --git a/...nterfaces/ecephys/ced/ceddatainterface.py → ...ces/ecephys/spike2/spike2datainterface.py b/...nterfaces/ecephys/ced/ceddatainterface.py → ...ces/ecephys/spike2/spike2datainterface.py
@@ -1,5 +1,6 @@
 """Authors: Heberto Mayorquin, Luiz Tauffer."""
 from pathlib import Path
+from warnings import warn
 
 from ..baserecordingextractorinterface import BaseRecordingExtractorInterface
 from ....tools import get_package
@@ -14,8 +15,9 @@ def _test_sonpy_installation() -> None:
     )
 
 
-class CEDRecordingInterface(BaseRecordingExtractorInterface):
-    """Primary data interface class for converting data from CED (Cambridge Electronic
+class Spike2RecordingInterface(BaseRecordingExtractorInterface):
+    """
+    Data interface class for converting Spike2 data from CED (Cambridge Electronic
     Design) using the :py:class:`~spikeinterface.extractors.CedRecordingExtractor`."""
 
     ExtractorName = "CedRecordingExtractor"
@@ -35,7 +37,8 @@ def get_all_channels_info(cls, file_path: FilePathType):
 
     def __init__(self, file_path: FilePathType, verbose: bool = True, es_key: str = "ElectricalSeries"):
         """
-        Initialize reading of CED file.
+        Initialize reading of Spike2 file. CEDRecordingInterface will soon be deprecated. Please use
+        Spike2RecordingInterface instead.
 
         Parameters
         ----------
@@ -53,3 +56,22 @@ def __init__(self, file_path: FilePathType, verbose: bool = True, es_key: str =
         signal_channels = self.recording_extractor.neo_reader.header["signal_channels"]
         channel_ids_of_raw_data = [channel_info[1] for channel_info in signal_channels if channel_info[4] == "mV"]
         self.recording_extractor = self.recording_extractor.channel_slice(channel_ids=channel_ids_of_raw_data)
+
+
+class CEDRecordingInterface(Spike2RecordingInterface):
+    def __init__(self, file_path: FilePathType, verbose: bool = True, es_key: str = "ElectricalSeries"):
+        """
+        Initialize reading of CED file.
+
+        Parameters
+        ----------
+        file_path : FilePathType
+            Path to .smr or .smrx file.
+        verbose : bool, default: True
+        es_key : str, default: "ElectricalSeries"
+        """
+        warn(
+            message="CEDRecordingInterface will soon be deprecated. Please use Spike2RecordingInterface instead.",
+            category=DeprecationWarning,
+        )
+        super().__init__(file_path=file_path, verbose=verbose, es_key=es_key)