Merge pull request #3153 from alejoe91/clean-extractor-class-attrs

Remove unused legacy class name/mode from extractors

src/spikeinterface/core/binaryfolder.py

@@ -25,9 +25,6 @@ class BinaryFolderRecording(BinaryRecordingExtractor):
         The recording
     """
 
-    mode = "folder"
-    name = "binaryfolder"
-
     def __init__(self, folder_path):
         folder_path = Path(folder_path)
 

src/spikeinterface/core/binaryrecordingextractor.py

@@ -52,9 +52,6 @@ class BinaryRecordingExtractor(BaseRecording):
         The recording Extractor
     """
 
-    mode = "file"
-    name = "binary"
-
     def __init__(
         self,
         file_paths,

src/spikeinterface/core/npzsortingextractor.py

@@ -16,9 +16,6 @@ class NpzSortingExtractor(BaseSorting):
     All spike are store in two columns maner index+labels
     """
 
-    mode = "file"
-    name = "npz"
-
     def __init__(self, file_path):
         self.npz_filename = file_path
 

src/spikeinterface/core/numpyextractors.py

@@ -37,9 +37,6 @@ class NumpyRecording(BaseRecording):
         An optional list of channel_ids. If None, linear channels are assumed
     """
 
-    mode = "memory"
-    name = "numpy"
-
     def __init__(self, traces_list, sampling_frequency, t_starts=None, channel_ids=None):
         if isinstance(traces_list, list):
             all_elements_are_list = all(isinstance(e, list) for e in traces_list)
@@ -142,9 +139,6 @@ class SharedMemoryRecording(BaseRecording):
         If True, the main instance will unlink the sharedmem buffer when deleted
     """
 
-    mode = "memory"
-    name = "SharedMemory"
-
     def __init__(
         self, shm_names, shape_list, dtype, sampling_frequency, channel_ids=None, t_starts=None, main_shm_owner=True
     ):
@@ -252,8 +246,6 @@ class NumpySorting(BaseSorting):
         A list of unit_ids.
     """
 
-    name = "numpy"
-
     def __init__(self, spikes, sampling_frequency, unit_ids):
         """ """
         BaseSorting.__init__(self, sampling_frequency, unit_ids)

src/spikeinterface/core/zarrextractors.py

@@ -31,13 +31,7 @@ class ZarrRecordingExtractor(BaseRecording):
         The recording Extractor
     """
 
-    installed = True
-    mode = "folder"
-    installation_mesg = ""
-    name = "zarr"
-
     def __init__(self, folder_path: Path | str, storage_options: dict | None = None):
-        assert self.installed, self.installation_mesg
 
         folder_path, folder_path_kwarg = resolve_zarr_path(folder_path)
 
@@ -167,13 +161,7 @@ class ZarrSortingExtractor(BaseSorting):
         The sorting Extractor
     """
 
-    installed = True
-    mode = "folder"
-    installation_mesg = ""
-    name = "zarr"
-
     def __init__(self, folder_path: Path | str, storage_options: dict | None = None, zarr_group: str | None = None):
-        assert self.installed, self.installation_mesg
 
         folder_path, folder_path_kwarg = resolve_zarr_path(folder_path)
 

src/spikeinterface/extractors/alfsortingextractor.py

@@ -25,12 +25,11 @@ class ALFSortingExtractor(BaseSorting):
     """
 
     installation_mesg = "To use the ALF extractors, install ONE-api: \n\n pip install ONE-api\n\n"
-    name = "alf"
 
     def __init__(self, folder_path, sampling_frequency=30000):
         try:
             import one.alf.io as alfio
-        except ImportError as e:
+        except ImportError:
             raise ImportError(self.installation_mesg)
 
         self._folder_path = Path(folder_path)

src/spikeinterface/extractors/cbin_ibl.py

@@ -39,16 +39,14 @@ class CompressedBinaryIblExtractor(BaseRecording):
         The loaded data.
     """
 
-    mode = "folder"
     installation_mesg = "To use the CompressedBinaryIblExtractor, install mtscomp: \n\n pip install mtscomp\n\n"
-    name = "cbin_ibl"
 
     def __init__(self, folder_path=None, load_sync_channel=False, stream_name="ap", cbin_file=None):
         from neo.rawio.spikeglxrawio import read_meta_file
 
         try:
             import mtscomp
-        except:
+        except ImportError:
             raise ImportError(self.installation_mesg)
         if cbin_file is None:
             folder_path = Path(folder_path)

src/spikeinterface/extractors/cellexplorersortingextractor.py

@@ -29,7 +29,6 @@ class CellExplorerSortingExtractor(BaseSorting):
         Path to the `sessionInfo.mat` file. If None, it will be inferred from the file_path.
     """
 
-    mode = "file"
     installation_mesg = "To use the CellExplorerSortingExtractor install pymatreader"
 
     def __init__(

src/spikeinterface/extractors/combinatoextractors.py

@@ -7,13 +7,6 @@
 from spikeinterface.core import BaseSorting, BaseSortingSegment
 from spikeinterface.core.core_tools import define_function_from_class
 
-try:
-    import h5py
-
-    HAVE_H5PY = True
-except ImportError:
-    HAVE_H5PY = False
-
 
 class CombinatoSortingExtractor(BaseSorting):
     """Load Combinato format data as a sorting extractor.
@@ -37,11 +30,14 @@ class CombinatoSortingExtractor(BaseSorting):
         The loaded data.
     """
 
-    installed = HAVE_H5PY
     installation_mesg = "To use the CombinatoSortingExtractor install h5py: \n\n pip install h5py\n\n"
-    name = "combinato"
 
     def __init__(self, folder_path, sampling_frequency=None, user="simple", det_sign="both", keep_good_only=True):
+        try:
+            import h5py
+        except ImportError:
+            raise ImportError(self.installation_mesg)
+
         folder_path = Path(folder_path)
         assert folder_path.is_dir(), "Folder {} doesn't exist".format(folder_path)
         if sampling_frequency is None:

src/spikeinterface/extractors/extractorlist.py

@@ -116,52 +116,3 @@
 event_extractor_full_list += neo_event_extractors_list
 
 snippets_extractor_full_list = [NpySnippetsExtractor, WaveClusSnippetsExtractor]
-
-
-recording_extractor_full_dict = {recext.name: recext for recext in recording_extractor_full_list}
-sorting_extractor_full_dict = {recext.name: recext for recext in sorting_extractor_full_list}
-snippets_extractor_full_dict = {recext.name: recext for recext in snippets_extractor_full_list}
-
-
-def get_recording_extractor_from_name(name: str) -> Type[BaseRecording]:
-    """
-    Returns the Recording Extractor class based on its name.
-
-    Parameters
-    ----------
-    name: str
-        The Recording Extractor's name.
-
-    Returns
-    -------
-    recording_extractor: BaseRecording
-        The Recording Extractor class.
-    """
-
-    for recording_extractor in recording_extractor_full_list:
-        if recording_extractor.__name__ == name:
-            return recording_extractor
-
-    raise ValueError(f"Recording extractor '{name}' not found.")
-
-
-def get_sorting_extractor_from_name(name: str) -> Type[BaseSorting]:
-    """
-    Returns the Sorting Extractor class based on its name.
-
-    Parameters
-    ----------
-    name: str
-        The Sorting Extractor's name.
-
-    Returns
-    -------
-    sorting_extractor: BaseSorting
-        The Sorting Extractor class.
-    """
-
-    for sorting_extractor in sorting_extractor_full_list:
-        if sorting_extractor.__name__ == name:
-            return sorting_extractor
-
-    raise ValueError(f"Sorting extractor '{name}' not found.")

src/spikeinterface/extractors/hdsortextractors.py

@@ -25,9 +25,6 @@ class HDSortSortingExtractor(MatlabHelper, BaseSorting):
         The loaded data.
     """
 
-    mode = "file"
-    name = "hdsort"
-
     def __init__(self, file_path, keep_good_only=True):
         MatlabHelper.__init__(self, file_path)
 

src/spikeinterface/extractors/herdingspikesextractors.py

@@ -7,13 +7,6 @@
 from spikeinterface.core import BaseSorting, BaseSortingSegment
 from spikeinterface.core.core_tools import define_function_from_class
 
-try:
-    import h5py
-
-    HAVE_HS2SX = True
-except ImportError:
-    HAVE_HS2SX = False
-
 
 class HerdingspikesSortingExtractor(BaseSorting):
     """Load HerdingSpikes format data as a sorting extractor.
@@ -31,15 +24,13 @@ class HerdingspikesSortingExtractor(BaseSorting):
         The loaded data.
     """
 
-    installed = HAVE_HS2SX  # check at class level if installed or not
-    mode = "file"
-    installation_mesg = (
-        "To use the HS2SortingExtractor install h5py: \n\n pip install h5py\n\n"  # error message when not installed
-    )
-    name = "herdingspikes"
+    installation_mesg = "To use the HS2SortingExtractor install h5py: \n\n pip install h5py\n\n"
 
     def __init__(self, file_path, load_unit_info=True):
-        assert self.installed, self.installation_mesg
+        try:
+            import h5py
+        except ImportError:
+            raise ImportError(self.installation_mesg)
 
         self._recording_file = file_path
         self._rf = h5py.File(self._recording_file, mode="r")

src/spikeinterface/extractors/iblextractors.py

@@ -65,9 +65,7 @@ class IblRecordingExtractor(BaseRecording):
         The recording extractor which allows access to the traces.
     """
 
-    mode = "folder"
     installation_mesg = "To use the IblRecordingSegment, install ibllib: \n\n pip install ONE-api\npip install ibllib\n"
-    name = "ibl_recording"
 
     @staticmethod
     def _get_default_one(cache_folder: Optional[Union[Path, str]] = None):
@@ -304,7 +302,6 @@ class IblSortingExtractor(BaseSorting):
         The loaded data.
     """
 
-    name = "ibl"
     installation_mesg = "IBL extractors require ibllib as a dependency." " To install, run: \n\n pip install ibllib\n\n"
 
     def __init__(self, pid: str, good_clusters_only: bool = False, load_unit_properties: bool = True, one=None):

src/spikeinterface/extractors/klustaextractors.py

@@ -18,13 +18,6 @@
 from spikeinterface.core import BaseRecording, BaseSorting, BaseRecordingSegment, BaseSortingSegment, read_python
 from spikeinterface.core.core_tools import define_function_from_class
 
-try:
-    import h5py
-
-    HAVE_H5PY = True
-except ImportError:
-    HAVE_H5PY = False
-
 
 # noinspection SpellCheckingInspection
 class KlustaSortingExtractor(BaseSorting):
@@ -43,18 +36,15 @@ class KlustaSortingExtractor(BaseSorting):
         The loaded data.
     """
 
-    installed = HAVE_H5PY  # check at class level if installed or not
-    installation_mesg = (
-        "To use the KlustaSortingExtractor install h5py: \n\n pip install h5py\n\n"  # error message when not installed
-    )
-    mode = "file_or_folder"
-    name = "klusta"
+    installation_mesg = "To use the KlustaSortingExtractor install h5py: \n\n pip install h5py\n\n"
 
     default_cluster_groups = {0: "Noise", 1: "MUA", 2: "Good", 3: "Unsorted"}
 
     def __init__(self, file_or_folder_path, exclude_cluster_groups=None):
-        assert HAVE_H5PY, self.installation_mesg
-        # ~ SortingExtractor.__init__(self)
+        try:
+            import h5py
+        except ImportError:
+            raise ImportError(self.installation_mesg)
 
         kwik_file_or_folder = Path(file_or_folder_path)
         kwikfile = None

src/spikeinterface/extractors/mclustextractors.py

@@ -29,8 +29,6 @@ class MClustSortingExtractor(BaseSorting):
         Loaded data.
     """
 
-    name = "mclust"
-
     def __init__(self, folder_path, sampling_frequency, sampling_frequency_raw=None):
         end_header_str = "%%ENDHEADER"
         ext_list = ["t64", "t32", "t", "raw64", "raw32"]

src/spikeinterface/extractors/mcsh5extractors.py

@@ -24,18 +24,12 @@ class MCSH5RecordingExtractor(BaseRecording):
         The loaded data.
     """
 
-    mode = "file"
-    installation_mesg = (
-        "To use the MCSH5RecordingExtractor install h5py: \n\n pip install h5py\n\n"  # error message when not installed
-    )
-    name = "mcsh5"
+    installation_mesg = "To use the MCSH5RecordingExtractor install h5py: \n\n pip install h5py\n\n"
 
     def __init__(self, file_path, stream_id=0):
 
         try:
             import h5py
-
-            HAVE_MCSH5 = True
         except ImportError:
             raise ImportError(self.installation_mesg)
 

src/spikeinterface/extractors/mdaextractors.py

@@ -36,9 +36,6 @@ class MdaRecordingExtractor(BaseRecording):
         The loaded data.
     """
 
-    mode = "folder"
-    name = "mda"
-
     def __init__(self, folder_path, raw_fname="raw.mda", params_fname="params.json", geom_fname="geom.csv"):
         folder_path = Path(folder_path)
         self._folder_path = folder_path
@@ -192,9 +189,6 @@ class MdaSortingExtractor(BaseSorting):
         The loaded data.
     """
 
-    mode = "file"
-    name = "mda"
-
     def __init__(self, file_path, sampling_frequency):
         firings = readmda(str(Path(file_path).absolute()))
         labels = firings[2, :]

src/spikeinterface/extractors/neoextractors/alphaomega.py

@@ -27,9 +27,7 @@ class AlphaOmegaRecordingExtractor(NeoBaseRecordingExtractor):
         Load exhaustively all annotations from neo.
     """
 
-    mode = "folder"
     NeoRawIOClass = "AlphaOmegaRawIO"
-    name = "alphaomega"
 
     def __init__(self, folder_path, lsx_files=None, stream_id="RAW", stream_name=None, all_annotations=False):
         neo_kwargs = self.map_to_neo_kwargs(folder_path, lsx_files)

src/spikeinterface/extractors/neoextractors/axona.py

@@ -21,9 +21,7 @@ class AxonaRecordingExtractor(NeoBaseRecordingExtractor):
         Load exhaustively all annotations from neo.
     """
 
-    mode = "folder"
     NeoRawIOClass = "AxonaRawIO"
-    name = "axona"
 
     def __init__(self, file_path, all_annotations=False):
         neo_kwargs = self.map_to_neo_kwargs(file_path)

src/spikeinterface/extractors/neoextractors/biocam.py

@@ -31,9 +31,7 @@ class BiocamRecordingExtractor(NeoBaseRecordingExtractor):
         Load exhaustively all annotations from neo.
     """
 
-    mode = "file"
     NeoRawIOClass = "BiocamRawIO"
-    name = "biocam"
 
     def __init__(
         self,