spikeinterface 0.100.2__tar.gz → 0.100.4__tar.gz

{spikeinterface-0.100.2/src/spikeinterface.egg-info → spikeinterface-0.100.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spikeinterface
-Version: 0.100.2
+Version: 0.100.4
 Summary: Python toolkit for analysis, visualization, and comparison of spike sorting output
 Author-email: Alessio Buccino <alessiop.buccino@gmail.com>, Samuel Garcia <sam.garcia.die@gmail.com>
 Project-URL: homepage, https://github.com/SpikeInterface/spikeinterface

{spikeinterface-0.100.2 → spikeinterface-0.100.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.100.2"
+version = "0.100.4"
 authors = [
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },

{spikeinterface-0.100.2 → spikeinterface-0.100.4}/src/spikeinterface/core/base.py

@@ -967,9 +967,24 @@ class BaseExtractor:
             For cloud storage locations, this should not be None (in case of default values, use an empty dict)
         channel_chunk_size: int or None, default: None
             Channels per chunk (only for BaseRecording)
+        compressor: numcodecs.Codec or None, default: None
+            Global compressor. If None, Blosc-zstd level 5 is used.
+        filters: list[numcodecs.Codec] or None, default: None
+            Global filters for zarr (global)
+        compressor_by_dataset: dict or None, default: None
+            Optional compressor per dataset:
+                - traces
+                - times
+            If None, the global compressor is used
+        filters_by_dataset: dict or None, default: None
+            Optional filters per dataset:
+                - traces
+                - times
+            If None, the global filters are used
         verbose: bool, default: True
             If True, the output is verbose
-        **save_kwargs: Keyword arguments for saving to zarr
+        auto_cast_uint: bool, default: True
+            If True, unsigned integers are cast to signed integers to avoid issues with zarr (only for BaseRecording)
 
         Returns
         -------

{spikeinterface-0.100.2 → spikeinterface-0.100.4}/src/spikeinterface/core/zarrextractors.py

@@ -255,7 +255,7 @@ def read_zarr(
         The loaded extractor
     """
     # TODO @alessio : we should have something more explicit in our zarr format to tell which object it is.
-    # for the futur SortingResult we will have this 2 fields!!!
+    # for the futur SortingAnalyzer we will have this 2 fields!!!
     root = zarr.open(str(folder_path), mode="r", storage_options=storage_options)
     if "channel_ids" in root.keys():
         return read_zarr_recording(folder_path, storage_options=storage_options)
@@ -366,7 +366,9 @@ def add_sorting_to_zarr_group(sorting: BaseSorting, zarr_group: zarr.hierarchy.G
 
 
 # Recording
-def add_recording_to_zarr_group(recording: BaseRecording, zarr_group: zarr.hierarchy.Group, **kwargs):
+def add_recording_to_zarr_group(
+    recording: BaseRecording, zarr_group: zarr.hierarchy.Group, verbose=False, auto_cast_uint=True, dtype=None, **kwargs
+):
     zarr_kwargs, job_kwargs = split_job_kwargs(kwargs)
 
     if recording.check_if_json_serializable():
@@ -380,19 +382,29 @@ def add_recording_to_zarr_group(recording: BaseRecording, zarr_group: zarr.hiera
     zarr_group.create_dataset(name="channel_ids", data=recording.get_channel_ids(), compressor=None)
     dataset_paths = [f"traces_seg{i}" for i in range(recording.get_num_segments())]
 
-    zarr_kwargs["dtype"] = kwargs.get("dtype", None) or recording.get_dtype()
-    if "compressor" not in zarr_group:
-        zarr_kwargs["compressor"] = get_default_zarr_compressor()
+    dtype = recording.get_dtype() if dtype is None else dtype
+    channel_chunk_size = zarr_kwargs.get("channel_chunk_size", None)
+    global_compressor = zarr_kwargs.pop("compressor", get_default_zarr_compressor())
+    compressor_by_dataset = zarr_kwargs.pop("compressor_by_dataset", {})
+    global_filters = zarr_kwargs.pop("filters", None)
+    filters_by_dataset = zarr_kwargs.pop("filters_by_dataset", {})
 
+    compressor_traces = compressor_by_dataset.get("traces", global_compressor)
+    filters_traces = filters_by_dataset.get("traces", global_filters)
     add_traces_to_zarr(
         recording=recording,
         zarr_group=zarr_group,
         dataset_paths=dataset_paths,
-        **zarr_kwargs,
+        compressor=compressor_traces,
+        filters=filters_traces,
+        dtype=dtype,
+        channel_chunk_size=channel_chunk_size,
+        auto_cast_uint=auto_cast_uint,
+        verbose=verbose,
         **job_kwargs,
     )
 
-    # # save probe
+    # save probe
     if recording.get_property("contact_vector") is not None:
         probegroup = recording.get_probegroup()
         zarr_group.attrs["probe"] = check_json(probegroup.to_dict(array_as_list=True))
@@ -402,12 +414,16 @@ def add_recording_to_zarr_group(recording: BaseRecording, zarr_group: zarr.hiera
     for segment_index, rs in enumerate(recording._recording_segments):
         d = rs.get_times_kwargs()
         time_vector = d["time_vector"]
+
+        compressor_times = compressor_by_dataset.get("times", global_compressor)
+        filters_times = filters_by_dataset.get("times", global_filters)
+
         if time_vector is not None:
             _ = zarr_group.create_dataset(
                 name=f"times_seg{segment_index}",
                 data=time_vector,
-                filters=zarr_kwargs.get("filters", None),
-                compressor=zarr_kwargs["compressor"],
+                filters=filters_times,
+                compressor=compressor_times,
             )
         elif d["t_start"] is not None:
             t_starts[segment_index] = d["t_start"]

{spikeinterface-0.100.2 → spikeinterface-0.100.4}/src/spikeinterface/extractors/nwbextractors.py

@@ -10,15 +10,6 @@ from spikeinterface.core import BaseRecording, BaseRecordingSegment, BaseSorting
 from spikeinterface.core.core_tools import define_function_from_class
 
 
-def import_lazily():
-    "Makes annotations / typing available lazily"
-    global NWBFile, ElectricalSeries, Units, NWBHDF5IO
-    from pynwb import NWBFile
-    from pynwb.ecephys import ElectricalSeries
-    from pynwb.misc import Units
-    from pynwb import NWBHDF5IO
-
-
 def read_file_from_backend(
     *,
     file_path: str | Path | None,
@@ -111,7 +102,7 @@ def read_nwbfile(
     cache: bool = False,
     stream_cache_path: str | Path | None = None,
     storage_options: dict | None = None,
-) -> NWBFile:
+) -> "NWBFile":
     """
     Read an NWB file and return the NWBFile object.
 
@@ -176,8 +167,8 @@ def read_nwbfile(
 
 
 def _retrieve_electrical_series_pynwb(
-    nwbfile: NWBFile, electrical_series_path: Optional[str] = None
-) -> ElectricalSeries:
+    nwbfile: "NWBFile", electrical_series_path: Optional[str] = None
+) -> "ElectricalSeries":
     """
     Get an ElectricalSeries object from an NWBFile.
 
@@ -230,7 +221,7 @@ def _retrieve_electrical_series_pynwb(
     return electrical_series
 
 
-def _retrieve_unit_table_pynwb(nwbfile: NWBFile, unit_table_path: Optional[str] = None) -> Units:
+def _retrieve_unit_table_pynwb(nwbfile: "NWBFile", unit_table_path: Optional[str] = None) -> "Units":
     """
     Get an Units object from an NWBFile.
     Units tables can be either the main unit table (nwbfile.units) or in the processing module.
@@ -568,8 +559,10 @@ class NwbRecordingExtractor(BaseRecording):
         # fetch and add main recording properties
         if use_pynwb:
             gains, offsets, locations, groups = self._fetch_main_properties_pynwb()
+            self.extra_requirements.append("pynwb")
         else:
             gains, offsets, locations, groups = self._fetch_main_properties_backend()
+            self.extra_requirements.append("h5py")
         self.set_channel_gains(gains)
         self.set_channel_offsets(offsets)
         if locations is not None:
@@ -781,8 +774,6 @@ class NwbRecordingExtractor(BaseRecording):
         #########
         # Extract and re-name properties from nwbfile TODO: Should be a function
         ########
-        from pynwb.ecephys import ElectrodeGroup
-
         properties = dict()
         properties_to_skip = [
             "id",
@@ -798,9 +789,7 @@ class NwbRecordingExtractor(BaseRecording):
 
         for column in columns:
             first_value = electrodes_table[column][0]
-            if isinstance(first_value, ElectrodeGroup):
-                continue
-            elif column in properties_to_skip:
+            if column in properties_to_skip:
                 continue
             else:
                 column_name = rename_properties.get(column, column)
@@ -1024,8 +1013,10 @@ class NwbSortingExtractor(BaseSorting):
         if load_unit_properties:
             if use_pynwb:
                 columns = [c.name for c in self.units_table.columns]
+                self.extra_requirements.append("pynwb")
             else:
                 columns = list(self.units_table.keys())
+                self.extra_requirements.append("h5py")
             properties = self._fetch_properties(columns)
             for property_name, property_values in properties.items():
                 values = [x.decode("utf-8") if isinstance(x, bytes) else x for x in property_values]

{spikeinterface-0.100.2 → spikeinterface-0.100.4}/src/spikeinterface/postprocessing/template_similarity.py

@@ -112,7 +112,9 @@ def compute_template_similarity(
         similarity = tmc.get_data()
         return similarity
     else:
-        return _compute_template_similarity(waveform_extractor, waveform_extractor_other, method)
+        return _compute_template_similarity(
+            waveform_extractor=waveform_extractor, waveform_extractor_other=waveform_extractor_other, method=method
+        )
 
 
 def check_equal_template_with_distribution_overlap(

{spikeinterface-0.100.2 → spikeinterface-0.100.4/src/spikeinterface.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spikeinterface
-Version: 0.100.2
+Version: 0.100.4
 Summary: Python toolkit for analysis, visualization, and comparison of spike sorting output
 Author-email: Alessio Buccino <alessiop.buccino@gmail.com>, Samuel Garcia <sam.garcia.die@gmail.com>
 Project-URL: homepage, https://github.com/SpikeInterface/spikeinterface