spikeinterface 0.100.3__tar.gz → 0.100.4__tar.gz

{spikeinterface-0.100.3/src/spikeinterface.egg-info → spikeinterface-0.100.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spikeinterface
-Version: 0.100.3
+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-0.100.3 → spikeinterface-0.100.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.100.3"
+version = "0.100.4"
 authors = [
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },

{spikeinterface-0.100.3 → 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-0.100.3 → 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():
@@ -380,15 +382,25 @@ 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_kwargs:
-        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,
     )
 
@@ -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-0.100.3 → spikeinterface-0.100.4/src/spikeinterface.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spikeinterface
-Version: 0.100.3
+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