spikeinterface 0.104.0__tar.gz → 0.104.2__tar.gz

{spikeinterface-0.104.0/src/spikeinterface.egg-info → spikeinterface-0.104.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spikeinterface
-Version: 0.104.0
+Version: 0.104.2
 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-0.104.0 → spikeinterface-0.104.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.104.0"
+version = "0.104.2"
 authors = [
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },

{spikeinterface-0.104.0 → spikeinterface-0.104.2}/src/spikeinterface/core/base.py

@@ -1138,14 +1138,8 @@ def _load_extractor_from_dict(dic) -> BaseExtractor:
 
     assert extractor_class is not None and class_name is not None, "Could not load spikeinterface class"
     is_old_version = not _check_same_version(class_name, dic["version"])
-    if is_old_version:
-        warnings.warn(
-            f"Versions are not the same. This might lead to compatibility errors. "
-            f"Using {class_name.split('.')[0]}=={dic['version']} is recommended"
-        )
-
-        if hasattr(extractor_class, "_handle_backward_compatibility"):
-            new_kwargs = extractor_class._handle_backward_compatibility(new_kwargs, dic)
+    if is_old_version and hasattr(extractor_class, "_handle_backward_compatibility"):
+        new_kwargs = extractor_class._handle_backward_compatibility(new_kwargs, dic)
 
     # Initialize the extractor
     extractor = extractor_class(**new_kwargs)

{spikeinterface-0.104.0 → spikeinterface-0.104.2}/src/spikeinterface/core/waveforms_extractor_backwards_compatibility.py

@@ -628,12 +628,16 @@ def _read_old_waveforms_extractor_binary(folder, sorting):
                     pc_all[mask, ...] = pc_one
                 ext.data["pca_projection"] = pc_all
 
-        # update params
-        new_params = ext._set_params()
-        updated_params = make_ext_params_up_to_date(ext, params, new_params)
-        ext.set_params(**updated_params, save=False)
+        # Install raw on-disk params and run compat handler first,
+        # matching what AnalyzerExtension.load does for non-legacy folders.
+        ext.params = dict(params)
         if ext.need_backward_compatibility_on_load:
             ext._handle_backward_compatibility_on_load()
+
+        # Now merge and validate — deprecated names are already migrated.
+        new_params = ext._set_params()
+        updated_params = make_ext_params_up_to_date(ext, ext.params, new_params)
+        ext.set_params(**updated_params, save=False)
         ext.run_info = None
 
         sorting_analyzer.extensions[new_name] = ext

{spikeinterface-0.104.0 → spikeinterface-0.104.2}/src/spikeinterface/extractors/cbin_ibl.py

@@ -106,14 +106,7 @@ class CompressedBinaryIblExtractor(BaseRecording):
             else:
                 self.set_probe(probe, in_place=True)
 
-            # load num_channels_per_adc depending on probe type
-            ptype = probe.annotations["probe_type"]
-
-            if ptype in [21, 24]:  # NP2.0
-                num_channels_per_adc = 16
-            else:  # NP1.0
-                num_channels_per_adc = 12
-            sample_shifts = get_neuropixels_sample_shifts_from_probe(probe, num_channels_per_adc)
+            sample_shifts = get_neuropixels_sample_shifts_from_probe(probe)
             self.set_property("inter_sample_shift", sample_shifts)
 
         self._kwargs = {

{spikeinterface-0.104.0 → spikeinterface-0.104.2}/src/spikeinterface/extractors/neoextractors/openephys.py

@@ -229,6 +229,8 @@ class OpenEphysBinaryRecordingExtractor(NeoBaseRecordingExtractor):
         experiment_names: str | list | None = None,
         all_annotations: bool = False,
     ):
+        folder_path = Path(folder_path)
+
         # Handle experiment_names deprecation
         if experiment_names is not None:
             warnings.warn(
@@ -348,8 +350,15 @@ class OpenEphysBinaryRecordingExtractor(NeoBaseRecordingExtractor):
                     if sample_shifts is not None:
                         self.set_property("inter_sample_shift", sample_shifts)
 
-            # load synchronized timestamps and set_times to recording
-            recording_folder = Path(folder_path) / record_node
+            # folder_path can point to different levels of the OE folder structure
+            # (root, record node, experiment, or recording). We need to find the root folder
+            # in order to load the sync timestamps and set them as times to the recording.
+            if record_node in folder_path.parts:
+                root_index = len(folder_path.parts) - folder_path.parts.index(record_node) - 1
+                root_folder = folder_path.parents[root_index]
+            else:
+                root_folder = folder_path
+            recording_folder = root_folder / record_node
             stream_folders = []
             for segment_index, rec_id in enumerate(rec_ids):
                 stream_folder = (

{spikeinterface-0.104.0 → spikeinterface-0.104.2}/src/spikeinterface/metrics/quality/quality_metrics.py

@@ -77,6 +77,20 @@ class ComputeQualityMetrics(BaseMetricExtension):
             if "peak_sign" in self.params["metric_params"]["amplitude_median"]:
                 del self.params["metric_params"]["amplitude_median"]["peak_sign"]
 
+        # TODO: update this once `main_channel_index` PR is merged
+        # global peak_sign used to find appropriate channels for pca metric computation
+        # If not found, use a "peak_sign" set by any metric
+        global_peak_sign_from_params = self.params.get("peak_sign")
+        if global_peak_sign_from_params is None:
+            for metric_params in self.params["metric_params"].values():
+                if "peak_sign" in metric_params:
+                    global_peak_sign_from_params = metric_params["peak_sign"]
+                    break
+            # If still not found, use <0.104.0 default, "neg"
+            if global_peak_sign_from_params is None:
+                global_peak_sign_from_params = "neg"
+            self.params["peak_sign"] = global_peak_sign_from_params
+
     def _set_params(
         self,
         metric_names: list[str] | None = None,

{spikeinterface-0.104.0 → spikeinterface-0.104.2}/src/spikeinterface/metrics/template/template_metrics.py

@@ -169,6 +169,11 @@ class ComputeTemplateMetrics(BaseMetricExtension):
             if "waveform_ratios" not in self.params["metric_names"]:
                 self.params["metric_names"].append("waveform_ratios")
 
+        # If original analyzer doesn't have "peaks_data" or "main_channel_templates",
+        # then we can't save this tmp data (important for merges/splits)
+        if "peaks_data" not in self.data:
+            self.tmp_data_to_save = []
+
     def _set_params(
         self,
         metric_names: list[str] | None = None,
@@ -234,12 +239,12 @@ class ComputeTemplateMetrics(BaseMetricExtension):
             unit_ids = sorting_analyzer.unit_ids
         peak_sign = self.params["peak_sign"]
         upsampling_factor = self.params["upsampling_factor"]
-        min_thresh_detect_peaks_troughs = self.params["min_thresh_detect_peaks_troughs"]
-        edge_exclusion_ms = self.params.get("edge_exclusion_ms", 0.1)
+        min_thresh_detect_peaks_troughs = self.params.get("min_thresh_detect_peaks_troughs", 0.3)
+        edge_exclusion_ms = self.params.get("edge_exclusion_ms", 0.09)
         min_peak_trough_distance_ratio = self.params.get("min_peak_trough_distance_ratio", 0.2)
         min_extremum_distance_samples = self.params.get("min_extremum_distance_samples", 3)
         sampling_frequency = sorting_analyzer.sampling_frequency
-        if self.params["upsampling_factor"] > 1:
+        if upsampling_factor > 1:
             sampling_frequency_up = upsampling_factor * sampling_frequency
         else:
             sampling_frequency_up = sampling_frequency
@@ -249,7 +254,7 @@ class ComputeTemplateMetrics(BaseMetricExtension):
             m in get_multi_channel_template_metric_names() for m in self.params["metrics_to_compute"]
         )
 
-        operator = self.params["template_operator"]
+        operator = self.params.get("template_operator", "average")
         extremum_channel_indices = get_template_extremum_channel(
             sorting_analyzer, peak_sign=peak_sign, outputs="index", operator=operator
         )
@@ -312,7 +317,7 @@ class ComputeTemplateMetrics(BaseMetricExtension):
             # multi_channel_templates is a list of 2D arrays of shape (n_times, n_channels)
             tmp_data["multi_channel_templates"] = multi_channel_templates
             tmp_data["channel_locations_multi"] = channel_locations_multi
-            tmp_data["depth_direction"] = self.params["depth_direction"]
+            tmp_data["depth_direction"] = self.params.get("depth_direction", "y")
 
         # Add peaks_info and preprocessed templates to self.data for storage in extension
         columns = []

{spikeinterface-0.104.0 → spikeinterface-0.104.2}/src/spikeinterface/postprocessing/valid_unit_periods.py

@@ -548,12 +548,12 @@ class ComputeValidUnitPeriods(AnalyzerExtension):
             for segment_index in range(self.sorting_analyzer.get_num_segments()):
                 segment_mask = good_periods_array["segment_index"] == segment_index
                 periods_dict = {}
-                for unit_index in unit_ids:
-                    periods_dict[unit_index] = []
+                for unit_index, unit_id in enumerate(unit_ids):
+                    periods_dict[unit_id] = []
                     unit_mask = good_periods_array["unit_index"] == unit_index
                     good_periods_unit_segment = good_periods_array[segment_mask & unit_mask]
                     for start, end in good_periods_unit_segment[["start_sample_index", "end_sample_index"]]:
-                        periods_dict[unit_index].append((start, end))
+                        periods_dict[unit_id].append((start, end))
                 good_periods.append(periods_dict)
 
         return good_periods

{spikeinterface-0.104.0 → spikeinterface-0.104.2/src/spikeinterface.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spikeinterface
-Version: 0.104.0
+Version: 0.104.2
 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