spikeinterface 0.104.2__tar.gz → 0.104.4__tar.gz

{spikeinterface-0.104.2/src/spikeinterface.egg-info → spikeinterface-0.104.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spikeinterface
-Version: 0.104.2
+Version: 0.104.4
 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-0.104.2 → spikeinterface-0.104.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.104.2"
+version = "0.104.4"
 authors = [
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },

{spikeinterface-0.104.2 → spikeinterface-0.104.4}/src/spikeinterface/preprocessing/correct_lsb.py

@@ -10,6 +10,11 @@ def correct_lsb(recording, num_chunks_per_segment=20, chunk_size=10000, seed=Non
     Estimates the LSB of the recording and divide traces by LSB
     to ensure LSB = 1. Medians are also subtracted to avoid rounding errors.
 
+    Since the LSB is set at the acquisition level, it is shared across channels. The global
+    LSB is therefore estimated as the mode (most frequent value) of the per-channel LSBs,
+    which is robust both to undersampled channels (that overestimate the LSB) and to
+    spuriously small per-channel values arising from rounding errors.
+
     Parameters
     ----------
     recording : RecordingExtractor
@@ -64,7 +69,12 @@ def correct_lsb(recording, num_chunks_per_segment=20, chunk_size=10000, seed=Non
 
 def _estimate_lsb_from_data(data):
     """
-    Estimate LSB by taking the minimum LSB found across channels.
+    Estimate the global LSB as the mode of the per-channel LSBs.
+
+    For each channel the LSB is the smallest difference between consecutive unique values.
+    Since the LSB is shared across channels, the global estimate is the most frequent
+    per-channel value, which is robust to undersampled channels (that overestimate the LSB)
+    and to spuriously small values from rounding errors.
 
     Parameters
     ----------
@@ -76,20 +86,23 @@ def _estimate_lsb_from_data(data):
     lsb_value : int
         The estimated LSB value. -1 indicates that lsb could not be estimated
     """
-    lsb_value = None
     num_channels = data.shape[1]
+    per_channel_lsb = []
     for ch in np.arange(num_channels):
-        unique_values = np.unique(data[:, ch])
+        # cast to int64 to avoid integer overflow in np.diff when consecutive
+        # unique values are farther apart than the dtype range (e.g. int16)
+        unique_values = np.unique(data[:, ch]).astype(np.int64)
         # It might happen that there is a single unique value (e.g. a channel is broken, or all zeros)
         if len(unique_values) > 1:
-            chan_lsb_val = np.min(np.diff(unique_values))
+            per_channel_lsb.append(np.min(np.diff(unique_values)))
         else:
             # in this case we can't estimate the LSB for the channel
             continue
 
-        if lsb_value is None:
-            lsb_value = chan_lsb_val
-        lsb_value = min(lsb_value, chan_lsb_val)
-    if lsb_value is None:
-        lsb_value = -1
+    if len(per_channel_lsb) == 0:
+        return -1
+
+    # mode: most frequent per-channel LSB (ties broken towards the smaller value)
+    values, counts = np.unique(per_channel_lsb, return_counts=True)
+    lsb_value = int(values[np.argmax(counts)])
     return lsb_value

{spikeinterface-0.104.2 → spikeinterface-0.104.4}/src/spikeinterface/preprocessing/filter.py

@@ -339,7 +339,13 @@ class HighpassFilterRecording(FilterRecording):
             self, recording, band=freq_min, margin_ms=margin_ms, dtype=dtype, btype="highpass", **filter_kwargs
         )
         dtype = fix_dtype(recording, dtype)
-        self._kwargs = dict(recording=recording, freq_min=freq_min, margin_ms=margin_ms, dtype=dtype.str)
+        self._kwargs = dict(
+            recording=recording,
+            freq_min=freq_min,
+            margin_ms=margin_ms,
+            dtype=dtype.str,
+            ignore_low_freq_error=ignore_low_freq_error,
+        )
         self._kwargs.update(filter_kwargs)
 
     @classmethod

{spikeinterface-0.104.2 → spikeinterface-0.104.4}/src/spikeinterface/widgets/sorting_summary.py

@@ -125,6 +125,7 @@ class SortingSummaryWidget(BaseWidget):
 
         use_sortingview = backend_kwargs.get("use_sortingview", False)
         vv_base, vv_views = import_figpack_or_sortingview(use_sortingview)
+        backend = "sortingview" if use_sortingview else "figpack"
 
         dp = to_attr(data_plot)
         sorting_analyzer = dp.sorting_analyzer
@@ -141,7 +142,7 @@ class SortingSummaryWidget(BaseWidget):
             hide_unit_selector=True,
             generate_url=False,
             display=False,
-            backend="figpack",
+            backend=backend,
         ).view
         v_average_waveforms = UnitTemplatesWidget(
             sorting_analyzer,
@@ -150,7 +151,7 @@ class SortingSummaryWidget(BaseWidget):
             hide_unit_selector=True,
             generate_url=False,
             display=False,
-            backend="figpack",
+            backend=backend,
         ).view
         v_cross_correlograms = CrossCorrelogramsWidget(
             sorting_analyzer,
@@ -159,7 +160,7 @@ class SortingSummaryWidget(BaseWidget):
             hide_unit_selector=True,
             generate_url=False,
             display=False,
-            backend="figpack",
+            backend=backend,
         ).view
 
         v_unit_locations = UnitLocationsWidget(
@@ -168,7 +169,7 @@ class SortingSummaryWidget(BaseWidget):
             hide_unit_selector=True,
             generate_url=False,
             display=False,
-            backend="figpack",
+            backend=backend,
         ).view
 
         w = TemplateSimilarityWidget(
@@ -177,7 +178,7 @@ class SortingSummaryWidget(BaseWidget):
             immediate_plot=False,
             generate_url=False,
             display=False,
-            backend="figpack",
+            backend=backend,
         )
         similarity = w.data_plot["similarity"]
 

{spikeinterface-0.104.2 → spikeinterface-0.104.4/src/spikeinterface.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spikeinterface
-Version: 0.104.2
+Version: 0.104.4
 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