figpack-spike-sorting 0.1.9__py3-none-any.whl → 0.1.10__py3-none-any.whl

figpack_spike_sorting/views/AverageWaveforms.py

@@ -2,7 +2,7 @@
 AverageWaveforms view for figpack - displays multiple average waveforms
 """
 
-from typing import List, Optional, Union
+from typing import List, Optional, Union, Dict, Any
 
 import numpy as np
 import figpack
@@ -54,7 +54,12 @@ class AverageWaveforms(figpack.ExtensionView):
     A view that displays multiple average waveforms for spike sorting analysis
     """
 
-    def __init__(self, *, average_waveforms: List[AverageWaveformItem]):
+    def __init__(
+        self,
+        *,
+        average_waveforms: List[AverageWaveformItem],
+        channel_locations: Union[None, Dict[str, Any]] = None,
+    ):
         """
         Initialize an AverageWaveforms view
 
@@ -66,6 +71,7 @@ class AverageWaveforms(figpack.ExtensionView):
             view_type="spike_sorting.AverageWaveforms",
         )
         self.average_waveforms = average_waveforms
+        self.channel_locations = channel_locations
 
     @staticmethod
     def from_sorting_analyzer(sorting_analyzer):
@@ -112,6 +118,12 @@ class AverageWaveforms(figpack.ExtensionView):
         # Store the number of average waveforms
         group.attrs["num_average_waveforms"] = len(self.average_waveforms)
 
+        if self.channel_locations is not None:
+            channel_locations_dict = {}
+            for ch_id, loc in self.channel_locations.items():
+                channel_locations_dict[str(ch_id)] = [float(a) for a in loc]
+            group.attrs["channel_locations"] = channel_locations_dict
+
         # Store metadata for each average waveform
         average_waveform_metadata = []
         for i, waveform in enumerate(self.average_waveforms):
@@ -136,12 +148,15 @@ class AverageWaveforms(figpack.ExtensionView):
                     data=waveform.waveform_std_dev,
                 )
             if waveform.waveform_percentiles is not None:
-                for j, p in enumerate(waveform.waveform_percentiles):
-                    group.create_dataset(
-                        f"{waveform_name}/waveform_percentile_{j}",
-                        data=p,
-                        dtype=p.dtype,
-                    )
+                # concat along first axis
+                waveform_percentiles_concat = np.stack(
+                    waveform.waveform_percentiles, axis=0
+                )
+                group.create_dataset(
+                    f"{waveform_name}/waveform_percentiles",
+                    data=waveform_percentiles_concat,
+                    dtype=waveform_percentiles_concat.dtype,
+                )
 
         # Store the average waveform metadata
         group.attrs["average_waveforms"] = average_waveform_metadata

{figpack_spike_sorting-0.1.9.dist-info → figpack_spike_sorting-0.1.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: figpack_spike_sorting
-Version: 0.1.9
+Version: 0.1.10
 Summary: Spike Sorting specific extension for figpack
 Home-page: https://github.com/flatironinstitute/figpack
 Author: figpack contributors

{figpack_spike_sorting-0.1.9.dist-info → figpack_spike_sorting-0.1.10.dist-info}/RECORD

@@ -1,10 +1,10 @@
-figpack_spike_sorting/__init__.py,sha256=_Zs1NXfy-jeCBgjeBaeYj1NoBwKLegGZekA7GWk4QOg,100
-figpack_spike_sorting/figpack_spike_sorting.js,sha256=V2ytXiMK1So90UeOZAIqzbrYlQh_jYT2jwTlq7CJq9U,1509840
+figpack_spike_sorting/__init__.py,sha256=cOe9uUkswDw9ukyVyHxTNtcSe0JSXZiNT3BhSR8VYKs,101
+figpack_spike_sorting/figpack_spike_sorting.js,sha256=_ejq5vMz6_AbLfNd6l1615MOlBnBJbm5C8rKdF4p9ig,1510577
 figpack_spike_sorting/spike_sorting_extension.py,sha256=ugpk8hDsO4RmyQRNjfhB4Pw5p10FmhQeu3koBynSPHU,755
 figpack_spike_sorting/style.css,sha256=R4pcnrpSMpOsBn7X1t-JBP8ODktsc5e8o95Fl_0LVps,3208
 figpack_spike_sorting/views/AutocorrelogramItem.py,sha256=qHmvIdHpbfVA_utPb5N2oP3hSP2cGnlT8VLaxOXV4UM,738
 figpack_spike_sorting/views/Autocorrelograms.py,sha256=-vyBayJPnJsGY6fMXKOJyA4qfmKlUBngTXCYzali4sY,3742
-figpack_spike_sorting/views/AverageWaveforms.py,sha256=mqbQeAbunvMnMU1vS7_u4nDThBoCrvaciRuoBdyvWD8,5218
+figpack_spike_sorting/views/AverageWaveforms.py,sha256=65U7FN7LjCLQWT0Mc08EVYt0s7K9LhcPBSPhyVjWlBw,5804
 figpack_spike_sorting/views/CrossCorrelogramItem.py,sha256=uSd0i2hupteuILi_aKp7bYPYpL_PdC3CUDRMOEKUEM0,880
 figpack_spike_sorting/views/CrossCorrelograms.py,sha256=uDq27k2ixpc3yQVvzpZzogXbq2uCIPKoKCcTRlPBG6w,4490
 figpack_spike_sorting/views/RasterPlot.py,sha256=jk5mDGjGPhgGu6YtYJJhMSZgLdH4o9qmJqT3juONNPg,9982
@@ -20,7 +20,7 @@ figpack_spike_sorting/views/UnitsTable.py,sha256=8aluJ2tCnwsFOLbjbJDyY2z1ml9VK7S
 figpack_spike_sorting/views/UnitsTableColumn.py,sha256=zBnuoeILTuiVLDvtcOxqa37E5WlbR12rlwNJUeWXxY4,847
 figpack_spike_sorting/views/UnitsTableRow.py,sha256=rEb2hMTA_pl2fTW1nOvnGir0ysfNx4uww3aekZzfWjk,720
 figpack_spike_sorting/views/__init__.py,sha256=gUt261Id35gNiJyne6GY-NzIGyTfRDmL25tNjyC2dLY,1409
-figpack_spike_sorting-0.1.9.dist-info/METADATA,sha256=5DJesKdTLJAM2yTEtowLS99HbeTu4S-ZY7kCF2X8GTo,1218
-figpack_spike_sorting-0.1.9.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-figpack_spike_sorting-0.1.9.dist-info/top_level.txt,sha256=CAkWrQc1wGK5laYDkT2GBjGgAuNwWNXKodTQlTcpxus,22
-figpack_spike_sorting-0.1.9.dist-info/RECORD,,
+figpack_spike_sorting-0.1.10.dist-info/METADATA,sha256=9JMa7jm-uV7wRUwa-S7H9fG30RrxF2bjTNQaLkP3MSk,1219
+figpack_spike_sorting-0.1.10.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+figpack_spike_sorting-0.1.10.dist-info/top_level.txt,sha256=CAkWrQc1wGK5laYDkT2GBjGgAuNwWNXKodTQlTcpxus,22
+figpack_spike_sorting-0.1.10.dist-info/RECORD,,