figpack-spike-sorting 0.1.10__py3-none-any.whl → 0.1.12__py3-none-any.whl

figpack_spike_sorting/views/SpikeLocations.py

@@ -0,0 +1,138 @@
+"""
+SpikeLocations view for figpack - displays spike locations in 2D space
+"""
+
+from typing import Dict, List, Optional, Tuple, Union
+
+import numpy as np
+import figpack
+from ..spike_sorting_extension import spike_sorting_extension
+
+
+class SpikeLocationsItem:
+    """
+    Represents spike locations for a single unit
+    """
+
+    def __init__(
+        self,
+        *,
+        unit_id: Union[str, int],
+        spike_times_sec: np.ndarray,
+        x_locations: np.ndarray,
+        y_locations: np.ndarray,
+    ):
+        """
+        Initialize a SpikeLocationsItem
+
+        Args:
+            unit_id: Identifier for the unit
+            spike_times_sec: Array of spike times in seconds
+            x_locations: Array of x coordinates for each spike
+            y_locations: Array of y coordinates for each spike
+        """
+        self.unit_id = unit_id
+        self.spike_times_sec = np.array(spike_times_sec, dtype=np.float32)
+        self.x_locations = np.array(x_locations, dtype=np.float32)
+        self.y_locations = np.array(y_locations, dtype=np.float32)
+
+        # Validate that all arrays have the same length
+        if not (
+            len(self.spike_times_sec) == len(self.x_locations) == len(self.y_locations)
+        ):
+            raise ValueError(
+                "spike_times_sec, x_locations, and y_locations must have the same length"
+            )
+
+
+class SpikeLocations(figpack.ExtensionView):
+    """
+    A view that displays spike locations in 2D space
+    """
+
+    def __init__(
+        self,
+        *,
+        units: List[SpikeLocationsItem],
+        x_range: Tuple[float, float],
+        y_range: Tuple[float, float],
+        channel_locations: Optional[Dict[str, np.ndarray]] = None,
+        hide_unit_selector: bool = False,
+        disable_auto_rotate: bool = False,
+    ):
+        """
+        Initialize a SpikeLocations view
+
+        Args:
+            units: List of SpikeLocationsItem objects
+            x_range: Tuple specifying the x-axis range (min, max)
+            y_range: Tuple specifying the y-axis range (min, max)
+            channel_locations: Optional dictionary mapping channel IDs to (x, y) coordinates
+            hide_unit_selector: Whether to hide the unit selector
+            disable_auto_rotate: Whether to disable automatic rotation of the view
+        """
+        super().__init__(
+            extension=spike_sorting_extension,
+            view_type="spike_sorting.SpikeLocations",
+        )
+        self.units = units
+        self.x_range = x_range
+        self.y_range = y_range
+        self.channel_locations = channel_locations
+        self.hide_unit_selector = hide_unit_selector
+        self.disable_auto_rotate = disable_auto_rotate
+
+    def write_to_zarr_group(self, group: figpack.Group) -> None:
+        """
+        Write the SpikeLocations data to a Zarr group
+
+        Args:
+            group: Zarr group to write data into
+        """
+        super().write_to_zarr_group(group)
+
+        # Store metadata
+        group.attrs["x_range"] = list(self.x_range)
+        group.attrs["y_range"] = list(self.y_range)
+
+        if self.hide_unit_selector:
+            group.attrs["hide_unit_selector"] = True
+
+        if self.disable_auto_rotate:
+            group.attrs["disable_auto_rotate"] = True
+
+        # Store channel locations if provided
+        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 unit data
+        unit_metadata = []
+        for i, unit_item in enumerate(self.units):
+            unit_name = f"unit_{i}"
+
+            # Store metadata
+            metadata = {
+                "name": unit_name,
+                "unit_id": str(unit_item.unit_id),
+            }
+            unit_metadata.append(metadata)
+
+            # Create datasets for this unit
+            group.create_dataset(
+                f"{unit_name}/spike_times_sec",
+                data=unit_item.spike_times_sec,
+            )
+            group.create_dataset(
+                f"{unit_name}/x_locations",
+                data=unit_item.x_locations,
+            )
+            group.create_dataset(
+                f"{unit_name}/y_locations",
+                data=unit_item.y_locations,
+            )
+
+        # Store the unit metadata
+        group.attrs["units"] = unit_metadata

figpack_spike_sorting/views/UnitSimilarityMatrix.py

@@ -0,0 +1,58 @@
+"""
+UnitSimilarityMatrix view for figpack - displays a similarity matrix between units
+"""
+
+from typing import List, Optional, Tuple, Union
+
+import figpack
+from ..spike_sorting_extension import spike_sorting_extension
+from .UnitSimilarityScore import UnitSimilarityScore
+
+
+class UnitSimilarityMatrix(figpack.ExtensionView):
+    """
+    A view that displays a similarity matrix between units
+    """
+
+    def __init__(
+        self,
+        *,
+        unit_ids: List[Union[str, int]],
+        similarity_scores: List[UnitSimilarityScore],
+        range: Optional[Tuple[float, float]] = None,
+    ):
+        """
+        Initialize a UnitSimilarityMatrix view
+
+        Args:
+            unit_ids: List of unit identifiers
+            similarity_scores: List of UnitSimilarityScore objects representing pairwise similarities
+            range: Optional tuple specifying the range for the color scale (min, max)
+        """
+        super().__init__(
+            extension=spike_sorting_extension,
+            view_type="spike_sorting.UnitSimilarityMatrix",
+        )
+        self.unit_ids = unit_ids
+        self.similarity_scores = similarity_scores
+        self.range = range
+
+    def write_to_zarr_group(self, group: figpack.Group) -> None:
+        """
+        Write the UnitSimilarityMatrix data to a Zarr group
+
+        Args:
+            group: Zarr group to write data into
+        """
+        super().write_to_zarr_group(group)
+
+        # Store unit IDs as strings
+        group.attrs["unit_ids"] = [str(uid) for uid in self.unit_ids]
+
+        # Store similarity scores as a list of dictionaries
+        similarity_scores_data = [score.to_dict() for score in self.similarity_scores]
+        group.attrs["similarity_scores"] = similarity_scores_data
+
+        # Store optional range parameter
+        if self.range is not None:
+            group.attrs["range"] = list(self.range)

figpack_spike_sorting/views/__init__.py

@@ -8,11 +8,13 @@ from .UnitsTableRow import UnitsTableRow
 from .UnitsTableColumn import UnitsTableColumn
 from .UnitsTable import UnitsTable
 from .UnitSimilarityScore import UnitSimilarityScore
+from .UnitSimilarityMatrix import UnitSimilarityMatrix
 from .AverageWaveforms import AverageWaveforms, AverageWaveformItem
 from .CrossCorrelograms import CrossCorrelograms, CrossCorrelogramItem
 from .RasterPlot import RasterPlot
 from .RasterPlotItem import RasterPlotItem
 from .SpikeAmplitudes import SpikeAmplitudes, SpikeAmplitudesItem
+from .SpikeLocations import SpikeLocations, SpikeLocationsItem
 from .UnitLocations import UnitLocations, UnitLocationsItem
 from .UnitMetricsGraph import (
     UnitMetricsGraph,
@@ -29,6 +31,7 @@ __all__ = [
     "UnitsTableColumn",
     "UnitsTable",
     "UnitSimilarityScore",
+    "UnitSimilarityMatrix",
     "AverageWaveforms",
     "AverageWaveformItem",
     "CrossCorrelograms",
@@ -37,6 +40,8 @@ __all__ = [
     "RasterPlotItem",
     "SpikeAmplitudes",
     "SpikeAmplitudesItem",
+    "SpikeLocations",
+    "SpikeLocationsItem",
     "UnitLocations",
     "UnitLocationsItem",
     "UnitMetricsGraph",

{figpack_spike_sorting-0.1.10.dist-info → figpack_spike_sorting-0.1.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: figpack_spike_sorting
-Version: 0.1.10
+Version: 0.1.12
 Summary: Spike Sorting specific extension for figpack
 Home-page: https://github.com/flatironinstitute/figpack
 Author: figpack contributors

{figpack_spike_sorting-0.1.10.dist-info → figpack_spike_sorting-0.1.12.dist-info}/RECORD

@@ -1,5 +1,5 @@
-figpack_spike_sorting/__init__.py,sha256=cOe9uUkswDw9ukyVyHxTNtcSe0JSXZiNT3BhSR8VYKs,101
-figpack_spike_sorting/figpack_spike_sorting.js,sha256=_ejq5vMz6_AbLfNd6l1615MOlBnBJbm5C8rKdF4p9ig,1510577
+figpack_spike_sorting/__init__.py,sha256=KmrACoB-IMTH3OdbGdJt4N1jk2huodjYbRErU6P2rlM,101
+figpack_spike_sorting/figpack_spike_sorting.js,sha256=TMfa_sfgauvw1CL4LXXkiTv0AjA2CeU6fLe1iC6f7Yw,1521126
 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
@@ -12,15 +12,17 @@ figpack_spike_sorting/views/RasterPlotItem.py,sha256=iW7fuDEjSfvf5YMIwrF_6cmKvD7
 figpack_spike_sorting/views/SortingCuration.py,sha256=J3p9vrhbnRt05qeihZk_i6EBWDcTGYs293WVW_9qLSk,1243
 figpack_spike_sorting/views/SpikeAmplitudes.py,sha256=H_VV0Z1kAVCztNaTYnOW8tqyu6FLtgFPWNrlmokVKeI,13290
 figpack_spike_sorting/views/SpikeAmplitudesItem.py,sha256=j5Na-diY-vRUAPu0t0VkyFCSKFnQ_f5HT077mB3Cy8c,1134
+figpack_spike_sorting/views/SpikeLocations.py,sha256=uSJVGZZ8nen1YOjePTA7SAQD8RtOzLTeQmKNQqKhUrs,4485
 figpack_spike_sorting/views/TiledImage.py,sha256=_nvFhvRoGWd7MN84d9CphB0bK4j0txlx035zm-hCDic,5457
 figpack_spike_sorting/views/UnitLocations.py,sha256=K18oJFnKshn0fZ9NtgKXcWGroJGc_OaF3f_ZEEInZPA,2336
 figpack_spike_sorting/views/UnitMetricsGraph.py,sha256=8YZo2-5d-RHKSfyUKYAfDvW9hZDCTzmnUAyb3fPWo3I,3373
+figpack_spike_sorting/views/UnitSimilarityMatrix.py,sha256=fO1vC9Ih-UipjczOqlsZCE0jQl35DLVaPQ75JwIqxlE,1880
 figpack_spike_sorting/views/UnitSimilarityScore.py,sha256=cJA9MkETos9qHhV1tqgA7SfNEaPo-duXYCE76hSFGnA,948
 figpack_spike_sorting/views/UnitsTable.py,sha256=8aluJ2tCnwsFOLbjbJDyY2z1ml9VK7Sz5_bxdRUAeDI,2758
 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-0.1.10.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,,
+figpack_spike_sorting/views/__init__.py,sha256=_Ffl0GtgA5hgVRt1hLlod60nGmgTbwplaPPS59uC2hA,1603
+figpack_spike_sorting-0.1.12.dist-info/METADATA,sha256=R9AIdvxvGLasVI5O5-6XQJv6aHSINYjJ329k6P9V84g,1219
+figpack_spike_sorting-0.1.12.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+figpack_spike_sorting-0.1.12.dist-info/top_level.txt,sha256=CAkWrQc1wGK5laYDkT2GBjGgAuNwWNXKodTQlTcpxus,22
+figpack_spike_sorting-0.1.12.dist-info/RECORD,,