figpack 0.2.15__py3-none-any.whl → 0.2.17__py3-none-any.whl

figpack/spike_sorting/views/SpikeAmplitudesItem.py

@@ -1,38 +0,0 @@
-"""
-SpikeAmplitudesItem for figpack - represents spike amplitudes for a single unit
-"""
-
-from typing import Union
-
-import numpy as np
-
-
-class SpikeAmplitudesItem:
-    """
-    Represents spike amplitudes for a single unit
-    """
-
-    def __init__(
-        self,
-        *,
-        unit_id: Union[str, int],
-        spike_times_sec: np.ndarray,
-        spike_amplitudes: np.ndarray,
-    ):
-        """
-        Initialize a SpikeAmplitudesItem
-
-        Args:
-            unit_id: Identifier for the unit
-            spike_times_sec: 1D numpy array of spike times in seconds
-            spike_amplitudes: 1D numpy array of spike amplitudes
-        """
-        assert spike_times_sec.ndim == 1, "Spike times must be 1-dimensional"
-        assert spike_amplitudes.ndim == 1, "Spike amplitudes must be 1-dimensional"
-        assert len(spike_times_sec) == len(
-            spike_amplitudes
-        ), "Spike times and amplitudes must have the same length"
-
-        self.unit_id = unit_id
-        self.spike_times_sec = np.array(spike_times_sec, dtype=np.float32)
-        self.spike_amplitudes = np.array(spike_amplitudes, dtype=np.float32)

figpack/spike_sorting/views/UnitMetricsGraph.py

@@ -1,129 +0,0 @@
-"""
-UnitMetricsGraph view for figpack - displays unit metrics in a graph format
-"""
-
-from typing import List, Optional, Union, Dict
-import json
-
-import numpy as np
-import zarr
-
-from ...core.figpack_view import FigpackView
-
-
-class UnitMetricsGraphMetric:
-    """
-    Defines a metric with key, label, and data type
-    """
-
-    def __init__(
-        self,
-        *,
-        key: str,
-        label: str,
-        dtype: str,
-    ):
-        """
-        Initialize a UnitMetricsGraphMetric
-
-        Args:
-            key: Unique identifier for the metric
-            label: Human-readable label for display
-            dtype: Data type of the metric ("int", "float", etc.)
-        """
-        self.key = key
-        self.label = label
-        self.dtype = dtype
-
-    def to_dict(self) -> Dict:
-        """Convert to dictionary for serialization"""
-        return {
-            "key": self.key,
-            "label": self.label,
-            "dtype": self.dtype,
-        }
-
-
-class UnitMetricsGraphUnit:
-    """
-    Represents a unit with its metric values
-    """
-
-    def __init__(
-        self,
-        *,
-        unit_id: Union[str, int],
-        values: Dict[str, Union[int, float]],
-    ):
-        """
-        Initialize a UnitMetricsGraphUnit
-
-        Args:
-            unit_id: Identifier for the unit
-            values: Dictionary mapping metric keys to their values
-        """
-        self.unit_id = unit_id
-        self.values = values
-
-    def to_dict(self) -> Dict:
-        """Convert to dictionary for serialization"""
-        return {
-            "unit_id": str(self.unit_id),
-            "values": self.values,
-        }
-
-
-class UnitMetricsGraph(FigpackView):
-    """
-    A view that displays unit metrics in a graph format
-    """
-
-    def __init__(
-        self,
-        *,
-        units: List[UnitMetricsGraphUnit],
-        metrics: List[UnitMetricsGraphMetric],
-        height: Optional[int] = None,
-    ):
-        """
-        Initialize a UnitMetricsGraph view
-
-        Args:
-            units: List of UnitMetricsGraphUnit objects containing the data
-            metrics: List of UnitMetricsGraphMetric objects defining the metrics
-            height: Height of the view in pixels
-        """
-        self.units = units
-        self.metrics = metrics
-        self.height = height
-
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
-        """
-        Write the UnitMetricsGraph data to a Zarr group
-
-        Args:
-            group: Zarr group to write data into
-        """
-        # Set the view type
-        group.attrs["view_type"] = "UnitMetricsGraph"
-
-        # Set view properties
-        if self.height is not None:
-            group.attrs["height"] = self.height
-
-        # Store metrics metadata
-        metrics_metadata = [metric.to_dict() for metric in self.metrics]
-        group.attrs["metrics"] = metrics_metadata
-
-        # Store units data in a zarr array
-        units_data = [unit.to_dict() for unit in self.units]
-        units_json = json.dumps(units_data).encode("utf-8")
-        units_array = np.frombuffer(units_json, dtype=np.uint8)
-        group.create_dataset(
-            "units_data",
-            data=units_array,
-            dtype=np.uint8,
-            chunks=True,
-            compressor=zarr.Blosc(cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE),
-        )
-        group.attrs["units_data_size"] = len(units_json)

figpack/spike_sorting/views/UnitSimilarityScore.py

@@ -1,40 +0,0 @@
-"""
-UnitSimilarityScore for spike sorting views
-"""
-
-from typing import Union
-
-
-class UnitSimilarityScore:
-    """
-    Represents a similarity score between two units
-    """
-
-    def __init__(
-        self,
-        *,
-        unit_id1: Union[str, int],
-        unit_id2: Union[str, int],
-        similarity: float,
-    ):
-        """
-        Initialize a UnitSimilarityScore
-
-        Args:
-            unit_id1: Identifier for the first unit
-            unit_id2: Identifier for the second unit
-            similarity: Similarity score between the units (typically 0-1)
-        """
-        self.unit_id1 = unit_id1
-        self.unit_id2 = unit_id2
-        self.similarity = similarity
-
-    def to_dict(self):
-        """
-        Convert the similarity score to a dictionary representation
-        """
-        return {
-            "unitId1": self.unit_id1,
-            "unitId2": self.unit_id2,
-            "similarity": self.similarity,
-        }

figpack/spike_sorting/views/UnitsTable.py

@@ -1,89 +0,0 @@
-"""
-UnitsTable view for figpack - displays a table of units with their properties
-"""
-
-from typing import List, Optional
-import json
-
-import numpy as np
-import zarr
-
-from ...core.figpack_view import FigpackView
-from .UnitSimilarityScore import UnitSimilarityScore
-from .UnitsTableColumn import UnitsTableColumn
-from .UnitsTableRow import UnitsTableRow
-
-
-class UnitsTable(FigpackView):
-    """
-    A view that displays a table of units with their properties and optional similarity scores
-    """
-
-    def __init__(
-        self,
-        *,
-        columns: List[UnitsTableColumn],
-        rows: List[UnitsTableRow],
-        similarity_scores: Optional[List[UnitSimilarityScore]] = None,
-        height: Optional[int] = 600,
-    ):
-        """
-        Initialize a UnitsTable view
-
-        Args:
-            columns: List of UnitsTableColumn objects defining the table structure
-            rows: List of UnitsTableRow objects containing the data
-            similarity_scores: Optional list of UnitSimilarityScore objects
-            height: Height of the view in pixels
-        """
-        self.columns = columns
-        self.rows = rows
-        self.similarity_scores = similarity_scores or []
-        self.height = height
-
-    def _write_to_zarr_group(self, group: zarr.Group) -> None:
-        """
-        Write the UnitsTable data to a Zarr group
-
-        Args:
-            group: Zarr group to write data into
-        """
-        # Set the view type
-        group.attrs["view_type"] = "UnitsTable"
-
-        # Set view properties
-        if self.height is not None:
-            group.attrs["height"] = self.height
-
-        # Store columns metadata
-        columns_metadata = [col.to_dict() for col in self.columns]
-        group.attrs["columns"] = columns_metadata
-
-        # Store rows data in a zarr array
-        rows_data = [row.to_dict() for row in self.rows]
-        rows_json = json.dumps(rows_data).encode("utf-8")
-        rows_array = np.frombuffer(rows_json, dtype=np.uint8)
-        group.create_dataset(
-            "rows_data",
-            data=rows_array,
-            dtype=np.uint8,
-            chunks=True,
-            compressor=zarr.Blosc(cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE),
-        )
-        group.attrs["rows_data_size"] = len(rows_json)
-
-        # Store similarity scores in a zarr array
-        if self.similarity_scores:
-            scores_data = [score.to_dict() for score in self.similarity_scores]
-            scores_json = json.dumps(scores_data).encode("utf-8")
-            scores_array = np.frombuffer(scores_json, dtype=np.uint8)
-            group.create_dataset(
-                "similarity_scores_data",
-                data=scores_array,
-                dtype=np.uint8,
-                chunks=True,
-                compressor=zarr.Blosc(
-                    cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE
-                ),
-            )
-            group.attrs["similarity_scores_data_size"] = len(scores_json)

figpack/spike_sorting/views/UnitsTableColumn.py

@@ -1,40 +0,0 @@
-"""
-UnitsTableColumn for spike sorting views
-"""
-
-from typing import Literal
-
-
-class UnitsTableColumn:
-    """
-    Represents a column in a units table
-    """
-
-    def __init__(
-        self,
-        *,
-        key: str,
-        label: str,
-        dtype: Literal["int", "float", "str", "bool"],
-    ):
-        """
-        Initialize a UnitsTableColumn
-
-        Args:
-            key: The key used to access values in the row data
-            label: Display label for the column
-            dtype: Data type of the column values
-        """
-        self.key = key
-        self.label = label
-        self.dtype = dtype
-
-    def to_dict(self):
-        """
-        Convert the column to a dictionary representation
-        """
-        return {
-            "key": self.key,
-            "label": self.label,
-            "dtype": self.dtype,
-        }

figpack/spike_sorting/views/UnitsTableRow.py

@@ -1,36 +0,0 @@
-"""
-UnitsTableRow for spike sorting views
-"""
-
-from typing import Any, Dict, Union
-
-
-class UnitsTableRow:
-    """
-    Represents a row in a units table
-    """
-
-    def __init__(
-        self,
-        *,
-        unit_id: Union[str, int],
-        values: Dict[str, Any],
-    ):
-        """
-        Initialize a UnitsTableRow
-
-        Args:
-            unit_id: Identifier for the unit
-            values: Dictionary of column key to value mappings
-        """
-        self.unit_id = unit_id
-        self.values = values
-
-    def to_dict(self):
-        """
-        Convert the row to a dictionary representation
-        """
-        return {
-            "unitId": self.unit_id,
-            "values": self.values,
-        }

figpack/spike_sorting/views/__init__.py

@@ -1,41 +0,0 @@
-"""
-Spike sorting views for figpack
-"""
-
-from .AutocorrelogramItem import AutocorrelogramItem
-from .Autocorrelograms import Autocorrelograms
-from .CrossCorrelogramItem import CrossCorrelogramItem
-from .CrossCorrelograms import CrossCorrelograms
-from .UnitSimilarityScore import UnitSimilarityScore
-from .UnitsTable import UnitsTable
-from .UnitsTableColumn import UnitsTableColumn
-from .UnitsTableRow import UnitsTableRow
-from .AverageWaveforms import AverageWaveforms
-from .SpikeAmplitudesItem import SpikeAmplitudesItem
-from .SpikeAmplitudes import SpikeAmplitudes
-from .RasterPlotItem import RasterPlotItem
-from .RasterPlot import RasterPlot
-from .UnitMetricsGraph import (
-    UnitMetricsGraph,
-    UnitMetricsGraphMetric,
-    UnitMetricsGraphUnit,
-)
-
-__all__ = [
-    "AutocorrelogramItem",
-    "Autocorrelograms",
-    "CrossCorrelogramItem",
-    "CrossCorrelograms",
-    "UnitsTableColumn",
-    "UnitsTableRow",
-    "UnitSimilarityScore",
-    "UnitsTable",
-    "AverageWaveforms",
-    "SpikeAmplitudesItem",
-    "SpikeAmplitudes",
-    "RasterPlotItem",
-    "RasterPlot",
-    "UnitMetricsGraph",
-    "UnitMetricsGraphMetric",
-    "UnitMetricsGraphUnit",
-]

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