PyPI - figpack - Versions diffs - 0.2.1__py3-none-any.whl → 0.2.3__py3-none-any.whl - Mend

figpack 0.2.1py3-none-any.whl → 0.2.3py3-none-any.whl

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Files changed (27) hide show

figpack/__init__.py +1 -1
figpack/cli.py +60 -3
figpack/core/_server_manager.py +304 -0
figpack/core/_show_view.py +128 -92
figpack/core/_upload_bundle.py +19 -9
figpack/core/figpack_view.py +34 -2
figpack/figpack-gui-dist/assets/index-DUR9Dmwh.js +847 -0
figpack/figpack-gui-dist/index.html +1 -1
figpack/franklab/__init__.py +5 -0
figpack/franklab/views/TrackAnimation.py +153 -0
figpack/franklab/views/__init__.py +9 -0
figpack/spike_sorting/views/AutocorrelogramItem.py +0 -10
figpack/spike_sorting/views/Autocorrelograms.py +2 -0
figpack/spike_sorting/views/AverageWaveforms.py +147 -0
figpack/spike_sorting/views/CrossCorrelogramItem.py +0 -11
figpack/spike_sorting/views/CrossCorrelograms.py +2 -0
figpack/spike_sorting/views/SpikeAmplitudes.py +89 -0
figpack/spike_sorting/views/SpikeAmplitudesItem.py +38 -0
figpack/spike_sorting/views/__init__.py +6 -0
{figpack-0.2.1.dist-info → figpack-0.2.3.dist-info}/METADATA +3 -2
figpack-0.2.3.dist-info/RECORD +47 -0
figpack/figpack-gui-dist/assets/index-BqYF6BN-.js +0 -846
figpack-0.2.1.dist-info/RECORD +0 -40
{figpack-0.2.1.dist-info → figpack-0.2.3.dist-info}/WHEEL +0 -0
{figpack-0.2.1.dist-info → figpack-0.2.3.dist-info}/entry_points.txt +0 -0
{figpack-0.2.1.dist-info → figpack-0.2.3.dist-info}/licenses/LICENSE +0 -0
{figpack-0.2.1.dist-info → figpack-0.2.3.dist-info}/top_level.txt +0 -0

figpack/figpack-gui-dist/index.html CHANGED Viewed

@@ -5,7 +5,7 @@
     <link rel="icon" type="image/png" href="./assets/neurosift-logo-CLsuwLMO.png" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>figpack figure</title>
-    <script type="module" crossorigin src="./assets/index-BqYF6BN-.js"></script>
+    <script type="module" crossorigin src="./assets/index-DUR9Dmwh.js"></script>
     <link rel="stylesheet" crossorigin href="./assets/index-Cmae55E4.css">
   </head>
   <body>

figpack/franklab/__init__.py ADDED Viewed

@@ -0,0 +1,5 @@
+"""
+Franklab views for figpack
+"""
+from . import views

figpack/franklab/views/TrackAnimation.py ADDED Viewed

@@ -0,0 +1,153 @@
+"""
+TrackAnimation view for figpack - displays animated tracking data
+"""
+from typing import Optional
+import numpy as np
+import zarr
+from ...core.figpack_view import FigpackView
+class TrackAnimation(FigpackView):
+    """
+    A track animation visualization component for displaying animal tracking data
+    """
+    def __init__(
+        self,
+        *,
+        bin_height: float,
+        bin_width: float,
+        frame_bounds: np.ndarray,
+        locations: np.ndarray,
+        values: np.ndarray,
+        xcount: int,
+        ycount: int,
+        xmin: float,
+        ymin: float,
+        head_direction: np.ndarray,
+        positions: np.ndarray,
+        timestamps: np.ndarray,
+        track_bin_corners: np.ndarray,
+        sampling_frequency_hz: float,
+        timestamp_start: float,
+        total_recording_frame_length: int,
+        track_bin_height: float,
+        track_bin_width: float,
+        xmax: float,
+        ymax: float,
+    ):
+        """
+        Initialize a TrackAnimation view
+        Args:
+            bin_height: Height of spatial bins
+            bin_width: Width of spatial bins
+            frame_bounds: Array of frame boundaries
+            locations: Array of spatial locations
+            values: Array of values at each location
+            xcount: Number of bins in x direction
+            ycount: Number of bins in y direction
+            xmin: Minimum x coordinate
+            ymin: Minimum y coordinate
+            head_direction: Array of head direction angles
+            positions: Array of position coordinates (2D)
+            timestamps: Array of timestamps
+            track_bin_corners: Array of track bin corner coordinates
+            sampling_frequency_hz: Sampling frequency in Hz
+            timestamp_start: Start timestamp
+            total_recording_frame_length: Total number of frames
+            track_bin_height: Height of track bins
+            track_bin_width: Width of track bins
+            xmax: Maximum x coordinate
+            ymax: Maximum y coordinate
+        """
+        # Validate input arrays
+        assert isinstance(
+            frame_bounds, np.ndarray
+        ), "frame_bounds must be a numpy array"
+        assert isinstance(locations, np.ndarray), "locations must be a numpy array"
+        assert isinstance(values, np.ndarray), "values must be a numpy array"
+        assert isinstance(
+            head_direction, np.ndarray
+        ), "head_direction must be a numpy array"
+        assert isinstance(positions, np.ndarray), "positions must be a numpy array"
+        assert isinstance(timestamps, np.ndarray), "timestamps must be a numpy array"
+        assert isinstance(
+            track_bin_corners, np.ndarray
+        ), "track_bin_corners must be a numpy array"
+        assert len(locations) == len(
+            values
+        ), "locations and values must have same length"
+        assert len(head_direction) == len(
+            timestamps
+        ), "head_direction and timestamps must have same length"
+        assert positions.shape[1] == len(
+            timestamps
+        ), "positions second dimension must match timestamps length"
+        assert positions.shape[0] == 2, "positions must have shape (2, N)"
+        # Store spatial binning parameters
+        self.bin_height = bin_height
+        self.bin_width = bin_width
+        self.xcount = xcount
+        self.ycount = ycount
+        self.xmin = xmin
+        self.ymin = ymin
+        self.xmax = xmax
+        self.ymax = ymax
+        # Store arrays
+        self.frame_bounds = frame_bounds
+        self.locations = locations
+        self.values = values
+        self.head_direction = head_direction
+        self.positions = positions
+        self.timestamps = timestamps
+        self.track_bin_corners = track_bin_corners
+        # Store metadata
+        self.sampling_frequency_hz = sampling_frequency_hz
+        self.timestamp_start = timestamp_start
+        self.total_recording_frame_length = total_recording_frame_length
+        self.track_bin_height = track_bin_height
+        self.track_bin_width = track_bin_width
+    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the track animation data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set view type
+        group.attrs["view_type"] = "TrackAnimation"
+        # Store spatial binning parameters
+        group.attrs["bin_height"] = self.bin_height
+        group.attrs["bin_width"] = self.bin_width
+        group.attrs["xcount"] = self.xcount
+        group.attrs["ycount"] = self.ycount
+        group.attrs["xmin"] = self.xmin
+        group.attrs["ymin"] = self.ymin
+        group.attrs["xmax"] = self.xmax
+        group.attrs["ymax"] = self.ymax
+        # Store metadata
+        group.attrs["sampling_frequency_hz"] = self.sampling_frequency_hz
+        group.attrs["timestamp_start"] = self.timestamp_start
+        group.attrs["total_recording_frame_length"] = self.total_recording_frame_length
+        group.attrs["track_bin_height"] = self.track_bin_height
+        group.attrs["track_bin_width"] = self.track_bin_width
+        # Store arrays as datasets
+        group.create_dataset("frame_bounds", data=self.frame_bounds)
+        group.create_dataset("locations", data=self.locations)
+        group.create_dataset("values", data=self.values)
+        group.create_dataset("head_direction", data=self.head_direction)
+        group.create_dataset("positions", data=self.positions)
+        group.create_dataset("timestamps", data=self.timestamps)
+        group.create_dataset("track_bin_corners", data=self.track_bin_corners)

figpack/franklab/views/__init__.py ADDED Viewed

@@ -0,0 +1,9 @@
+"""
+Franklab views for figpack
+"""
+from .TrackAnimation import TrackAnimation
+__all__ = [
+    "TrackAnimation",
+]

figpack/spike_sorting/views/AutocorrelogramItem.py CHANGED Viewed

@@ -30,13 +30,3 @@ class AutocorrelogramItem:
         self.unit_id = unit_id
         self.bin_edges_sec = np.array(bin_edges_sec, dtype=np.float32)
         self.bin_counts = np.array(bin_counts, dtype=np.int32)
-    def to_dict(self):
-        """
-        Convert the autocorrelogram item to a dictionary representation
-        """
-        return {
-            "unit_id": str(self.unit_id),
-            "bin_edges_sec": self.bin_edges_sec.tolist(),
-            "bin_counts": self.bin_counts.tolist(),
-        }

figpack/spike_sorting/views/Autocorrelograms.py CHANGED Viewed

@@ -29,6 +29,7 @@ class Autocorrelograms(FigpackView):
         """
         self.autocorrelograms = autocorrelograms
+    @staticmethod
     def from_sorting(sorting):
         import spikeinterface as si
         import spikeinterface.widgets as sw
@@ -37,6 +38,7 @@ class Autocorrelograms(FigpackView):
         W = sw.plot_autocorrelograms(sorting)
         return Autocorrelograms.from_spikeinterface_widget(W)
+    @staticmethod
     def from_spikeinterface_widget(W):
         from spikeinterface.widgets.base import to_attr
         from spikeinterface.widgets.utils_sortingview import make_serializable

figpack/spike_sorting/views/AverageWaveforms.py ADDED Viewed

@@ -0,0 +1,147 @@
+"""
+AverageWaveforms view for figpack - displays multiple average waveforms
+"""
+from typing import List, Optional, Union
+import numpy as np
+import zarr
+from ...core.figpack_view import FigpackView
+class AverageWaveformItem:
+    """
+    Represents a single average waveform for a unit
+    """
+    def __init__(
+        self,
+        *,
+        unit_id: Union[str, int],
+        channel_ids: List[Union[str, int]],
+        waveform: np.ndarray,
+        waveform_std_dev: Optional[np.ndarray] = None,
+        waveform_percentiles: Optional[List[np.ndarray]] = None,
+    ):
+        """
+        Initialize an AverageWaveformItem
+        Args:
+            unit_id: Identifier for the unit
+            channel_ids: List of channel identifiers
+            waveform: 2D numpy array representing the average waveform (num_samples x num_channels)
+            waveform_std_dev: Optional 2D numpy array representing the standard deviation of the waveform
+            waveform_percentiles: Optional list of 2D numpy arrays representing percentiles of the waveform
+        """
+        self.unit_id = unit_id
+        self.channel_ids = channel_ids
+        self.waveform = np.array(waveform, dtype=np.float32)
+        self.waveform_std_dev = (
+            np.array(waveform_std_dev, dtype=np.float32)
+            if waveform_std_dev is not None
+            else None
+        )
+        if waveform_percentiles is not None:
+            self.waveform_percentiles = [
+                np.array(p, dtype=np.float32) for p in waveform_percentiles
+            ]
+        else:
+            self.waveform_percentiles = None
+class AverageWaveforms(FigpackView):
+    """
+    A view that displays multiple average waveforms for spike sorting analysis
+    """
+    def __init__(self, *, average_waveforms: List[AverageWaveformItem]):
+        """
+        Initialize an AverageWaveforms view
+        Args:
+            average_waveforms: List of AverageWaveformItem objects
+        """
+        self.average_waveforms = average_waveforms
+    @staticmethod
+    def from_sorting_analyzer(sorting_analyzer):
+        sorting_analyzer.compute(
+            ["random_spikes", "waveforms", "templates", "noise_levels"]
+        )
+        ext_templates = sorting_analyzer.get_extension("templates")
+        # shape is num_units, num_samples, num_channels
+        av_templates = ext_templates.get_data(operator="average")
+        ext_noise_levels = sorting_analyzer.get_extension("noise_levels")
+        noise_levels = ext_noise_levels.get_data()
+        waveform_std_dev = np.zeros(
+            (av_templates.shape[1], av_templates.shape[2]), dtype=np.float32
+        )
+        for i in range(av_templates.shape[2]):
+            waveform_std_dev[:, i] = noise_levels[i]
+        average_waveform_items = []
+        for i, unit_id in enumerate(sorting_analyzer.unit_ids):
+            waveform = av_templates[i]
+            channel_ids = list(sorting_analyzer.recording.get_channel_ids())
+            average_waveform_items.append(
+                AverageWaveformItem(
+                    unit_id=unit_id,
+                    waveform=waveform,
+                    channel_ids=channel_ids,
+                    waveform_std_dev=waveform_std_dev,
+                )
+            )
+        view = AverageWaveforms(average_waveforms=average_waveform_items)
+        return view
+    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the AverageWaveforms data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set the view type
+        group.attrs["view_type"] = "AverageWaveforms"
+        # Store the number of average waveforms
+        group.attrs["num_average_waveforms"] = len(self.average_waveforms)
+        # Store metadata for each average waveform
+        average_waveform_metadata = []
+        for i, waveform in enumerate(self.average_waveforms):
+            waveform_name = f"waveform_{i}"
+            # Store metadata
+            metadata = {
+                "name": waveform_name,
+                "unit_id": str(waveform.unit_id),
+                "channel_ids": [str(ch) for ch in waveform.channel_ids],
+            }
+            average_waveform_metadata.append(metadata)
+            # Create arrays for this average waveform
+            group.create_dataset(
+                f"{waveform_name}/waveform",
+                data=waveform.waveform,
+                dtype=waveform.waveform.dtype,
+            )
+            if waveform.waveform_std_dev is not None:
+                group.create_dataset(
+                    f"{waveform_name}/waveform_std_dev",
+                    data=waveform.waveform_std_dev,
+                    dtype=waveform.waveform_std_dev.dtype,
+                )
+            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,
+                    )
+        # Store the average waveform metadata
+        group.attrs["average_waveforms"] = average_waveform_metadata

figpack/spike_sorting/views/CrossCorrelogramItem.py CHANGED Viewed

@@ -33,14 +33,3 @@ class CrossCorrelogramItem:
         self.unit_id2 = unit_id2
         self.bin_edges_sec = np.array(bin_edges_sec, dtype=np.float32)
         self.bin_counts = np.array(bin_counts, dtype=np.int32)
-    def to_dict(self):
-        """
-        Convert the cross-correlogram item to a dictionary representation
-        """
-        return {
-            "unit_id1": str(self.unit_id1),
-            "unit_id2": str(self.unit_id2),
-            "bin_edges_sec": self.bin_edges_sec.tolist(),
-            "bin_counts": self.bin_counts.tolist(),
-        }

figpack/spike_sorting/views/CrossCorrelograms.py CHANGED Viewed

@@ -32,6 +32,7 @@ class CrossCorrelograms(FigpackView):
         self.cross_correlograms = cross_correlograms
         self.hide_unit_selector = hide_unit_selector
+    @staticmethod
     def from_sorting(sorting):
         import spikeinterface as si
         import spikeinterface.widgets as sw
@@ -40,6 +41,7 @@ class CrossCorrelograms(FigpackView):
         W = sw.CrossCorrelogramsWidget(sorting)
         return CrossCorrelograms.from_spikeinterface_widget(W)
+    @staticmethod
     def from_spikeinterface_widget(W):
         from spikeinterface.widgets.base import to_attr
         from spikeinterface.widgets.utils_sortingview import make_serializable

figpack/spike_sorting/views/SpikeAmplitudes.py ADDED Viewed

@@ -0,0 +1,89 @@
+"""
+SpikeAmplitudes view for figpack - displays spike amplitudes over time
+"""
+from typing import List, Optional
+import numpy as np
+import zarr
+from ...core.figpack_view import FigpackView
+from .SpikeAmplitudesItem import SpikeAmplitudesItem
+class SpikeAmplitudes(FigpackView):
+    """
+    A view that displays spike amplitudes over time for multiple units
+    """
+    def __init__(
+        self,
+        *,
+        start_time_sec: float,
+        end_time_sec: float,
+        plots: List[SpikeAmplitudesItem],
+        hide_unit_selector: bool = False,
+        height: int = 500,
+    ):
+        """
+        Initialize a SpikeAmplitudes view
+        Args:
+            start_time_sec: Start time of the view in seconds
+            end_time_sec: End time of the view in seconds
+            plots: List of SpikeAmplitudesItem objects
+            hide_unit_selector: Whether to hide the unit selector
+            height: Height of the view in pixels
+        """
+        self.start_time_sec = start_time_sec
+        self.end_time_sec = end_time_sec
+        self.plots = plots
+        self.hide_unit_selector = hide_unit_selector
+        self.height = height
+    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the SpikeAmplitudes data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set the view type
+        group.attrs["view_type"] = "SpikeAmplitudes"
+        # Store view parameters
+        group.attrs["start_time_sec"] = self.start_time_sec
+        group.attrs["end_time_sec"] = self.end_time_sec
+        group.attrs["hide_unit_selector"] = self.hide_unit_selector
+        group.attrs["height"] = self.height
+        # Store the number of plots
+        group.attrs["num_plots"] = len(self.plots)
+        # Store metadata for each plot
+        plot_metadata = []
+        for i, plot in enumerate(self.plots):
+            plot_name = f"plot_{i}"
+            # Store metadata
+            metadata = {
+                "name": plot_name,
+                "unit_id": str(plot.unit_id),
+                "num_spikes": len(plot.spike_times_sec),
+            }
+            plot_metadata.append(metadata)
+            # Create arrays for this plot
+            group.create_dataset(
+                f"{plot_name}/spike_times_sec",
+                data=plot.spike_times_sec,
+                dtype=np.float32,
+            )
+            group.create_dataset(
+                f"{plot_name}/spike_amplitudes",
+                data=plot.spike_amplitudes,
+                dtype=np.float32,
+            )
+        # Store the plot metadata
+        group.attrs["plots"] = plot_metadata

figpack/spike_sorting/views/SpikeAmplitudesItem.py ADDED Viewed

@@ -0,0 +1,38 @@
+"""
+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/__init__.py CHANGED Viewed

@@ -10,6 +10,9 @@ 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
 __all__ = [
     "AutocorrelogramItem",
@@ -20,4 +23,7 @@ __all__ = [
     "UnitsTableRow",
     "UnitSimilarityScore",
     "UnitsTable",
+    "AverageWaveforms",
+    "SpikeAmplitudesItem",
+    "SpikeAmplitudes",
 ]

{figpack-0.2.1.dist-info → figpack-0.2.3.dist-info}/METADATA RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: figpack
-Version: 0.2.1
+Version: 0.2.3
 Summary: A Python package for creating shareable, interactive visualizations in the browser
 Author-email: Jeremy Magland <jmagland@flatironinstitute.org>
 License: Apache-2.0
@@ -25,8 +25,9 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
-Requires-Dist: zarr
+Requires-Dist: zarr<3
 Requires-Dist: requests
+Requires-Dist: psutil
 Provides-Extra: test
 Requires-Dist: pytest>=7.0; extra == "test"
 Requires-Dist: pytest-cov>=4.0; extra == "test"

figpack-0.2.3.dist-info/RECORD ADDED Viewed

@@ -0,0 +1,47 @@
+figpack/__init__.py,sha256=qKVa2XgXzmxB506Y98CMOKvDXy8y-xdiDmkDLGJ3YE8,124
+figpack/cli.py,sha256=DYV-DxzWnQTMNywW-ZzhlTEFOEIt11rAKdobdBmRQFk,12051
+figpack/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+figpack/core/_bundle_utils.py,sha256=73E6FinAvrt1QATGncIqyg6JLeiWVmlGF8NOcFyeYSs,1913
+figpack/core/_server_manager.py,sha256=8uxJftMgJ7EcVXtLo_VQuaiCZIyqgE89yDfCXKEgyeQ,10922
+figpack/core/_show_view.py,sha256=WeHbQ1qdq5Lr54XTuNqmCIrwR4jbPWu8dT7Sm_UNcsk,5194
+figpack/core/_upload_bundle.py,sha256=8D3M778E7nvkl9xnyrFOBlFhOOhywdiwLzOSPCMm4KE,13351
+figpack/core/config.py,sha256=6EU9CMvzGk9308Xlx8iJ2cIHJV6pqhXyiZGkK2snA4g,108
+figpack/core/figpack_view.py,sha256=q-Xxk9X4dnLy_kGX0POC7FLB6qwmBfqrWD6uelPJZVE,3708
+figpack/figpack-gui-dist/index.html,sha256=HU8Dv1EzISPzQjibGxDA6tAz7VpzjL6o-HXOPKv4s4E,486
+figpack/figpack-gui-dist/assets/index-Cmae55E4.css,sha256=Yg0apcYehJwQvSQIUH13S7tsfqWQDevpJsAho0dDf0g,5499
+figpack/figpack-gui-dist/assets/index-DUR9Dmwh.js,sha256=iHbhpBXkfKoDzn-ZDxh2_uktWyzSTwes9gzgdBEM7PU,1590964
+figpack/figpack-gui-dist/assets/neurosift-logo-CLsuwLMO.png,sha256=g5m-TwrGh5f6-9rXtWV-znH4B0nHgc__0GWclRDLUHs,9307
+figpack/franklab/__init__.py,sha256=HkehqGImJE_sE2vbPDo-HbgtEYaMICb9-230xTYvRTU,56
+figpack/franklab/views/TrackAnimation.py,sha256=3Jv1Ri4FIwTyqNahinqhHsBH1Bv_iZrEGx12w6diJ2M,5636
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+figpack/spike_sorting/__init__.py,sha256=09njqh-oFaCTdZUsc4HAOFTliUYV9DClddfZ0Q_dm0I,61
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figpack 0.2.1__py3-none-any.whl → 0.2.3__py3-none-any.whl

Potentially problematic release.

figpack 0.2.1py3-none-any.whl → 0.2.3py3-none-any.whl