PyPI - figpack - Versions diffs - 0.1.3__py3-none-any.whl → 0.1.5__py3-none-any.whl - Mend

figpack 0.1.3py3-none-any.whl → 0.1.5py3-none-any.whl

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Files changed (34) hide show

figpack/__init__.py +1 -5
figpack/cli.py +8 -7
figpack/core/_bundle_utils.py +2 -0
figpack/core/_show_view.py +4 -8
figpack/core/_upload_bundle.py +13 -11
figpack/core/figpack_view.py +1 -0
figpack/figpack-gui-dist/assets/{index-ByLxmrzp.js → index-DeyVLaXh.js} +88 -88
figpack/figpack-gui-dist/index.html +1 -1
figpack/spike_sorting/views/AutocorrelogramItem.py +1 -0
figpack/spike_sorting/views/Autocorrelograms.py +39 -9
figpack/spike_sorting/views/CrossCorrelogramItem.py +1 -0
figpack/spike_sorting/views/CrossCorrelograms.py +45 -7
figpack/spike_sorting/views/UnitsTable.py +5 -3
figpack/spike_sorting/views/UnitsTableRow.py +1 -1
figpack/spike_sorting/views/__init__.py +2 -2
figpack/views/Box.py +3 -1
figpack/views/Image.py +4 -2
figpack/views/LayoutItem.py +1 -0
figpack/views/Markdown.py +1 -0
figpack/views/MatplotlibFigure.py +4 -2
figpack/views/MultiChannelTimeseries.py +226 -0
figpack/views/PlotlyFigure.py +5 -3
figpack/views/Splitter.py +3 -1
figpack/views/TabLayout.py +3 -1
figpack/views/TabLayoutItem.py +1 -0
figpack/views/TimeseriesGraph.py +3 -2
figpack/views/__init__.py +7 -6
{figpack-0.1.3.dist-info → figpack-0.1.5.dist-info}/METADATA +48 -7
figpack-0.1.5.dist-info/RECORD +39 -0
figpack-0.1.3.dist-info/RECORD +0 -38
{figpack-0.1.3.dist-info → figpack-0.1.5.dist-info}/WHEEL +0 -0
{figpack-0.1.3.dist-info → figpack-0.1.5.dist-info}/entry_points.txt +0 -0
{figpack-0.1.3.dist-info → figpack-0.1.5.dist-info}/licenses/LICENSE +0 -0
{figpack-0.1.3.dist-info → figpack-0.1.5.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-ByLxmrzp.js"></script>
+    <script type="module" crossorigin src="./assets/index-DeyVLaXh.js"></script>
     <link rel="stylesheet" crossorigin href="./assets/index-BDa2iJW9.css">
   </head>
   <body>

figpack/spike_sorting/views/AutocorrelogramItem.py CHANGED Viewed

@@ -3,6 +3,7 @@ AutocorrelogramItem for spike sorting views
 """
 from typing import Union
 import numpy as np

figpack/spike_sorting/views/Autocorrelograms.py CHANGED Viewed

@@ -2,9 +2,11 @@
 Autocorrelograms view for figpack - displays multiple autocorrelograms
 """
-import zarr
-import numpy as np
 from typing import List, Optional
+import numpy as np
+import zarr
 from ...core.figpack_view import FigpackView
 from .AutocorrelogramItem import AutocorrelogramItem
@@ -18,17 +20,49 @@ class Autocorrelograms(FigpackView):
         self,
         *,
         autocorrelograms: List[AutocorrelogramItem],
-        height: Optional[int] = 400,
     ):
         """
         Initialize an Autocorrelograms view
         Args:
             autocorrelograms: List of AutocorrelogramItem objects
-            height: Height of the view in pixels
         """
         self.autocorrelograms = autocorrelograms
-        self.height = height
+    def from_sorting(sorting):
+        import spikeinterface as si
+        import spikeinterface.widgets as sw
+        assert isinstance(sorting, si.BaseSorting), "Input must be a BaseSorting object"
+        W = sw.plot_autocorrelograms(sorting)
+        return Autocorrelograms.from_spikeinterface_widget(W)
+    def from_spikeinterface_widget(W):
+        from spikeinterface.widgets.base import to_attr
+        from spikeinterface.widgets.utils_sortingview import make_serializable
+        from .AutocorrelogramItem import AutocorrelogramItem
+        data_plot = W.data_plot
+        dp = to_attr(data_plot)
+        unit_ids = make_serializable(dp.unit_ids)
+        ac_items = []
+        for i in range(len(unit_ids)):
+            for j in range(i, len(unit_ids)):
+                if i == j:
+                    ac_items.append(
+                        AutocorrelogramItem(
+                            unit_id=unit_ids[i],
+                            bin_edges_sec=(dp.bins / 1000.0).astype("float32"),
+                            bin_counts=dp.correlograms[i, j].astype("int32"),
+                        )
+                    )
+        view = Autocorrelograms(autocorrelograms=ac_items)
+        return view
     def _write_to_zarr_group(self, group: zarr.Group) -> None:
         """
@@ -40,10 +74,6 @@ class Autocorrelograms(FigpackView):
         # Set the view type
         group.attrs["view_type"] = "Autocorrelograms"
-        # Set view properties
-        if self.height is not None:
-            group.attrs["height"] = self.height
         # Store the number of autocorrelograms
         group.attrs["num_autocorrelograms"] = len(self.autocorrelograms)

figpack/spike_sorting/views/CrossCorrelogramItem.py CHANGED Viewed

@@ -3,6 +3,7 @@ CrossCorrelogramItem for spike sorting views
 """
 from typing import Union
 import numpy as np

figpack/spike_sorting/views/CrossCorrelograms.py CHANGED Viewed

@@ -2,9 +2,11 @@
 CrossCorrelograms view for figpack - displays multiple cross-correlograms
 """
-import zarr
-import numpy as np
 from typing import List, Optional
+import numpy as np
+import zarr
 from ...core.figpack_view import FigpackView
 from .CrossCorrelogramItem import CrossCorrelogramItem
@@ -19,7 +21,6 @@ class CrossCorrelograms(FigpackView):
         *,
         cross_correlograms: List[CrossCorrelogramItem],
         hide_unit_selector: Optional[bool] = False,
-        height: Optional[int] = 500,
     ):
         """
         Initialize a CrossCorrelograms view
@@ -27,11 +28,50 @@ class CrossCorrelograms(FigpackView):
         Args:
             cross_correlograms: List of CrossCorrelogramItem objects
             hide_unit_selector: Whether to hide the unit selector widget
-            height: Height of the view in pixels
         """
         self.cross_correlograms = cross_correlograms
         self.hide_unit_selector = hide_unit_selector
-        self.height = height
+    def from_sorting(sorting):
+        import spikeinterface as si
+        import spikeinterface.widgets as sw
+        assert isinstance(sorting, si.BaseSorting), "Input must be a BaseSorting object"
+        W = sw.CrossCorrelogramsWidget(sorting)
+        return CrossCorrelograms.from_spikeinterface_widget(W)
+    def from_spikeinterface_widget(W):
+        from spikeinterface.widgets.base import to_attr
+        from spikeinterface.widgets.utils_sortingview import make_serializable
+        from .CrossCorrelogramItem import CrossCorrelogramItem
+        data_plot = W.data_plot
+        dp = to_attr(data_plot)
+        unit_ids = make_serializable(dp.unit_ids)
+        if dp.similarity is not None:
+            similarity = dp.similarity
+        else:
+            similarity = np.ones((len(unit_ids), len(unit_ids)))
+        cc_items = []
+        for i in range(len(unit_ids)):
+            for j in range(i, len(unit_ids)):
+                if similarity[i, j] >= dp.min_similarity_for_correlograms:
+                    cc_items.append(
+                        CrossCorrelogramItem(
+                            unit_id1=unit_ids[i],
+                            unit_id2=unit_ids[j],
+                            bin_edges_sec=(dp.bins / 1000.0).astype("float32"),
+                            bin_counts=dp.correlograms[i, j].astype("int32"),
+                        )
+                    )
+        view = CrossCorrelograms(cross_correlograms=cc_items, hide_unit_selector=False)
+        return view
     def _write_to_zarr_group(self, group: zarr.Group) -> None:
         """
@@ -44,8 +84,6 @@ class CrossCorrelograms(FigpackView):
         group.attrs["view_type"] = "CrossCorrelograms"
         # Set view properties
-        if self.height is not None:
-            group.attrs["height"] = self.height
         if self.hide_unit_selector is not None:
             group.attrs["hide_unit_selector"] = self.hide_unit_selector

figpack/spike_sorting/views/UnitsTable.py CHANGED Viewed

@@ -2,13 +2,15 @@
 UnitsTable view for figpack - displays a table of units with their properties
 """
-import zarr
-import numpy as np
 from typing import List, Optional
+import numpy as np
+import zarr
 from ...core.figpack_view import FigpackView
+from .UnitSimilarityScore import UnitSimilarityScore
 from .UnitsTableColumn import UnitsTableColumn
 from .UnitsTableRow import UnitsTableRow
-from .UnitSimilarityScore import UnitSimilarityScore
 class UnitsTable(FigpackView):

figpack/spike_sorting/views/UnitsTableRow.py CHANGED Viewed

@@ -2,7 +2,7 @@
 UnitsTableRow for spike sorting views
 """
-from typing import Union, Dict, Any
+from typing import Any, Dict, Union
 class UnitsTableRow:

figpack/spike_sorting/views/__init__.py CHANGED Viewed

@@ -6,10 +6,10 @@ from .AutocorrelogramItem import AutocorrelogramItem
 from .Autocorrelograms import Autocorrelograms
 from .CrossCorrelogramItem import CrossCorrelogramItem
 from .CrossCorrelograms import CrossCorrelograms
-from .UnitsTableColumn import UnitsTableColumn
-from .UnitsTableRow import UnitsTableRow
 from .UnitSimilarityScore import UnitSimilarityScore
 from .UnitsTable import UnitsTable
+from .UnitsTableColumn import UnitsTableColumn
+from .UnitsTableRow import UnitsTableRow
 __all__ = [
     "AutocorrelogramItem",

figpack/views/Box.py CHANGED Viewed

@@ -2,8 +2,10 @@
 Box view for figpack - a layout container that handles other views
 """
+from typing import Any, Dict, List, Literal, Optional
 import zarr
-from typing import List, Literal, Optional, Dict, Any
 from ..core.figpack_view import FigpackView
 from .LayoutItem import LayoutItem

figpack/views/Image.py CHANGED Viewed

@@ -2,9 +2,11 @@
 Image view for figpack - displays PNG and JPG images
 """
-import zarr
-import numpy as np
 from typing import Union
+import numpy as np
+import zarr
 from ..core.figpack_view import FigpackView

figpack/views/LayoutItem.py CHANGED Viewed

@@ -3,6 +3,7 @@ LayoutItem class for figpack Box view - represents an item in a layout container
 """
 from typing import Optional, Union
 from ..core.figpack_view import FigpackView

figpack/views/Markdown.py CHANGED Viewed

@@ -3,6 +3,7 @@ Markdown view for figpack - displays markdown content
 """
 import zarr
 from ..core.figpack_view import FigpackView

figpack/views/MatplotlibFigure.py CHANGED Viewed

@@ -2,9 +2,11 @@
 MatplotlibFigure view for figpack - displays matplotlib figures
 """
-import zarr
 import io
-from typing import Union, Any
+from typing import Any, Union
+import zarr
 from ..core.figpack_view import FigpackView

figpack/views/MultiChannelTimeseries.py ADDED Viewed

@@ -0,0 +1,226 @@
+"""
+Multi-channel timeseries visualization component
+"""
+import math
+from typing import List, Optional, Union
+import numpy as np
+import zarr
+from ..core.figpack_view import FigpackView
+class MultiChannelTimeseries(FigpackView):
+    """
+    A multi-channel timeseries visualization component
+    """
+    def __init__(
+        self,
+        *,
+        start_time_sec: float,
+        sampling_frequency_hz: float,
+        data: np.ndarray,
+        channel_ids: Optional[List[Union[str, int]]] = None,
+    ):
+        """
+        Initialize a MultiChannelTimeseries view
+        Args:
+            start_time_sec: Starting time in seconds
+            sampling_frequency_hz: Sampling rate in Hz
+            data: N×M numpy array where N is timepoints and M is channels
+            channel_ids: Optional list of channel identifiers
+        """
+        assert data.ndim == 2, "Data must be a 2D array (timepoints × channels)"
+        assert sampling_frequency_hz > 0, "Sampling frequency must be positive"
+        self.start_time_sec = start_time_sec
+        self.sampling_frequency_hz = sampling_frequency_hz
+        self.data = data.astype(np.float32)  # Ensure float32 for efficiency
+        n_timepoints, n_channels = data.shape
+        # Set channel IDs
+        if channel_ids is None:
+            self.channel_ids = [f"ch_{i}" for i in range(n_channels)]
+        else:
+            assert len(channel_ids) == n_channels, (
+                f"Number of channel_ids ({len(channel_ids)}) must match "
+                f"number of channels ({n_channels})"
+            )
+            self.channel_ids = [str(ch_id) for ch_id in channel_ids]
+        # Prepare downsampled arrays for efficient rendering
+        self.downsampled_data = self._compute_downsampled_data()
+    def _compute_downsampled_data(self) -> dict:
+        """
+        Compute downsampled arrays at power-of-4 factors using a vectorized
+        min/max pyramid with NaN padding for partial bins.
+        Returns:
+            dict: {factor: (ceil(N/factor), 2, M) float32 array}, where the second
+                axis stores [min, max] per bin per channel.
+        """
+        data = self.data  # (N, M), float32
+        n_timepoints, n_channels = data.shape
+        downsampled = {}
+        if n_timepoints < 4:
+            # No level with factor >= 4 fits the stop condition (factor < N)
+            return downsampled
+        def _first_level_from_raw(x: np.ndarray) -> np.ndarray:
+            """Build the factor=4 level directly from the raw data."""
+            N, M = x.shape
+            n_bins = math.ceil(N / 4)
+            pad = n_bins * 4 - N
+            # Pad time axis with NaNs so min/max ignore the padded tail
+            x_pad = np.pad(
+                x, ((0, pad), (0, 0)), mode="constant", constant_values=np.nan
+            )
+            blk = x_pad.reshape(n_bins, 4, M)  # (B, 4, M)
+            mins = np.nanmin(blk, axis=1)  # (B, M)
+            maxs = np.nanmax(blk, axis=1)  # (B, M)
+            out = np.empty((n_bins, 2, M), dtype=np.float32)
+            out[:, 0, :] = mins
+            out[:, 1, :] = maxs
+            return out
+        def _downsample4_bins(level_minmax: np.ndarray) -> np.ndarray:
+            """
+            Build the next pyramid level from the previous one by grouping every 4
+            bins. Input is (B, 2, M) -> Output is (ceil(B/4), 2, M).
+            """
+            B, two, M = level_minmax.shape
+            assert two == 2
+            n_bins_next = math.ceil(B / 4)
+            pad = n_bins_next * 4 - B
+            lvl_pad = np.pad(
+                level_minmax,
+                ((0, pad), (0, 0), (0, 0)),
+                mode="constant",
+                constant_values=np.nan,
+            )
+            blk = lvl_pad.reshape(n_bins_next, 4, 2, M)  # (B', 4, 2, M)
+            # Next mins from mins; next maxs from maxs
+            mins = np.nanmin(blk[:, :, 0, :], axis=1)  # (B', M)
+            maxs = np.nanmax(blk[:, :, 1, :], axis=1)  # (B', M)
+            out = np.empty((n_bins_next, 2, M), dtype=np.float32)
+            out[:, 0, :] = mins
+            out[:, 1, :] = maxs
+            return out
+        # Level 1: factor = 4 from raw data
+        factor = 4
+        level = _first_level_from_raw(data)
+        downsampled[factor] = level
+        # Higher levels: factor *= 4 each time, built from previous level
+        factor *= 4  # -> 16
+        while factor < n_timepoints / 1000:
+            level = _downsample4_bins(level)
+            downsampled[factor] = level
+            factor *= 4
+        return downsampled
+    def _calculate_optimal_chunk_size(
+        self, shape: tuple, target_size_mb: float = 5.0
+    ) -> tuple:
+        """
+        Calculate optimal chunk size for Zarr storage targeting ~5MB per chunk
+        Args:
+            shape: Array shape (n_timepoints, ..., n_channels)
+            target_size_mb: Target chunk size in MB
+        Returns:
+            Tuple of chunk dimensions
+        """
+        # Calculate bytes per element (float32 = 4 bytes)
+        bytes_per_element = 4
+        target_size_bytes = target_size_mb * 1024 * 1024
+        if len(shape) == 2:  # Original data: (n_timepoints, n_channels)
+            n_timepoints, n_channels = shape
+            elements_per_timepoint = n_channels
+        elif len(shape) == 3:  # Downsampled data: (n_timepoints, 2, n_channels)
+            n_timepoints, _, n_channels = shape
+            elements_per_timepoint = 2 * n_channels
+        else:
+            raise ValueError(f"Unsupported shape: {shape}")
+        # Calculate chunk size in timepoints
+        max_timepoints_per_chunk = target_size_bytes // (
+            elements_per_timepoint * bytes_per_element
+        )
+        # Round down to nearest power of 2 for efficiency
+        chunk_timepoints = 2 ** int(math.log2(max_timepoints_per_chunk))
+        chunk_timepoints = max(chunk_timepoints, 1)  # At least 1
+        chunk_timepoints = min(chunk_timepoints, n_timepoints)  # At most n_timepoints
+        if len(shape) == 2:
+            return (chunk_timepoints, n_channels)
+        else:  # len(shape) == 3
+            return (chunk_timepoints, 2, n_channels)
+    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the multi-channel timeseries data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        group.attrs["view_type"] = "MultiChannelTimeseries"
+        # Store metadata
+        group.attrs["start_time_sec"] = self.start_time_sec
+        group.attrs["sampling_frequency_hz"] = self.sampling_frequency_hz
+        group.attrs["channel_ids"] = self.channel_ids
+        n_timepoints, n_channels = self.data.shape
+        group.attrs["n_timepoints"] = n_timepoints
+        group.attrs["n_channels"] = n_channels
+        # Store original data with optimal chunking
+        original_chunks = self._calculate_optimal_chunk_size(self.data.shape)
+        group.create_dataset(
+            "data",
+            data=self.data,
+            chunks=original_chunks,
+            compression="blosc",
+            compression_opts={"cname": "lz4", "clevel": 5, "shuffle": 1},
+        )
+        # Store downsampled data arrays
+        downsample_factors = list(self.downsampled_data.keys())
+        group.attrs["downsample_factors"] = downsample_factors
+        for factor, downsampled_array in self.downsampled_data.items():
+            dataset_name = f"data_ds_{factor}"
+            # Calculate optimal chunks for this downsampled array
+            ds_chunks = self._calculate_optimal_chunk_size(downsampled_array.shape)
+            group.create_dataset(
+                dataset_name,
+                data=downsampled_array,
+                chunks=ds_chunks,
+                compression="blosc",
+                compression_opts={"cname": "lz4", "clevel": 5, "shuffle": 1},
+            )
+        print(
+            f"Stored MultiChannelTimeseries with {len(downsample_factors)} downsampled levels:"
+        )
+        print(f"  Original: {self.data.shape} (chunks: {original_chunks})")
+        for factor in downsample_factors:
+            ds_shape = self.downsampled_data[factor].shape
+            ds_chunks = self._calculate_optimal_chunk_size(ds_shape)
+            print(f"  Factor {factor}: {ds_shape} (chunks: {ds_chunks})")

figpack/views/PlotlyFigure.py CHANGED Viewed

@@ -2,11 +2,13 @@
 PlotlyFigure view for figpack - displays plotly figures
 """
-import zarr
 import json
+from datetime import date, datetime
+from typing import Any, Dict, Union
 import numpy as np
-from typing import Union, Any, Dict
-from datetime import datetime, date
+import zarr
 from ..core.figpack_view import FigpackView

figpack/views/Splitter.py CHANGED Viewed

@@ -2,8 +2,10 @@
 Splitter view for figpack - a resizable split layout container
 """
-import zarr
 from typing import Literal
+import zarr
 from ..core.figpack_view import FigpackView
 from .LayoutItem import LayoutItem

figpack/views/TabLayout.py CHANGED Viewed

@@ -2,8 +2,10 @@
 TabLayout view for figpack - a tabbed layout container that handles other views
 """
+from typing import Any, Dict, List, Optional
 import zarr
-from typing import List, Optional, Dict, Any
 from ..core.figpack_view import FigpackView
 from .TabLayoutItem import TabLayoutItem

figpack/views/TabLayoutItem.py CHANGED Viewed

@@ -3,6 +3,7 @@ TabLayoutItem class for figpack TabLayout view - represents a tab in a tab layou
 """
 from typing import Optional
 from ..core.figpack_view import FigpackView

figpack/views/TimeseriesGraph.py CHANGED Viewed

@@ -2,10 +2,11 @@
 Views module for figpack - contains visualization components
 """
-import numpy as np
-from typing import Optional, List, Dict, Any
+from typing import Any, Dict, List, Optional
+import numpy as np
 import zarr
 from ..core.figpack_view import FigpackView

figpack/views/__init__.py CHANGED Viewed

@@ -1,10 +1,11 @@
-from .TimeseriesGraph import TimeseriesGraph
 from .Box import Box
-from .Splitter import Splitter
-from .TabLayout import TabLayout
+from .Image import Image
 from .LayoutItem import LayoutItem
-from .TabLayoutItem import TabLayoutItem
 from .Markdown import Markdown
-from .PlotlyFigure import PlotlyFigure
 from .MatplotlibFigure import MatplotlibFigure
-from .Image import Image
+from .MultiChannelTimeseries import MultiChannelTimeseries
+from .PlotlyFigure import PlotlyFigure
+from .Splitter import Splitter
+from .TabLayout import TabLayout
+from .TabLayoutItem import TabLayoutItem
+from .TimeseriesGraph import TimeseriesGraph

figpack 0.1.3__py3-none-any.whl → 0.1.5__py3-none-any.whl

Potentially problematic release.

figpack 0.1.3py3-none-any.whl → 0.1.5py3-none-any.whl