figpack 0.2.3__py3-none-any.whl → 0.2.5__py3-none-any.whl
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- figpack/__init__.py +5 -1
- figpack/cli.py +2 -118
- figpack/core/_bundle_utils.py +3 -4
- figpack/core/_save_figure.py +31 -0
- figpack/core/_server_manager.py +9 -5
- figpack/core/_show_view.py +20 -21
- figpack/core/_upload_bundle.py +46 -22
- figpack/core/_view_figure.py +138 -0
- figpack/core/config.py +2 -0
- figpack/core/figpack_view.py +79 -22
- figpack/figpack-gui-dist/assets/{index-DUR9Dmwh.js → index-CrYQmIda.js} +70 -70
- figpack/figpack-gui-dist/index.html +1 -1
- figpack/spike_sorting/views/RasterPlot.py +77 -0
- figpack/spike_sorting/views/RasterPlotItem.py +28 -0
- figpack/spike_sorting/views/__init__.py +4 -0
- figpack/views/Gallery.py +88 -0
- figpack/views/GalleryItem.py +47 -0
- figpack/views/Image.py +37 -0
- figpack/views/__init__.py +2 -0
- figpack-0.2.5.dist-info/METADATA +96 -0
- {figpack-0.2.3.dist-info → figpack-0.2.5.dist-info}/RECORD +25 -19
- figpack-0.2.3.dist-info/METADATA +0 -168
- {figpack-0.2.3.dist-info → figpack-0.2.5.dist-info}/WHEEL +0 -0
- {figpack-0.2.3.dist-info → figpack-0.2.5.dist-info}/entry_points.txt +0 -0
- {figpack-0.2.3.dist-info → figpack-0.2.5.dist-info}/licenses/LICENSE +0 -0
- {figpack-0.2.3.dist-info → figpack-0.2.5.dist-info}/top_level.txt +0 -0
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<link rel="icon" type="image/png" href="./assets/neurosift-logo-CLsuwLMO.png" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>figpack figure</title>
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<script type="module" crossorigin src="./assets/index-
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<script type="module" crossorigin src="./assets/index-CrYQmIda.js"></script>
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<link rel="stylesheet" crossorigin href="./assets/index-Cmae55E4.css">
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</head>
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<body>
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"""
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RasterPlot view for figpack - displays multiple raster plots
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"""
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from typing import List
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import numpy as np
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import zarr
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from ...core.figpack_view import FigpackView
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from .RasterPlotItem import RasterPlotItem
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class RasterPlot(FigpackView):
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"""
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A view that displays multiple raster plots for spike sorting analysis
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"""
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def __init__(
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self,
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*,
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start_time_sec: float,
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end_time_sec: float,
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plots: List[RasterPlotItem],
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height: int = 500,
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):
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"""
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Initialize a RasterPlot view
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Args:
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start_time_sec: Start time in seconds for the plot range
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end_time_sec: End time in seconds for the plot range
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plots: List of RasterPlotItem objects
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height: Height of the plot in pixels (default: 500)
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"""
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self.start_time_sec = float(start_time_sec)
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self.end_time_sec = float(end_time_sec)
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self.plots = plots
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self.height = height
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def _write_to_zarr_group(self, group: zarr.Group) -> None:
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"""
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Write the RasterPlot data to a Zarr group
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Args:
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group: Zarr group to write data into
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"""
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# Set the view type
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group.attrs["view_type"] = "RasterPlot"
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# Store view-level attributes
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group.attrs["start_time_sec"] = self.start_time_sec
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group.attrs["end_time_sec"] = self.end_time_sec
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group.attrs["height"] = self.height
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group.attrs["num_plots"] = len(self.plots)
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# Store metadata for each plot
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plot_metadata = []
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for i, plot in enumerate(self.plots):
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plot_name = f"plot_{i}"
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# Store metadata
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metadata = {
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"name": plot_name,
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"unit_id": str(plot.unit_id),
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"num_spikes": len(plot.spike_times_sec),
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}
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plot_metadata.append(metadata)
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# Create arrays for this plot
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group.create_dataset(
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f"{plot_name}/spike_times_sec",
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data=plot.spike_times_sec,
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dtype=np.float32,
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)
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# Store the plot metadata
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group.attrs["plots"] = plot_metadata
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"""
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RasterPlotItem for figpack - represents a single unit's raster plot
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"""
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from typing import Union
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import numpy as np
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class RasterPlotItem:
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"""
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Represents spike times for a single unit in a raster plot
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"""
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def __init__(
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self,
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*,
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unit_id: Union[str, int],
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spike_times_sec: np.ndarray,
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):
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"""
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Initialize a RasterPlotItem
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Args:
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unit_id: Identifier for the unit
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spike_times_sec: Numpy array of spike times in seconds
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"""
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self.unit_id = unit_id
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self.spike_times_sec = np.array(spike_times_sec, dtype=np.float32)
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from .AverageWaveforms import AverageWaveforms
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from .SpikeAmplitudesItem import SpikeAmplitudesItem
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from .SpikeAmplitudes import SpikeAmplitudes
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from .RasterPlotItem import RasterPlotItem
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from .RasterPlot import RasterPlot
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__all__ = [
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"AutocorrelogramItem",
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"AverageWaveforms",
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"SpikeAmplitudesItem",
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"SpikeAmplitudes",
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"RasterPlotItem",
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"RasterPlot",
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figpack/views/Gallery.py
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"""
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Gallery view for figpack - a gallery layout container that handles other views with separate timeseries contexts
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"""
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from typing import Any, Dict, List, Optional
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import zarr
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from ..core.figpack_view import FigpackView
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from .GalleryItem import GalleryItem
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class Gallery(FigpackView):
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"""
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A gallery layout container view that arranges other views in a gallery format.
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The Gallery view is functionally similar to TabLayout, but with a key difference:
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each gallery item maintains its own independent timeseries selection context.
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This means that time range selections, current time, and visible time ranges
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are isolated between different gallery items, allowing for independent navigation
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and analysis of timeseries data in each item.
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This is particularly useful when comparing different datasets or views that
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should not share the same time selection state.
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"""
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def __init__(
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self,
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*,
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items: List[GalleryItem],
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initial_item_index: int = 0,
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):
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"""
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Initialize a Gallery view
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Args:
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items: List of GalleryItem objects containing the child views.
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Each item will have its own independent timeseries selection context.
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initial_item_index: Index of the initially selected gallery item (default: 0).
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Will be clamped to valid range if out of bounds.
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"""
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self.items = items
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# Ensure initial_item_index is within valid bounds
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self.initial_item_index = (
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max(0, min(initial_item_index, len(items) - 1)) if items else 0
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)
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def _write_to_zarr_group(self, group: zarr.Group) -> None:
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"""
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Write the Gallery data to a Zarr group
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This method serializes the gallery structure and all its child views
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into a Zarr group format that can be read by the frontend components.
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Each gallery item's view is written to its own subgroup within the
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main gallery group.
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Args:
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group: Zarr group to write data into
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"""
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# Set the view type identifier for the frontend
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group.attrs["view_type"] = "Gallery"
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# Store gallery-specific properties
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group.attrs["initial_item_index"] = self.initial_item_index
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# Create a list to store metadata for all gallery items
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items_metadata = []
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# Process each gallery item
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for i, item in enumerate(self.items):
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# Generate a unique name for this item's subgroup
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item_name = f"gallery_item_{i}"
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# Store item metadata (label, etc.) for the frontend
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item_metadata = item.to_dict()
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item_metadata["name"] = item_name
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items_metadata.append(item_metadata)
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# Create a subgroup for this gallery item's view
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item_group = group.create_group(item_name)
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# Recursively write the child view to the subgroup
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# This allows any figpack view to be contained within a gallery item
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item.view._write_to_zarr_group(item_group)
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# Store the complete items metadata in the group attributes
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# This will be used by the frontend to render the gallery structure
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group.attrs["items"] = items_metadata
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"""
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GalleryItem class for figpack Gallery view - represents an item in a gallery layout container
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"""
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from typing import Optional
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from ..core.figpack_view import FigpackView
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class GalleryItem:
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"""
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Represents an item in a Gallery with a label and view.
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Similar to TabLayoutItem, but designed for gallery layouts where each item
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maintains its own independent timeseries selection context.
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"""
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def __init__(
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self,
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view: FigpackView,
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label: str,
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):
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"""
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Initialize a GalleryItem
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Args:
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view: The figpack view to be contained in this gallery item
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label: The label text to display for this gallery item
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"""
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self.view = view
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self.label = label
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def to_dict(self) -> dict:
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"""
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Convert the GalleryItem to a dictionary for serialization
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This method is used when writing the gallery data to Zarr format.
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The dictionary contains metadata about the item that will be stored
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in the Zarr group attributes.
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Returns:
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Dictionary representation of the GalleryItem containing the label
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"""
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return {
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"label": self.label,
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}
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figpack/views/Image.py
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self.image_path_or_data = image_path_or_data
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@staticmethod
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def from_image_file(image_path: str) -> "Image":
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"""
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Create an Image view from a file path
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Args:
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image_path: Path to the image file
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Returns:
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An Image view instance
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"""
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return Image(image_path)
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@staticmethod
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def from_image_url(image_url: str) -> "Image":
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"""
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Create an Image view from an image URL by downloading the image
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Args:
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image_url: URL of the image to download
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Returns:
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An Image view instance
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Raises:
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ValueError: If the image cannot be downloaded
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"""
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import requests
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try:
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response = requests.get(image_url)
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response.raise_for_status()
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image_data = response.content
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return Image(image_data)
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except Exception as e:
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raise ValueError(f"Failed to download image from URL: {str(e)}")
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def _write_to_zarr_group(self, group: zarr.Group) -> None:
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"""
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Write the image data to a Zarr group
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figpack/views/__init__.py
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Metadata-Version: 2.4
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Name: figpack
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Version: 0.2.5
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Summary: A Python package for creating shareable, interactive visualizations in the browser
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Author-email: Jeremy Magland <jmagland@flatironinstitute.org>
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License: Apache-2.0
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Project-URL: Homepage, https://github.com/flatironinstitute/figpack
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# figpack
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[](https://github.com/flatironinstitute/figpack/actions/workflows/test.yml)
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[](https://codecov.io/gh/flatironinstitute/figpack)
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[](https://badge.fury.io/py/figpack)
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A Python package for creating shareable, interactive visualizations in the browser.
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## Documentation
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For detailed guidance, tutorials, and API reference, visit our **[documentation](https://flatironinstitute.github.io/figpack)**.
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## Quick Start
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Want to jump right in? Here's how to get started:
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pip install figpack
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```
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```python
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# Add some data
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t = np.linspace(0, 10, 1000)
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y = np.sin(2 * np.pi * t)
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graph.add_line_series(name="sine wave", t=t, y=y, color="blue")
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```
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# Create a timeseries graph
|
|
77
|
-
graph = vv.TimeseriesGraph(y_label="Signal")
|
|
78
|
-
|
|
79
|
-
# Add some data
|
|
80
|
-
t = np.linspace(0, 10, 1000)
|
|
81
|
-
y = np.sin(2 * np.pi * t)
|
|
82
|
-
graph.add_line_series(name="sine wave", t=t, y=y, color="blue")
|
|
83
|
-
|
|
84
|
-
# Display the visualization
|
|
85
|
-
graph.show(open_in_browser=True, title="Quick Start Example")
|
|
86
|
-
```
|
|
87
|
-
|
|
88
|
-
## Available Views
|
|
89
|
-
|
|
90
|
-
figpack provides a comprehensive set of view components for creating interactive visualizations:
|
|
91
|
-
|
|
92
|
-
### Core Views
|
|
93
|
-
|
|
94
|
-
- **[TimeseriesGraph](docs/timeseries-graph.md)** - Interactive line plots, markers, and intervals ([example](examples/example_timeseries_graph.py))
|
|
95
|
-
- **[MultiChannelTimeseries](docs/multichannel-timeseries.md)** - Multi-channel timeseries visualization ([example](examples/example_multichannel_timeseries.py))
|
|
96
|
-
- **[Image](docs/image.md)** - Display images with optional annotations ([example](examples/example_image.py))
|
|
97
|
-
- **[Markdown](docs/markdown.md)** - Render markdown content ([example](examples/example_markdown.py))
|
|
98
|
-
|
|
99
|
-
### Layout Views
|
|
100
|
-
|
|
101
|
-
- **[Box](docs/box.md)** - Flexible container with horizontal/vertical layouts ([example](examples/example_box.py))
|
|
102
|
-
- **[Splitter](docs/splitter.md)** - Resizable split panes ([example](examples/example_splitter.py))
|
|
103
|
-
- **[TabLayout](docs/tab-layout.md)** - Tabbed interface for multiple views ([example](examples/example_tablayout.py))
|
|
104
|
-
|
|
105
|
-
### External Figure Support
|
|
106
|
-
|
|
107
|
-
- **[MatplotlibFigure](docs/matplotlib-figure.md)** - Embed matplotlib plots ([example](examples/example_matplotlib.py))
|
|
108
|
-
- **[PlotlyFigure](docs/plotly-figure.md)** - Embed plotly visualizations ([example](examples/example_plotly.py))
|
|
109
|
-
|
|
110
|
-
### Spike Sorting Views
|
|
111
|
-
|
|
112
|
-
- **[Autocorrelograms](docs/autocorrelograms.md)** - Auto-correlation analysis ([example](examples/example_autocorrelograms.py))
|
|
113
|
-
- **[CrossCorrelograms](docs/cross-correlograms.md)** - Cross-correlation analysis ([example](examples/example_cross_correlograms.py))
|
|
114
|
-
- **[UnitsTable](docs/units-table.md)** - Sortable table for spike sorting units ([example](examples/example_units_table.py))
|
|
115
|
-
|
|
116
|
-
## Examples
|
|
117
|
-
|
|
118
|
-
See the `examples/` directory for working examples of each view type.
|
|
119
|
-
|
|
120
|
-
## Usage Modes
|
|
121
|
-
|
|
122
|
-
### Local-only Mode
|
|
123
|
-
|
|
124
|
-
```python
|
|
125
|
-
view.show(open_in_browser=True, title="Local Visualization")
|
|
126
|
-
```
|
|
127
|
-
|
|
128
|
-
### Sharing Online
|
|
129
|
-
|
|
130
|
-
Set the `FIGPACK_API_KEY` environment variable and use:
|
|
131
|
-
|
|
132
|
-
```python
|
|
133
|
-
view.show(upload=True, open_in_browser=True, title="Shared Visualization")
|
|
134
|
-
```
|
|
135
|
-
|
|
136
|
-
### Development Mode
|
|
137
|
-
|
|
138
|
-
Set `_dev=True` in the call to show() to enable development mode, which allows for live updates and development of figpack-gui.
|
|
139
|
-
|
|
140
|
-
## Command Line Interface
|
|
141
|
-
|
|
142
|
-
figpack includes a command-line interface for working with figures:
|
|
143
|
-
|
|
144
|
-
### Download a Figure
|
|
145
|
-
|
|
146
|
-
```bash
|
|
147
|
-
figpack download <figure-url> <dest.tar.gz>
|
|
148
|
-
```
|
|
149
|
-
|
|
150
|
-
Download a figure from any figpack URL and save it as a local archive.
|
|
151
|
-
|
|
152
|
-
### View a Figure Archive
|
|
153
|
-
|
|
154
|
-
```bash
|
|
155
|
-
figpack view <figure.tar.gz>
|
|
156
|
-
```
|
|
157
|
-
|
|
158
|
-
Extract and view a figure archive in your browser. The server will run locally until you press Enter.
|
|
159
|
-
|
|
160
|
-
Use `--port <number>` to specify a custom port.
|
|
161
|
-
|
|
162
|
-
## License
|
|
163
|
-
|
|
164
|
-
Apache-2.0
|
|
165
|
-
|
|
166
|
-
## Contributing
|
|
167
|
-
|
|
168
|
-
Visit the [GitHub repository](https://github.com/magland/figpack) for issues, contributions, and the latest updates.
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|
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