PyPI - figpack - Versions diffs - 0.2.4__py3-none-any.whl → 0.2.6__py3-none-any.whl - Mend

figpack 0.2.4py3-none-any.whl → 0.2.6py3-none-any.whl

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figpack/__init__.py +5 -1
figpack/cli.py +2 -118
figpack/core/_bundle_utils.py +5 -6
figpack/core/_save_figure.py +31 -0
figpack/core/_server_manager.py +0 -2
figpack/core/_show_view.py +22 -22
figpack/core/_upload_bundle.py +61 -22
figpack/core/_view_figure.py +138 -0
figpack/core/figpack_view.py +74 -25
figpack/{figpack-gui-dist/assets/index-CuFseOGX.js → figpack-figure-dist/assets/index-HXdk2TtM.js} +58 -58
figpack/{figpack-gui-dist → figpack-figure-dist}/index.html +1 -1
figpack/spike_sorting/views/Autocorrelograms.py +29 -19
figpack/spike_sorting/views/CrossCorrelograms.py +29 -19
figpack/spike_sorting/views/UnitsTable.py +27 -8
figpack/views/Gallery.py +88 -0
figpack/views/GalleryItem.py +47 -0
figpack/views/Image.py +37 -0
figpack/views/Markdown.py +12 -2
figpack/views/MatplotlibFigure.py +26 -3
figpack/views/PlotlyFigure.py +18 -2
figpack/views/__init__.py +2 -0
figpack-0.2.6.dist-info/METADATA +96 -0
figpack-0.2.6.dist-info/RECORD +53 -0
figpack-0.2.4.dist-info/METADATA +0 -168
figpack-0.2.4.dist-info/RECORD +0 -49
/figpack/{figpack-gui-dist → figpack-figure-dist}/assets/index-Cmae55E4.css +0 -0
/figpack/{figpack-gui-dist → figpack-figure-dist}/assets/neurosift-logo-CLsuwLMO.png +0 -0
{figpack-0.2.4.dist-info → figpack-0.2.6.dist-info}/WHEEL +0 -0
{figpack-0.2.4.dist-info → figpack-0.2.6.dist-info}/entry_points.txt +0 -0
{figpack-0.2.4.dist-info → figpack-0.2.6.dist-info}/licenses/LICENSE +0 -0
{figpack-0.2.4.dist-info → figpack-0.2.6.dist-info}/top_level.txt +0 -0

figpack/{figpack-gui-dist → figpack-figure-dist}/index.html RENAMED 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-CuFseOGX.js"></script>
+    <script type="module" crossorigin src="./assets/index-HXdk2TtM.js"></script>
     <link rel="stylesheet" crossorigin href="./assets/index-Cmae55E4.css">
   </head>
   <body>

figpack/spike_sorting/views/Autocorrelograms.py CHANGED Viewed

@@ -77,32 +77,42 @@ class Autocorrelograms(FigpackView):
         group.attrs["view_type"] = "Autocorrelograms"
         # Store the number of autocorrelograms
-        group.attrs["num_autocorrelograms"] = len(self.autocorrelograms)
+        num_autocorrelograms = len(self.autocorrelograms)
+        group.attrs["num_autocorrelograms"] = num_autocorrelograms
-        # Store metadata for each autocorrelogram
+        if num_autocorrelograms == 0:
+            return
+        # Get dimensions from first autocorrelogram
+        num_bins = len(self.autocorrelograms[0].bin_counts)
+        # Store bin edges (same for all autocorrelograms)
+        group.create_dataset(
+            "bin_edges_sec",
+            data=self.autocorrelograms[0].bin_edges_sec,
+            dtype=np.float32,
+        )
+        # Create 2D array for all bin counts
+        bin_counts = np.zeros((num_autocorrelograms, num_bins), dtype=np.int32)
+        # Store metadata for each autocorrelogram and populate bin counts array
         autocorrelogram_metadata = []
         for i, autocorr in enumerate(self.autocorrelograms):
-            autocorr_name = f"autocorrelogram_{i}"
-            # Store metadata
             metadata = {
-                "name": autocorr_name,
                 "unit_id": str(autocorr.unit_id),
-                "num_bins": len(autocorr.bin_counts),
+                "index": i,  # Store index to map to bin_counts array
+                "num_bins": num_bins,
             }
             autocorrelogram_metadata.append(metadata)
-            # Create arrays for this autocorrelogram
-            group.create_dataset(
-                f"{autocorr_name}/bin_edges_sec",
-                data=autocorr.bin_edges_sec,
-                dtype=np.float32,
-            )
-            group.create_dataset(
-                f"{autocorr_name}/bin_counts",
-                data=autocorr.bin_counts,
-                dtype=np.int32,
-            )
+            bin_counts[i] = autocorr.bin_counts
+        # Store the bin counts as a single 2D dataset
+        group.create_dataset(
+            "bin_counts",
+            data=bin_counts,
+            dtype=np.int32,
+        )
         # Store the autocorrelogram metadata
         group.attrs["autocorrelograms"] = autocorrelogram_metadata

figpack/spike_sorting/views/CrossCorrelograms.py CHANGED Viewed

@@ -90,33 +90,43 @@ class CrossCorrelograms(FigpackView):
             group.attrs["hide_unit_selector"] = self.hide_unit_selector
         # Store the number of cross-correlograms
-        group.attrs["num_cross_correlograms"] = len(self.cross_correlograms)
+        num_cross_correlograms = len(self.cross_correlograms)
+        group.attrs["num_cross_correlograms"] = num_cross_correlograms
-        # Store metadata for each cross-correlogram
+        if num_cross_correlograms == 0:
+            return
+        # Get dimensions from first cross-correlogram
+        num_bins = len(self.cross_correlograms[0].bin_counts)
+        # Store bin edges (same for all cross-correlograms)
+        group.create_dataset(
+            "bin_edges_sec",
+            data=self.cross_correlograms[0].bin_edges_sec,
+            dtype=np.float32,
+        )
+        # Create 2D array for all bin counts
+        bin_counts = np.zeros((num_cross_correlograms, num_bins), dtype=np.int32)
+        # Store metadata for each cross-correlogram and populate bin counts array
         cross_correlogram_metadata = []
         for i, cross_corr in enumerate(self.cross_correlograms):
-            cross_corr_name = f"cross_correlogram_{i}"
-            # Store metadata
             metadata = {
-                "name": cross_corr_name,
                 "unit_id1": str(cross_corr.unit_id1),
                 "unit_id2": str(cross_corr.unit_id2),
-                "num_bins": len(cross_corr.bin_counts),
+                "index": i,  # Store index to map to bin_counts array
+                "num_bins": num_bins,
             }
             cross_correlogram_metadata.append(metadata)
-            # Create arrays for this cross-correlogram
-            group.create_dataset(
-                f"{cross_corr_name}/bin_edges_sec",
-                data=cross_corr.bin_edges_sec,
-                dtype=np.float32,
-            )
-            group.create_dataset(
-                f"{cross_corr_name}/bin_counts",
-                data=cross_corr.bin_counts,
-                dtype=np.int32,
-            )
+            bin_counts[i] = cross_corr.bin_counts
+        # Store the bin counts as a single 2D dataset
+        group.create_dataset(
+            "bin_counts",
+            data=bin_counts,
+            dtype=np.int32,
+        )
         # Store the cross-correlogram metadata
         group.attrs["cross_correlograms"] = cross_correlogram_metadata

figpack/spike_sorting/views/UnitsTable.py CHANGED Viewed

@@ -3,6 +3,7 @@ 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
@@ -58,13 +59,31 @@ class UnitsTable(FigpackView):
         columns_metadata = [col.to_dict() for col in self.columns]
         group.attrs["columns"] = columns_metadata
-        # Store rows metadata
-        rows_metadata = [row.to_dict() for row in self.rows]
-        group.attrs["rows"] = rows_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 if provided
+        # Store similarity scores in a zarr array
         if self.similarity_scores:
-            similarity_scores_metadata = [
-                score.to_dict() for score in self.similarity_scores
-            ]
-            group.attrs["similarityScores"] = similarity_scores_metadata
+            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/views/Gallery.py ADDED Viewed

@@ -0,0 +1,88 @@
+"""
+Gallery view for figpack - a gallery layout container that handles other views with separate timeseries contexts
+"""
+from typing import Any, Dict, List, Optional
+import zarr
+from ..core.figpack_view import FigpackView
+from .GalleryItem import GalleryItem
+class Gallery(FigpackView):
+    """
+    A gallery layout container view that arranges other views in a gallery format.
+    The Gallery view is functionally similar to TabLayout, but with a key difference:
+    each gallery item maintains its own independent timeseries selection context.
+    This means that time range selections, current time, and visible time ranges
+    are isolated between different gallery items, allowing for independent navigation
+    and analysis of timeseries data in each item.
+    This is particularly useful when comparing different datasets or views that
+    should not share the same time selection state.
+    """
+    def __init__(
+        self,
+        *,
+        items: List[GalleryItem],
+        initial_item_index: int = 0,
+    ):
+        """
+        Initialize a Gallery view
+        Args:
+            items: List of GalleryItem objects containing the child views.
+                   Each item will have its own independent timeseries selection context.
+            initial_item_index: Index of the initially selected gallery item (default: 0).
+                               Will be clamped to valid range if out of bounds.
+        """
+        self.items = items
+        # Ensure initial_item_index is within valid bounds
+        self.initial_item_index = (
+            max(0, min(initial_item_index, len(items) - 1)) if items else 0
+        )
+    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the Gallery data to a Zarr group
+        This method serializes the gallery structure and all its child views
+        into a Zarr group format that can be read by the frontend components.
+        Each gallery item's view is written to its own subgroup within the
+        main gallery group.
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set the view type identifier for the frontend
+        group.attrs["view_type"] = "Gallery"
+        # Store gallery-specific properties
+        group.attrs["initial_item_index"] = self.initial_item_index
+        # Create a list to store metadata for all gallery items
+        items_metadata = []
+        # Process each gallery item
+        for i, item in enumerate(self.items):
+            # Generate a unique name for this item's subgroup
+            item_name = f"gallery_item_{i}"
+            # Store item metadata (label, etc.) for the frontend
+            item_metadata = item.to_dict()
+            item_metadata["name"] = item_name
+            items_metadata.append(item_metadata)
+            # Create a subgroup for this gallery item's view
+            item_group = group.create_group(item_name)
+            # Recursively write the child view to the subgroup
+            # This allows any figpack view to be contained within a gallery item
+            item.view._write_to_zarr_group(item_group)
+        # Store the complete items metadata in the group attributes
+        # This will be used by the frontend to render the gallery structure
+        group.attrs["items"] = items_metadata

figpack/views/GalleryItem.py ADDED Viewed

@@ -0,0 +1,47 @@
+"""
+GalleryItem class for figpack Gallery view - represents an item in a gallery layout container
+"""
+from typing import Optional
+from ..core.figpack_view import FigpackView
+class GalleryItem:
+    """
+    Represents an item in a Gallery with a label and view.
+    Similar to TabLayoutItem, but designed for gallery layouts where each item
+    maintains its own independent timeseries selection context.
+    """
+    def __init__(
+        self,
+        view: FigpackView,
+        *,
+        label: str,
+    ):
+        """
+        Initialize a GalleryItem
+        Args:
+            view: The figpack view to be contained in this gallery item
+            label: The label text to display for this gallery item
+        """
+        self.view = view
+        self.label = label
+    def to_dict(self) -> dict:
+        """
+        Convert the GalleryItem to a dictionary for serialization
+        This method is used when writing the gallery data to Zarr format.
+        The dictionary contains metadata about the item that will be stored
+        in the Zarr group attributes.
+        Returns:
+            Dictionary representation of the GalleryItem containing the label
+        """
+        return {
+            "label": self.label,
+        }

figpack/views/Image.py CHANGED Viewed

@@ -32,6 +32,43 @@ class Image(FigpackView):
         self.image_path_or_data = image_path_or_data
+    @staticmethod
+    def from_image_file(image_path: str) -> "Image":
+        """
+        Create an Image view from a file path
+        Args:
+            image_path: Path to the image file
+        Returns:
+            An Image view instance
+        """
+        return Image(image_path)
+    @staticmethod
+    def from_image_url(image_url: str) -> "Image":
+        """
+        Create an Image view from an image URL by downloading the image
+        Args:
+            image_url: URL of the image to download
+        Returns:
+            An Image view instance
+        Raises:
+            ValueError: If the image cannot be downloaded
+        """
+        import requests
+        try:
+            response = requests.get(image_url)
+            response.raise_for_status()
+            image_data = response.content
+            return Image(image_data)
+        except Exception as e:
+            raise ValueError(f"Failed to download image from URL: {str(e)}")
     def _write_to_zarr_group(self, group: zarr.Group) -> None:
         """
         Write the image data to a Zarr group

figpack/views/Markdown.py CHANGED Viewed

@@ -2,6 +2,7 @@
 Markdown view for figpack - displays markdown content
 """
+import numpy as np
 import zarr
 from ..core.figpack_view import FigpackView
@@ -31,5 +32,14 @@ class Markdown(FigpackView):
         # Set the view type
         group.attrs["view_type"] = "Markdown"
-        # Store the markdown content
-        group.attrs["content"] = self.content
+        # Convert string content to numpy array of bytes
+        content_bytes = self.content.encode("utf-8")
+        content_array = np.frombuffer(content_bytes, dtype=np.uint8)
+        # Store the markdown content as a zarr array
+        group.create_dataset(
+            "content_data", data=content_array, dtype=np.uint8, chunks=True
+        )
+        # Store content size in attrs
+        group.attrs["data_size"] = len(content_bytes)

figpack/views/MatplotlibFigure.py CHANGED Viewed

@@ -3,6 +3,7 @@ MatplotlibFigure view for figpack - displays matplotlib figures
 """
 import io
+import numpy as np
 from typing import Any, Union
 import zarr
@@ -47,8 +48,18 @@ class MatplotlibFigure(FigpackView):
             svg_string = svg_buffer.getvalue()
             svg_buffer.close()
-            # Store the SVG data
-            group.attrs["svg_data"] = svg_string
+            # Convert SVG string to numpy array and store in zarr array
+            svg_bytes = svg_string.encode("utf-8")
+            svg_array = np.frombuffer(svg_bytes, dtype=np.uint8)
+            group.create_dataset(
+                "svg_data",
+                data=svg_array,
+                dtype=np.uint8,
+                chunks=True,
+                compressor=zarr.Blosc(
+                    cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE
+                ),
+            )
             # Store figure dimensions for reference
             fig_width, fig_height = self.fig.get_size_inches()
@@ -58,10 +69,22 @@ class MatplotlibFigure(FigpackView):
             # Store DPI for reference
             group.attrs["figure_dpi"] = float(self.fig.dpi)
+            # Store data size for reference
+            group.attrs["data_size"] = len(svg_bytes)
         except Exception as e:
             # If SVG export fails, store error information
-            group.attrs["svg_data"] = ""
+            group.create_dataset(
+                "svg_data",
+                data=np.array([], dtype=np.uint8),
+                dtype=np.uint8,
+                chunks=True,
+                compressor=zarr.Blosc(
+                    cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE
+                ),
+            )
             group.attrs["error"] = f"Failed to export matplotlib figure: {str(e)}"
             group.attrs["figure_width_inches"] = 6.0
             group.attrs["figure_height_inches"] = 4.0
             group.attrs["figure_dpi"] = 100.0
+            group.attrs["data_size"] = 0

figpack/views/PlotlyFigure.py CHANGED Viewed

@@ -56,5 +56,21 @@ class PlotlyFigure(FigpackView):
         # Convert the plotly figure to a dictionary
         fig_dict = self.fig.to_dict()
-        # Store the figure data as JSON string using custom encoder
-        group.attrs["figure_data"] = json.dumps(fig_dict, cls=CustomJSONEncoder)
+        # Convert figure data to JSON string using custom encoder
+        json_string = json.dumps(fig_dict, cls=CustomJSONEncoder)
+        # Convert JSON string to bytes and store in numpy array
+        json_bytes = json_string.encode("utf-8")
+        json_array = np.frombuffer(json_bytes, dtype=np.uint8)
+        # Store the figure data as compressed array
+        group.create_dataset(
+            "figure_data",
+            data=json_array,
+            dtype=np.uint8,
+            chunks=True,
+            compressor=zarr.Blosc(cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE),
+        )
+        # Store data size for reference
+        group.attrs["data_size"] = len(json_bytes)

figpack/views/__init__.py CHANGED Viewed

@@ -1,4 +1,6 @@
 from .Box import Box
+from .Gallery import Gallery
+from .GalleryItem import GalleryItem
 from .Image import Image
 from .LayoutItem import LayoutItem
 from .Markdown import Markdown

figpack-0.2.6.dist-info/METADATA ADDED Viewed

@@ -0,0 +1,96 @@
+Metadata-Version: 2.4
+Name: figpack
+Version: 0.2.6
+Summary: A Python package for creating shareable, interactive visualizations in the browser
+Author-email: Jeremy Magland <jmagland@flatironinstitute.org>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/flatironinstitute/figpack
+Project-URL: Repository, https://github.com/flatironinstitute/figpack
+Project-URL: Documentation, https://flatironinstitute.github.io/figpack
+Project-URL: Bug Tracker, https://github.com/flatironinstitute/figpack/issues
+Keywords: visualization,plotting,timeseries,interactive
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+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"
+Requires-Dist: pytest-mock>=3.10; extra == "test"
+Requires-Dist: spikeinterface; extra == "test"
+Requires-Dist: matplotlib; extra == "test"
+Requires-Dist: plotly; extra == "test"
+Requires-Dist: Pillow; extra == "test"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: pytest-mock>=3.10; extra == "dev"
+Requires-Dist: black>=24.0; extra == "dev"
+Requires-Dist: pre-commit>=3.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.0; extra == "docs"
+Requires-Dist: myst-parser>=2.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=2.0; extra == "docs"
+Requires-Dist: sphinx-autobuild>=2021.3.14; extra == "docs"
+Requires-Dist: linkify-it-py>=2.0; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5; extra == "docs"
+Dynamic: license-file
+# figpack
+[![Tests](https://github.com/flatironinstitute/figpack/actions/workflows/test.yml/badge.svg)](https://github.com/flatironinstitute/figpack/actions/workflows/test.yml)
+[![codecov](https://codecov.io/gh/flatironinstitute/figpack/branch/main/graph/badge.svg)](https://codecov.io/gh/flatironinstitute/figpack)
+[![PyPI version](https://badge.fury.io/py/figpack.svg)](https://badge.fury.io/py/figpack)
+A Python package for creating shareable, interactive visualizations in the browser.
+## Documentation
+For detailed guidance, tutorials, and API reference, visit our **[documentation](https://flatironinstitute.github.io/figpack)**.
+## Quick Start
+Want to jump right in? Here's how to get started:
+```bash
+pip install figpack
+```
+```python
+import numpy as np
+import figpack.views as vv
+# Create a timeseries graph
+graph = vv.TimeseriesGraph(y_label="Signal")
+# Add some data
+t = np.linspace(0, 10, 1000)
+y = np.sin(2 * np.pi * t)
+graph.add_line_series(name="sine wave", t=t, y=y, color="blue")
+# Display the visualization in your browser
+graph.show(open_in_browser=True, title="Quick Start Example")
+```
+## License
+Apache-2.0
+## Contributing
+Visit the [GitHub repository](https://github.com/flatironinstitute/figpack) for issues, contributions, and the latest updates.

figpack-0.2.6.dist-info/RECORD ADDED Viewed

@@ -0,0 +1,53 @@
+figpack/__init__.py,sha256=0qLJ7E5m_1HlQz2yVbgdZj__rO56AZjWGC3NDzswq7U,181
+figpack/cli.py,sha256=xWF7J2BxUqOLvPu-Kje7Q6oGukTroXsLq8WN8vJgyw0,8321
+figpack/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+figpack/core/_bundle_utils.py,sha256=JBZh2LJyu0oYHQBBVw5fF3uUNQJY_2bxVf6V7CN10FM,1884
+figpack/core/_save_figure.py,sha256=52ny-m1ThGgxY4ZgMn7m33n8A2OCyezj8H8TMvw0Y8Q,1043
+figpack/core/_server_manager.py,sha256=BTLeZtSbaJtAmtslAfgvp9C-SV0aJnn4WCpUJzd1Mlg,10997
+figpack/core/_show_view.py,sha256=-5HT1MYSeVuEoaL3RNNyoCjYsZy4Jy9XLjljUqLuvV4,5146
+figpack/core/_upload_bundle.py,sha256=54hdWayJJdRZdx7N9V2aH_X33KkR6hImMjN6tkBTLi8,14894
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figpack 0.2.4__py3-none-any.whl → 0.2.6__py3-none-any.whl

Potentially problematic release.

figpack 0.2.4py3-none-any.whl → 0.2.6py3-none-any.whl