PyPI - figpack - Versions diffs - 0.2.27__py3-none-any.whl → 0.2.40__py3-none-any.whl - Mend

figpack 0.2.27py3-none-any.whl → 0.2.40py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (32) hide show

figpack/__init__.py +1 -1
figpack/cli.py +214 -2
figpack/core/_bundle_utils.py +12 -8
figpack/core/_file_handler.py +4 -1
figpack/core/_save_figure.py +12 -8
figpack/core/_server_manager.py +106 -3
figpack/core/_show_view.py +1 -1
figpack/core/_upload_bundle.py +63 -51
figpack/core/_view_figure.py +15 -10
figpack/core/_zarr_consolidate.py +185 -0
figpack/core/extension_view.py +8 -4
figpack/core/figpack_extension.py +1 -1
figpack/core/figpack_view.py +29 -13
figpack/core/zarr.py +2 -2
figpack/figpack-figure-dist/assets/{index-DnHZdWys.js → index-ST_DU17U.js} +39 -39
figpack/figpack-figure-dist/index.html +2 -2
figpack/views/Box.py +2 -2
figpack/views/CaptionedView.py +64 -0
figpack/views/Iframe.py +43 -0
figpack/views/Image.py +1 -2
figpack/views/Markdown.py +7 -3
figpack/views/PlotlyExtension/PlotlyExtension.py +12 -12
figpack/views/Spectrogram.py +2 -0
figpack/views/TimeseriesGraph.py +84 -15
figpack/views/__init__.py +2 -0
{figpack-0.2.27.dist-info → figpack-0.2.40.dist-info}/METADATA +22 -1
figpack-0.2.40.dist-info/RECORD +50 -0
figpack-0.2.27.dist-info/RECORD +0 -47
{figpack-0.2.27.dist-info → figpack-0.2.40.dist-info}/WHEEL +0 -0
{figpack-0.2.27.dist-info → figpack-0.2.40.dist-info}/entry_points.txt +0 -0
{figpack-0.2.27.dist-info → figpack-0.2.40.dist-info}/licenses/LICENSE +0 -0
{figpack-0.2.27.dist-info → figpack-0.2.40.dist-info}/top_level.txt +0 -0

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

@@ -7,9 +7,9 @@
     <title>figpack figure</title>
     <script>
       // Allow script injection from trusted domains (see src/main.tsx)
-      window.script_injection_allowed_domains = ['https://manage.figpack.org', 'https://figpack.org'];
+      window.script_injection_allowed_domains = ['https://manage.figpack.org', 'https://figpack.org', "https://documents.figpack.org"];
     </script>
-    <script type="module" crossorigin src="./assets/index-DnHZdWys.js"></script>
+    <script type="module" crossorigin src="./assets/index-ST_DU17U.js"></script>
     <link rel="stylesheet" crossorigin href="./assets/index-V5m_wCvw.css">
   </head>
   <body>

figpack/views/Box.py CHANGED Viewed

@@ -2,7 +2,7 @@
 Box view for figpack - a layout container that handles other views
 """
-from typing import Any, Dict, List, Literal, Optional
+from typing import List, Literal, Optional
 from ..core.figpack_view import FigpackView
 from ..core.zarr import Group
@@ -21,7 +21,7 @@ class Box(FigpackView):
         show_titles: bool = True,
         items: List[LayoutItem],
         title: Optional[str] = None,
-    ):
+    ) -> None:
         """
         Initialize a Box layout view

figpack/views/CaptionedView.py ADDED Viewed

@@ -0,0 +1,64 @@
+"""
+CaptionedView for figpack - displays a view with a caption below it
+"""
+from typing import Optional
+import numpy as np
+from ..core.figpack_view import FigpackView
+from ..core.zarr import Group
+class CaptionedView(FigpackView):
+    """
+    A view that displays a child view with a text caption below it.
+    The caption height dynamically adjusts based on text length and container width.
+    """
+    def __init__(
+        self,
+        *,
+        view: FigpackView,
+        caption: str,
+        font_size: Optional[int] = None,
+    ):
+        """
+        Initialize a CaptionedView
+        Args:
+            view: The child view to display above the caption
+            caption: The text caption to display below the view
+            font_size: Optional font size for the caption text (default: 14)
+        """
+        self.view = view
+        self.caption = caption
+        self.font_size = font_size if font_size is not None else 14
+    def write_to_zarr_group(self, group: Group) -> None:
+        """
+        Write the CaptionedView data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set the view type
+        group.attrs["view_type"] = "CaptionedView"
+        # Set caption properties
+        group.attrs["font_size"] = self.font_size
+        # Convert caption string to numpy array of bytes
+        caption_bytes = self.caption.encode("utf-8")
+        caption_array = np.frombuffer(caption_bytes, dtype=np.uint8)
+        # Store the caption as a zarr array
+        group.create_dataset("caption_data", data=caption_array)
+        # Store caption size in attrs
+        group.attrs["caption_size"] = len(caption_bytes)
+        # Create a subgroup for the child view
+        child_group = group.create_group("child_view")
+        # Recursively write the child view to the subgroup
+        self.view.write_to_zarr_group(child_group)

figpack/views/Iframe.py ADDED Viewed

@@ -0,0 +1,43 @@
+"""
+Iframe view for figpack - displays content in an iframe
+"""
+import numpy as np
+from ..core.figpack_view import FigpackView
+from ..core.zarr import Group
+class Iframe(FigpackView):
+    """
+    An iframe visualization component for displaying web content
+    """
+    def __init__(self, url: str):
+        """
+        Initialize an Iframe view
+        Args:
+            url: The URL to display in the iframe
+        """
+        self.url = url
+    def write_to_zarr_group(self, group: Group) -> None:
+        """
+        Write the iframe data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set the view type
+        group.attrs["view_type"] = "Iframe"
+        # Convert URL to numpy array of bytes
+        url_bytes = self.url.encode("utf-8")
+        url_array = np.frombuffer(url_bytes, dtype=np.uint8)
+        # Store the URL as a zarr array
+        group.create_dataset("url_data", data=url_array)
+        # Store URL size in attrs
+        group.attrs["data_size"] = len(url_bytes)

figpack/views/Image.py CHANGED Viewed

@@ -5,7 +5,6 @@ Image view for figpack - displays PNG and JPG images
 from typing import Union
 import numpy as np
-import zarr
 from ..core.figpack_view import FigpackView
 from ..core.zarr import Group
@@ -16,7 +15,7 @@ class Image(FigpackView):
     An image visualization component for PNG and JPG files
     """
-    def __init__(self, image_path_or_data: Union[str, bytes]):
+    def __init__(self, image_path_or_data: Union[str, bytes]) -> None:
         """
         Initialize an Image view

figpack/views/Markdown.py CHANGED Viewed

@@ -2,8 +2,8 @@
 Markdown view for figpack - displays markdown content
 """
+from typing import Optional
 import numpy as np
-import zarr
 from ..core.figpack_view import FigpackView
 from ..core.zarr import Group
@@ -14,7 +14,7 @@ class Markdown(FigpackView):
     A markdown content visualization component
     """
-    def __init__(self, content: str):
+    def __init__(self, content: str, *, font_size: Optional[int] = None):
         """
         Initialize a Markdown view
@@ -22,6 +22,7 @@ class Markdown(FigpackView):
             content: The markdown content to display
         """
         self.content = content
+        self.font_size = font_size
     def write_to_zarr_group(self, group: Group) -> None:
         """
@@ -33,12 +34,15 @@ class Markdown(FigpackView):
         # Set the view type
         group.attrs["view_type"] = "Markdown"
+        if self.font_size is not None:
+            group.attrs["font_size"] = self.font_size
         # 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, chunks=True)
+        group.create_dataset("content_data", data=content_array)
         # Store content size in attrs
         group.attrs["data_size"] = len(content_bytes)

figpack/views/PlotlyExtension/PlotlyExtension.py CHANGED Viewed

@@ -55,15 +55,15 @@ class PlotlyFigure(figpack.ExtensionView):
 class CustomJSONEncoder(json.JSONEncoder):
     """Custom JSON encoder that handles numpy arrays and datetime objects"""
-    def default(self, obj):
-        if isinstance(obj, np.ndarray):
-            return obj.tolist()
-        elif isinstance(obj, (np.integer, np.floating)):
-            return obj.item()
-        elif isinstance(obj, (datetime, date)):
-            return obj.isoformat()
-        elif isinstance(obj, np.datetime64):
-            return str(obj)
-        elif hasattr(obj, "isoformat"):  # Handle other datetime-like objects
-            return obj.isoformat()
-        return super().default(obj)
+    def default(self, o):
+        if isinstance(o, np.ndarray):
+            return o.tolist()
+        elif isinstance(o, (np.integer, np.floating)):
+            return o.item()
+        elif isinstance(o, (datetime, date)):
+            return o.isoformat()
+        elif isinstance(o, np.datetime64):
+            return str(o)
+        elif hasattr(o, "isoformat"):  # Handle other datetime-like objects
+            return o.isoformat()
+        return super().default(o)

figpack/views/Spectrogram.py CHANGED Viewed

@@ -62,12 +62,14 @@ class Spectrogram(FigpackView):
         # Store frequency information
         if uniform_specified:
+            assert frequency_delta_hz is not None, "Frequency delta must be provided"
             assert frequency_delta_hz > 0, "Frequency delta must be positive"
             self.uniform_frequencies = True
             self.frequency_min_hz = frequency_min_hz
             self.frequency_delta_hz = frequency_delta_hz
             self.frequencies = None
         else:
+            assert frequencies is not None, "Frequencies array must be provided"
             assert (
                 len(frequencies) == data.shape[1]
             ), f"Number of frequencies ({len(frequencies)}) must match data frequency dimension ({data.shape[1]})"

figpack/views/TimeseriesGraph.py CHANGED Viewed

@@ -3,7 +3,7 @@ Views module for figpack - contains visualization components
 """
 import math
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, Dict, List, Optional, Tuple, Union
 import numpy as np
@@ -26,7 +26,7 @@ class TimeseriesGraph(FigpackView):
         hide_nav_toolbar: bool = False,
         hide_time_axis_labels: bool = False,
         y_label: str = "",
-    ):
+    ) -> None:
         """
         Initialize a TimeseriesGraph
@@ -54,8 +54,8 @@ class TimeseriesGraph(FigpackView):
         self,
         *,
         name: str,
-        t: np.ndarray,
-        y: np.ndarray,
+        t: Union[np.ndarray, List[float]],
+        y: Union[np.ndarray, List[float]],
         color: str = "blue",
         width: float = 1.0,
         dash: Optional[List[float]] = None,
@@ -71,6 +71,13 @@ class TimeseriesGraph(FigpackView):
             width: Line width
             dash: Dash pattern as [dash_length, gap_length]
         """
+        if isinstance(t, list):
+            t = np.array(t)
+        if isinstance(y, list):
+            y = np.array(y)
+        assert t.ndim == 1, "Time array must be 1-dimensional"
+        assert y.ndim == 1, "Y array must be 1-dimensional"
+        assert len(t) == len(y), "Time and Y arrays must have the same length"
         self._series.append(
             TGLineSeries(name=name, t=t, y=y, color=color, width=width, dash=dash)
         )
@@ -96,6 +103,13 @@ class TimeseriesGraph(FigpackView):
             radius: Marker radius
             shape: Marker shape ("circle", "square", etc.)
         """
+        if isinstance(t, list):
+            t = np.array(t)
+        if isinstance(y, list):
+            y = np.array(y)
+        assert t.ndim == 1, "Time array must be 1-dimensional"
+        assert y.ndim == 1, "Y array must be 1-dimensional"
+        assert len(t) == len(y), "Time and Y arrays must have the same length"
         self._series.append(
             TGMarkerSeries(name=name, t=t, y=y, color=color, radius=radius, shape=shape)
         )
@@ -119,6 +133,18 @@ class TimeseriesGraph(FigpackView):
             color: Fill color
             alpha: Transparency (0-1)
         """
+        if isinstance(t_start, list):
+            t_start = np.array(t_start)
+        if isinstance(t_end, list):
+            t_end = np.array(t_end)
+        assert t_start.ndim == 1, "Start time array must be 1-dimensional"
+        assert t_end.ndim == 1, "End time array must be 1-dimensional"
+        assert len(t_start) == len(
+            t_end
+        ), "Start and end time arrays must have the same length"
+        assert np.all(
+            t_start <= t_end
+        ), "Start times must be less than or equal to end times"
         self._series.append(
             TGIntervalSeries(
                 name=name, t_start=t_start, t_end=t_end, color=color, alpha=alpha
@@ -137,6 +163,7 @@ class TimeseriesGraph(FigpackView):
         width: float = 1.0,
         channel_spacing: Optional[float] = None,
         auto_channel_spacing: Optional[float] = None,
+        timestamps_for_inserting_nans: Optional[np.ndarray] = None,
     ) -> None:
         """
         Add a uniform timeseries to the graph with optional multi-channel support
@@ -151,7 +178,10 @@ class TimeseriesGraph(FigpackView):
             width: Line width
             channel_spacing: Vertical spacing between channels
             auto_channel_spacing: sets channel spacing to this multiple of the estimated RMS noise level
+            timestamps_for_inserting_nans: Optional array of timestamps used to determine where to insert NaNs in the data
         """
+        if isinstance(data, list):
+            data = np.array(data)
         self._series.append(
             TGUniformSeries(
                 name=name,
@@ -163,6 +193,7 @@ class TimeseriesGraph(FigpackView):
                 width=width,
                 channel_spacing=channel_spacing,
                 auto_channel_spacing=auto_channel_spacing,
+                timestamps_for_inserting_nans=timestamps_for_inserting_nans,
             )
         )
@@ -210,7 +241,7 @@ class TGLineSeries:
         color: str,
         width: float,
         dash: Optional[List[float]],
-    ):
+    ) -> None:
         assert t.ndim == 1, "Time array must be 1-dimensional"
         assert y.ndim == 1, "Y array must be 1-dimensional"
         assert len(t) == len(y), "Time and Y arrays must have the same length"
@@ -243,7 +274,7 @@ class TGMarkerSeries:
         color: str,
         radius: float,
         shape: str,
-    ):
+    ) -> None:
         assert t.ndim == 1, "Time array must be 1-dimensional"
         assert y.ndim == 1, "Y array must be 1-dimensional"
         assert len(t) == len(y), "Time and Y arrays must have the same length"
@@ -278,7 +309,7 @@ class TGIntervalSeries:
         t_end: np.ndarray,
         color: str,
         alpha: float,
-    ):
+    ) -> None:
         assert t_start.ndim == 1, "Start time array must be 1-dimensional"
         assert t_end.ndim == 1, "End time array must be 1-dimensional"
         assert len(t_start) == len(
@@ -320,7 +351,8 @@ class TGUniformSeries:
         width: float = 1.0,
         channel_spacing: Optional[float] = None,
         auto_channel_spacing: Optional[float] = None,
-    ):
+        timestamps_for_inserting_nans: Optional[np.ndarray] = None,
+    ) -> None:
         assert sampling_frequency_hz > 0, "Sampling frequency must be positive"
         # Handle both 1D and 2D data
@@ -340,16 +372,31 @@ class TGUniformSeries:
         self.sampling_frequency_hz = sampling_frequency_hz
         self.data = data.astype(np.float32)  # Ensure float32 for efficiency
+        if timestamps_for_inserting_nans is not None:
+            self.data = insert_nans_based_on_timestamps(
+                self.data,
+                start_time_sec=start_time_sec,
+                sampling_frequency_hz=sampling_frequency_hz,
+                timestamps=timestamps_for_inserting_nans,
+            )
         if auto_channel_spacing is not None:
             if channel_spacing is not None:
                 raise ValueError(
                     "Specify either channel_spacing or auto_channel_spacing, not both."
                 )
             # Estimate RMS noise level across all channels using median absolute deviation
-            mad = np.median(np.abs(self.data - np.median(self.data, axis=0)), axis=0)
+            # Use nanmedian to handle NaN values properly
+            mad = np.nanmedian(
+                np.abs(self.data - np.nanmedian(self.data, axis=0)), axis=0
+            )
             rms_estimate = mad / 0.6745  # Convert MAD to RMS estimate
-            channel_spacing = auto_channel_spacing * np.median(rms_estimate)
-            if channel_spacing <= 0:
+            channel_spacing = auto_channel_spacing * np.nanmedian(rms_estimate)
+            if (
+                channel_spacing is None
+                or (channel_spacing <= 0)
+                or np.isnan(channel_spacing)
+            ):
                 channel_spacing = 1.0  # Fallback to default spacing if estimate fails
         self.channel_spacing = channel_spacing
@@ -394,7 +441,7 @@ class TGUniformSeries:
         # Prepare downsampled arrays for efficient rendering
         self.downsampled_data = self._compute_downsampled_data()
-    def _compute_downsampled_data(self) -> dict:
+    def _compute_downsampled_data(self) -> Dict[int, np.ndarray]:
         """
         Compute downsampled arrays at power-of-4 factors using a vectorized
         min/max pyramid with NaN padding for partial bins.
@@ -469,8 +516,8 @@ class TGUniformSeries:
         return downsampled
     def _calculate_optimal_chunk_size(
-        self, shape: tuple, target_size_mb: float = 5.0
-    ) -> tuple:
+        self, shape: Tuple[int, ...], target_size_mb: float = 5.0
+    ) -> Tuple[int, ...]:
         """
         Calculate optimal chunk size for Zarr storage targeting ~5MB per chunk
@@ -534,7 +581,7 @@ class TGUniformSeries:
         group.attrs["n_channels"] = n_channels
         if self.channel_spacing is not None:
-            group.attrs["channel_spacing"] = self.channel_spacing
+            group.attrs["channel_spacing"] = float(self.channel_spacing)
         # Store original data with optimal chunking
         original_chunks = self._calculate_optimal_chunk_size(self.data.shape)
@@ -559,3 +606,25 @@ class TGUniformSeries:
                 data=downsampled_array,
                 chunks=ds_chunks,
             )
+def insert_nans_based_on_timestamps(
+    x: np.ndarray,
+    *,
+    start_time_sec: float,
+    sampling_frequency_hz: float,
+    timestamps: np.ndarray,
+) -> np.ndarray:
+    end_timestamps = timestamps[-1]
+    ret_length = int((end_timestamps - start_time_sec) * sampling_frequency_hz) + 1
+    # Handle both 1D and 2D (multi-channel) data
+    if x.ndim == 1:
+        ret = np.nan * np.ones((ret_length,), dtype=x.dtype)
+    else:  # x.ndim == 2
+        n_channels = x.shape[1]
+        ret = np.nan * np.ones((ret_length, n_channels), dtype=x.dtype)
+    indices = ((timestamps - start_time_sec) * sampling_frequency_hz).astype(int)
+    ret[indices] = x
+    return ret

figpack/views/__init__.py CHANGED Viewed

@@ -1,7 +1,9 @@
 from .Box import Box
+from .CaptionedView import CaptionedView
 from .DataFrame import DataFrame
 from .Gallery import Gallery
 from .GalleryItem import GalleryItem
+from .Iframe import Iframe
 from .Image import Image
 from .LayoutItem import LayoutItem
 from .Markdown import Markdown

{figpack-0.2.27.dist-info → figpack-0.2.40.dist-info}/METADATA RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: figpack
-Version: 0.2.27
+Version: 0.2.40
 Summary: A Python package for creating shareable, interactive visualizations in the browser
 Author-email: Jeremy Magland <jmagland@flatironinstitute.org>
 License: Apache-2.0
@@ -114,6 +114,27 @@ graph.show(open_in_browser=True, title="Quick Start Example")
 Apache-2.0
+## Citation
+If you use figpack in your research, please cite it:
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17419621.svg)](https://doi.org/10.5281/zenodo.17419621)
+```bibtex
+@software{magland_figpack_2025,
+  author       = {Magland, Jeremy},
+  title        = {figpack},
+  year         = 2025,
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.17419621},
+  url          = {https://doi.org/10.5281/zenodo.17419621}
+}
+```
+Or in APA format:
+> Magland, J. (2025). figpack (Version 0.2.40) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.17419621
 ## Contributing
 Visit the [GitHub repository](https://github.com/flatironinstitute/figpack) for issues, contributions, and the latest updates.

figpack-0.2.40.dist-info/RECORD ADDED Viewed

@@ -0,0 +1,50 @@
+figpack/__init__.py,sha256=skZ1R6k19F5UFsi2LdLti5jyUb4LzRtZT1VVaXWy0cE,358
+figpack/cli.py,sha256=TfSGSw2YUlO0JPlNb4DYko636rk7vV91tqL6QHBSgoQ,18464
+figpack/extensions.py,sha256=mILB4_F1RHkca4I7t88zh74IX8VCmfT7XFZZT4XYdNw,13009
+figpack/core/__init__.py,sha256=7zU6O1piTk07aeCfbU81QqTgSHIO2n5MZ4LFNmsrtfs,192
+figpack/core/_bundle_utils.py,sha256=a0oPsqRsaQbrNcUKXHZTfE5uPtgmtqLJdQQPE1jS4_0,9299
+figpack/core/_file_handler.py,sha256=T_Yq3aGcgfqbGCW31Ge9MseApH3zoZ8iZ2wTyb9cYuw,7113
+figpack/core/_save_figure.py,sha256=ZboTlu5N609GmBlQ7rni5p7AP1mvCelEjHBHWeLWGOM,1166
+figpack/core/_server_manager.py,sha256=2F1fo1aEcbbmQXiZ5wjJ1SpV4BqgtwAqq8KvQFrFVPo,16262
+figpack/core/_show_view.py,sha256=nLsVOuuy5-NLSAK8qMjxmRart3TAL1wH1duTcIH_mGA,5187
+figpack/core/_upload_bundle.py,sha256=cNoLSbsulmZ8R8BzohZLACDmwxdDN9f8TwO_fpDeSHc,15020
+figpack/core/_view_figure.py,sha256=FVPvSOa1hW2Th-X778VwKytfNpudoFNb1LK7eY43p44,5568
+figpack/core/_zarr_consolidate.py,sha256=uKcSq_ml0pBVztJJZwinXAiyyk2P28Ao12IbEA3niSU,6052
+figpack/core/config.py,sha256=oOR7SlP192vuFhYlS-h14HnG-kd_3gaz0vshXch2RNc,173
+figpack/core/extension_view.py,sha256=qh1g7H_YfOF0eLAl-c7uZlv7A8Ssm8VbrhRfGsjtHto,1322
+figpack/core/figpack_extension.py,sha256=F4q6poPihwVnjWQtasZjvzB0IkqFfgJuv8Xb9N4eNOA,2260
+figpack/core/figpack_view.py,sha256=LCwydF_M03gvlAGjU9CMWFMyXGlV0EkfhzgAU9gxPWc,7292
+figpack/core/zarr.py,sha256=wKi8G2MksdTbZUA3Yc-huhIplrOWCgkmYnn8NMftA7k,1666
+figpack/figpack-figure-dist/index.html,sha256=hclmcIxQE4wsyJhUGc_VEn_mOIIwYNlPxMYiu-5Rl0Q,721
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