PyPI - figpack - Versions diffs - 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl - Mend

figpack 0.1.1py3-none-any.whl → 0.1.3py3-none-any.whl

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Files changed (37) hide show

figpack/__init__.py +3 -1
figpack/cli.py +312 -0
figpack/core/_bundle_utils.py +11 -1
figpack/core/_show_view.py +34 -8
figpack/core/{_upload_view.py → _upload_bundle.py} +140 -49
figpack/core/figpack_view.py +32 -24
figpack/figpack-gui-dist/assets/index-BDa2iJW9.css +1 -0
figpack/figpack-gui-dist/assets/index-ByLxmrzp.js +846 -0
figpack/figpack-gui-dist/assets/neurosift-logo-CLsuwLMO.png +0 -0
figpack/figpack-gui-dist/index.html +4 -4
figpack/spike_sorting/__init__.py +5 -0
figpack/spike_sorting/views/AutocorrelogramItem.py +41 -0
figpack/spike_sorting/views/Autocorrelograms.py +76 -0
figpack/spike_sorting/views/CrossCorrelogramItem.py +45 -0
figpack/spike_sorting/views/CrossCorrelograms.py +82 -0
figpack/spike_sorting/views/UnitSimilarityScore.py +40 -0
figpack/spike_sorting/views/UnitsTable.py +68 -0
figpack/spike_sorting/views/UnitsTableColumn.py +40 -0
figpack/spike_sorting/views/UnitsTableRow.py +36 -0
figpack/spike_sorting/views/__init__.py +23 -0
figpack/views/Image.py +82 -0
figpack/views/Markdown.py +34 -0
figpack/views/MatplotlibFigure.py +65 -0
figpack/views/PlotlyFigure.py +58 -0
figpack/views/__init__.py +4 -0
figpack-0.1.3.dist-info/METADATA +126 -0
figpack-0.1.3.dist-info/RECORD +38 -0
figpack-0.1.3.dist-info/entry_points.txt +2 -0
figpack-0.1.3.dist-info/top_level.txt +1 -0
figpack/figpack-gui-dist/assets/index-BW-ONVCL.js +0 -65
figpack/figpack-gui-dist/assets/index-CeWL3OeJ.css +0 -1
figpack-0.1.1.dist-info/METADATA +0 -33
figpack-0.1.1.dist-info/RECORD +0 -22
figpack-0.1.1.dist-info/top_level.txt +0 -2
figpack-gui/node_modules/flatted/python/flatted.py +0 -149
{figpack-0.1.1.dist-info → figpack-0.1.3.dist-info}/WHEEL +0 -0
{figpack-0.1.1.dist-info → figpack-0.1.3.dist-info}/licenses/LICENSE +0 -0

figpack/figpack-gui-dist/assets/neurosift-logo-CLsuwLMO.png ADDED Viewed

Binary file

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

@@ -2,11 +2,11 @@
 <html lang="en">
   <head>
     <meta charset="UTF-8" />
-    <link rel="icon" type="image/svg+xml" href="/vite.svg" />
+    <link rel="icon" type="image/png" href="./assets/neurosift-logo-CLsuwLMO.png" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Vite + React + TS</title>
-    <script type="module" crossorigin src="./assets/index-BW-ONVCL.js"></script>
-    <link rel="stylesheet" crossorigin href="./assets/index-CeWL3OeJ.css">
+    <title>figpack figure</title>
+    <script type="module" crossorigin src="./assets/index-ByLxmrzp.js"></script>
+    <link rel="stylesheet" crossorigin href="./assets/index-BDa2iJW9.css">
   </head>
   <body>
     <div id="root"></div>

figpack/spike_sorting/__init__.py ADDED Viewed

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

figpack/spike_sorting/views/AutocorrelogramItem.py ADDED Viewed

@@ -0,0 +1,41 @@
+"""
+AutocorrelogramItem for spike sorting views
+"""
+from typing import Union
+import numpy as np
+class AutocorrelogramItem:
+    """
+    Represents a single autocorrelogram for a unit
+    """
+    def __init__(
+        self,
+        *,
+        unit_id: Union[str, int],
+        bin_edges_sec: np.ndarray,
+        bin_counts: np.ndarray,
+    ):
+        """
+        Initialize an AutocorrelogramItem
+        Args:
+            unit_id: Identifier for the unit
+            bin_edges_sec: Array of bin edges in seconds
+            bin_counts: Array of bin counts
+        """
+        self.unit_id = unit_id
+        self.bin_edges_sec = np.array(bin_edges_sec, dtype=np.float32)
+        self.bin_counts = np.array(bin_counts, dtype=np.int32)
+    def to_dict(self):
+        """
+        Convert the autocorrelogram item to a dictionary representation
+        """
+        return {
+            "unit_id": str(self.unit_id),
+            "bin_edges_sec": self.bin_edges_sec.tolist(),
+            "bin_counts": self.bin_counts.tolist(),
+        }

figpack/spike_sorting/views/Autocorrelograms.py ADDED Viewed

@@ -0,0 +1,76 @@
+"""
+Autocorrelograms view for figpack - displays multiple autocorrelograms
+"""
+import zarr
+import numpy as np
+from typing import List, Optional
+from ...core.figpack_view import FigpackView
+from .AutocorrelogramItem import AutocorrelogramItem
+class Autocorrelograms(FigpackView):
+    """
+    A view that displays multiple autocorrelograms for spike sorting analysis
+    """
+    def __init__(
+        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 _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the Autocorrelograms data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # 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)
+        # Store metadata for each autocorrelogram
+        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),
+            }
+            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,
+            )
+        # Store the autocorrelogram metadata
+        group.attrs["autocorrelograms"] = autocorrelogram_metadata

figpack/spike_sorting/views/CrossCorrelogramItem.py ADDED Viewed

@@ -0,0 +1,45 @@
+"""
+CrossCorrelogramItem for spike sorting views
+"""
+from typing import Union
+import numpy as np
+class CrossCorrelogramItem:
+    """
+    Represents a single cross-correlogram between two units
+    """
+    def __init__(
+        self,
+        *,
+        unit_id1: Union[str, int],
+        unit_id2: Union[str, int],
+        bin_edges_sec: np.ndarray,
+        bin_counts: np.ndarray,
+    ):
+        """
+        Initialize a CrossCorrelogramItem
+        Args:
+            unit_id1: Identifier for the first unit
+            unit_id2: Identifier for the second unit
+            bin_edges_sec: Array of bin edges in seconds
+            bin_counts: Array of bin counts
+        """
+        self.unit_id1 = unit_id1
+        self.unit_id2 = unit_id2
+        self.bin_edges_sec = np.array(bin_edges_sec, dtype=np.float32)
+        self.bin_counts = np.array(bin_counts, dtype=np.int32)
+    def to_dict(self):
+        """
+        Convert the cross-correlogram item to a dictionary representation
+        """
+        return {
+            "unit_id1": str(self.unit_id1),
+            "unit_id2": str(self.unit_id2),
+            "bin_edges_sec": self.bin_edges_sec.tolist(),
+            "bin_counts": self.bin_counts.tolist(),
+        }

figpack/spike_sorting/views/CrossCorrelograms.py ADDED Viewed

@@ -0,0 +1,82 @@
+"""
+CrossCorrelograms view for figpack - displays multiple cross-correlograms
+"""
+import zarr
+import numpy as np
+from typing import List, Optional
+from ...core.figpack_view import FigpackView
+from .CrossCorrelogramItem import CrossCorrelogramItem
+class CrossCorrelograms(FigpackView):
+    """
+    A view that displays multiple cross-correlograms for spike sorting analysis
+    """
+    def __init__(
+        self,
+        *,
+        cross_correlograms: List[CrossCorrelogramItem],
+        hide_unit_selector: Optional[bool] = False,
+        height: Optional[int] = 500,
+    ):
+        """
+        Initialize a CrossCorrelograms view
+        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 _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the CrossCorrelograms data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set the view type
+        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
+        # Store the number of cross-correlograms
+        group.attrs["num_cross_correlograms"] = len(self.cross_correlograms)
+        # Store metadata for each cross-correlogram
+        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),
+            }
+            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,
+            )
+        # Store the cross-correlogram metadata
+        group.attrs["cross_correlograms"] = cross_correlogram_metadata

figpack/spike_sorting/views/UnitSimilarityScore.py ADDED Viewed

@@ -0,0 +1,40 @@
+"""
+UnitSimilarityScore for spike sorting views
+"""
+from typing import Union
+class UnitSimilarityScore:
+    """
+    Represents a similarity score between two units
+    """
+    def __init__(
+        self,
+        *,
+        unit_id1: Union[str, int],
+        unit_id2: Union[str, int],
+        similarity: float,
+    ):
+        """
+        Initialize a UnitSimilarityScore
+        Args:
+            unit_id1: Identifier for the first unit
+            unit_id2: Identifier for the second unit
+            similarity: Similarity score between the units (typically 0-1)
+        """
+        self.unit_id1 = unit_id1
+        self.unit_id2 = unit_id2
+        self.similarity = similarity
+    def to_dict(self):
+        """
+        Convert the similarity score to a dictionary representation
+        """
+        return {
+            "unitId1": self.unit_id1,
+            "unitId2": self.unit_id2,
+            "similarity": self.similarity,
+        }

figpack/spike_sorting/views/UnitsTable.py ADDED Viewed

@@ -0,0 +1,68 @@
+"""
+UnitsTable view for figpack - displays a table of units with their properties
+"""
+import zarr
+import numpy as np
+from typing import List, Optional
+from ...core.figpack_view import FigpackView
+from .UnitsTableColumn import UnitsTableColumn
+from .UnitsTableRow import UnitsTableRow
+from .UnitSimilarityScore import UnitSimilarityScore
+class UnitsTable(FigpackView):
+    """
+    A view that displays a table of units with their properties and optional similarity scores
+    """
+    def __init__(
+        self,
+        *,
+        columns: List[UnitsTableColumn],
+        rows: List[UnitsTableRow],
+        similarity_scores: Optional[List[UnitSimilarityScore]] = None,
+        height: Optional[int] = 600,
+    ):
+        """
+        Initialize a UnitsTable view
+        Args:
+            columns: List of UnitsTableColumn objects defining the table structure
+            rows: List of UnitsTableRow objects containing the data
+            similarity_scores: Optional list of UnitSimilarityScore objects
+            height: Height of the view in pixels
+        """
+        self.columns = columns
+        self.rows = rows
+        self.similarity_scores = similarity_scores or []
+        self.height = height
+    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the UnitsTable data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set the view type
+        group.attrs["view_type"] = "UnitsTable"
+        # Set view properties
+        if self.height is not None:
+            group.attrs["height"] = self.height
+        # Store columns metadata
+        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 similarity scores if provided
+        if self.similarity_scores:
+            similarity_scores_metadata = [
+                score.to_dict() for score in self.similarity_scores
+            ]
+            group.attrs["similarityScores"] = similarity_scores_metadata

figpack/spike_sorting/views/UnitsTableColumn.py ADDED Viewed

@@ -0,0 +1,40 @@
+"""
+UnitsTableColumn for spike sorting views
+"""
+from typing import Literal
+class UnitsTableColumn:
+    """
+    Represents a column in a units table
+    """
+    def __init__(
+        self,
+        *,
+        key: str,
+        label: str,
+        dtype: Literal["int", "float", "str", "bool"],
+    ):
+        """
+        Initialize a UnitsTableColumn
+        Args:
+            key: The key used to access values in the row data
+            label: Display label for the column
+            dtype: Data type of the column values
+        """
+        self.key = key
+        self.label = label
+        self.dtype = dtype
+    def to_dict(self):
+        """
+        Convert the column to a dictionary representation
+        """
+        return {
+            "key": self.key,
+            "label": self.label,
+            "dtype": self.dtype,
+        }

figpack/spike_sorting/views/UnitsTableRow.py ADDED Viewed

@@ -0,0 +1,36 @@
+"""
+UnitsTableRow for spike sorting views
+"""
+from typing import Union, Dict, Any
+class UnitsTableRow:
+    """
+    Represents a row in a units table
+    """
+    def __init__(
+        self,
+        *,
+        unit_id: Union[str, int],
+        values: Dict[str, Any],
+    ):
+        """
+        Initialize a UnitsTableRow
+        Args:
+            unit_id: Identifier for the unit
+            values: Dictionary of column key to value mappings
+        """
+        self.unit_id = unit_id
+        self.values = values
+    def to_dict(self):
+        """
+        Convert the row to a dictionary representation
+        """
+        return {
+            "unitId": self.unit_id,
+            "values": self.values,
+        }

figpack/spike_sorting/views/__init__.py ADDED Viewed

@@ -0,0 +1,23 @@
+"""
+Spike sorting views for figpack
+"""
+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
+__all__ = [
+    "AutocorrelogramItem",
+    "Autocorrelograms",
+    "CrossCorrelogramItem",
+    "CrossCorrelograms",
+    "UnitsTableColumn",
+    "UnitsTableRow",
+    "UnitSimilarityScore",
+    "UnitsTable",
+]

figpack/views/Image.py ADDED Viewed

@@ -0,0 +1,82 @@
+"""
+Image view for figpack - displays PNG and JPG images
+"""
+import zarr
+import numpy as np
+from typing import Union
+from ..core.figpack_view import FigpackView
+class Image(FigpackView):
+    """
+    An image visualization component for PNG and JPG files
+    """
+    def __init__(self, image_path_or_data: Union[str, bytes]):
+        """
+        Initialize an Image view
+        Args:
+            image_path_or_data: Path to image file or raw image bytes
+        """
+        self.image_path_or_data = image_path_or_data
+    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the image data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set the view type
+        group.attrs["view_type"] = "Image"
+        try:
+            # Get the raw image data
+            if isinstance(self.image_path_or_data, str):
+                # Load from file path
+                with open(self.image_path_or_data, "rb") as f:
+                    image_data = f.read()
+            elif isinstance(self.image_path_or_data, bytes):
+                # Use bytes directly
+                image_data = self.image_path_or_data
+            else:
+                raise ValueError("image_path_or_data must be a file path or bytes")
+            # Convert bytes to numpy array of uint8
+            image_array = np.frombuffer(image_data, dtype=np.uint8)
+            # Store the raw image data as a zarr array
+            group.create_dataset(
+                "image_data",
+                data=image_array,
+                dtype=np.uint8,
+                chunks=True,
+                compressor=zarr.Blosc(
+                    cname="zstd", clevel=3, shuffle=zarr.Blosc.SHUFFLE
+                ),
+            )
+            # Try to determine format from file signature
+            format_type = "Unknown"
+            if len(image_data) >= 8:
+                # Check PNG signature
+                if image_data[:8] == b"\x89PNG\r\n\x1a\n":
+                    format_type = "PNG"
+                # Check JPEG signature
+                elif image_data[:2] == b"\xff\xd8":
+                    format_type = "JPEG"
+            group.attrs["image_format"] = format_type
+            group.attrs["data_size"] = len(image_data)
+        except Exception as e:
+            # If image loading fails, store error information
+            group.attrs["error"] = f"Failed to load image: {str(e)}"
+            group.attrs["image_format"] = "Unknown"
+            group.attrs["data_size"] = 0
+            # Create empty array as placeholder
+            group.create_dataset(
+                "image_data", data=np.array([], dtype=np.uint8), dtype=np.uint8
+            )

figpack/views/Markdown.py ADDED Viewed

@@ -0,0 +1,34 @@
+"""
+Markdown view for figpack - displays markdown content
+"""
+import zarr
+from ..core.figpack_view import FigpackView
+class Markdown(FigpackView):
+    """
+    A markdown content visualization component
+    """
+    def __init__(self, content: str):
+        """
+        Initialize a Markdown view
+        Args:
+            content: The markdown content to display
+        """
+        self.content = content
+    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the markdown data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set the view type
+        group.attrs["view_type"] = "Markdown"
+        # Store the markdown content
+        group.attrs["content"] = self.content

figpack/views/MatplotlibFigure.py ADDED Viewed

@@ -0,0 +1,65 @@
+"""
+MatplotlibFigure view for figpack - displays matplotlib figures
+"""
+import zarr
+import io
+from typing import Union, Any
+from ..core.figpack_view import FigpackView
+class MatplotlibFigure(FigpackView):
+    """
+    A matplotlib figure visualization component
+    """
+    def __init__(self, fig):
+        """
+        Initialize a MatplotlibFigure view
+        Args:
+            fig: The matplotlib figure object
+        """
+        self.fig = fig
+    def _write_to_zarr_group(self, group: zarr.Group) -> None:
+        """
+        Write the matplotlib figure data to a Zarr group
+        Args:
+            group: Zarr group to write data into
+        """
+        # Set the view type
+        group.attrs["view_type"] = "MatplotlibFigure"
+        try:
+            # Convert matplotlib figure to SVG string
+            svg_buffer = io.StringIO()
+            self.fig.savefig(
+                svg_buffer,
+                format="svg",
+                bbox_inches="tight",
+                facecolor="white",
+                edgecolor="none",
+            )
+            svg_string = svg_buffer.getvalue()
+            svg_buffer.close()
+            # Store the SVG data
+            group.attrs["svg_data"] = svg_string
+            # Store figure dimensions for reference
+            fig_width, fig_height = self.fig.get_size_inches()
+            group.attrs["figure_width_inches"] = float(fig_width)
+            group.attrs["figure_height_inches"] = float(fig_height)
+            # Store DPI for reference
+            group.attrs["figure_dpi"] = float(self.fig.dpi)
+        except Exception as e:
+            # If SVG export fails, store error information
+            group.attrs["svg_data"] = ""
+            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

figpack 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

Potentially problematic release.

figpack 0.1.1py3-none-any.whl → 0.1.3py3-none-any.whl