scitex 2.14.0__py3-none-any.whl

scitex/canvas/io/_bundle.py

@@ -0,0 +1,1121 @@
+#!/usr/bin/env python3
+# Timestamp: "2025-12-14 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/fig/io/_bundle.py
+
+"""
+SciTeX Figure Bundle I/O - Figure-specific bundle operations.
+
+Handles:
+    - Figure specification validation
+    - Panel composition and layout
+    - Nested .plot bundle management
+    - Export file handling
+"""
+
+import json
+import shutil
+from pathlib import Path
+from typing import Any, Dict, List
+
+__all__ = [
+    "validate_figure_spec",
+    "load_figure_bundle",
+    "save_figure_bundle",
+    "FIGURE_SCHEMA_SPEC",
+]
+
+# Schema specification for .figure bundles
+FIGURE_SCHEMA_SPEC = {
+    "name": "scitex.canvas.figure",
+    "version": "1.0.0",
+    "required_fields": ["schema"],
+    "optional_fields": ["figure", "panels", "notations"],
+}
+
+
+def validate_figure_spec(spec: Dict[str, Any]) -> List[str]:
+    """Validate .figure-specific fields.
+
+    Args:
+        spec: The specification dictionary to validate.
+
+    Returns:
+        List of validation error messages (empty if valid).
+    """
+    errors = []
+
+    if "panels" in spec:
+        panels = spec["panels"]
+        if not isinstance(panels, list):
+            errors.append("'panels' must be a list")
+        else:
+            for i, panel in enumerate(panels):
+                if not isinstance(panel, dict):
+                    errors.append(f"panels[{i}] must be a dictionary")
+                    continue
+                if "id" not in panel:
+                    errors.append(f"panels[{i}].id is required")
+
+    if "figure" in spec:
+        figure = spec["figure"]
+        if not isinstance(figure, dict):
+            errors.append("'figure' must be a dictionary")
+
+    return errors
+
+
+def load_figure_bundle(bundle_dir: Path) -> Dict[str, Any]:
+    """Load .figure bundle contents from directory.
+
+    Supports both:
+    - New format: spec.json + style.json (separate semantic/appearance)
+    - Legacy format: {basename}.json (embedded styles)
+
+    Args:
+        bundle_dir: Path to the bundle directory.
+
+    Returns:
+        Dictionary with loaded bundle contents:
+        - spec: Figure specification (semantic)
+        - style: Figure style (appearance)
+        - plots: Dict of nested plot bundles
+        - basename: Base filename
+    """
+    result = {}
+    bundle_dir = Path(bundle_dir)
+
+    # Determine basename from directory name
+    basename = bundle_dir.stem.replace(".figure", "")
+    result["basename"] = basename
+
+    # Try to load spec.json (new format) first
+    spec_file = bundle_dir / "spec.json"
+    if spec_file.exists():
+        with open(spec_file) as f:
+            result["spec"] = json.load(f)
+    else:
+        # Fallback to {basename}.json (legacy format)
+        legacy_file = bundle_dir / f"{basename}.json"
+        if legacy_file.exists():
+            with open(legacy_file) as f:
+                result["spec"] = json.load(f)
+        else:
+            # Try any .json file
+            for f in bundle_dir.glob("*.json"):
+                if not f.name.startswith(".") and f.name != "style.json":
+                    with open(f) as fp:
+                        result["spec"] = json.load(fp)
+                    break
+            else:
+                result["spec"] = None
+
+    # Load style.json if exists
+    style_file = bundle_dir / "style.json"
+    if style_file.exists():
+        with open(style_file) as f:
+            result["style"] = json.load(f)
+    else:
+        # Extract from embedded styles in spec (legacy)
+        if result.get("spec"):
+            figure = result["spec"].get("figure", {})
+            if "styles" in figure:
+                result["style"] = figure["styles"]
+            else:
+                result["style"] = {}
+        else:
+            result["style"] = {}
+
+    # Load nested .plot bundles
+    result["plots"] = {}
+
+    # Load from .plot directories
+    for plot_dir in bundle_dir.glob("*.plot"):
+        plot_name = plot_dir.stem.replace(".plot", "")
+        from scitex.io.bundle import load
+
+        result["plots"][plot_name] = load(plot_dir)
+
+    # Load from .plot.zip files
+    for plot_zip in bundle_dir.glob("*.plot.zip"):
+        if plot_zip.is_file():
+            plot_name = plot_zip.stem.replace(".plot", "")
+            from scitex.io.bundle import load
+
+            result["plots"][plot_name] = load(plot_zip)
+
+    return result
+
+
+def save_figure_bundle(data: Dict[str, Any], dir_path: Path) -> None:
+    """Save .figure bundle contents to directory.
+
+    Structure:
+        figure.figure/
+            spec.json              # Figure-level specification
+            style.json             # Figure-level style (optional)
+            exports/               # Figure-level exports
+                figure.png
+                figure.svg
+                figure_hitmap.png
+                figure_overview.png
+            cache/                 # Figure-level cache
+                geometry_px.json   # Combined geometry for all panels
+                render_manifest.json
+            panels/                # Nested panel bundles (or *.plot at root)
+                A.plot/
+                B.plot/
+            README.md
+
+    Args:
+        data: Bundle data dictionary.
+        dir_path: Path to the bundle directory.
+    """
+    import logging
+
+    logger = logging.getLogger("scitex")
+
+    # Get basename from directory name (e.g., "Figure1" from "Figure1.figure")
+    basename = dir_path.stem.replace(".figure", "")
+
+    # Create directories
+    exports_dir = dir_path / "exports"
+    cache_dir = dir_path / "cache"
+    exports_dir.mkdir(parents=True, exist_ok=True)
+    cache_dir.mkdir(parents=True, exist_ok=True)
+
+    # Split spec into spec.json (semantic) and style.json (appearance)
+    spec = data.get("spec", {})
+    style = data.get("style", {})
+
+    # Extract style from spec.figure.styles if not provided separately
+    figure_data = spec.get("figure", {})
+    if not style and "styles" in figure_data:
+        style = figure_data.get("styles", {})
+
+    # Build clean spec (semantic data only)
+    clean_spec = {
+        "schema": spec.get(
+            "schema", {"name": "scitex.canvas.figure", "version": "1.0.0"}
+        ),
+        "figure": {
+            "id": figure_data.get("id", "figure"),
+            "title": figure_data.get("title", ""),
+            "caption": figure_data.get("caption", ""),
+        },
+        "panels": spec.get("panels", []),
+    }
+    if "notations" in spec:
+        clean_spec["notations"] = spec["notations"]
+
+    # Build style (appearance data)
+    figure_style = {
+        "schema": {"name": "scitex.canvas.style", "version": "1.0.0"},
+        "size": style.get("size", {"width_mm": 180, "height_mm": 120}),
+        "background": style.get("background", "#ffffff"),
+        "theme": style.get("theme", {"mode": "light"}),
+        "panel_labels": style.get(
+            "panel_labels",
+            {
+                "visible": True,
+                "fontsize": 12,
+                "fontweight": "bold",
+                "position": "top-left",
+            },
+        ),
+    }
+
+    # Save spec.json (semantic)
+    spec_file = dir_path / "spec.json"
+    with open(spec_file, "w") as f:
+        json.dump(clean_spec, f, indent=2)
+
+    # Save style.json (appearance)
+    style_file = dir_path / "style.json"
+    with open(style_file, "w") as f:
+        json.dump(figure_style, f, indent=2)
+
+    # Also save as {basename}.json for backward compatibility (full spec with embedded style)
+    compat_spec = dict(clean_spec)
+    compat_spec["figure"]["styles"] = {
+        "size": figure_style["size"],
+        "background": figure_style["background"],
+    }
+    compat_spec_file = dir_path / f"{basename}.json"
+    with open(compat_spec_file, "w") as f:
+        json.dump(compat_spec, f, indent=2)
+
+    # Save exports to exports/ directory
+    _save_figure_exports(data, exports_dir, spec, basename)
+
+    # Copy nested .plot bundles directly (preserving all files)
+    if "plots" in data:
+        _copy_nested_plot_bundles(data["plots"], dir_path)
+
+    # Generate composed figure in exports/ (Figure1.png, Figure1.svg)
+    try:
+        _generate_composed_figure(dir_path, spec, basename)
+    except Exception as e:
+        logger.debug(f"Could not generate composed figure: {e}")
+
+    # Generate figure overview in exports/
+    try:
+        _generate_figure_overview(dir_path, spec, data, basename)
+    except Exception as e:
+        logger.debug(f"Could not generate figure overview: {e}")
+
+    # Generate figure-level geometry cache
+    try:
+        _generate_figure_geometry_cache(dir_path, spec, basename)
+    except Exception as e:
+        logger.debug(f"Could not generate figure geometry cache: {e}")
+
+    # Generate README.md
+    try:
+        _generate_figure_readme(dir_path, spec, data, basename)
+    except Exception as e:
+        logger.debug(f"Could not generate figure README: {e}")
+
+
+def _save_figure_exports(
+    data: Dict[str, Any], exports_dir: Path, spec: Dict, basename: str
+) -> None:
+    """Save figure-level export files to exports/ directory.
+
+    Args:
+        data: Bundle data containing PNG/SVG/PDF bytes or paths.
+        exports_dir: Path to exports/ directory.
+        spec: Figure specification.
+        basename: Base filename for exports.
+    """
+    for fmt in ["png", "svg", "pdf"]:
+        if fmt not in data:
+            continue
+
+        out_file = exports_dir / f"{basename}.{fmt}"
+        export_data = data[fmt]
+
+        if isinstance(export_data, bytes):
+            with open(out_file, "wb") as f:
+                f.write(export_data)
+        elif isinstance(export_data, (str, Path)) and Path(export_data).exists():
+            shutil.copy(export_data, out_file)
+
+        # Embed metadata into PNG and PDF files
+        if out_file.exists() and spec:
+            try:
+                _embed_metadata_in_export(out_file, spec, fmt)
+            except Exception as e:
+                import logging
+
+                logging.getLogger("scitex").debug(
+                    f"Could not embed metadata in {out_file}: {e}"
+                )
+
+
+def _save_exports(
+    data: Dict[str, Any], dir_path: Path, spec: Dict, basename: str = "figure"
+) -> None:
+    """Save export files (PNG, SVG, PDF) with embedded metadata. (Legacy - root level)"""
+    for fmt in ["png", "svg", "pdf"]:
+        if fmt not in data:
+            continue
+
+        out_file = dir_path / f"{basename}.{fmt}"
+        export_data = data[fmt]
+
+        if isinstance(export_data, bytes):
+            with open(out_file, "wb") as f:
+                f.write(export_data)
+        elif isinstance(export_data, (str, Path)) and Path(export_data).exists():
+            shutil.copy(export_data, out_file)
+
+        # Embed metadata into PNG and PDF files
+        if out_file.exists() and spec:
+            try:
+                _embed_metadata_in_export(out_file, spec, fmt)
+            except Exception as e:
+                import logging
+
+                logging.getLogger("scitex").debug(
+                    f"Could not embed metadata in {out_file}: {e}"
+                )
+
+
+def _copy_nested_plot_bundles(plots: Dict[str, Any], dir_path: Path) -> None:
+    """Copy nested .plot bundles directly, preserving all files.
+
+    Args:
+        plots: Dict mapping panel IDs to either:
+            - source_path: Path to existing .plot directory or .plot.zip
+            - bundle_data: Dict with spec/data (will use save_bundle)
+        dir_path: Target figure directory.
+    """
+    for panel_id, plot_source in plots.items():
+        if isinstance(plot_source, (str, Path)):
+            # Direct copy from source path
+            source_path = Path(plot_source)
+
+            if source_path.is_dir() and str(source_path).endswith(".plot"):
+                # Source is .plot directory - copy as directory
+                target_path = dir_path / f"{panel_id}.plot"
+                if target_path.exists():
+                    shutil.rmtree(target_path)
+                shutil.copytree(source_path, target_path)
+
+            elif source_path.is_file() and str(source_path).endswith(".plot.zip"):
+                # Source is .plot.zip file - copy as zip file (preserving zip format)
+                target_path = dir_path / f"{panel_id}.plot.zip"
+                if target_path.exists():
+                    target_path.unlink()
+                shutil.copy2(source_path, target_path)
+
+            elif source_path.exists():
+                # Unknown format - try to copy as directory
+                target_path = dir_path / f"{panel_id}.plot"
+                if source_path.is_dir():
+                    if target_path.exists():
+                        shutil.rmtree(target_path)
+                    shutil.copytree(source_path, target_path)
+
+        elif isinstance(plot_source, dict):
+            # Check if it has source_path for direct copy
+            if "source_path" in plot_source:
+                source_path = Path(plot_source["source_path"])
+                if source_path.is_file() and str(source_path).endswith(".plot.zip"):
+                    # .plot.zip file
+                    target_path = dir_path / f"{panel_id}.plot.zip"
+                    if target_path.exists():
+                        target_path.unlink()
+                    shutil.copy2(source_path, target_path)
+                elif source_path.exists() and source_path.is_dir():
+                    # .plot directory
+                    target_path = dir_path / f"{panel_id}.plot"
+                    if target_path.exists():
+                        shutil.rmtree(target_path)
+                    shutil.copytree(source_path, target_path)
+            else:
+                # Fallback to save (will lose images)
+                from scitex.io.bundle import BundleType, save
+
+                target_path = dir_path / f"{panel_id}.plot"
+                save(plot_source, target_path, bundle_type=BundleType.PLOT)
+
+
+def _generate_figure_overview(
+    dir_path: Path, spec: Dict, data: Dict, basename: str
+) -> None:
+    """Generate overview image for figure bundle showing panels with hitmaps, overlays, and bboxes.
+
+    Args:
+        dir_path: Bundle directory path.
+        spec: Bundle specification.
+        data: Bundle data dictionary.
+        basename: Base filename for bundle files.
+    """
+    import tempfile
+    import warnings
+    import zipfile
+
+    import matplotlib.gridspec as gridspec
+    import matplotlib.pyplot as plt
+    import numpy as np
+    from PIL import Image
+
+    # Find all panel bundles (both .plot directories and .plot.zip files)
+    panel_dirs = []
+    temp_dirs_to_cleanup = []
+
+    for item in dir_path.iterdir():
+        if item.is_dir() and str(item).endswith(".plot"):
+            panel_dirs.append(item)
+        elif item.is_file() and str(item).endswith(".plot.zip"):
+            # Extract .plot.zip to temp directory for overview generation
+            temp_dir = tempfile.mkdtemp(prefix=f"scitex_overview_{item.stem}_")
+            temp_dirs_to_cleanup.append(temp_dir)
+            with zipfile.ZipFile(item, "r") as zf:
+                zf.extractall(temp_dir)
+            # Find the extracted .plot directory
+            extracted = Path(temp_dir)
+            for subitem in extracted.iterdir():
+                if subitem.is_dir() and str(subitem).endswith(".plot"):
+                    panel_dirs.append(subitem)
+                    break
+            else:
+                # Use temp dir directly if no .plot subfolder
+                panel_dirs.append(extracted)
+
+    panel_dirs = sorted(panel_dirs, key=lambda x: x.name)
+    n_panels = len(panel_dirs)
+
+    if n_panels == 0:
+        return
+
+    # Create figure with 2 rows per panel:
+    # Row 1: Plot | Hitmap | Overlay
+    # Row 2: Bboxes | (empty) | (empty)
+    fig_width = 15
+    fig_height = 6 * n_panels + 1
+    fig = plt.figure(figsize=(fig_width, fig_height), facecolor="white")
+
+    # Title
+    title = spec.get("figure", {}).get("title", basename)
+    fig.suptitle(f"Figure Overview: {title}", fontsize=14, fontweight="bold", y=0.99)
+
+    # Create gridspec - 2 rows per panel, 3 columns
+    gs = gridspec.GridSpec(
+        n_panels * 2,
+        3,
+        figure=fig,
+        hspace=0.3,
+        wspace=0.15,
+        height_ratios=[1, 1] * n_panels,
+    )
+
+    # Add each panel
+    for idx, panel_dir in enumerate(panel_dirs):
+        panel_id = panel_dir.stem.replace(".plot", "")
+        row_base = idx * 2  # Two rows per panel
+
+        # Find PNG in panel directory (check exports/ first for layered format, then root)
+        png_files = list(panel_dir.glob("exports/*.png"))
+        if not png_files:
+            png_files = list(panel_dir.glob("*.png"))
+        main_pngs = [
+            f
+            for f in png_files
+            if "_hitmap" not in f.name and "_overview" not in f.name
+        ]
+
+        # Find hitmap PNG
+        hitmap_files = list(panel_dir.glob("exports/*_hitmap.png"))
+        if not hitmap_files:
+            hitmap_files = list(panel_dir.glob("*_hitmap.png"))
+
+        # Load geometry for bboxes
+        geometry_data = {}
+        geometry_path = panel_dir / "cache" / "geometry_px.json"
+        if geometry_path.exists():
+            with open(geometry_path) as f:
+                geometry_data = json.load(f)
+
+        # === Row 1: Plot | Hitmap | Overlay ===
+        # Left subplot: main image
+        ax_main = fig.add_subplot(gs[row_base, 0])
+        ax_main.set_title(f"Panel {panel_id}", fontweight="bold", fontsize=11)
+
+        main_img = None
+        if main_pngs:
+            main_img = Image.open(main_pngs[0])
+            ax_main.imshow(main_img)
+        else:
+            ax_main.text(
+                0.5,
+                0.5,
+                "No image",
+                ha="center",
+                va="center",
+                transform=ax_main.transAxes,
+            )
+        ax_main.axis("off")
+
+        # Middle subplot: hitmap
+        ax_hitmap = fig.add_subplot(gs[row_base, 1])
+        ax_hitmap.set_title(f"Hitmap {panel_id}", fontweight="bold", fontsize=11)
+
+        hitmap_img = None
+        if hitmap_files:
+            hitmap_img = Image.open(hitmap_files[0])
+            ax_hitmap.imshow(hitmap_img)
+        else:
+            ax_hitmap.text(
+                0.5,
+                0.5,
+                "No hitmap",
+                ha="center",
+                va="center",
+                transform=ax_hitmap.transAxes,
+            )
+        ax_hitmap.axis("off")
+
+        # Right subplot: overlay
+        ax_overlay = fig.add_subplot(gs[row_base, 2])
+        ax_overlay.set_title(f"Overlay {panel_id}", fontweight="bold", fontsize=11)
+
+        if main_img is not None:
+            ax_overlay.imshow(main_img)
+            if hitmap_img is not None:
+                hitmap_rgba = hitmap_img.convert("RGBA")
+                hitmap_array = np.array(hitmap_rgba)
+                # Create semi-transparent overlay
+                hitmap_array[:, :, 3] = (hitmap_array[:, :, 3] * 0.5).astype(np.uint8)
+                ax_overlay.imshow(hitmap_array, alpha=0.5)
+        else:
+            ax_overlay.text(
+                0.5,
+                0.5,
+                "No overlay",
+                ha="center",
+                va="center",
+                transform=ax_overlay.transAxes,
+            )
+        ax_overlay.axis("off")
+
+        # === Row 2: Bboxes ===
+        ax_bboxes = fig.add_subplot(gs[row_base + 1, 0])
+        ax_bboxes.set_title(f"Bboxes {panel_id}", fontweight="bold", fontsize=11)
+
+        if main_img is not None:
+            ax_bboxes.imshow(main_img)
+            # Draw bboxes from geometry
+            _draw_bboxes_from_geometry(ax_bboxes, geometry_data)
+        else:
+            ax_bboxes.text(
+                0.5,
+                0.5,
+                "No image",
+                ha="center",
+                va="center",
+                transform=ax_bboxes.transAxes,
+            )
+        ax_bboxes.axis("off")
+
+        # Info panel
+        ax_info = fig.add_subplot(gs[row_base + 1, 1:])
+        ax_info.set_title(f"Info {panel_id}", fontweight="bold", fontsize=11)
+        ax_info.axis("off")
+
+        # Show spec/style summary
+        spec_path = panel_dir / "spec.json"
+        style_path = panel_dir / "style.json"
+        info_text = ""
+
+        if spec_path.exists():
+            with open(spec_path) as f:
+                spec_data = json.load(f)
+            info_text += f"Axes: {len(spec_data.get('axes', []))}\n"
+            info_text += f"Traces: {len(spec_data.get('traces', []))}\n"
+
+        if style_path.exists():
+            with open(style_path) as f:
+                style_data = json.load(f)
+            size = style_data.get("size", {})
+            info_text += f"Size: {size.get('width_mm', 0):.1f} × {size.get('height_mm', 0):.1f} mm\n"
+            info_text += f"Theme: {style_data.get('theme', {}).get('mode', 'light')}\n"
+
+        manifest_path = panel_dir / "cache" / "render_manifest.json"
+        if manifest_path.exists():
+            with open(manifest_path) as f:
+                manifest_data = json.load(f)
+            info_text += f"DPI: {manifest_data.get('dpi', 300)}\n"
+            render_px = manifest_data.get("render_px", [0, 0])
+            info_text += f"Pixels: {render_px[0]} × {render_px[1]}\n"
+
+        ax_info.text(
+            0.02,
+            0.98,
+            info_text,
+            transform=ax_info.transAxes,
+            fontsize=10,
+            fontfamily="monospace",
+            verticalalignment="top",
+            bbox=dict(boxstyle="round", facecolor="wheat", alpha=0.5),
+        )
+
+    # Save overview to exports/ directory
+    exports_dir = dir_path / "exports"
+    exports_dir.mkdir(parents=True, exist_ok=True)
+    overview_path = exports_dir / f"{basename}_overview.png"
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", message=".*tight_layout.*")
+        fig.savefig(overview_path, dpi=150, bbox_inches="tight", facecolor="white")
+    plt.close(fig)
+
+    # Cleanup temp directories
+    for temp_dir in temp_dirs_to_cleanup:
+        try:
+            shutil.rmtree(temp_dir)
+        except Exception:
+            pass
+
+
+def _draw_bboxes_from_geometry(ax, geometry_data: Dict) -> None:
+    """Draw bboxes from geometry data on an axes.
+
+    Args:
+        ax: Matplotlib axes.
+        geometry_data: Geometry data dictionary.
+    """
+
+    colors = ["red", "blue", "green", "orange", "purple", "cyan"]
+    selectable = geometry_data.get("selectable_regions", {})
+
+    for ax_idx, ax_region in enumerate(selectable.get("axes", [])):
+        color = colors[ax_idx % len(colors)]
+
+        # Title bbox
+        if "title" in ax_region:
+            bbox = ax_region["title"].get("bbox_px", [])
+            if len(bbox) == 4:
+                _draw_single_bbox(ax, bbox, color, "title")
+
+        # xlabel bbox
+        if "xlabel" in ax_region:
+            bbox = ax_region["xlabel"].get("bbox_px", [])
+            if len(bbox) == 4:
+                _draw_single_bbox(ax, bbox, color, "xlabel")
+
+        # ylabel bbox
+        if "ylabel" in ax_region:
+            bbox = ax_region["ylabel"].get("bbox_px", [])
+            if len(bbox) == 4:
+                _draw_single_bbox(ax, bbox, color, "ylabel")
+
+        # xaxis spine
+        if "xaxis" in ax_region and "spine" in ax_region["xaxis"]:
+            bbox = ax_region["xaxis"]["spine"].get("bbox_px", [])
+            if len(bbox) == 4:
+                _draw_single_bbox(ax, bbox, "gray", "xaxis", lw=1)
+
+        # yaxis spine
+        if "yaxis" in ax_region and "spine" in ax_region["yaxis"]:
+            bbox = ax_region["yaxis"]["spine"].get("bbox_px", [])
+            if len(bbox) == 4:
+                _draw_single_bbox(ax, bbox, "gray", "yaxis", lw=1)
+
+        # legend bbox
+        if "legend" in ax_region:
+            bbox = ax_region["legend"].get("bbox_px", [])
+            if len(bbox) == 4:
+                _draw_single_bbox(ax, bbox, "magenta", "legend")
+
+
+def _draw_single_bbox(ax, bbox: List, color: str, label: str, lw: int = 2) -> None:
+    """Draw a single bbox rectangle on axes.
+
+    Args:
+        ax: Matplotlib axes.
+        bbox: [x0, y0, x1, y1] bounding box (corner coordinates).
+        color: Rectangle color.
+        label: Label text.
+        lw: Line width.
+    """
+    import matplotlib.patches as patches
+
+    # bbox is [x0, y0, x1, y1] format
+    x0, y0, x1, y1 = bbox
+    width = x1 - x0
+    height = y1 - y0
+    rect = patches.Rectangle(
+        (x0, y0), width, height, linewidth=lw, edgecolor=color, facecolor="none"
+    )
+    ax.add_patch(rect)
+    # Add label
+    ax.text(x0 + 2, y0 + height / 2, label, fontsize=6, color=color, fontweight="bold")
+
+
+def _generate_composed_figure(dir_path: Path, spec: Dict, basename: str) -> None:
+    """Generate composed figure from panel images.
+
+    Composes all panel PNG images into a single figure based on the layout
+    specified in the figz spec.
+
+    Args:
+        dir_path: Bundle directory path.
+        spec: Bundle specification with panel layout.
+        basename: Base filename for exports.
+    """
+
+    from PIL import Image
+
+    exports_dir = dir_path / "exports"
+    exports_dir.mkdir(parents=True, exist_ok=True)
+
+    # Load style from style.json if exists, else from spec
+    style_file = dir_path / "style.json"
+    if style_file.exists():
+        with open(style_file) as f:
+            style = json.load(f)
+        size = style.get("size", {})
+        background = style.get("background", "#ffffff")
+    else:
+        # Fallback to embedded styles in spec
+        figure = spec.get("figure", {})
+        styles = figure.get("styles", {})
+        size = styles.get("size", {})
+        background = styles.get("background", "#ffffff")
+
+    fig_width_mm = size.get("width_mm", 180)
+    fig_height_mm = size.get("height_mm", 120)
+
+    # Use 300 DPI for composition
+    dpi = 300
+    mm_to_inch = 1 / 25.4
+    fig_width_px = int(fig_width_mm * mm_to_inch * dpi)
+    fig_height_px = int(fig_height_mm * mm_to_inch * dpi)
+
+    # Create canvas
+    canvas = Image.new("RGB", (fig_width_px, fig_height_px), background)
+
+    # Get panels from spec
+    panels = spec.get("panels", [])
+
+    for panel in panels:
+        panel_id = panel.get("id", "")
+        plot_ref = panel.get("plot", "")
+
+        # Find the panel's plot bundle
+        if plot_ref.endswith(".plot"):
+            panel_dir = dir_path / plot_ref
+        else:
+            panel_dir = dir_path / f"{panel_id}.plot"
+
+        if not panel_dir.exists():
+            continue
+
+        # Find panel PNG in exports/
+        panel_png = None
+        exports_subdir = panel_dir / "exports"
+        if exports_subdir.exists():
+            for png_file in exports_subdir.glob("*.png"):
+                if "_hitmap" not in png_file.name and "_overview" not in png_file.name:
+                    panel_png = png_file
+                    break
+
+        # Fallback: look in panel root
+        if not panel_png:
+            for png_file in panel_dir.glob("*.png"):
+                if "_hitmap" not in png_file.name and "_overview" not in png_file.name:
+                    panel_png = png_file
+                    break
+
+        if not panel_png or not panel_png.exists():
+            continue
+
+        # Load panel image
+        panel_img = Image.open(panel_png)
+
+        # Get panel position and size from spec
+        pos = panel.get("position", {})
+        panel_size = panel.get("size", {})
+
+        x_mm = pos.get("x_mm", 0)
+        y_mm = pos.get("y_mm", 0)
+        width_mm = panel_size.get("width_mm", 80)
+        height_mm = panel_size.get("height_mm", 68)
+
+        # Convert to pixels
+        x_px = int(x_mm * mm_to_inch * dpi)
+        y_px = int(y_mm * mm_to_inch * dpi)
+        target_width = int(width_mm * mm_to_inch * dpi)
+        target_height = int(height_mm * mm_to_inch * dpi)
+
+        # Resize panel to fit
+        panel_img = panel_img.resize(
+            (target_width, target_height), Image.Resampling.LANCZOS
+        )
+
+        # Convert to RGB if necessary (for transparent PNGs)
+        if panel_img.mode == "RGBA":
+            # Create white background
+            bg = Image.new("RGB", panel_img.size, background)
+            bg.paste(panel_img, mask=panel_img.split()[3])
+            panel_img = bg
+        elif panel_img.mode != "RGB":
+            panel_img = panel_img.convert("RGB")
+
+        # Paste onto canvas
+        canvas.paste(panel_img, (x_px, y_px))
+
+    # Save composed figure
+    png_path = exports_dir / f"{basename}.png"
+    canvas.save(png_path, "PNG", dpi=(dpi, dpi))
+
+    # Also save as SVG (embed PNG in SVG for now)
+    svg_path = exports_dir / f"{basename}.svg"
+    svg_width_in = fig_width_mm * mm_to_inch
+    svg_height_in = fig_height_mm * mm_to_inch
+
+    # Create simple SVG wrapper with embedded image
+    import base64
+
+    with open(png_path, "rb") as f:
+        png_b64 = base64.b64encode(f.read()).decode("utf-8")
+
+    svg_content = f"""<?xml version="1.0" encoding="UTF-8"?>
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"
+     width="{fig_width_px}" height="{fig_height_px}"
+     viewBox="0 0 {fig_width_px} {fig_height_px}">
+  <image width="{fig_width_px}" height="{fig_height_px}"
+         xlink:href="data:image/png;base64,{png_b64}"/>
+</svg>"""
+
+    with open(svg_path, "w") as f:
+        f.write(svg_content)
+
+
+def _generate_figure_geometry_cache(dir_path: Path, spec: Dict, basename: str) -> None:
+    """Generate figure-level geometry cache combining all panel geometries.
+
+    Creates:
+        cache/geometry_px.json - Combined geometry for all panels
+        cache/render_manifest.json - Figure-level render metadata
+
+    Args:
+        dir_path: Bundle directory path.
+        spec: Bundle specification.
+        basename: Base filename for bundle files.
+    """
+    import tempfile
+    import zipfile
+    from datetime import datetime
+
+    cache_dir = dir_path / "cache"
+    cache_dir.mkdir(parents=True, exist_ok=True)
+
+    # Collect geometry from all panel bundles
+    combined_geometry = {
+        "figure_id": basename,
+        "panels": {},
+        "generated_at": datetime.now().isoformat(),
+    }
+
+    # Find all panel bundles (both .plot directories and .plot.zip files)
+    panel_sources = []
+    temp_dirs_to_cleanup = []
+
+    for item in dir_path.iterdir():
+        if item.is_dir() and str(item).endswith(".plot"):
+            panel_sources.append((item.stem.replace(".plot", ""), item))
+        elif item.is_file() and str(item).endswith(".plot.zip"):
+            # Extract .plot.zip to temp directory
+            temp_dir = tempfile.mkdtemp(prefix=f"scitex_geom_{item.stem}_")
+            temp_dirs_to_cleanup.append(temp_dir)
+            with zipfile.ZipFile(item, "r") as zf:
+                zf.extractall(temp_dir)
+            extracted = Path(temp_dir)
+            for subitem in extracted.iterdir():
+                if subitem.is_dir() and str(subitem).endswith(".plot"):
+                    panel_sources.append((item.stem, subitem))
+                    break
+            else:
+                panel_sources.append((item.stem, extracted))
+
+    panel_sources = sorted(panel_sources, key=lambda x: x[0])
+
+    for panel_id, panel_dir in panel_sources:
+        # Load panel geometry
+        panel_geometry_path = panel_dir / "cache" / "geometry_px.json"
+        if panel_geometry_path.exists():
+            with open(panel_geometry_path) as f:
+                panel_geometry = json.load(f)
+            combined_geometry["panels"][panel_id] = panel_geometry
+
+    # Add panel positions from spec
+    panels_spec = spec.get("panels", [])
+    for panel in panels_spec:
+        panel_id = panel.get("id")
+        if panel_id and panel_id in combined_geometry["panels"]:
+            combined_geometry["panels"][panel_id]["position_mm"] = panel.get(
+                "position", {}
+            )
+            combined_geometry["panels"][panel_id]["size_mm"] = panel.get("size", {})
+
+    # Save combined geometry
+    geometry_path = cache_dir / "geometry_px.json"
+    with open(geometry_path, "w") as f:
+        json.dump(combined_geometry, f, indent=2)
+
+    # Generate render manifest
+    figure_styles = spec.get("figure", {}).get("styles", {})
+    size = figure_styles.get("size", {})
+
+    manifest = {
+        "figure_id": basename,
+        "generated_at": datetime.now().isoformat(),
+        "size_mm": [size.get("width_mm", 0), size.get("height_mm", 0)],
+        "panels_count": len(panel_sources),
+        "schema": spec.get("schema", {}),
+    }
+
+    manifest_path = cache_dir / "render_manifest.json"
+    with open(manifest_path, "w") as f:
+        json.dump(manifest, f, indent=2)
+
+    # Cleanup temp directories
+    for temp_dir in temp_dirs_to_cleanup:
+        try:
+            shutil.rmtree(temp_dir)
+        except Exception:
+            pass
+
+
+def _embed_metadata_in_export(file_path: Path, spec: Dict[str, Any], fmt: str) -> None:
+    """Embed bundle spec metadata into exported image files."""
+    from scitex.io._metadata import embed_metadata
+
+    embed_data = {
+        "scitex_bundle": True,
+        "schema": spec.get("schema", {}),
+    }
+
+    for key in ["figure", "panels", "notations"]:
+        if key in spec:
+            embed_data[key] = spec[key]
+
+    if fmt in ("png", "pdf"):
+        embed_metadata(str(file_path), embed_data)
+
+
+def _generate_figure_readme(
+    dir_path: Path, spec: Dict, data: Dict, basename: str
+) -> None:
+    """Generate a dynamic README.md for figure bundle.
+
+    Args:
+        dir_path: Bundle directory path.
+        spec: Bundle specification.
+        data: Bundle data dictionary.
+        basename: Base filename for bundle files.
+    """
+    from datetime import datetime
+
+    # Extract figure info
+    figure = spec.get("figure", {})
+    title = figure.get("title", basename)
+    caption = figure.get("caption", "")
+
+    # Load style from style.json if exists, else from spec.figure.styles
+    style_file = dir_path / "style.json"
+    if style_file.exists():
+        with open(style_file) as f:
+            style = json.load(f)
+        size = style.get("size", {})
+        background = style.get("background", "#ffffff")
+    else:
+        styles = figure.get("styles", {})
+        size = styles.get("size", {})
+        background = styles.get("background", "#ffffff")
+
+    width_mm = size.get("width_mm", 0)
+    height_mm = size.get("height_mm", 0)
+
+    # Count panels
+    panels = spec.get("panels", [])
+    n_panels = len(panels)
+
+    # Find panel directories
+    panel_dirs = sorted(dir_path.glob("*.plot"))
+
+    # Build panel table
+    panel_rows = ""
+    for panel in panels:
+        panel_id = panel.get("id", "?")
+        label = panel.get("label", panel_id)
+        plot_ref = panel.get("plot", "")
+        pos = panel.get("position", {})
+        panel_size = panel.get("size", {})
+        panel_rows += f"| {label} | {plot_ref} | ({pos.get('x_mm', 0)}, {pos.get('y_mm', 0)}) | {panel_size.get('width_mm', 0)} × {panel_size.get('height_mm', 0)} mm |\n"
+
+    # Build panel directory list
+    panel_dir_list = ""
+    for pd in panel_dirs:
+        panel_dir_list += f"│   ├── {pd.name}/\n"
+
+    readme_content = f"""# {basename}.figure
+
+> SciTeX Figure Bundle - Auto-generated README
+
+## Overview
+
+![Figure Overview](exports/{basename}_overview.png)
+
+## Bundle Structure
+
+```
+{basename}.figure/
+├── spec.json              # Figure specification (semantic: what to draw)
+├── style.json             # Figure style (appearance: how it looks)
+├── {basename}.json        # Combined spec+style
+├── exports/               # Figure-level exports
+│   ├── {basename}.png          # Rendered figure (raster)
+│   ├── {basename}.svg          # Rendered figure (vector)
+│   └── {basename}_overview.png # Visual summary with hitmaps
+├── cache/                 # Figure-level cache (regenerable)
+│   ├── geometry_px.json        # Combined geometry for all panels
+│   └── render_manifest.json    # Render metadata
+{panel_dir_list}└── README.md              # This file
+```
+
+## Figure Information
+
+| Property | Value |
+|----------|-------|
+| Title | {title or "(none)"} |
+| Panels | {n_panels} |
+| Size | {width_mm:.1f} × {height_mm:.1f} mm |
+| Background | `{background}` |
+
+{f"**Caption**: {caption}" if caption else ""}
+
+## Panel Layout
+
+| Label | Plot Bundle | Position (x, y) | Size |
+|-------|-------------|-----------------|------|
+{panel_rows}
+
+## Nested Bundles
+
+Each panel is stored as a separate `.plot` bundle containing:
+- `spec.json` - What to plot (data, axes, traces)
+- `style.json` - How it looks (colors, fonts, theme)
+- `exports/` - Rendered images (PNG, SVG, hitmap)
+- `cache/` - Computed geometry (regenerable)
+
+## Usage
+
+### Python
+
+```python
+import scitex as stx
+
+# Load the figure bundle
+bundle = stx.load("{dir_path}")
+
+# Access components
+spec = bundle["spec"]       # Figure layout
+plots = bundle["plots"]     # Dict of panel bundles
+
+# Access specific panel
+panel_a = plots["A"]        # Get panel A's plot bundle
+```
+
+### Editing
+
+Edit `spec.json` to change semantic content:
+- Panel positions and sizes
+- Figure title and caption
+- Panel layout
+
+Edit `style.json` to change appearance:
+- Figure size (width_mm, height_mm)
+- Background color
+- Panel label styling
+- Theme (light/dark)
+
+Edit individual `*.plot/spec.json` and `*.plot/style.json` to change:
+- Plot data and axes (spec.json)
+- Trace specifications (spec.json)
+- Colors, fonts, theme (style.json)
+
+---
+
+*Generated: {datetime.now().strftime("%Y-%m-%d %H:%M:%S")}*
+*Schema: {spec.get("schema", {}).get("name", "scitex.canvas.figure")} v{spec.get("schema", {}).get("version", "1.0.0")}*
+"""
+
+    readme_path = dir_path / "README.md"
+    with open(readme_path, "w") as f:
+        f.write(readme_content)
+
+
+# EOF