"""Document processing: markdown extraction, figure handling, and caption enrichment.""" from __future__ import annotations import ast import base64 import json import logging import re from io import BytesIO from pathlib import Path from typing import Any, Dict, List, Tuple import numpy as np from PIL import Image, ImageDraw, ImageFont from .config import FigureMetadata LOGGER = logging.getLogger(__name__) GROUNDING_PATTERN = re.compile( r"<\|ref\|>(.*?)<\|/ref\|><\|det\|>(.*?)<\|/det\|>", re.DOTALL, ) # Matches both old path format and new figure: URI format FIGURE_MARKDOWN_PATTERN = re.compile( r"!\[(?:Figure )?(?P[^\]]+)\]\((?P[^)]+)\)" ) def encode_image(image: Image.Image) -> str: """Encode a PIL Image to base64 PNG string.""" buffer = BytesIO() image.save(buffer, format="PNG") return base64.b64encode(buffer.getvalue()).decode("utf-8") def extract_grounding_blocks(text: str) -> List[Dict[str, Any]]: """Extract grounding blocks (ref/det tags) from model response.""" matches: List[Dict[str, Any]] = [] for match in GROUNDING_PATTERN.finditer(text): label = match.group(1).strip() coords_text = match.group(2).strip() coordinates = None if coords_text: try: coordinates = ast.literal_eval(coords_text) except Exception: coordinates = None matches.append( { "label": label, "coordinates": coordinates, "raw": match.group(0), "span": match.span(), } ) return matches def postprocess_markdown(text: str) -> str: """Clean up markdown text from model output.""" cleaned = ( text.replace("\\coloneqq", ":=") .replace("\\eqqcolon", "=:") .replace("<|image_pad|>", "") ) cleaned = re.sub(r"\n{3,}", "\n\n", cleaned) return cleaned.strip() def apply_replacements(text: str, replacements: List[Tuple[int, int, str]]) -> str: """Apply text replacements at specified spans.""" if not replacements: return postprocess_markdown(text) sorted_replacements = sorted(replacements, key=lambda item: item[0]) segments: List[str] = [] cursor = 0 for start, end, replacement in sorted_replacements: segments.append(text[cursor:start]) segments.append(replacement) cursor = end segments.append(text[cursor:]) return postprocess_markdown("".join(segments)) def crop_figure( image: Image.Image, sample_id: str, figure_index: int, pixel_box: List[int], label: str, ) -> Tuple[FigureMetadata, Image.Image]: """Crop a figure region from the source image. Args: pixel_box: [x1, y1, x2, y2] bounding box in pixels Returns: (metadata, cropped_image) tuple for embedding in dataset """ x1, y1, x2, y2 = pixel_box crop = image.crop((x1, y1, x2, y2)).copy() figure_id = f"{sample_id}_fig{figure_index:02d}" metadata = FigureMetadata( figure_id=figure_id, label=label, bounding_box_pixels={"x1": x1, "y1": y1, "x2": x2, "y2": y2}, ) return metadata, crop def write_text(path: Path, content: str) -> None: """Write text content to a file.""" path.parent.mkdir(parents=True, exist_ok=True) path.write_text(content, encoding="utf-8") def write_json(path: Path, payload: Any) -> None: """Write JSON content to a file.""" path.parent.mkdir(parents=True, exist_ok=True) with path.open("w", encoding="utf-8") as handle: json.dump(payload, handle, indent=2, ensure_ascii=False) def build_document_markdown( image: Image.Image, response_text: str, sample_id: str, ) -> Tuple[str, List[FigureMetadata], List[Image.Image], Image.Image]: """Process model response to extract markdown and figures. Returns: (markdown, figure_metadata, figure_images, annotated_image) tuple """ blocks = extract_grounding_blocks(response_text) replacements: List[Tuple[int, int, str]] = [] figures: List[FigureMetadata] = [] figure_images: List[Image.Image] = [] figure_index = 1 img_draw = image.copy() draw = ImageDraw.Draw(img_draw) overlay = Image.new("RGBA", img_draw.size, (0, 0, 0, 0)) draw_overlay = ImageDraw.Draw(overlay) font = ImageFont.load_default() width, height = image.size for block in blocks: label = block["label"].lower() start, end = block["span"] # Random color for this block color = ( np.random.randint(0, 200), np.random.randint(0, 200), np.random.randint(0, 255), ) color_alpha = color + (20,) # Convert normalized coords to pixels raw_box = block["coordinates"][0] x1 = int(raw_box[0] / 999 * width) y1 = int(raw_box[1] / 999 * height) x2 = int(raw_box[2] / 999 * width) y2 = int(raw_box[3] / 999 * height) pixel_box = (x1, y1, x2, y2) # Extract figures (images) if label == "image": metadata, crop = crop_figure( image=image, sample_id=sample_id, figure_index=figure_index, pixel_box=pixel_box, label=block["label"], ) figures.append(metadata) figure_images.append(crop) # Use figure:{id} URI format - clearly an identifier, not a file path replacements.append( ( start, end, f"![{metadata.figure_id}](figure:{metadata.figure_id})", ) ) figure_index += 1 else: replacements.append((start, end, "")) # Draw bounding box box_width = 4 if label == "title" else 2 draw.rectangle([x1, y1, x2, y2], outline=color, width=box_width) draw_overlay.rectangle([x1, y1, x2, y2], fill=color_alpha) # Draw label text_x, text_y = x1, max(0, y1 - 15) text_bbox = draw.textbbox((0, 0), label, font=font) text_w, text_h = text_bbox[2] - text_bbox[0], text_bbox[3] - text_bbox[1] draw.rectangle( [text_x, text_y, text_x + text_w, text_y + text_h], fill=(255, 255, 255, 30) ) draw.text((text_x, text_y), label, font=font, fill=color) img_draw.paste(overlay, (0, 0), overlay) markdown = apply_replacements(response_text, replacements) return markdown, figures, figure_images, img_draw def _truncate_for_alt(description: str, max_length: int = 120) -> str: """Create a short alt text from a description (first sentence, truncated).""" # Take first sentence first_sentence = description.split(". ")[0].split(".\n")[0] if len(first_sentence) <= max_length: return first_sentence.strip() # Truncate at word boundary truncated = first_sentence[:max_length].rsplit(" ", 1)[0] return truncated.strip() + "..." def enrich_markdown_with_captions( markdown: str, description_map: Dict[str, Dict[str, Any]], ) -> str: """Add figure captions to markdown. Alt text is truncated; full description below.""" used: set[str] = set() def replace(match: re.Match[str]) -> str: alt_text = match.group("figure_id").strip() path = match.group("path").strip() # Extract figure_id from figure:{id} URI or from alt text if path.startswith("figure:"): figure_id = path[7:] # Remove "figure:" prefix else: # Legacy format - figure_id is in alt text after "Figure " figure_id = alt_text.replace("Figure ", "").split(":")[0].strip() entry = description_map.get(figure_id) if not entry: return match.group(0) description = (entry.get("description") or "").strip() if not description: return match.group(0) # Alt text: short summary (first sentence, max 120 chars) short_alt = _truncate_for_alt(description) # Image tag with short alt text rendered = f"![{figure_id}: {short_alt}]({path})" # Add full caption below (only once per figure) if figure_id not in used: rendered += f"\n\n*Figure {figure_id}: {description}*\n" used.add(figure_id) return rendered return FIGURE_MARKDOWN_PATTERN.sub(replace, markdown) def render_markdown_with_images( markdown: str, figure_images: List[Image.Image], figure_metadata: List[Dict[str, Any]], ) -> str: """Replace figure:{id} URIs in markdown with base64-encoded images.""" # Build figure_id -> image mapping id_to_image: Dict[str, Image.Image] = {} for i, meta in enumerate(figure_metadata): fig_id = meta.get("figure_id", "") if fig_id and i < len(figure_images) and figure_images[i] is not None: id_to_image[fig_id] = figure_images[i] def replace(match: re.Match[str]) -> str: alt_text = match.group("figure_id").strip() path = match.group("path").strip() # Extract figure_id from figure:{id} URI or use alt_text as fallback if path.startswith("figure:"): figure_id = path[7:] # Remove "figure:" prefix else: # Legacy path format - extract figure_id from alt_text figure_id = alt_text.replace("Figure ", "").split(":")[0].strip() img = id_to_image.get(figure_id) if img is None: return match.group(0) # Keep original if image not found # Embed as base64 data URI data_uri = f"data:image/png;base64,{encode_image(img)}" return f"![{alt_text}]({data_uri})" return FIGURE_MARKDOWN_PATTERN.sub(replace, markdown) def render_sample_markdown(sample: Dict[str, Any]) -> str: """Render dataset sample's markdown with embedded base64 images.""" markdown = ( sample.get("document_final_markdown") or sample.get("document_markdown") or "" ) # Parse metadata raw_metadata = sample.get("extracted_figures_metadata") or [] metadata = [] for m in raw_metadata: if isinstance(m, str): metadata.append(json.loads(m)) else: metadata.append(m) images = sample.get("extracted_figures") or [] return render_markdown_with_images( markdown=markdown, figure_images=images, figure_metadata=metadata, ) def display_markdown(sample: Dict[str, Any]) -> None: """Display sample's markdown with embedded images in Jupyter.""" from IPython.display import display, Markdown rendered = render_sample_markdown(sample) display(Markdown(rendered)) def display_samples(dataset, num_samples: int = 2) -> None: """Display samples with source images, markdown, and figure descriptions.""" from IPython.display import display print(f"Dataset: {len(dataset)} samples") print(f"Columns: {list(dataset.column_names)}") print() for i in range(min(num_samples, len(dataset))): sample = dataset[i] print(f"=== Sample {i}: {sample.get('sample_id', i)} ===") # Show source image if sample.get("source_image"): print("Source image:") img = sample["source_image"] img.thumbnail((500, 500)) # Resize to max 500px display(img) # Show markdown preview md = sample.get("document_markdown") or sample.get("document_markdown_text", "") if md: print(f"\nMarkdown preview ({len(md)} chars):") print(md[:500] + "..." if len(md) > 500 else md) # Show final markdown if available final_md = sample.get("document_final_markdown") or sample.get( "document_final_markdown_text", "" ) if final_md: print(f"\nFinal markdown preview ({len(final_md)} chars):") print(final_md[:500] + "..." if len(final_md) > 500 else final_md) # Show figures and their descriptions figures = sample.get("extracted_figures", []) metadata = sample.get("extracted_figures_metadata", []) if figures: print(f"\nExtracted figures: {len(figures)}") for j, fig in enumerate(figures[:2]): # Show max 2 figures fig.thumbnail((500, 500)) display(fig) # Show figure description if available if j < len(metadata): try: meta = ( json.loads(metadata[j]) if isinstance(metadata[j], str) else metadata[j] ) if meta.get("description"): print(f" 📝 Description: {meta['description'][:200]}...") except Exception: pass print()