@research-copilot/plugin 1.1.16 → 1.1.18

package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/reference.md

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+# PDF Processing Advanced Reference
+
+This document contains advanced PDF processing features, detailed examples, and additional libraries not covered in the main skill instructions.
+
+## pypdfium2 Library (Apache/BSD License)
+
+### Overview
+pypdfium2 is a Python binding for PDFium (Chromium's PDF library). It's excellent for fast PDF rendering, image generation, and serves as a PyMuPDF replacement.
+
+### Render PDF to Images
+```python
+import pypdfium2 as pdfium
+from PIL import Image
+
+# Load PDF
+pdf = pdfium.PdfDocument("document.pdf")
+
+# Render page to image
+page = pdf[0]  # First page
+bitmap = page.render(
+    scale=2.0,  # Higher resolution
+    rotation=0  # No rotation
+)
+
+# Convert to PIL Image
+img = bitmap.to_pil()
+img.save("page_1.png", "PNG")
+
+# Process multiple pages
+for i, page in enumerate(pdf):
+    bitmap = page.render(scale=1.5)
+    img = bitmap.to_pil()
+    img.save(f"page_{i+1}.jpg", "JPEG", quality=90)
+```
+
+### Extract Text with pypdfium2
+```python
+import pypdfium2 as pdfium
+
+pdf = pdfium.PdfDocument("document.pdf")
+for i, page in enumerate(pdf):
+    text = page.get_text()
+    print(f"Page {i+1} text length: {len(text)} chars")
+```
+
+## JavaScript Libraries
+
+### pdf-lib (MIT License)
+
+pdf-lib is a powerful JavaScript library for creating and modifying PDF documents in any JavaScript environment.
+
+#### Load and Manipulate Existing PDF
+```javascript
+import { PDFDocument } from 'pdf-lib';
+import fs from 'fs';
+
+async function manipulatePDF() {
+    // Load existing PDF
+    const existingPdfBytes = fs.readFileSync('input.pdf');
+    const pdfDoc = await PDFDocument.load(existingPdfBytes);
+
+    // Get page count
+    const pageCount = pdfDoc.getPageCount();
+    console.log(`Document has ${pageCount} pages`);
+
+    // Add new page
+    const newPage = pdfDoc.addPage([600, 400]);
+    newPage.drawText('Added by pdf-lib', {
+        x: 100,
+        y: 300,
+        size: 16
+    });
+
+    // Save modified PDF
+    const pdfBytes = await pdfDoc.save();
+    fs.writeFileSync('modified.pdf', pdfBytes);
+}
+```
+
+#### Create Complex PDFs from Scratch
+```javascript
+import { PDFDocument, rgb, StandardFonts } from 'pdf-lib';
+import fs from 'fs';
+
+async function createPDF() {
+    const pdfDoc = await PDFDocument.create();
+
+    // Add fonts
+    const helveticaFont = await pdfDoc.embedFont(StandardFonts.Helvetica);
+    const helveticaBold = await pdfDoc.embedFont(StandardFonts.HelveticaBold);
+
+    // Add page
+    const page = pdfDoc.addPage([595, 842]); // A4 size
+    const { width, height } = page.getSize();
+
+    // Add text with styling
+    page.drawText('Invoice #12345', {
+        x: 50,
+        y: height - 50,
+        size: 18,
+        font: helveticaBold,
+        color: rgb(0.2, 0.2, 0.8)
+    });
+
+    // Add rectangle (header background)
+    page.drawRectangle({
+        x: 40,
+        y: height - 100,
+        width: width - 80,
+        height: 30,
+        color: rgb(0.9, 0.9, 0.9)
+    });
+
+    // Add table-like content
+    const items = [
+        ['Item', 'Qty', 'Price', 'Total'],
+        ['Widget', '2', '$50', '$100'],
+        ['Gadget', '1', '$75', '$75']
+    ];
+
+    let yPos = height - 150;
+    items.forEach(row => {
+        let xPos = 50;
+        row.forEach(cell => {
+            page.drawText(cell, {
+                x: xPos,
+                y: yPos,
+                size: 12,
+                font: helveticaFont
+            });
+            xPos += 120;
+        });
+        yPos -= 25;
+    });
+
+    const pdfBytes = await pdfDoc.save();
+    fs.writeFileSync('created.pdf', pdfBytes);
+}
+```
+
+#### Advanced Merge and Split Operations
+```javascript
+import { PDFDocument } from 'pdf-lib';
+import fs from 'fs';
+
+async function mergePDFs() {
+    // Create new document
+    const mergedPdf = await PDFDocument.create();
+
+    // Load source PDFs
+    const pdf1Bytes = fs.readFileSync('doc1.pdf');
+    const pdf2Bytes = fs.readFileSync('doc2.pdf');
+
+    const pdf1 = await PDFDocument.load(pdf1Bytes);
+    const pdf2 = await PDFDocument.load(pdf2Bytes);
+
+    // Copy pages from first PDF
+    const pdf1Pages = await mergedPdf.copyPages(pdf1, pdf1.getPageIndices());
+    pdf1Pages.forEach(page => mergedPdf.addPage(page));
+
+    // Copy specific pages from second PDF (pages 0, 2, 4)
+    const pdf2Pages = await mergedPdf.copyPages(pdf2, [0, 2, 4]);
+    pdf2Pages.forEach(page => mergedPdf.addPage(page));
+
+    const mergedPdfBytes = await mergedPdf.save();
+    fs.writeFileSync('merged.pdf', mergedPdfBytes);
+}
+```
+
+### pdfjs-dist (Apache License)
+
+PDF.js is Mozilla's JavaScript library for rendering PDFs in the browser.
+
+#### Basic PDF Loading and Rendering
+```javascript
+import * as pdfjsLib from 'pdfjs-dist';
+
+// Configure worker (important for performance)
+pdfjsLib.GlobalWorkerOptions.workerSrc = './pdf.worker.js';
+
+async function renderPDF() {
+    // Load PDF
+    const loadingTask = pdfjsLib.getDocument('document.pdf');
+    const pdf = await loadingTask.promise;
+
+    console.log(`Loaded PDF with ${pdf.numPages} pages`);
+
+    // Get first page
+    const page = await pdf.getPage(1);
+    const viewport = page.getViewport({ scale: 1.5 });
+
+    // Render to canvas
+    const canvas = document.createElement('canvas');
+    const context = canvas.getContext('2d');
+    canvas.height = viewport.height;
+    canvas.width = viewport.width;
+
+    const renderContext = {
+        canvasContext: context,
+        viewport: viewport
+    };
+
+    await page.render(renderContext).promise;
+    document.body.appendChild(canvas);
+}
+```
+
+#### Extract Text with Coordinates
+```javascript
+import * as pdfjsLib from 'pdfjs-dist';
+
+async function extractText() {
+    const loadingTask = pdfjsLib.getDocument('document.pdf');
+    const pdf = await loadingTask.promise;
+
+    let fullText = '';
+
+    // Extract text from all pages
+    for (let i = 1; i <= pdf.numPages; i++) {
+        const page = await pdf.getPage(i);
+        const textContent = await page.getTextContent();
+
+        const pageText = textContent.items
+            .map(item => item.str)
+            .join(' ');
+
+        fullText += `\n--- Page ${i} ---\n${pageText}`;
+
+        // Get text with coordinates for advanced processing
+        const textWithCoords = textContent.items.map(item => ({
+            text: item.str,
+            x: item.transform[4],
+            y: item.transform[5],
+            width: item.width,
+            height: item.height
+        }));
+    }
+
+    console.log(fullText);
+    return fullText;
+}
+```
+
+#### Extract Annotations and Forms
+```javascript
+import * as pdfjsLib from 'pdfjs-dist';
+
+async function extractAnnotations() {
+    const loadingTask = pdfjsLib.getDocument('annotated.pdf');
+    const pdf = await loadingTask.promise;
+
+    for (let i = 1; i <= pdf.numPages; i++) {
+        const page = await pdf.getPage(i);
+        const annotations = await page.getAnnotations();
+
+        annotations.forEach(annotation => {
+            console.log(`Annotation type: ${annotation.subtype}`);
+            console.log(`Content: ${annotation.contents}`);
+            console.log(`Coordinates: ${JSON.stringify(annotation.rect)}`);
+        });
+    }
+}
+```
+
+## Advanced Command-Line Operations
+
+### poppler-utils Advanced Features
+
+#### Extract Text with Bounding Box Coordinates
+```bash
+# Extract text with bounding box coordinates (essential for structured data)
+pdftotext -bbox-layout document.pdf output.xml
+
+# The XML output contains precise coordinates for each text element
+```
+
+#### Advanced Image Conversion
+```bash
+# Convert to PNG images with specific resolution
+pdftoppm -png -r 300 document.pdf output_prefix
+
+# Convert specific page range with high resolution
+pdftoppm -png -r 600 -f 1 -l 3 document.pdf high_res_pages
+
+# Convert to JPEG with quality setting
+pdftoppm -jpeg -jpegopt quality=85 -r 200 document.pdf jpeg_output
+```
+
+#### Extract Embedded Images
+```bash
+# Extract all embedded images with metadata
+pdfimages -j -p document.pdf page_images
+
+# List image info without extracting
+pdfimages -list document.pdf
+
+# Extract images in their original format
+pdfimages -all document.pdf images/img
+```
+
+### qpdf Advanced Features
+
+#### Complex Page Manipulation
+```bash
+# Split PDF into groups of pages
+qpdf --split-pages=3 input.pdf output_group_%02d.pdf
+
+# Extract specific pages with complex ranges
+qpdf input.pdf --pages input.pdf 1,3-5,8,10-end -- extracted.pdf
+
+# Merge specific pages from multiple PDFs
+qpdf --empty --pages doc1.pdf 1-3 doc2.pdf 5-7 doc3.pdf 2,4 -- combined.pdf
+```
+
+#### PDF Optimization and Repair
+```bash
+# Optimize PDF for web (linearize for streaming)
+qpdf --linearize input.pdf optimized.pdf
+
+# Remove unused objects and compress
+qpdf --optimize-level=all input.pdf compressed.pdf
+
+# Attempt to repair corrupted PDF structure
+qpdf --check input.pdf
+qpdf --fix-qdf damaged.pdf repaired.pdf
+
+# Show detailed PDF structure for debugging
+qpdf --show-all-pages input.pdf > structure.txt
+```
+
+#### Advanced Encryption
+```bash
+# Add password protection with specific permissions
+qpdf --encrypt user_pass owner_pass 256 --print=none --modify=none -- input.pdf encrypted.pdf
+
+# Check encryption status
+qpdf --show-encryption encrypted.pdf
+
+# Remove password protection (requires password)
+qpdf --password=secret123 --decrypt encrypted.pdf decrypted.pdf
+```
+
+## Advanced Python Techniques
+
+### pdfplumber Advanced Features
+
+#### Extract Text with Precise Coordinates
+```python
+import pdfplumber
+
+with pdfplumber.open("document.pdf") as pdf:
+    page = pdf.pages[0]
+    
+    # Extract all text with coordinates
+    chars = page.chars
+    for char in chars[:10]:  # First 10 characters
+        print(f"Char: '{char['text']}' at x:{char['x0']:.1f} y:{char['y0']:.1f}")
+    
+    # Extract text by bounding box (left, top, right, bottom)
+    bbox_text = page.within_bbox((100, 100, 400, 200)).extract_text()
+```
+
+#### Advanced Table Extraction with Custom Settings
+```python
+import pdfplumber
+import pandas as pd
+
+with pdfplumber.open("complex_table.pdf") as pdf:
+    page = pdf.pages[0]
+    
+    # Extract tables with custom settings for complex layouts
+    table_settings = {
+        "vertical_strategy": "lines",
+        "horizontal_strategy": "lines",
+        "snap_tolerance": 3,
+        "intersection_tolerance": 15
+    }
+    tables = page.extract_tables(table_settings)
+    
+    # Visual debugging for table extraction
+    img = page.to_image(resolution=150)
+    img.save("debug_layout.png")
+```
+
+### reportlab Advanced Features
+
+#### Create Professional Reports with Tables
+```python
+from reportlab.platypus import SimpleDocTemplate, Table, TableStyle, Paragraph
+from reportlab.lib.styles import getSampleStyleSheet
+from reportlab.lib import colors
+
+# Sample data
+data = [
+    ['Product', 'Q1', 'Q2', 'Q3', 'Q4'],
+    ['Widgets', '120', '135', '142', '158'],
+    ['Gadgets', '85', '92', '98', '105']
+]
+
+# Create PDF with table
+doc = SimpleDocTemplate("report.pdf")
+elements = []
+
+# Add title
+styles = getSampleStyleSheet()
+title = Paragraph("Quarterly Sales Report", styles['Title'])
+elements.append(title)
+
+# Add table with advanced styling
+table = Table(data)
+table.setStyle(TableStyle([
+    ('BACKGROUND', (0, 0), (-1, 0), colors.grey),
+    ('TEXTCOLOR', (0, 0), (-1, 0), colors.whitesmoke),
+    ('ALIGN', (0, 0), (-1, -1), 'CENTER'),
+    ('FONTNAME', (0, 0), (-1, 0), 'Helvetica-Bold'),
+    ('FONTSIZE', (0, 0), (-1, 0), 14),
+    ('BOTTOMPADDING', (0, 0), (-1, 0), 12),
+    ('BACKGROUND', (0, 1), (-1, -1), colors.beige),
+    ('GRID', (0, 0), (-1, -1), 1, colors.black)
+]))
+elements.append(table)
+
+doc.build(elements)
+```
+
+## Complex Workflows
+
+### Extract Figures/Images from PDF
+
+#### Method 1: Using pdfimages (fastest)
+```bash
+# Extract all images with original quality
+pdfimages -all document.pdf images/img
+```
+
+#### Method 2: Using pypdfium2 + Image Processing
+```python
+import pypdfium2 as pdfium
+from PIL import Image
+import numpy as np
+
+def extract_figures(pdf_path, output_dir):
+    pdf = pdfium.PdfDocument(pdf_path)
+    
+    for page_num, page in enumerate(pdf):
+        # Render high-resolution page
+        bitmap = page.render(scale=3.0)
+        img = bitmap.to_pil()
+        
+        # Convert to numpy for processing
+        img_array = np.array(img)
+        
+        # Simple figure detection (non-white regions)
+        mask = np.any(img_array != [255, 255, 255], axis=2)
+        
+        # Find contours and extract bounding boxes
+        # (This is simplified - real implementation would need more sophisticated detection)
+        
+        # Save detected figures
+        # ... implementation depends on specific needs
+```
+
+### Batch PDF Processing with Error Handling
+```python
+import os
+import glob
+from pypdf import PdfReader, PdfWriter
+import logging
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+def batch_process_pdfs(input_dir, operation='merge'):
+    pdf_files = glob.glob(os.path.join(input_dir, "*.pdf"))
+    
+    if operation == 'merge':
+        writer = PdfWriter()
+        for pdf_file in pdf_files:
+            try:
+                reader = PdfReader(pdf_file)
+                for page in reader.pages:
+                    writer.add_page(page)
+                logger.info(f"Processed: {pdf_file}")
+            except Exception as e:
+                logger.error(f"Failed to process {pdf_file}: {e}")
+                continue
+        
+        with open("batch_merged.pdf", "wb") as output:
+            writer.write(output)
+    
+    elif operation == 'extract_text':
+        for pdf_file in pdf_files:
+            try:
+                reader = PdfReader(pdf_file)
+                text = ""
+                for page in reader.pages:
+                    text += page.extract_text()
+                
+                output_file = pdf_file.replace('.pdf', '.txt')
+                with open(output_file, 'w', encoding='utf-8') as f:
+                    f.write(text)
+                logger.info(f"Extracted text from: {pdf_file}")
+                
+            except Exception as e:
+                logger.error(f"Failed to extract text from {pdf_file}: {e}")
+                continue
+```
+
+### Advanced PDF Cropping
+```python
+from pypdf import PdfWriter, PdfReader
+
+reader = PdfReader("input.pdf")
+writer = PdfWriter()
+
+# Crop page (left, bottom, right, top in points)
+page = reader.pages[0]
+page.mediabox.left = 50
+page.mediabox.bottom = 50
+page.mediabox.right = 550
+page.mediabox.top = 750
+
+writer.add_page(page)
+with open("cropped.pdf", "wb") as output:
+    writer.write(output)
+```
+
+## Performance Optimization Tips
+
+### 1. For Large PDFs
+- Use streaming approaches instead of loading entire PDF in memory
+- Use `qpdf --split-pages` for splitting large files
+- Process pages individually with pypdfium2
+
+### 2. For Text Extraction
+- `pdftotext -bbox-layout` is fastest for plain text extraction
+- Use pdfplumber for structured data and tables
+- Avoid `pypdf.extract_text()` for very large documents
+
+### 3. For Image Extraction
+- `pdfimages` is much faster than rendering pages
+- Use low resolution for previews, high resolution for final output
+
+### 4. For Form Filling
+- pdf-lib maintains form structure better than most alternatives
+- Pre-validate form fields before processing
+
+### 5. Memory Management
+```python
+# Process PDFs in chunks
+def process_large_pdf(pdf_path, chunk_size=10):
+    reader = PdfReader(pdf_path)
+    total_pages = len(reader.pages)
+    
+    for start_idx in range(0, total_pages, chunk_size):
+        end_idx = min(start_idx + chunk_size, total_pages)
+        writer = PdfWriter()
+        
+        for i in range(start_idx, end_idx):
+            writer.add_page(reader.pages[i])
+        
+        # Process chunk
+        with open(f"chunk_{start_idx//chunk_size}.pdf", "wb") as output:
+            writer.write(output)
+```
+
+## Troubleshooting Common Issues
+
+### Encrypted PDFs
+```python
+# Handle password-protected PDFs
+from pypdf import PdfReader
+
+try:
+    reader = PdfReader("encrypted.pdf")
+    if reader.is_encrypted:
+        reader.decrypt("password")
+except Exception as e:
+    print(f"Failed to decrypt: {e}")
+```
+
+### Corrupted PDFs
+```bash
+# Use qpdf to repair
+qpdf --check corrupted.pdf
+qpdf --replace-input corrupted.pdf
+```
+
+### Text Extraction Issues
+```python
+# Fallback to OCR for scanned PDFs
+import pytesseract
+from pdf2image import convert_from_path
+
+def extract_text_with_ocr(pdf_path):
+    images = convert_from_path(pdf_path)
+    text = ""
+    for i, image in enumerate(images):
+        text += pytesseract.image_to_string(image)
+    return text
+```
+
+## License Information
+
+- **pypdf**: BSD License
+- **pdfplumber**: MIT License
+- **pypdfium2**: Apache/BSD License
+- **reportlab**: BSD License
+- **poppler-utils**: GPL-2 License
+- **qpdf**: Apache License
+- **pdf-lib**: MIT License
+- **pdfjs-dist**: Apache License

package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/scripts/check_bounding_boxes.py

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+from dataclasses import dataclass
+import json
+import sys
+
+
+
+
+@dataclass
+class RectAndField:
+    rect: list[float]
+    rect_type: str
+    field: dict
+
+
+def get_bounding_box_messages(fields_json_stream) -> list[str]:
+    messages = []
+    fields = json.load(fields_json_stream)
+    messages.append(f"Read {len(fields['form_fields'])} fields")
+
+    def rects_intersect(r1, r2):
+        disjoint_horizontal = r1[0] >= r2[2] or r1[2] <= r2[0]
+        disjoint_vertical = r1[1] >= r2[3] or r1[3] <= r2[1]
+        return not (disjoint_horizontal or disjoint_vertical)
+
+    rects_and_fields = []
+    for f in fields["form_fields"]:
+        rects_and_fields.append(RectAndField(f["label_bounding_box"], "label", f))
+        rects_and_fields.append(RectAndField(f["entry_bounding_box"], "entry", f))
+
+    has_error = False
+    for i, ri in enumerate(rects_and_fields):
+        for j in range(i + 1, len(rects_and_fields)):
+            rj = rects_and_fields[j]
+            if ri.field["page_number"] == rj.field["page_number"] and rects_intersect(ri.rect, rj.rect):
+                has_error = True
+                if ri.field is rj.field:
+                    messages.append(f"FAILURE: intersection between label and entry bounding boxes for `{ri.field['description']}` ({ri.rect}, {rj.rect})")
+                else:
+                    messages.append(f"FAILURE: intersection between {ri.rect_type} bounding box for `{ri.field['description']}` ({ri.rect}) and {rj.rect_type} bounding box for `{rj.field['description']}` ({rj.rect})")
+                if len(messages) >= 20:
+                    messages.append("Aborting further checks; fix bounding boxes and try again")
+                    return messages
+        if ri.rect_type == "entry":
+            if "entry_text" in ri.field:
+                font_size = ri.field["entry_text"].get("font_size", 14)
+                entry_height = ri.rect[3] - ri.rect[1]
+                if entry_height < font_size:
+                    has_error = True
+                    messages.append(f"FAILURE: entry bounding box height ({entry_height}) for `{ri.field['description']}` is too short for the text content (font size: {font_size}). Increase the box height or decrease the font size.")
+                    if len(messages) >= 20:
+                        messages.append("Aborting further checks; fix bounding boxes and try again")
+                        return messages
+
+    if not has_error:
+        messages.append("SUCCESS: All bounding boxes are valid")
+    return messages
+
+if __name__ == "__main__":
+    if len(sys.argv) != 2:
+        print("Usage: check_bounding_boxes.py [fields.json]")
+        sys.exit(1)
+    with open(sys.argv[1]) as f:
+        messages = get_bounding_box_messages(f)
+    for msg in messages:
+        print(msg)

package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/scripts/check_fillable_fields.py

@@ -0,0 +1,11 @@
+import sys
+from pypdf import PdfReader
+
+
+
+
+reader = PdfReader(sys.argv[1])
+if (reader.get_fields()):
+    print("This PDF has fillable form fields")
+else:
+    print("This PDF does not have fillable form fields; you will need to visually determine where to enter data")