table-extractor

What this skill does

# Table Extractor

## Overview

Extract tables from PDF documents with high accuracy using camelot-py. Handles complex table structures including merged cells, multi-line rows, spanning headers, and borderless tables. Outputs clean DataFrames that can be exported to CSV, Excel, or JSON.

## Instructions

When a user asks you to extract tables from a PDF, follow this process:

### Step 1: Install and verify dependencies

```bash
# Install camelot and its dependencies
pip install "camelot-py[base]" ghostscript opencv-python-headless pandas

# Verify ghostscript is available (required by camelot)
gs --version 2>/dev/null || echo "Install ghostscript: sudo apt install ghostscript"
```

If ghostscript is not available, fall back to pdfplumber:

```bash
pip install pdfplumber pandas
```

### Step 2: Inspect the PDF to locate tables

```python
import camelot

# Quick scan: how many tables are in the document?
tables = camelot.read_pdf("document.pdf", pages="all", flavor="lattice")
print(f"Found {len(tables)} tables using lattice detection")

# If no tables found, try stream detection (for borderless tables)
if len(tables) == 0:
    tables = camelot.read_pdf("document.pdf", pages="all", flavor="stream")
    print(f"Found {len(tables)} tables using stream detection")

# Summary of each table
for i, table in enumerate(tables):
    print(f"\nTable {i}: {table.shape[0]} rows x {table.shape[1]} cols (page {table.page})")
    print(f"Accuracy: {table.accuracy:.1f}%")
    print(table.df.head(3))
```

### Step 3: Choose the right extraction flavor

**Lattice flavor** (for tables with visible borders/gridlines):

```python
tables = camelot.read_pdf(
    "document.pdf",
    pages="1,2,3",        # Specific pages
    flavor="lattice",
    line_scale=40,         # Adjust line detection sensitivity
    process_background=True # Detect lines on colored backgrounds
)
```

**Stream flavor** (for borderless tables, whitespace-separated):

```python
tables = camelot.read_pdf(
    "document.pdf",
    pages="1",
    flavor="stream",
    edge_tol=50,          # Tolerance for edge detection
    row_tol=10,           # Tolerance for grouping text into rows
    columns=["72,200,350,500"]  # Manual column boundaries if auto-detect fails
)
```

### Step 4: Clean and process extracted tables

```python
import pandas as pd

for i, table in enumerate(tables):
    df = table.df

    # Promote first row to header if it contains column names
    if df.iloc[0].str.match(r'^[A-Za-z]').all():
        df.columns = df.iloc[0]
        df = df[1:].reset_index(drop=True)

    # Clean whitespace and newlines within cells
    df = df.apply(lambda col: col.str.strip().str.replace(r'\n', ' ', regex=True))

    # Remove completely empty rows
    df = df.dropna(how='all').replace('', pd.NA).dropna(how='all')

    # Convert numeric columns
    for col in df.columns:
        try:
            df[col] = pd.to_numeric(df[col].str.replace(',', '').str.replace('$', ''))
        except (ValueError, AttributeError):
            pass  # Keep as string

    print(f"\nCleaned Table {i}:")
    print(df.head())
```

### Step 5: Handle complex table structures

**Merged cells and spanning headers:**

```python
# Forward-fill merged cells (common in row headers)
df.iloc[:, 0] = df.iloc[:, 0].replace('', pd.NA).ffill()

# Handle multi-level column headers
if df.iloc[0:2].apply(lambda x: x.str.len().mean()).mean() < 20:
    # Combine first two rows as multi-level header
    new_cols = df.iloc[0] + " - " + df.iloc[1]
    df.columns = new_cols.str.strip(" - ")
    df = df[2:].reset_index(drop=True)
```

**Tables spanning multiple pages:**

```python
# Extract from all pages and concatenate
all_tables = camelot.read_pdf("document.pdf", pages="all", flavor="lattice")

# Group tables that are continuations (same column count)
groups = {}
for t in all_tables:
    key = t.shape[1]
    groups.setdefault(key, []).append(t.df)

for col_count, dfs in groups.items():
    combined = pd.concat(dfs, ignore_index=True)
    # Remove duplicate header rows that appear at page breaks
    combined = combined[~combined.duplicated(keep='first')]
```

### Step 6: Export the results

```python
# CSV (one file per table)
for i, table in enumerate(tables):
    table.df.to_csv(f"table_{i+1}.csv", index=False)

# Excel (all tables as separate sheets)
with pd.ExcelWriter("extracted_tables.xlsx") as writer:
    for i, table in enumerate(tables):
        table.df.to_excel(writer, sheet_name=f"Table_{i+1}", index=False)

# JSON
for i, table in enumerate(tables):
    table.df.to_json(f"table_{i+1}.json", orient="records", indent=2)

print(f"Exported {len(tables)} tables")
```

## Examples

### Example 1: Extract financial tables from an annual report

**User request:** "Extract all tables from this annual report PDF"

**Actions:**

1. Scan all pages with lattice flavor (financial reports typically have bordered tables)
2. Identify income statement, balance sheet, and cash flow tables by column headers
3. Clean numeric values (remove $, commas, parentheses for negatives)
4. Export each table to a separate CSV and combine into one Excel workbook

**Output:** "Extracted 7 tables across 42 pages. Exported to extracted_tables.xlsx with sheets: Income_Statement, Balance_Sheet, Cash_Flow, Revenue_Breakdown, Expenses, Quarterly_Summary, KPIs."

### Example 2: Extract a specific table from a research paper

**User request:** "Get the results table from page 8 of this paper"

**Actions:**

1. Target page 8 specifically: `camelot.read_pdf("paper.pdf", pages="8")`
2. If multiple tables on the page, show summaries and let the user pick
3. Clean the extracted table and handle any multi-line cells
4. Export as CSV

**Output:** A single CSV file with the results table, plus a preview of the first few rows printed to the console.

### Example 3: Batch process multiple PDFs

**User request:** "Extract the summary table from each of these 20 monthly reports"

**Actions:**

```python
import glob

results = []
for pdf_path in sorted(glob.glob("reports/*.pdf")):
    tables = camelot.read_pdf(pdf_path, pages="1", flavor="lattice")
    if tables:
        df = tables[0].df  # First table on first page
        df["source_file"] = pdf_path
        results.append(df)

combined = pd.concat(results, ignore_index=True)
combined.to_csv("all_summaries.csv", index=False)
```

**Output:** A single CSV combining the summary table from all 20 reports with a source_file column for traceability.

## Guidelines

- Always try `lattice` flavor first (bordered tables). Fall back to `stream` for borderless tables.
- Check the `accuracy` score on each table. Below 80% indicates extraction issues that need manual review.
- For scanned PDFs, run OCR first (e.g., `ocrmypdf`) before table extraction.
- When camelot struggles, try pdfplumber as an alternative: `page.extract_table(table_settings={...})`.
- Clean numeric data aggressively: remove currency symbols, commas, and handle parenthesized negatives.
- For tables with merged cells, use forward-fill on the appropriate columns.
- When extracting from multiple pages, watch for repeated header rows at page breaks.
- Always preview the extracted data before exporting to catch alignment or parsing issues.
- Report extraction quality metrics (accuracy, row/column count) so the user can verify correctness.