scientific-writer 2.2.1__py3-none-any.whl → 2.2.3__py3-none-any.whl

scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py

@@ -0,0 +1,369 @@
+#!/usr/bin/env python3
+"""
+Treatment Timeline Generator
+Generates visual treatment timelines from treatment plan files.
+"""
+
+import sys
+import re
+import argparse
+from pathlib import Path
+from datetime import datetime, timedelta
+from typing import List, Dict, Tuple
+
+# Try to import matplotlib, but make it optional
+try:
+    import matplotlib.pyplot as plt
+    import matplotlib.dates as mdates
+    from matplotlib.patches import Rectangle
+    HAS_MATPLOTLIB = True
+except ImportError:
+    HAS_MATPLOTLIB = False
+
+
+def extract_timeline_info(content: str) -> Dict[str, List[Tuple[str, str]]]:
+    """
+    Extract timeline and schedule information from treatment plan.
+    Returns dict with phases, appointments, milestones.
+    """
+    timeline_data = {
+        'phases': [],
+        'appointments': [],
+        'milestones': []
+    }
+    
+    # Extract treatment phases
+    # Look for patterns like "Week 1-4: Description" or "Months 1-3: Description"
+    phase_patterns = [
+        r'(Week[s]?\s*\d+[-–]\d+|Month[s]?\s*\d+[-–]\d+)[:\s]+([^\n]+)',
+        r'(POD\s*\d+[-–]\d+)[:\s]+([^\n]+)',
+        r'(\d+[-–]\d+\s*week[s]?)[:\s]+([^\n]+)'
+    ]
+    
+    for pattern in phase_patterns:
+        matches = re.findall(pattern, content, re.IGNORECASE)
+        for timeframe, description in matches:
+            timeline_data['phases'].append((timeframe.strip(), description.strip()))
+    
+    # Extract appointments
+    # Look for patterns like "Week 2: Visit" or "Month 3: Follow-up"
+    apt_patterns = [
+        r'(Week\s*\d+|Month\s*\d+|POD\s*\d+)[:\s]+(Visit|Appointment|Follow-up|Check-up|Consultation)([^\n]*)',
+        r'(Every\s+\d+\s+\w+)[:\s]+(Visit|Appointment|therapy|session)([^\n]*)'
+    ]
+    
+    for pattern in apt_patterns:
+        matches = re.findall(pattern, content, re.IGNORECASE)
+        for timeframe, visit_type, details in matches:
+            timeline_data['appointments'].append((timeframe.strip(), f"{visit_type}{details}".strip()))
+    
+    # Extract milestones/assessments
+    # Look for "reassessment", "goal evaluation", "milestone" mentions
+    milestone_patterns = [
+        r'(Week\s*\d+|Month\s*\d+)[:\s]+(reassess|evaluation|assessment|milestone)([^\n]*)',
+        r'(\w+\s*\d+)[:\s]+(HbA1c|labs?|imaging|test)([^\n]*)'
+    ]
+    
+    for pattern in milestone_patterns:
+        matches = re.findall(pattern, content, re.IGNORECASE)
+        for timeframe, event_type, details in matches:
+            timeline_data['milestones'].append((timeframe.strip(), f"{event_type}{details}".strip()))
+    
+    return timeline_data
+
+
+def parse_timeframe_to_days(timeframe: str) -> Tuple[int, int]:
+    """
+    Parse timeframe string to start and end days.
+    Examples: "Week 1-4" -> (0, 28), "Month 3" -> (60, 90)
+    """
+    timeframe = timeframe.lower()
+    
+    # Week patterns
+    if 'week' in timeframe:
+        weeks = re.findall(r'\d+', timeframe)
+        if len(weeks) == 2:
+            start_week = int(weeks[0])
+            end_week = int(weeks[1])
+            return ((start_week - 1) * 7, end_week * 7)
+        elif len(weeks) == 1:
+            week = int(weeks[0])
+            return ((week - 1) * 7, week * 7)
+    
+    # Month patterns
+    if 'month' in timeframe:
+        months = re.findall(r'\d+', timeframe)
+        if len(months) == 2:
+            start_month = int(months[0])
+            end_month = int(months[1])
+            return ((start_month - 1) * 30, end_month * 30)
+        elif len(months) == 1:
+            month = int(months[0])
+            return ((month - 1) * 30, month * 30)
+    
+    # POD (post-operative day) patterns
+    if 'pod' in timeframe:
+        days = re.findall(r'\d+', timeframe)
+        if len(days) == 2:
+            return (int(days[0]), int(days[1]))
+        elif len(days) == 1:
+            day = int(days[0])
+            return (day, day + 1)
+    
+    # Default fallback
+    return (0, 7)
+
+
+def create_text_timeline(timeline_data: Dict, output_file: Path = None):
+    """Create a text-based timeline representation."""
+    
+    lines = []
+    lines.append("="*70)
+    lines.append("TREATMENT TIMELINE")
+    lines.append("="*70)
+    
+    # Treatment phases
+    if timeline_data['phases']:
+        lines.append("\nTREATMENT PHASES:")
+        lines.append("-"*70)
+        for timeframe, description in timeline_data['phases']:
+            lines.append(f"{timeframe:20s} | {description}")
+    
+    # Appointments
+    if timeline_data['appointments']:
+        lines.append("\nSCHEDULED APPOINTMENTS:")
+        lines.append("-"*70)
+        for timeframe, details in timeline_data['appointments']:
+            lines.append(f"{timeframe:20s} | {details}")
+    
+    # Milestones
+    if timeline_data['milestones']:
+        lines.append("\nMILESTONES & ASSESSMENTS:")
+        lines.append("-"*70)
+        for timeframe, event in timeline_data['milestones']:
+            lines.append(f"{timeframe:20s} | {event}")
+    
+    lines.append("\n" + "="*70)
+    
+    # Output
+    output_text = "\n".join(lines)
+    
+    if output_file:
+        with open(output_file, 'w') as f:
+            f.write(output_text)
+        print(f"\nText timeline saved to: {output_file}")
+    else:
+        print(output_text)
+    
+    return output_text
+
+
+def create_visual_timeline(timeline_data: Dict, output_file: Path, start_date: str = None):
+    """Create a visual Gantt-chart style timeline (requires matplotlib)."""
+    
+    if not HAS_MATPLOTLIB:
+        print("Error: matplotlib not installed. Install with: pip install matplotlib", file=sys.stderr)
+        print("Generating text timeline instead...", file=sys.stderr)
+        text_output = output_file.with_suffix('.txt')
+        create_text_timeline(timeline_data, text_output)
+        return
+    
+    # Parse start date
+    if start_date:
+        try:
+            start = datetime.strptime(start_date, '%Y-%m-%d')
+        except ValueError:
+            print(f"Invalid date format: {start_date}. Using today.", file=sys.stderr)
+            start = datetime.now()
+    else:
+        start = datetime.now()
+    
+    # Prepare data for plotting
+    phases = []
+    for timeframe, description in timeline_data['phases']:
+        start_day, end_day = parse_timeframe_to_days(timeframe)
+        phases.append({
+            'name': f"{timeframe}: {description[:40]}",
+            'start': start + timedelta(days=start_day),
+            'end': start + timedelta(days=end_day),
+            'type': 'phase'
+        })
+    
+    # Add appointments as events
+    events = []
+    for timeframe, details in timeline_data['appointments']:
+        start_day, _ = parse_timeframe_to_days(timeframe)
+        events.append({
+            'name': f"{timeframe}: {details[:40]}",
+            'date': start + timedelta(days=start_day),
+            'type': 'appointment'
+        })
+    
+    # Add milestones
+    for timeframe, event in timeline_data['milestones']:
+        start_day, _ = parse_timeframe_to_days(timeframe)
+        events.append({
+            'name': f"{timeframe}: {event[:40]}",
+            'date': start + timedelta(days=start_day),
+            'type': 'milestone'
+        })
+    
+    # Create figure
+    fig, ax = plt.subplots(figsize=(12, 8))
+    
+    # Plot phases as horizontal bars
+    y_position = len(phases) + len(events)
+    
+    for i, phase in enumerate(phases):
+        duration = (phase['end'] - phase['start']).days
+        ax.barh(y_position - i, duration, left=mdates.date2num(phase['start']),
+                height=0.6, color='steelblue', alpha=0.7, edgecolor='black')
+        ax.text(mdates.date2num(phase['start']) + duration/2, y_position - i,
+                phase['name'], va='center', ha='center', fontsize=9, color='white', weight='bold')
+    
+    # Plot events as markers
+    event_y = y_position - len(phases) - 1
+    
+    for i, event in enumerate(events):
+        marker = 'o' if event['type'] == 'appointment' else 's'
+        color = 'green' if event['type'] == 'appointment' else 'orange'
+        ax.plot(mdates.date2num(event['date']), event_y - i, marker=marker,
+                markersize=10, color=color, markeredgecolor='black')
+        ax.text(mdates.date2num(event['date']) + 2, event_y - i, event['name'],
+                va='center', ha='left', fontsize=8)
+    
+    # Format x-axis as dates
+    ax.xaxis.set_major_formatter(mdates.DateFormatter('%b %Y'))
+    ax.xaxis.set_major_locator(mdates.MonthLocator())
+    plt.xticks(rotation=45, ha='right')
+    
+    # Labels and title
+    ax.set_xlabel('Date', fontsize=12, weight='bold')
+    ax.set_title('Treatment Plan Timeline', fontsize=14, weight='bold', pad=20)
+    ax.set_yticks([])
+    ax.grid(axis='x', alpha=0.3, linestyle='--')
+    
+    # Legend
+    from matplotlib.lines import Line2D
+    legend_elements = [
+        Rectangle((0, 0), 1, 1, fc='steelblue', alpha=0.7, edgecolor='black', label='Treatment Phase'),
+        Line2D([0], [0], marker='o', color='w', markerfacecolor='green', markersize=10,
+               markeredgecolor='black', label='Appointment'),
+        Line2D([0], [0], marker='s', color='w', markerfacecolor='orange', markersize=10,
+               markeredgecolor='black', label='Milestone/Assessment')
+    ]
+    ax.legend(handles=legend_elements, loc='upper right', framealpha=0.9)
+    
+    plt.tight_layout()
+    
+    # Save
+    plt.savefig(output_file, dpi=300, bbox_inches='tight')
+    print(f"\nVisual timeline saved to: {output_file}")
+    
+    # Close plot
+    plt.close()
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='Generate treatment timeline visualization',
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  # Generate text timeline
+  python timeline_generator.py --plan my_plan.tex
+
+  # Generate visual timeline (requires matplotlib)
+  python timeline_generator.py --plan my_plan.tex --output timeline.png --visual
+
+  # Specify start date for visual timeline
+  python timeline_generator.py --plan my_plan.tex --output timeline.pdf --visual --start 2025-02-01
+
+Output formats:
+  Text: .txt
+  Visual: .png, .pdf, .svg (requires matplotlib)
+
+Note: Visual timeline generation requires matplotlib.
+  Install with: pip install matplotlib
+        """
+    )
+    
+    parser.add_argument(
+        '--plan',
+        type=Path,
+        required=True,
+        help='Treatment plan file to analyze (.tex format)'
+    )
+    
+    parser.add_argument(
+        '--output',
+        type=Path,
+        help='Output file (default: timeline.txt or timeline.png if --visual)'
+    )
+    
+    parser.add_argument(
+        '--visual',
+        action='store_true',
+        help='Generate visual timeline (requires matplotlib)'
+    )
+    
+    parser.add_argument(
+        '--start',
+        help='Start date for timeline (YYYY-MM-DD format, default: today)'
+    )
+    
+    args = parser.parse_args()
+    
+    # Check plan file exists
+    if not args.plan.exists():
+        print(f"Error: File not found: {args.plan}", file=sys.stderr)
+        sys.exit(1)
+    
+    # Read plan
+    try:
+        with open(args.plan, 'r', encoding='utf-8') as f:
+            content = f.read()
+    except Exception as e:
+        print(f"Error reading file: {e}", file=sys.stderr)
+        sys.exit(1)
+    
+    # Extract timeline information
+    print("Extracting timeline information from treatment plan...")
+    timeline_data = extract_timeline_info(content)
+    
+    # Check if any timeline info found
+    total_items = (len(timeline_data['phases']) +
+                   len(timeline_data['appointments']) +
+                   len(timeline_data['milestones']))
+    
+    if total_items == 0:
+        print("\nWarning: No timeline information detected in treatment plan.", file=sys.stderr)
+        print("The plan may not contain structured timeline/schedule sections.", file=sys.stderr)
+        print("\nTip: Include sections with timeframes like:", file=sys.stderr)
+        print("  - Week 1-4: Initial phase", file=sys.stderr)
+        print("  - Month 3: Follow-up visit", file=sys.stderr)
+        sys.exit(1)
+    
+    print(f"Found {len(timeline_data['phases'])} phase(s), "
+          f"{len(timeline_data['appointments'])} appointment(s), "
+          f"{len(timeline_data['milestones'])} milestone(s)")
+    
+    # Determine output file
+    if not args.output:
+        if args.visual:
+            args.output = Path('timeline.png')
+        else:
+            args.output = Path('timeline.txt')
+    
+    # Generate timeline
+    if args.visual:
+        create_visual_timeline(timeline_data, args.output, args.start)
+    else:
+        create_text_timeline(timeline_data, args.output)
+    
+    print(f"\nTimeline generation complete!")
+
+
+if __name__ == '__main__':
+    main()
+