Muscles: Types, Classification, and Function

from reportlab.lib.pagesizes import A4
from reportlab.lib import colors
from reportlab.lib.units import cm, mm
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.lib.enums import TA_LEFT, TA_CENTER, TA_JUSTIFY
from reportlab.platypus import (
    SimpleDocTemplate, Paragraph, Spacer, Table, TableStyle,
    HRFlowable, PageBreak, KeepTogether
)
from reportlab.platypus.flowables import HRFlowable
from reportlab.graphics.shapes import Drawing, Rect, String, Line, Polygon, Circle
from reportlab.graphics.charts.barcharts import VerticalBarChart
from reportlab.graphics import renderPDF
from reportlab.pdfbase import pdfmetrics

import os

OUTPUT_PATH = "/home/daytona/workspace/muscle-study-guide/Muscle_Classification_Study_Guide.pdf"

# ── Color Palette ──────────────────────────────────────────────────────────────
DARK_NAVY    = colors.HexColor("#1A2E4A")
MID_BLUE     = colors.HexColor("#2C5F8A")
ACCENT_BLUE  = colors.HexColor("#3B82C4")
LIGHT_BLUE   = colors.HexColor("#D6E8F5")
RED_TYPE1    = colors.HexColor("#C0392B")
ORANGE_TYPE2 = colors.HexColor("#D35400")
GREEN_ACCT   = colors.HexColor("#1E8449")
LIGHT_GREEN  = colors.HexColor("#D5F5E3")
LIGHT_RED    = colors.HexColor("#FADBD8")
LIGHT_ORANGE = colors.HexColor("#FDEBD0")
YELLOW_HL    = colors.HexColor("#FFF3CD")
GOLD         = colors.HexColor("#F39C12")
GRAY_LIGHT   = colors.HexColor("#F2F3F4")
GRAY_MID     = colors.HexColor("#BDC3C7")
GRAY_DARK    = colors.HexColor("#7F8C8D")
WHITE        = colors.white

# ── Styles ─────────────────────────────────────────────────────────────────────
styles = getSampleStyleSheet()

def make_style(name, parent='Normal', **kwargs):
    return ParagraphStyle(name, parent=styles[parent], **kwargs)

COVER_TITLE = make_style('CoverTitle',
    fontSize=34, leading=42, textColor=WHITE,
    fontName='Helvetica-Bold', alignment=TA_CENTER, spaceAfter=8)

COVER_SUB = make_style('CoverSub',
    fontSize=16, leading=22, textColor=colors.HexColor("#D6E8F5"),
    fontName='Helvetica', alignment=TA_CENTER, spaceAfter=6)

COVER_CAPTION = make_style('CoverCaption',
    fontSize=11, leading=15, textColor=GRAY_MID,
    fontName='Helvetica', alignment=TA_CENTER)

CH_TITLE = make_style('ChTitle',
    fontSize=22, leading=28, textColor=WHITE,
    fontName='Helvetica-Bold', alignment=TA_LEFT, spaceAfter=4)

SECTION_HEAD = make_style('SectionHead',
    fontSize=14, leading=18, textColor=DARK_NAVY,
    fontName='Helvetica-Bold', spaceBefore=14, spaceAfter=6)

SUBHEAD = make_style('Subhead',
    fontSize=12, leading=16, textColor=MID_BLUE,
    fontName='Helvetica-Bold', spaceBefore=10, spaceAfter=4)

BODY = make_style('Body',
    fontSize=10, leading=15, textColor=colors.HexColor("#2C3E50"),
    fontName='Helvetica', spaceAfter=4, alignment=TA_JUSTIFY)

BODY_BOLD = make_style('BodyBold',
    fontSize=10, leading=14, textColor=DARK_NAVY,
    fontName='Helvetica-Bold', spaceAfter=2)

BULLET = make_style('Bullet',
    fontSize=10, leading=14, textColor=colors.HexColor("#2C3E50"),
    fontName='Helvetica', leftIndent=18, spaceAfter=3,
    bulletIndent=6, bulletFontName='Helvetica')

NOTE_STYLE = make_style('NoteStyle',
    fontSize=9.5, leading=14, textColor=colors.HexColor("#5D4037"),
    fontName='Helvetica-Oblique', leftIndent=10, rightIndent=10,
    spaceAfter=4)

SMALL = make_style('Small',
    fontSize=8.5, leading=12, textColor=GRAY_DARK,
    fontName='Helvetica', alignment=TA_CENTER)

TABLE_HEADER = make_style('TableHeader',
    fontSize=9.5, leading=13, textColor=WHITE,
    fontName='Helvetica-Bold', alignment=TA_CENTER)

TABLE_CELL = make_style('TableCell',
    fontSize=9, leading=13, textColor=DARK_NAVY,
    fontName='Helvetica', alignment=TA_LEFT)

TABLE_CELL_C = make_style('TableCellC',
    fontSize=9, leading=13, textColor=DARK_NAVY,
    fontName='Helvetica', alignment=TA_CENTER)

# ── Helpers ────────────────────────────────────────────────────────────────────

def chapter_banner(title, subtitle="", color=DARK_NAVY):
    d = Drawing(500, 52)
    d.add(Rect(0, 0, 500, 52, fillColor=color, strokeColor=None))
    d.add(String(14, 30, title, fontSize=18, fontName='Helvetica-Bold',
                 fillColor=colors.white))
    if subtitle:
        d.add(String(14, 12, subtitle, fontSize=10, fontName='Helvetica',
                     fillColor=colors.HexColor("#D6E8F5")))
    return d

def section_rule():
    return HRFlowable(width="100%", thickness=1.5, color=ACCENT_BLUE,
                      spaceAfter=6, spaceBefore=4)

def info_box(title, body_paras, bg=LIGHT_BLUE, border=ACCENT_BLUE):
    inner = [[Paragraph(f"<b>{title}</b>", SUBHEAD)] + body_paras]
    t = Table(inner, colWidths=[470])
    t.setStyle(TableStyle([
        ('BACKGROUND', (0,0), (-1,-1), bg),
        ('BOX',        (0,0), (-1,-1), 1.5, border),
        ('TOPPADDING', (0,0), (-1,-1), 8),
        ('BOTTOMPADDING',(0,0),(-1,-1), 8),
        ('LEFTPADDING', (0,0), (-1,-1), 12),
        ('RIGHTPADDING',(0,0), (-1,-1), 12),
    ]))
    return t

def key_point_box(text, color=YELLOW_HL, border=GOLD):
    t = Table([[Paragraph(f"⚑  {text}", NOTE_STYLE)]], colWidths=[470])
    t.setStyle(TableStyle([
        ('BACKGROUND', (0,0),(-1,-1), color),
        ('BOX',        (0,0),(-1,-1), 1.2, border),
        ('TOPPADDING', (0,0),(-1,-1), 7),
        ('BOTTOMPADDING',(0,0),(-1,-1), 7),
        ('LEFTPADDING', (0,0),(-1,-1), 10),
        ('RIGHTPADDING',(0,0),(-1,-1), 10),
    ]))
    return t

def two_col_table(headers, rows, col_widths=None, header_color=DARK_NAVY):
    if col_widths is None:
        col_widths = [235, 235]
    data = [[Paragraph(h, TABLE_HEADER) for h in headers]]
    for row in rows:
        data.append([Paragraph(str(c), TABLE_CELL) for c in row])
    t = Table(data, colWidths=col_widths)
    n = len(rows)
    ts = [
        ('BACKGROUND', (0,0), (-1,0), header_color),
        ('ROWBACKGROUNDS', (0,1), (-1,-1), [WHITE, GRAY_LIGHT]),
        ('GRID', (0,0), (-1,-1), 0.5, GRAY_MID),
        ('TOPPADDING', (0,0), (-1,-1), 6),
        ('BOTTOMPADDING',(0,0),(-1,-1), 6),
        ('LEFTPADDING', (0,0), (-1,-1), 8),
        ('RIGHTPADDING',(0,0),(-1,-1), 8),
        ('VALIGN', (0,0), (-1,-1), 'TOP'),
    ]
    t.setStyle(TableStyle(ts))
    return t

def multi_col_table(headers, rows, col_widths, header_color=DARK_NAVY):
    data = [[Paragraph(h, TABLE_HEADER) for h in headers]]
    for row in rows:
        data.append([Paragraph(str(c), TABLE_CELL_C) for c in row])
    t = Table(data, colWidths=col_widths)
    ts = [
        ('BACKGROUND', (0,0), (-1,0), header_color),
        ('ROWBACKGROUNDS', (0,1), (-1,-1), [WHITE, GRAY_LIGHT]),
        ('GRID', (0,0), (-1,-1), 0.5, GRAY_MID),
        ('TOPPADDING', (0,0), (-1,-1), 5),
        ('BOTTOMPADDING',(0,0),(-1,-1), 5),
        ('LEFTPADDING', (0,0), (-1,-1), 6),
        ('RIGHTPADDING',(0,0),(-1,-1), 6),
        ('VALIGN', (0,0), (-1,-1), 'MIDDLE'),
        ('ALIGN', (0,0), (-1,-1), 'CENTER'),
    ]
    t.setStyle(TableStyle(ts))
    return t

# ── Fiber Type Comparison Diagram ─────────────────────────────────────────────

def fiber_type_diagram():
    d = Drawing(470, 200)
    # Background
    d.add(Rect(0, 0, 470, 200, fillColor=GRAY_LIGHT, strokeColor=None))

    # Type I column
    d.add(Rect(10, 10, 215, 180, fillColor=LIGHT_RED, strokeColor=RED_TYPE1, strokeWidth=2))
    d.add(String(20, 175, "TYPE I — Slow-Twitch (ST)", fontSize=11,
                 fontName='Helvetica-Bold', fillColor=RED_TYPE1))
    d.add(String(20, 158, "Postural / Red Muscles", fontSize=9,
                 fontName='Helvetica-Oblique', fillColor=colors.HexColor("#922B21")))

    items_1 = [
        "Twitch: ~100 ms (slow)",
        "Motor units: Large",
        "Myoglobin: Rich (red)",
        "Mitochondria: Abundant",
        "Metabolism: Aerobic (oxidative)",
        "Glycogen: Low (PAS–)",
        "Fatigue: Resistant",
        "Prone to: Shortening",
        "Athletes: Endurance (runners)",
    ]
    for i, item in enumerate(items_1):
        d.add(String(26, 142 - i*14, f"• {item}", fontSize=8.5,
                     fontName='Helvetica', fillColor=DARK_NAVY))

    # Type II column
    d.add(Rect(245, 10, 215, 180, fillColor=LIGHT_ORANGE, strokeColor=ORANGE_TYPE2, strokeWidth=2))
    d.add(String(255, 175, "TYPE II — Fast-Twitch (FT)", fontSize=11,
                 fontName='Helvetica-Bold', fillColor=ORANGE_TYPE2))
    d.add(String(255, 158, "Phasic / White Muscles", fontSize=9,
                 fontName='Helvetica-Oblique', fillColor=colors.HexColor("#A04000")))

    items_2 = [
        "Twitch: ~30 ms (fast)",
        "Motor units: Small (<100)",
        "Myoglobin: Scant (pale)",
        "Mitochondria: Few",
        "Metabolism: Anaerobic (glycolytic)",
        "Glycogen: Abundant (PAS+)",
        "Fatigue: Rapid",
        "Prone to: Atrophy",
        "Athletes: Explosive (sprinters)",
    ]
    for i, item in enumerate(items_2):
        d.add(String(261, 142 - i*14, f"• {item}", fontSize=8.5,
                     fontName='Helvetica', fillColor=DARK_NAVY))

    return d


# ── Pennate vs Non-pennate Diagram ─────────────────────────────────────────────

def pennate_diagram():
    d = Drawing(470, 130)
    d.add(Rect(0, 0, 470, 130, fillColor=GRAY_LIGHT, strokeColor=None))

    # --- Non-pennate ---
    d.add(Rect(10, 10, 135, 110, fillColor=LIGHT_BLUE, strokeColor=ACCENT_BLUE, strokeWidth=1.5))
    d.add(String(18, 108, "Non-Pennate", fontSize=10, fontName='Helvetica-Bold', fillColor=DARK_NAVY))
    d.add(String(18, 95, "(Parallel Fibered)", fontSize=8, fontName='Helvetica-Oblique', fillColor=MID_BLUE))
    # Draw parallel lines (fibers)
    for y in [80, 68, 56, 44, 32]:
        d.add(Line(25, y, 130, y, strokeColor=MID_BLUE, strokeWidth=2))
    # tendon at right
    d.add(Rect(128, 48, 8, 24, fillColor=DARK_NAVY, strokeColor=None))

    # --- Unipennate ---
    d.add(Rect(158, 10, 90, 110, fillColor=LIGHT_GREEN, strokeColor=GREEN_ACCT, strokeWidth=1.5))
    d.add(String(164, 108, "Unipennate", fontSize=9, fontName='Helvetica-Bold', fillColor=DARK_NAVY))
    # Tendon line
    d.add(Line(230, 25, 230, 105, strokeColor=DARK_NAVY, strokeWidth=3))
    for y in [90, 75, 60, 45, 30]:
        d.add(Line(168, y, 228, y+8, strokeColor=GREEN_ACCT, strokeWidth=2))

    # --- Bipennate ---
    d.add(Rect(260, 10, 90, 110, fillColor=LIGHT_GREEN, strokeColor=GREEN_ACCT, strokeWidth=1.5))
    d.add(String(266, 108, "Bipennate", fontSize=9, fontName='Helvetica-Bold', fillColor=DARK_NAVY))
    d.add(Line(305, 20, 305, 105, strokeColor=DARK_NAVY, strokeWidth=3))
    for y in [88, 74, 60, 46, 32]:
        d.add(Line(268, y, 303, y+8, strokeColor=GREEN_ACCT, strokeWidth=2))
        d.add(Line(342, y, 307, y+8, strokeColor=GREEN_ACCT, strokeWidth=2))

    # --- Multipennate ---
    d.add(Rect(362, 10, 98, 110, fillColor=LIGHT_GREEN, strokeColor=GREEN_ACCT, strokeWidth=1.5))
    d.add(String(368, 108, "Multipennate", fontSize=9, fontName='Helvetica-Bold', fillColor=DARK_NAVY))
    d.add(Line(380, 20, 380, 105, strokeColor=DARK_NAVY, strokeWidth=3))
    d.add(Line(420, 20, 420, 105, strokeColor=DARK_NAVY, strokeWidth=3))
    for y in [88, 72, 56, 40]:
        d.add(Line(366, y, 378, y+8, strokeColor=GREEN_ACCT, strokeWidth=2))
        d.add(Line(395, y, 382, y+8, strokeColor=GREEN_ACCT, strokeWidth=2))
        d.add(Line(395, y, 418, y+8, strokeColor=GREEN_ACCT, strokeWidth=2))
        d.add(Line(450, y, 422, y+8, strokeColor=GREEN_ACCT, strokeWidth=2))

    return d


# ── Connective Tissue Hierarchy Diagram ────────────────────────────────────────

def connective_tissue_diagram():
    d = Drawing(470, 90)
    d.add(Rect(0, 0, 470, 90, fillColor=GRAY_LIGHT, strokeColor=None))

    levels = [
        ("Epimysium", DARK_NAVY, 20, 62, 80),
        ("Perimysium", MID_BLUE, 120, 62, 80),
        ("Endomysium", ACCENT_BLUE, 220, 62, 80),
        ("Muscle Fiber", colors.HexColor("#E74C3C"), 320, 62, 80),
        ("Myofibril", colors.HexColor("#8E44AD"), 420, 62, 40),
    ]
    sub = [
        "Whole muscle",
        "Bundles",
        "200–250 fibers",
        "Single cell\n~60 µm dia",
        "Actin &\nMyosin",
    ]

    for i, (label, col, x, y, w) in enumerate(levels):
        d.add(Rect(x - w//2, y - 14, w, 28, fillColor=col, strokeColor=WHITE, strokeWidth=1))
        d.add(String(x - w//2 + 4, y - 2, label, fontSize=8,
                     fontName='Helvetica-Bold', fillColor=WHITE))
        d.add(String(x - w//2 + 2, 18, sub[i], fontSize=7.5,
                     fontName='Helvetica', fillColor=GRAY_DARK))
        if i < len(levels) - 1:
            nx = levels[i+1][2] - levels[i+1][4]//2
            d.add(Line(x + w//2, y, nx, y, strokeColor=GRAY_DARK,
                       strokeWidth=1.5, strokeDashArray=[3,2]))

    return d


# ── Motor Unit Diagram ─────────────────────────────────────────────────────────

def motor_unit_diagram():
    d = Drawing(470, 100)
    d.add(Rect(0, 0, 470, 100, fillColor=GRAY_LIGHT, strokeColor=None))

    # Type I motor unit (large)
    d.add(Rect(10, 10, 210, 80, fillColor=LIGHT_RED, strokeColor=RED_TYPE1, strokeWidth=1.5))
    d.add(String(18, 78, "TYPE I Motor Unit", fontSize=10,
                 fontName='Helvetica-Bold', fillColor=RED_TYPE1))
    d.add(String(18, 64, "Large (thousands of fibers)", fontSize=8.5,
                 fontName='Helvetica', fillColor=DARK_NAVY))
    d.add(String(18, 50, "Innervated by: Large alpha-MN", fontSize=8.5,
                 fontName='Helvetica', fillColor=DARK_NAVY))
    d.add(String(18, 36, "Force: Sustained / low force", fontSize=8.5,
                 fontName='Helvetica', fillColor=DARK_NAVY))
    d.add(String(18, 22, "Function: Posture & endurance", fontSize=8.5,
                 fontName='Helvetica', fillColor=DARK_NAVY))

    # Type II motor unit (small)
    d.add(Rect(250, 10, 210, 80, fillColor=LIGHT_ORANGE, strokeColor=ORANGE_TYPE2, strokeWidth=1.5))
    d.add(String(258, 78, "TYPE II Motor Unit", fontSize=10,
                 fontName='Helvetica-Bold', fillColor=ORANGE_TYPE2))
    d.add(String(258, 64, "Small (<100 fibers)", fontSize=8.5,
                 fontName='Helvetica', fillColor=DARK_NAVY))
    d.add(String(258, 50, "Innervated by: Small alpha-MN", fontSize=8.5,
                 fontName='Helvetica', fillColor=DARK_NAVY))
    d.add(String(258, 36, "Force: Brief / high force", fontSize=8.5,
                 fontName='Helvetica', fillColor=DARK_NAVY))
    d.add(String(258, 22, "Function: Power & speed", fontSize=8.5,
                 fontName='Helvetica', fillColor=DARK_NAVY))

    return d


# ── Cover Page ─────────────────────────────────────────────────────────────────

def build_cover():
    d = Drawing(595 - 72, 842 - 72)   # A4 minus margins
    d.add(Rect(0, 0, 523, 770, fillColor=DARK_NAVY, strokeColor=None))
    # Accent stripe
    d.add(Rect(0, 0, 523, 8, fillColor=GOLD, strokeColor=None))
    d.add(Rect(0, 762, 523, 8, fillColor=GOLD, strokeColor=None))
    # Decorative circles
    d.add(Circle(430, 680, 70, fillColor=MID_BLUE, strokeColor=None))
    d.add(Circle(80,  100, 50, fillColor=MID_BLUE, strokeColor=None))
    d.add(Circle(460, 100, 30, fillColor=ACCENT_BLUE, strokeColor=None))
    # Icon strip
    for x, lbl, col in [(120,'TYPE I', RED_TYPE1), (250,'TYPE II', ORANGE_TYPE2), (380,'MUSCLE', GREEN_ACCT)]:
        d.add(Rect(x-50, 380, 100, 55, fillColor=col, strokeColor=WHITE, strokeWidth=1.5))
        d.add(String(x-40, 402, lbl, fontSize=13, fontName='Helvetica-Bold', fillColor=WHITE))
    return d


# ── Build Document ─────────────────────────────────────────────────────────────

def build():
    doc = SimpleDocTemplate(
        OUTPUT_PATH,
        pagesize=A4,
        leftMargin=2.5*cm, rightMargin=2.5*cm,
        topMargin=2.2*cm, bottomMargin=2.2*cm,
        title="Muscle Classification & Fiber Types — Study Guide",
        author="Orris Medical Education",
        subject="General Anatomy"
    )

    story = []

    # ─── COVER ────────────────────────────────────────────────────────────────
    cover_bg = build_cover()
    story.append(cover_bg)
    story.append(Spacer(1, 2.5*cm))
    story.append(Paragraph("MUSCLE CLASSIFICATION", COVER_TITLE))
    story.append(Paragraph("&amp; FIBER TYPES", COVER_TITLE))
    story.append(Spacer(1, 0.6*cm))
    story.append(Paragraph("A Complete Study Guide for Medical Students", COVER_SUB))
    story.append(Spacer(1, 1.2*cm))
    story.append(Paragraph("General Anatomy | Musculoskeletal System", COVER_CAPTION))
    story.append(Paragraph("Based on THIEME Atlas of Anatomy — General Anatomy &amp; Musculoskeletal System", COVER_CAPTION))
    story.append(PageBreak())

    # ─── TABLE OF CONTENTS ────────────────────────────────────────────────────
    story.append(chapter_banner("TABLE OF CONTENTS", "Quick navigation guide"))
    story.append(Spacer(1, 0.4*cm))

    toc_data = [
        ["Section", "Topic", "Page"],
        ["1", "Overview: Three Types of Muscle Tissue", "3"],
        ["2", "Skeletal Muscle — General Classification", "3"],
        ["3", "Fiber Type Classification (Type I vs II)", "4"],
        ["4", "Type IIA vs IIB Subtypes", "5"],
        ["5", "Architectural Classification: Pennate vs Non-Pennate", "6"],
        ["6", "Histological Structure of Skeletal Muscle", "7"],
        ["7", "Motor Units", "8"],
        ["8", "Muscle Fasciae", "9"],
        ["9", "Functional Classification (Agonist/Antagonist etc.)", "9"],
        ["10", "Tendons: Types and Insertions", "10"],
        ["11", "Master Summary Table", "11"],
        ["12", "Quick-Recall Flashcard Points", "12"],
    ]
    toc_t = Table(toc_data, colWidths=[50, 300, 50])
    toc_t.setStyle(TableStyle([
        ('BACKGROUND', (0,0), (-1,0), DARK_NAVY),
        ('TEXTCOLOR', (0,0), (-1,0), WHITE),
        ('FONTNAME', (0,0), (-1,0), 'Helvetica-Bold'),
        ('FONTSIZE', (0,0), (-1,0), 10),
        ('FONTNAME', (0,1), (-1,-1), 'Helvetica'),
        ('FONTSIZE', (0,1), (-1,-1), 10),
        ('ROWBACKGROUNDS', (0,1), (-1,-1), [WHITE, GRAY_LIGHT]),
        ('GRID', (0,0), (-1,-1), 0.5, GRAY_MID),
        ('ALIGN', (0,0), (-1,-1), 'LEFT'),
        ('ALIGN', (2,0), (2,-1), 'CENTER'),
        ('TOPPADDING', (0,0), (-1,-1), 6),
        ('BOTTOMPADDING',(0,0),(-1,-1), 6),
        ('LEFTPADDING', (0,0), (-1,-1), 10),
    ]))
    story.append(toc_t)
    story.append(PageBreak())

    # ─── SECTION 1: THREE TYPES ───────────────────────────────────────────────
    story.append(chapter_banner("Section 1 — Overview: Three Types of Muscle", color=DARK_NAVY))
    story.append(Spacer(1, 0.3*cm))
    story.append(Paragraph("The human body contains three fundamental types of muscle tissue:", BODY))
    story.append(Spacer(1, 0.2*cm))

    three_types = multi_col_table(
        ["Feature", "Skeletal Muscle", "Cardiac Muscle", "Smooth Muscle"],
        [
            ["Location", "Attached to skeleton", "Heart wall", "Viscera, blood vessels"],
            ["Appearance", "Striated", "Striated", "Non-striated"],
            ["Control", "Voluntary", "Involuntary", "Involuntary"],
            ["Nuclei", "Multiple, peripheral", "Single, central", "Single, central"],
            ["Speed", "Fast", "Intermediate", "Slow"],
            ["Fatigue", "Yes (phasic)", "No (self-sustaining)", "No"],
            ["Special feature", "Motor end plate", "Intercalated discs", "Gap junctions"],
        ],
        col_widths=[90, 110, 110, 110],
        header_color=MID_BLUE,
    )
    story.append(three_types)
    story.append(Spacer(1, 0.3*cm))

    # ─── SECTION 2 ────────────────────────────────────────────────────────────
    story.append(section_rule())
    story.append(Paragraph("Section 2 — Skeletal Muscle: General Classification", SECTION_HEAD))
    story.append(Paragraph(
        "Skeletal muscle can be classified on multiple axes: fiber type (metabolic), architecture "
        "(pennation), functional role (agonist/antagonist), and lever type. The most clinically "
        "relevant is the <b>fiber type classification</b>.", BODY))
    story.append(Spacer(1, 0.25*cm))

    story.append(info_box("Why Classification Matters", [
        Paragraph("Understanding fiber type composition helps predict which muscles are prone to "
                  "<b>shortening vs. atrophy</b>, guides rehabilitation strategies, and explains why "
                  "different athletes develop different muscle profiles.", BODY),
    ]))
    story.append(PageBreak())

    # ─── SECTION 3: FIBER TYPES ───────────────────────────────────────────────
    story.append(chapter_banner("Section 3 — Fiber Type Classification", "Type I vs. Type II",
                                color=colors.HexColor("#7B241C")))
    story.append(Spacer(1, 0.3*cm))
    story.append(Paragraph(
        "All striated skeletal muscles consist of two primary fiber types. Since both respond to a "
        "single action potential with a single twitch (all-or-none response), they are called "
        "<b>twitch fibers</b>. In contrast, <b>tonic fibers</b> (found only in muscle spindles "
        "and external eye muscles) gradually depolarize, causing gradual fiber shortening.",
        BODY))
    story.append(Spacer(1, 0.3*cm))

    story.append(fiber_type_diagram())
    story.append(Spacer(1, 0.3*cm))

    story.append(Paragraph("Detailed Comparison Table", SUBHEAD))
    fiber_table = multi_col_table(
        ["Property", "Type I (ST)", "Type II (FT)"],
        [
            ["Twitch speed", "Slow (~100 ms)", "Fast (~30 ms)"],
            ["Myoglobin content", "High (red/dark)", "Low (pale/white)"],
            ["Mitochondria", "Abundant", "Few"],
            ["Primary metabolism", "Oxidative (aerobic)", "Glycolytic (anaerobic)"],
            ["Glycogen content", "Low (PAS-negative)", "High (PAS-positive)"],
            ["Capillary density", "High", "Low"],
            ["Motor unit size", "Large (1000s fibers)", "Small (<100 fibers)"],
            ["Fatigue resistance", "High (slow to fatigue)", "Low (fatigues quickly)"],
            ["Contraction force", "Lower per unit", "Higher per unit"],
            ["Primary function", "Sustained posture", "Rapid, powerful movement"],
            ["Plasticity", "Can convert to Type II with disuse", "Can convert to Type I with endurance training"],
        ],
        col_widths=[165, 155, 150],
        header_color=colors.HexColor("#7B241C"),
    )
    story.append(fiber_table)
    story.append(Spacer(1, 0.3*cm))

    story.append(key_point_box(
        "Key point: The basic distribution of Type I vs II fibers is GENETICALLY determined. "
        "However, skeletal muscle has phenotypic plasticity — neuro-muscular activity can shift the "
        "distribution. Endurance training ↑ Type I; explosive/resistance training ↑ Type II "
        "(Pette & Saron, 2001)."
    ))
    story.append(PageBreak())

    # ─── SECTION 4: TYPE IIA vs IIB ───────────────────────────────────────────
    story.append(chapter_banner("Section 4 — Type II Subtypes: IIA vs. IIB", color=ORANGE_TYPE2))
    story.append(Spacer(1, 0.3*cm))
    story.append(Paragraph(
        "Type II fibers are further subdivided based on the <b>weight of isoforms in their "
        "myosin heavy chains</b>:", BODY))
    story.append(Spacer(1, 0.2*cm))

    subtypes = multi_col_table(
        ["Property", "Type IIA", "Type IIB"],
        [
            ["Also called", "Fast oxidative-glycolytic (FOG)", "Fast glycolytic (FG)"],
            ["Myosin isoform", "IIa heavy chain", "IIb heavy chain"],
            ["Metabolism", "Oxidative + glycolytic (both)", "Mainly anaerobic glycolytic"],
            ["Mitochondria", "Moderate", "Few"],
            ["Fatigue", "Intermediate", "Fatigues fastest"],
            ["Force", "High", "Highest"],
            ["Speed", "Fast", "Fastest"],
            ["Typical use", "Prolonged high-intensity work", "Brief maximal efforts"],
            ["Examples", "Middle-distance running muscles", "Sprinting, jumping muscles"],
        ],
        col_widths=[130, 170, 170],
        header_color=ORANGE_TYPE2,
    )
    story.append(subtypes)
    story.append(Spacer(1, 0.3*cm))

    story.append(info_box("Fiber Type Distribution in Common Muscles", [
        Paragraph("• <b>Soleus:</b> ~80% Type I — classic postural muscle, sustains standing", BODY),
        Paragraph("• <b>Gastrocnemius:</b> ~50% Type II — generates force for jumping/sprinting", BODY),
        Paragraph("• <b>Deltoid:</b> ~60% Type I — holds arm up continuously", BODY),
        Paragraph("• <b>Biceps brachii:</b> ~50% mixed — both sustained & rapid elbow flexion", BODY),
        Paragraph("• <b>External eye muscles:</b> Tonic fibers (unique — gradual depolarization)", BODY),
    ], bg=LIGHT_ORANGE, border=ORANGE_TYPE2))
    story.append(PageBreak())

    # ─── SECTION 5: PENNATE ───────────────────────────────────────────────────
    story.append(chapter_banner("Section 5 — Architectural Classification: Pennate vs. Non-Pennate",
                                color=GREEN_ACCT))
    story.append(Spacer(1, 0.3*cm))
    story.append(Paragraph(
        "Skeletal muscles are classified by the <b>arrangement of fibers relative to their tendon</b>. "
        "This determines the trade-off between <i>force production</i> vs. <i>force development "
        "(lifting height)</i>.", BODY))
    story.append(Spacer(1, 0.3*cm))
    story.append(pennate_diagram())
    story.append(Spacer(1, 0.3*cm))

    penn_table = multi_col_table(
        ["Type", "Fiber Arrangement", "Physiological XS", "Advantage", "Examples"],
        [
            ["Non-pennate\n(parallel)", "Parallel to long axis of tendon",
             "= Anatomic XS", "Greater force production;\nlarger range of motion",
             "Sartorius, rectus abdominis"],
            ["Unipennate", "Fibers angle from ONE side of tendon",
             "> Anatomic XS", "More fibers per unit volume;\ngreater force development",
             "Flexor pollicis longus"],
            ["Bipennate", "Fibers angle from BOTH sides of tendon",
             ">> Anatomic XS", "Even more fibers; greater lifting height",
             "Rectus femoris, flexor digitorum longus"],
            ["Multipennate", "Multiple pennation angles; complex tendon",
             ">>> Anatomic XS", "Maximum fibers; maximum force in small space",
             "Deltoid, tibialis posterior"],
        ],
        col_widths=[75, 100, 75, 110, 110],
        header_color=GREEN_ACCT,
    )
    story.append(penn_table)
    story.append(Spacer(1, 0.3*cm))

    story.append(key_point_box(
        "In NON-pennate muscles: force production is greater (direct fiber-to-tendon axis). "
        "In PENNATE muscles: force development is greater (more fibers per cross-section, "
        "greater lifting height). Pennation allows the body to pack more powerful muscles "
        "into confined anatomical spaces — a critical evolutionary advantage."
    ))
    story.append(PageBreak())

    # ─── SECTION 6: HISTOLOGY ─────────────────────────────────────────────────
    story.append(chapter_banner("Section 6 — Histological Structure of Skeletal Muscle",
                                color=ACCENT_BLUE))
    story.append(Spacer(1, 0.3*cm))
    story.append(Paragraph(
        "Skeletal muscle has a hierarchical organization of muscle fibers and connective tissue "
        "sheaths that work together to transmit force efficiently.", BODY))
    story.append(Spacer(1, 0.3*cm))

    story.append(Paragraph("Connective Tissue Hierarchy", SUBHEAD))
    story.append(connective_tissue_diagram())
    story.append(Spacer(1, 0.2*cm))

    ct_table = multi_col_table(
        ["Layer", "What It Surrounds", "Thickness", "Function"],
        [
            ["Endomysium", "Individual muscle fibers;\n200–250 fibers → 1° bundles",
             "Thinnest", "Tensile strength; houses capillaries (300–400/mm²)\n& motor end plates"],
            ["Perimysium", "Primary bundles → secondary bundles\n(visible to naked eye = 'meat fibers')",
             "Intermediate", "Transmits tensile force to tendons"],
            ["Epimysium", "Entire muscle (beneath muscle fascia)",
             "Loose CT", "Connects muscle to fascial system;\npermits gliding"],
        ],
        col_widths=[80, 130, 80, 180],
        header_color=ACCENT_BLUE,
    )
    story.append(ct_table)
    story.append(Spacer(1, 0.3*cm))

    story.append(Paragraph("The Muscle Fiber (Cell)", SUBHEAD))
    story.append(Paragraph(
        "Skeletal muscle fibers are among the largest cells in the body:", BODY))
    fiber_stats = [
        [Paragraph("<b>Average diameter:</b>", BODY_BOLD),
         Paragraph("~60 µm (range: 10–100 µm)", BODY)],
        [Paragraph("<b>Length:</b>", BODY_BOLD),
         Paragraph("Up to 20 cm", BODY)],
        [Paragraph("<b>Nuclei:</b>", BODY_BOLD),
         Paragraph("Multiple, peripheral (subsarcolemmal)", BODY)],
        [Paragraph("<b>Dominant structures:</b>", BODY_BOLD),
         Paragraph("Myofibrils, mitochondria, L-system (sarcoplasmic reticulum), T-system (transverse tubules)", BODY)],
        [Paragraph("<b>L-system:</b>", BODY_BOLD),
         Paragraph("Longitudinal tubules — stores Ca²⁺, releases it on excitation to trigger contraction", BODY)],
        [Paragraph("<b>T-system:</b>", BODY_BOLD),
         Paragraph("Transverse tubules — conducts action potentials from sarcolemma to interior of fiber", BODY)],
    ]
    fs_t = Table(fiber_stats, colWidths=[150, 320])
    fs_t.setStyle(TableStyle([
        ('ROWBACKGROUNDS', (0,0), (-1,-1), [WHITE, GRAY_LIGHT]),
        ('GRID', (0,0), (-1,-1), 0.4, GRAY_MID),
        ('TOPPADDING', (0,0), (-1,-1), 5),
        ('BOTTOMPADDING', (0,0), (-1,-1), 5),
        ('LEFTPADDING', (0,0), (-1,-1), 8),
        ('VALIGN', (0,0), (-1,-1), 'TOP'),
    ]))
    story.append(fs_t)
    story.append(PageBreak())

    # ─── SECTION 7: MOTOR UNITS ───────────────────────────────────────────────
    story.append(chapter_banner("Section 7 — Motor Units", color=MID_BLUE))
    story.append(Spacer(1, 0.3*cm))
    story.append(Paragraph(
        "A <b>motor unit</b> = one alpha motor neuron + ALL the muscle fibers it innervates. "
        "All fibers within a motor unit are of the <b>same fiber type</b> (determined by the "
        "innervating neuron).", BODY))
    story.append(Spacer(1, 0.3*cm))
    story.append(motor_unit_diagram())
    story.append(Spacer(1, 0.3*cm))

    story.append(key_point_box(
        "Size Principle (Henneman, 1965): Motor units are recruited from smallest to largest. "
        "Type I (small, low-force) units are recruited first; Type II (large, high-force) units "
        "are added as force demand increases. This ensures metabolic efficiency."
    ))
    story.append(Spacer(1, 0.3*cm))

    mu_table = multi_col_table(
        ["Feature", "Type I Motor Unit", "Type II Motor Unit"],
        [
            ["Motor neuron size", "Small (slow-conducting)", "Large (fast-conducting)"],
            ["Number of fibers", "Hundreds to thousands", "< 100"],
            ["Force per unit", "Low", "High"],
            ["Recruitment order", "First (low effort)", "Last (high effort)"],
            ["Fatigue", "Resistant", "Rapid"],
        ],
        col_widths=[150, 160, 160],
        header_color=MID_BLUE,
    )
    story.append(mu_table)
    story.append(PageBreak())

    # ─── SECTION 8: FASCIAE ───────────────────────────────────────────────────
    story.append(chapter_banner("Section 8 — Muscle Fasciae", color=DARK_NAVY))
    story.append(Spacer(1, 0.3*cm))
    story.append(Paragraph(
        "Muscle fasciae are sheets of tough collagenous connective tissue forming a continuous "
        "three-dimensional network throughout the body.", BODY))
    story.append(Spacer(1, 0.2*cm))

    fascia_rows = [
        ["Structure", "Collagenous connective tissue in a weblike lattice pattern"],
        ["Lattice advantage", "Bears loads in ANY direction (not only along fiber axis)"],
        ["Function 1", "Maintains shape and position of muscles"],
        ["Function 2", "Permits adjacent muscles/groups to glide past each other with minimal friction"],
        ["Function 3", "Reduces force loss through friction between muscle groups"],
        ["Clinical relevance", "Compartment syndrome — fasciae can limit swelling and create dangerous pressure"],
        ["Modern concept", "Fasciae = continuous 3D network investing ALL body structures, supporting the entire musculoskeletal system"],
    ]
    f_t = Table(fascia_rows, colWidths=[140, 330])
    f_t.setStyle(TableStyle([
        ('ROWBACKGROUNDS', (0,0), (-1,-1), [LIGHT_BLUE, WHITE]),
        ('GRID', (0,0), (-1,-1), 0.4, GRAY_MID),
        ('FONTNAME', (0,0), (0,-1), 'Helvetica-Bold'),
        ('FONTSIZE', (0,0), (-1,-1), 9.5),
        ('TOPPADDING', (0,0), (-1,-1), 6),
        ('BOTTOMPADDING', (0,0), (-1,-1), 6),
        ('LEFTPADDING', (0,0), (-1,-1), 8),
        ('VALIGN', (0,0), (-1,-1), 'TOP'),
    ]))
    story.append(f_t)
    story.append(PageBreak())

    # ─── SECTION 9: FUNCTIONAL CLASSIFICATION ────────────────────────────────
    story.append(chapter_banner("Section 9 — Functional Classification", color=MID_BLUE))
    story.append(Spacer(1, 0.3*cm))
    story.append(Paragraph(
        "Muscles can be classified by their <b>functional role</b> during a movement:", BODY))
    story.append(Spacer(1, 0.2*cm))

    func_data = multi_col_table(
        ["Role", "Definition", "Contraction Type", "Example"],
        [
            ["Agonist\n(Prime mover)", "Primary muscle generating the movement",
             "Concentric (shortening)", "Biceps brachii in elbow flexion"],
            ["Antagonist", "Opposes the agonist; controls and smooths movement",
             "Eccentric (lengthening)", "Triceps brachii during elbow flexion"],
            ["Synergist", "Assists agonist; fine-tunes movement; stabilizes joints",
             "Varies", "Brachioradialis assists biceps in forearm flexion"],
            ["Fixator\n(Stabilizer)", "Contracts isometrically to stabilize proximal segment",
             "Isometric", "Rotator cuff stabilizes glenohumeral joint during arm abduction"],
        ],
        col_widths=[80, 130, 110, 150],
        header_color=MID_BLUE,
    )
    story.append(func_data)
    story.append(Spacer(1, 0.3*cm))

    story.append(Paragraph("Lever Mechanics", SUBHEAD))
    story.append(Paragraph(
        "Muscle force transmission follows lever principles. The <b>torque</b> = Force × Force arm.", BODY))
    lever_table = multi_col_table(
        ["Lever Class", "Description", "Example in Body"],
        [
            ["One-arm lever", "Muscle force and load act on the SAME side of the joint axis",
             "Elbow joint (biceps and load both act distal to joint)"],
            ["Two-arm lever", "Muscle force and body weight act on OPPOSITE sides of joint axis",
             "Hip joint in single-leg stance"],
        ],
        col_widths=[100, 185, 185],
        header_color=MID_BLUE,
    )
    story.append(lever_table)
    story.append(PageBreak())

    # ─── SECTION 10: TENDONS ─────────────────────────────────────────────────
    story.append(chapter_banner("Section 10 — Tendons: Types and Insertions", color=DARK_NAVY))
    story.append(Spacer(1, 0.3*cm))

    tendon_table = multi_col_table(
        ["Type", "Stress Borne", "Structure", "Vascularization", "Example"],
        [
            ["Traction tendon", "Tensile (pulling)", "Strong parallel collagen fibers",
             "Well vascularized", "Achilles tendon"],
            ["Pressure tendon", "Compressive (pressure)", "Fibrocartilage at bone contact;\nchanges direction around bone",
             "Avascular at compressed area", "Flexor tendons at pulleys"],
        ],
        col_widths=[80, 75, 120, 100, 95],
        header_color=DARK_NAVY,
    )
    story.append(tendon_table)
    story.append(Spacer(1, 0.3*cm))

    story.append(Paragraph("Tendon Insertion Types", SUBHEAD))
    ins_table = multi_col_table(
        ["Insertion Type", "Structure at Bone Interface", "Principle"],
        [
            ["Periosteal diaphyseal", "Collagen fibers → fibrocartilage → mineralized\nfibrocartilage → bone (Sharpey's fibers)",
             "Gradual force dissipation across 4 transitional zones"],
            ["Chondral apophyseal", "Non-mineralized fibrocartilage layer with cartilage cells",
             "Stretch protection: cartilage cells act like springs,\nresisting transverse shortening during contraction"],
        ],
        col_widths=[110, 200, 160],
        header_color=DARK_NAVY,
    )
    story.append(ins_table)
    story.append(PageBreak())

    # ─── SECTION 11: MASTER TABLE ─────────────────────────────────────────────
    story.append(chapter_banner("Section 11 — Master Summary Classification Table", color=colors.HexColor("#4A235A")))
    story.append(Spacer(1, 0.3*cm))

    master = multi_col_table(
        ["Classification Basis", "Categories"],
        [
            ["Control", "Voluntary (skeletal) | Involuntary (cardiac, smooth)"],
            ["Histology", "Striated (skeletal, cardiac) | Non-striated (smooth)"],
            ["Fiber type", "Type I (slow, oxidative) | Type IIA (fast, mixed) | Type IIB (fast, glycolytic)"],
            ["Functional role", "Postural (red) | Phasic/movement (white)"],
            ["Architecture", "Non-pennate (parallel) | Unipennate | Bipennate | Multipennate"],
            ["Action", "Agonist | Antagonist | Synergist | Fixator"],
            ["Lever type", "One-arm lever | Two-arm lever"],
            ["Tendon type", "Traction | Pressure"],
            ["Insertion type", "Periosteal diaphyseal | Chondral apophyseal"],
            ["Motor unit size", "Large (Type I) | Small (Type II)"],
        ],
        col_widths=[180, 290],
        header_color=colors.HexColor("#4A235A"),
    )
    story.append(master)
    story.append(PageBreak())

    # ─── SECTION 12: FLASHCARDS ───────────────────────────────────────────────
    story.append(chapter_banner("Section 12 — Quick-Recall Flashcard Points", color=colors.HexColor("#7D6608")))
    story.append(Spacer(1, 0.3*cm))

    flashcards = [
        ("Q: What is a twitch fiber?",
         "A fiber that responds to a single action potential with a single twitch (all-or-none). Both Type I and II are twitch fibers."),
        ("Q: What is a tonic fiber?",
         "A fiber that gradually depolarizes, causing gradual shortening. Found ONLY in muscle spindles and external eye muscles."),
        ("Q: Which fiber type is PAS-positive?",
         "Type II (fast-twitch) — rich in glycogen; stains positive with Periodic Acid-Schiff."),
        ("Q: Which fiber type fatigues rapidly?",
         "Type II (fast-twitch) — relies on anaerobic glycolysis, which depletes quickly."),
        ("Q: What determines fiber type within a motor unit?",
         "The innervating motor neuron determines the fiber type of all fibers in that motor unit."),
        ("Q: In which athletes do Type I fibers predominate?",
         "Endurance athletes — long-distance runners, cyclists, rowers, cross-country skiers."),
        ("Q: What is the advantage of pennate muscle architecture?",
         "More fibers per physiological cross-section → greater force development and lifting height in a smaller anatomical space."),
        ("Q: What is the 'principle of stretch protection' in tendon insertions?",
         "In chondral apophyseal insertions, cartilage cells in the non-mineralized fibrocartilage zone act like springs, resisting transverse shortening during muscle contraction."),
        ("Q: Name the 3 connective tissue sheaths of skeletal muscle (deep to superficial)",
         "Endomysium → Perimysium → Epimysium"),
        ("Q: What is physiological cross-section?",
         "The cross-section through ALL muscle fibers perpendicular to their long axis. In pennate muscles, this exceeds the anatomic cross-section, allowing more force development."),
        ("Q: What happens to Type I fibers if a muscle is not stretched regularly?",
         "They are prone to SHORTENING (increased resting tonus). Regular stretching is required."),
        ("Q: What happens to Type II fibers with disuse?",
         "They are prone to ATROPHY. Regular strengthening exercises are required."),
    ]

    for i, (q, a) in enumerate(flashcards):
        bg = LIGHT_BLUE if i % 2 == 0 else LIGHT_GREEN
        border = ACCENT_BLUE if i % 2 == 0 else GREEN_ACCT
        card_data = [
            [Paragraph(q, BODY_BOLD)],
            [Paragraph(a, BODY)],
        ]
        card_t = Table(card_data, colWidths=[470])
        card_t.setStyle(TableStyle([
            ('BACKGROUND', (0,0), (-1,0), bg),
            ('BACKGROUND', (0,1), (-1,1), WHITE),
            ('BOX', (0,0), (-1,-1), 1.2, border),
            ('LINEBELOW', (0,0), (-1,0), 0.8, border),
            ('TOPPADDING', (0,0), (-1,-1), 6),
            ('BOTTOMPADDING', (0,0), (-1,-1), 6),
            ('LEFTPADDING', (0,0), (-1,-1), 10),
            ('RIGHTPADDING', (0,0), (-1,-1), 10),
        ]))
        story.append(card_t)
        story.append(Spacer(1, 0.15*cm))

    # ─── FOOTER PAGE ──────────────────────────────────────────────────────────
    story.append(PageBreak())
    story.append(Spacer(1, 3*cm))
    story.append(Paragraph("References & Source", SECTION_HEAD))
    story.append(section_rule())
    story.append(Paragraph(
        "Primary source: <b>General Anatomy and Musculoskeletal System</b>, "
        "THIEME Atlas of Anatomy (ISBN 978-1-62623-718-6), Sections 5.1–5.3, pp. 76–81.",
        BODY))
    story.append(Paragraph(
        "Pette D, Saron RS (2001). Transitions of muscle fiber phenotypic profiles. "
        "<i>Histochem Cell Biol</i>. 115(5):359–72.",
        BODY))
    story.append(Paragraph(
        "Henneman E (1965). Relationship between size of neurons and their susceptibility to discharge. "
        "<i>Science</i>. 126(3287):1345–7. [Size Principle]",
        BODY))
    story.append(Spacer(1, 1*cm))
    story.append(Paragraph(
        "Study Guide compiled by Orris Medical Education · June 2026",
        SMALL))

    # ─── BUILD ────────────────────────────────────────────────────────────────
    doc.build(story)
    print(f"PDF generated: {OUTPUT_PATH}")


if __name__ == "__main__":
    build()

Successfully replaced 1 instance(s) of the string in '/home/daytona/workspace/muscle-study-guide/generate_study_guide.py'

Successfully replaced 1 instance(s) of the string in '/home/daytona/workspace/muscle-study-guide/generate_study_guide.py'