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app/services/pdf_generator.py

@@ -8,7 +8,7 @@ Supports multiple report types:
   - conversation    : Export of chat conversation
 """
 from __future__ import annotations
-import csv, json, io
+import csv, json, io, re
 from datetime import datetime
 from pathlib import Path
 from sqlalchemy.orm import Session
@@ -17,6 +17,8 @@ from .groq_client import complete_once
 from .medical_context import build_context
 from ..models import Scan, Patient, ChatMessage
 
+import markdown as _md
+
 
 # ── colour palette ──────────────────────────────────────────────────────
 _PRIMARY   = "#1e40af"
@@ -31,17 +33,21 @@ _TEXT      = "#1e293b"
 _TEXT_MUTED = "#64748b"
 
 
+def _md_to_html(text: str) -> str:
+    """Convert LLM markdown output to proper HTML for PDF rendering."""
+    cleaned = text.replace("[REPORT_READY]", "").strip()
+    html = _md.markdown(cleaned, extensions=["tables", "fenced_code", "nl2br"])
+    return html
+
+
 def _base_css() -> str:
     return f"""
 @page {{
   size: A4;
-  margin: 20mm 18mm 25mm 18mm;
-  @top-center {{
-    content: "";
-  }}
+  margin: 18mm 16mm 22mm 16mm;
   @bottom-center {{
     content: counter(page) " of " counter(pages);
-    font-size: 9px;
+    font-size: 8px;
     color: {_TEXT_MUTED};
     font-family: 'Helvetica Neue', Arial, sans-serif;
   }}
@@ -51,74 +57,69 @@ body {{
   font-family: 'Helvetica Neue', Arial, sans-serif;
   color: {_TEXT};
   line-height: 1.55;
-  font-size: 11px;
+  font-size: 10.5px;
   margin: 0;
   padding: 0;
 }}
 
-/* header band */
+/* ─── header band ─── */
 .report-header {{
-  display: flex;
-  justify-content: space-between;
-  align-items: flex-start;
   border-bottom: 3px solid {_PRIMARY};
-  padding-bottom: 14px;
-  margin-bottom: 18px;
+  padding-bottom: 12px;
+  margin-bottom: 14px;
 }}
-.report-header .brand {{
+.report-header table {{ border: none; margin: 0; }}
+.report-header td {{ border: none; padding: 0; vertical-align: top; background: transparent; }}
+.brand {{
   font-size: 22px;
   font-weight: 700;
   color: {_PRIMARY};
   letter-spacing: -0.5px;
 }}
-.report-header .brand-sub {{
-  font-size: 9px;
+.brand-sub {{
+  font-size: 8px;
   color: {_TEXT_MUTED};
   text-transform: uppercase;
   letter-spacing: 1.5px;
   margin-top: 2px;
 }}
-.report-header .doc-info {{
+.doc-info {{
   text-align: right;
   font-size: 9px;
   color: {_TEXT_MUTED};
   line-height: 1.6;
 }}
 
-/* patient info box */
-.patient-box {{
-  display: flex;
-  flex-wrap: wrap;
-  gap: 0;
-  background: {_BG_LIGHT};
+/* ─── patient info grid (table-based for WeasyPrint) ─── */
+.patient-grid {{
+  width: 100%;
+  border-collapse: collapse;
+  margin-bottom: 14px;
   border: 1px solid {_BORDER};
   border-radius: 6px;
-  padding: 0;
-  margin-bottom: 16px;
-  overflow: hidden;
-}}
-.patient-box .cell {{
-  flex: 1 1 auto;
-  min-width: 120px;
-  padding: 10px 14px;
-  border-right: 1px solid {_BORDER};
-  border-bottom: 1px solid {_BORDER};
 }}
-.patient-box .cell:last-child {{ border-right: none; }}
-.patient-box .cell-label {{
-  font-size: 8px;
+.patient-grid td {{
+  padding: 8px 12px;
+  border: 1px solid {_BORDER};
+  background: {_BG_LIGHT};
+  vertical-align: top;
+}}
+.patient-grid .plabel {{
+  font-size: 7.5px;
   text-transform: uppercase;
-  letter-spacing: 1px;
+  letter-spacing: 0.8px;
   color: {_TEXT_MUTED};
-  margin-bottom: 3px;
+  margin-bottom: 2px;
+  display: block;
 }}
-.patient-box .cell-value {{
-  font-size: 12px;
+.patient-grid .pval {{
+  font-size: 11.5px;
   font-weight: 600;
   color: {_TEXT};
+  display: block;
 }}
 
-/* badges */
+/* ─── badges ─── */
 .badge {{
   display: inline-block;
   padding: 2px 10px;
@@ -131,118 +132,179 @@ body {{
 .badge-red    {{ background: #fee2e2; color: #991b1b; }}
 .badge-blue   {{ background: #dbeafe; color: #1e40af; }}
 
-/* section headings */
+/* ─── highlight cards (table-based) ─── */
+.hl-table {{ width: 100%; border-collapse: separate; border-spacing: 6px; margin: 6px 0 14px 0; }}
+.hl-table td {{
+  text-align: center;
+  background: {_BG_LIGHT};
+  border: 1px solid {_BORDER};
+  border-radius: 6px;
+  padding: 10px 6px;
+  width: 20%;
+  vertical-align: middle;
+}}
+.hl-val {{
+  font-size: 18px;
+  font-weight: 700;
+  color: {_PRIMARY};
+  display: block;
+}}
+.hl-lbl {{
+  font-size: 7px;
+  text-transform: uppercase;
+  letter-spacing: 0.8px;
+  color: {_TEXT_MUTED};
+  margin-top: 3px;
+  display: block;
+}}
+
+/* ─── section headings ─── */
 h2 {{
-  font-size: 14px;
+  font-size: 13px;
   font-weight: 700;
   color: {_PRIMARY};
   border-left: 4px solid {_SECONDARY};
   padding-left: 10px;
-  margin: 20px 0 10px 0;
+  margin: 18px 0 8px 0;
   text-transform: uppercase;
   letter-spacing: 0.5px;
 }}
 h3 {{
-  font-size: 12px;
+  font-size: 11.5px;
   font-weight: 600;
+  color: {_PRIMARY};
+  margin: 12px 0 5px 0;
+  border-bottom: 1px solid {_BORDER};
+  padding-bottom: 3px;
+}}
+h4 {{
+  font-size: 10.5px;
+  font-weight: 600;
+  color: {_TEXT};
+  margin: 10px 0 4px 0;
+}}
+
+/* ─── narrative content (rendered from markdown) ─── */
+.narrative {{
+  font-size: 10.5px;
+  line-height: 1.65;
   color: {_TEXT};
+}}
+.narrative p {{
+  margin: 5px 0;
+}}
+.narrative strong {{
+  color: {_PRIMARY};
+  font-weight: 700;
+}}
+.narrative em {{
+  font-style: italic;
+  color: {_TEXT_MUTED};
+}}
+.narrative ul, .narrative ol {{
+  margin: 4px 0 8px 0;
+  padding-left: 20px;
+}}
+.narrative li {{
+  margin-bottom: 3px;
+}}
+.narrative h1 {{
+  font-size: 14px;
+  font-weight: 700;
+  color: {_PRIMARY};
+  border-left: 4px solid {_SECONDARY};
+  padding-left: 10px;
+  margin: 16px 0 8px 0;
+  text-transform: uppercase;
+  letter-spacing: 0.5px;
+}}
+.narrative h2 {{
+  font-size: 12px;
+  font-weight: 700;
+  color: {_PRIMARY};
+  border-left: 4px solid {_ACCENT};
+  padding-left: 8px;
   margin: 14px 0 6px 0;
 }}
+.narrative h3 {{
+  font-size: 11px;
+  font-weight: 600;
+  color: {_TEXT};
+  margin: 10px 0 4px 0;
+  border-bottom: 1px dotted {_BORDER};
+  padding-bottom: 2px;
+}}
+.narrative hr {{
+  border: none;
+  border-top: 1px solid {_BORDER};
+  margin: 12px 0;
+}}
+.narrative blockquote {{
+  border-left: 3px solid {_ACCENT};
+  margin: 8px 0;
+  padding: 4px 12px;
+  background: #eff6ff;
+  color: {_PRIMARY};
+  font-size: 10px;
+}}
 
-/* tables */
+/* ─── tables (data) ─── */
 table {{
   width: 100%;
   border-collapse: collapse;
-  font-size: 10px;
-  margin: 8px 0 14px 0;
+  font-size: 9.5px;
+  margin: 8px 0 12px 0;
 }}
-table thead th {{
+thead th {{
   background: {_PRIMARY};
   color: #ffffff;
-  padding: 8px 10px;
+  padding: 7px 8px;
   text-align: left;
   font-weight: 600;
-  font-size: 9px;
+  font-size: 8.5px;
   text-transform: uppercase;
   letter-spacing: 0.5px;
 }}
-table thead th:first-child {{ border-radius: 4px 0 0 0; }}
-table thead th:last-child  {{ border-radius: 0 4px 0 0; }}
-table tbody td {{
-  padding: 6px 10px;
+thead th:first-child {{ border-radius: 4px 0 0 0; }}
+thead th:last-child  {{ border-radius: 0 4px 0 0; }}
+tbody td {{
+  padding: 5px 8px;
   border-bottom: 1px solid {_BORDER};
   vertical-align: top;
 }}
-table tbody tr:nth-child(even) {{ background: {_BG_LIGHT}; }}
-table tbody tr:hover {{ background: #f1f5f9; }}
+tbody tr:nth-child(even) {{ background: {_BG_LIGHT}; }}
 .z-cell {{ font-weight: 600; font-variant-numeric: tabular-nums; }}
 .z-pos {{ color: {_DANGER}; }}
 .z-neg {{ color: {_SUCCESS}; }}
 .z-typ {{ color: {_TEXT_MUTED}; }}
 
-/* narrative text */
-.narrative {{
-  font-size: 11px;
-  line-height: 1.7;
-  white-space: pre-wrap;
-  color: {_TEXT};
-}}
-.narrative p {{ margin: 6px 0; }}
-
-/* info box */
+/* ─── info / warning boxes ─── */
 .info-box {{
   background: #eff6ff;
   border: 1px solid #bfdbfe;
   border-radius: 6px;
-  padding: 10px 14px;
-  font-size: 10px;
+  padding: 8px 12px;
+  font-size: 9.5px;
   color: #1e40af;
-  margin: 10px 0;
+  margin: 8px 0;
 }}
 .warn-box {{
   background: #fffbeb;
   border: 1px solid #fde68a;
   border-radius: 6px;
-  padding: 10px 14px;
-  font-size: 10px;
+  padding: 8px 12px;
+  font-size: 9.5px;
   color: #92400e;
-  margin: 10px 0;
-}}
-
-/* key findings highlight */
-.highlight-row {{
-  display: flex;
-  gap: 10px;
-  margin: 10px 0;
-}}
-.highlight-card {{
-  flex: 1;
-  background: {_BG_LIGHT};
-  border: 1px solid {_BORDER};
-  border-radius: 6px;
-  padding: 12px;
-  text-align: center;
-}}
-.highlight-card .val {{
-  font-size: 20px;
-  font-weight: 700;
-  color: {_PRIMARY};
-}}
-.highlight-card .lbl {{
-  font-size: 8px;
-  text-transform: uppercase;
-  letter-spacing: 1px;
-  color: {_TEXT_MUTED};
-  margin-top: 4px;
+  margin: 8px 0;
 }}
 
-/* conversation style */
+/* ─── conversation style ─── */
 .chat-msg {{
-  margin: 8px 0;
+  margin: 6px 0;
   padding: 8px 12px;
   border-radius: 8px;
-  font-size: 11px;
-  line-height: 1.6;
+  font-size: 10px;
+  line-height: 1.55;
   page-break-inside: avoid;
 }}
 .chat-user {{
@@ -250,11 +312,10 @@ table tbody tr:hover {{ background: #f1f5f9; }}
   border: 1px solid #93c5fd;
   margin-left: 40px;
 }}
-.chat-user::before {{
-  content: "You";
+.chat-user-label {{
   font-weight: 700;
   color: {_PRIMARY};
-  font-size: 9px;
+  font-size: 8px;
   text-transform: uppercase;
   display: block;
   margin-bottom: 2px;
@@ -264,29 +325,28 @@ table tbody tr:hover {{ background: #f1f5f9; }}
   border: 1px solid {_BORDER};
   margin-right: 40px;
 }}
-.chat-bot::before {{
-  content: "AI Assistant";
+.chat-bot-label {{
   font-weight: 700;
   color: {_SECONDARY};
-  font-size: 9px;
+  font-size: 8px;
   text-transform: uppercase;
   display: block;
   margin-bottom: 2px;
 }}
 
-/* footer */
+/* ─── footer ─── */
 .report-footer {{
-  margin-top: 30px;
-  padding-top: 12px;
+  margin-top: 24px;
+  padding-top: 10px;
   border-top: 2px solid {_BORDER};
-  font-size: 9px;
+  font-size: 8px;
   color: {_TEXT_MUTED};
   text-align: center;
-  line-height: 1.6;
+  line-height: 1.5;
 }}
 .report-footer .disclaimer {{
   font-style: italic;
-  margin-top: 4px;
+  margin-top: 3px;
 }}
 """
 
@@ -294,16 +354,18 @@ table tbody tr:hover {{ background: #f1f5f9; }}
 def _header_html(report_title: str, report_type: str, now_str: str) -> str:
     return f"""
 <div class="report-header">
-  <div>
-    <div class="brand">BrainAge AI</div>
-    <div class="brand-sub">Neuroimaging Analytics Platform</div>
-  </div>
-  <div class="doc-info">
-    <strong>{report_title}</strong><br>
-    Report Type: {report_type}<br>
-    Generated: {now_str}<br>
-    Document ID: RPT-{datetime.now().strftime('%Y%m%d%H%M%S')}
-  </div>
+  <table width="100%"><tr>
+    <td>
+      <div class="brand">BrainAge AI</div>
+      <div class="brand-sub">Neuroimaging Analytics Platform</div>
+    </td>
+    <td class="doc-info">
+      <strong>{report_title}</strong><br>
+      Report Type: {report_type}<br>
+      Generated: {now_str}<br>
+      Document ID: RPT-{datetime.now().strftime('%Y%m%d%H%M%S')}
+    </td>
+  </tr></table>
 </div>"""
 
 
@@ -311,21 +373,23 @@ def _patient_box(ctx: dict, scan: Scan, bag_badge: str) -> str:
     pred = f"{ctx['predicted_age']:.1f}" if ctx.get('predicted_age') else "N/A"
     bag_val = ctx.get('brain_age_gap') or 0
     bag_str = f"{bag_val:+.1f}" if ctx.get('brain_age_gap') is not None else "N/A"
+    age_display = ctx.get('patient_age', 'N/A')
+    if age_display is None:
+        age_display = "N/A"
+    scan_date = scan.created_at.strftime('%Y-%m-%d') if scan and scan.created_at else 'N/A'
     return f"""
-<div class="patient-box">
-  <div class="cell"><div class="cell-label">Patient Name</div>
-    <div class="cell-value">{ctx['patient_name']}</div></div>
-  <div class="cell"><div class="cell-label">Age</div>
-    <div class="cell-value">{ctx.get('patient_age', 'N/A')}y</div></div>
-  <div class="cell"><div class="cell-label">Sex</div>
-    <div class="cell-value">{ctx['patient_sex']}</div></div>
-  <div class="cell"><div class="cell-label">Predicted Brain Age</div>
-    <div class="cell-value">{pred}y</div></div>
-  <div class="cell"><div class="cell-label">Brain Age Gap</div>
-    <div class="cell-value"><span class="badge {bag_badge}">{bag_str}y</span></div></div>
-  <div class="cell"><div class="cell-label">Scan Date</div>
-    <div class="cell-value">{scan.created_at.strftime('%Y-%m-%d') if scan.created_at else 'N/A'}</div></div>
-</div>"""
+<table class="patient-grid">
+  <tr>
+    <td><span class="plabel">Patient Name</span><span class="pval">{ctx['patient_name']}</span></td>
+    <td><span class="plabel">Age</span><span class="pval">{age_display}y</span></td>
+    <td><span class="plabel">Sex</span><span class="pval">{'Male' if ctx['patient_sex']=='M' else 'Female' if ctx['patient_sex']=='F' else ctx['patient_sex']}</span></td>
+  </tr>
+  <tr>
+    <td><span class="plabel">Predicted Brain Age</span><span class="pval">{pred}y</span></td>
+    <td><span class="plabel">Brain Age Gap</span><span class="pval"><span class="badge {bag_badge}">{bag_str}y</span></span></td>
+    <td><span class="plabel">Scan Date</span><span class="pval">{scan_date}</span></td>
+  </tr>
+</table>"""
 
 
 def _highlight_cards(ctx: dict) -> str:
@@ -335,41 +399,23 @@ def _highlight_cards(ctx: dict) -> str:
     n_regions = len(ctx.get('measurements', []))
     abnormal = [r for r in ctx.get('regions', []) if abs(r.get('z_score', 0)) >= 2]
     return f"""
-<div class="highlight-row">
-  <div class="highlight-card">
-    <div class="val">{age if age else '—'}y</div>
-    <div class="lbl">Chronological Age</div>
-  </div>
-  <div class="highlight-card">
-    <div class="val">{f'{pred:.1f}' if pred else '—'}y</div>
-    <div class="lbl">Predicted Brain Age</div>
-  </div>
-  <div class="highlight-card">
-    <div class="val">{f'{bag:+.1f}' if bag is not None else '—'}y</div>
-    <div class="lbl">Brain Age Gap</div>
-  </div>
-  <div class="highlight-card">
-    <div class="val">{n_regions}</div>
-    <div class="lbl">Regions Analyzed</div>
-  </div>
-  <div class="highlight-card">
-    <div class="val">{len(abnormal)}</div>
-    <div class="lbl">Abnormal Regions</div>
-  </div>
-</div>"""
+<table class="hl-table"><tr>
+  <td><span class="hl-val">{age if age else '—'}y</span><span class="hl-lbl">Chronological Age</span></td>
+  <td><span class="hl-val">{f'{pred:.1f}' if pred else '—'}y</span><span class="hl-lbl">Predicted Brain Age</span></td>
+  <td><span class="hl-val">{f'{bag:+.1f}' if bag is not None else '—'}y</span><span class="hl-lbl">Brain Age Gap</span></td>
+  <td><span class="hl-val">{n_regions}</span><span class="hl-lbl">Regions Analyzed</span></td>
+  <td><span class="hl-val">{len(abnormal)}</span><span class="hl-lbl">Abnormal Regions</span></td>
+</tr></table>"""
 
 
 def _region_table(ctx: dict) -> str:
     """Build an HTML table of top regions by |z-score|."""
-    out_dir = None
-    if ctx.get("meta") and ctx["meta"].get("n_regions"):
-        pass  # we have regions from ctx
     regions = ctx.get("regions", [])
     if not regions:
         return ""
     sorted_r = sorted(regions, key=lambda r: abs(r.get("z_score", 0)), reverse=True)
     rows_html = ""
-    for r in sorted_r[:15]:
+    for i, r in enumerate(sorted_r[:20]):
         z = r.get("z_score", 0)
         z_cls = "z-pos" if z > 1 else "z-neg" if z < -1 else "z-typ"
         sev = "normal"
@@ -377,33 +423,42 @@ def _region_table(ctx: dict) -> str:
         if az >= 3: sev = "severe"
         elif az >= 2: sev = "moderate"
         elif az >= 1: sev = "borderline"
-        pct = 50 + 50 * (2 / (1 + 2.718 ** (-z / 1.4)) - 1)  # approx percentile
+        pct = 50 + 50 * (2 / (1 + 2.718 ** (-z / 1.4)) - 1)
+        badge_cls = "badge-red" if sev == "severe" else "badge-yellow" if sev in ("moderate", "borderline") else "badge-green"
+        exp = r.get("expected_mm3")
+        exp_str = f"{float(exp):,.0f}" if exp else "—"
         rows_html += f"""<tr>
-          <td>{r.get('region', '?')}</td>
-          <td style="text-align:right">{float(r.get('volume_mm3', 0)):.0f}</td>
+          <td style="font-weight:{'600' if az>=2 else '400'}">{r.get('region', '?')}</td>
+          <td style="text-align:right">{float(r.get('volume_mm3', 0)):,.0f}</td>
+          <td style="text-align:right;color:{_TEXT_MUTED}">{exp_str}</td>
           <td class="z-cell {z_cls}" style="text-align:right">{z:+.2f}</td>
           <td style="text-align:right">p{pct:.0f}</td>
-          <td><span class="badge badge-{'red' if sev=='severe' else 'yellow' if sev in ('moderate','borderline') else 'green'}">{sev}</span></td>
+          <td><span class="badge {badge_cls}">{sev}</span></td>
         </tr>"""
     return f"""
 <h2>Regional Volumetric Analysis</h2>
 <table>
   <thead><tr>
-    <th>Region</th><th style="text-align:right">Volume (mm³)</th>
-    <th style="text-align:right">Z-Score</th><th style="text-align:right">Percentile</th>
+    <th>Region</th>
+    <th style="text-align:right">Volume (mm&sup3;)</th>
+    <th style="text-align:right">Expected (mm&sup3;)</th>
+    <th style="text-align:right">Z-Score</th>
+    <th style="text-align:right">Percentile</th>
     <th>Severity</th>
   </tr></thead>
   <tbody>{rows_html}</tbody>
-</table>"""
+</table>
+<div class="info-box">Showing top {min(20, len(sorted_r))} of {len(regions)} regions sorted by |z-score|.
+Z-scores compare measured volumes against age-appropriate normative expectations.</div>"""
 
 
 def _footer_html() -> str:
     return """
 <div class="report-footer">
-  <div>BrainAge AI &bull; Neuroimaging Analytics Platform</div>
+  <div><strong>BrainAge AI</strong> &bull; Neuroimaging Analytics Platform</div>
   <div>Model: SFCN Dual-Branch &bull; Trained on 6,050 healthy subjects &bull; MAE: 2.5y (lifespan), 1.05y (pediatric)</div>
   <div class="disclaimer">This report is AI-generated and intended to support, not replace, clinical decision-making.
-  All findings should be reviewed by a qualified healthcare professional.</div>
+  All findings should be reviewed and interpreted by a qualified healthcare professional.</div>
 </div>"""
 
 
@@ -432,51 +487,66 @@ def _get_report_prompt(report_type: str, ctx: dict) -> str:
             z = r.get("z_score", 0)
             base_data += f"  - {r.get('region')}: {float(r.get('volume_mm3',0)):.0f}mm³, z={z:+.2f}\n"
 
+    fmt_instruction = (
+        "\n\nIMPORTANT formatting rules for this report:\n"
+        "- Use markdown: ## for section headers, ### for sub-headers\n"
+        "- Use **bold** for important terms and values\n"
+        "- Use bullet lists with * for itemized content\n"
+        "- Do NOT include [REPORT_READY] or any metadata markers\n"
+    )
+
     prompts = {
         "comprehensive": (
-            base_data + "\nGenerate a comprehensive clinical brain MRI analysis report with these sections:\n"
-            "1. **Executive Summary** (2-3 sentences)\n"
-            "2. **Brain Age Analysis** (interpretation of predicted vs chronological age)\n"
-            "3. **Volumetric Findings** (key regional observations)\n"
-            "4. **Abnormal Regions** (detail each significant deviation)\n"
-            "5. **Tissue Composition** (GM/WM/CSF observations)\n"
-            "6. **Clinical Significance** (what these findings mean)\n"
-            "7. **Recommendations** (next steps, follow-up)\n"
-            "Use clear section headers with **bold**. Be thorough but clinical."
+            base_data +
+            "\nGenerate a comprehensive clinical brain MRI analysis report with these sections:\n"
+            "## Executive Summary\n(2-3 sentences)\n"
+            "## Brain Age Analysis\n(interpretation of predicted vs chronological age)\n"
+            "## Volumetric Findings\n(key regional observations)\n"
+            "## Abnormal Regions\n(detail each significant deviation)\n"
+            "## Clinical Significance\n(what these findings mean)\n"
+            "## Recommendations\n(next steps, follow-up)\n"
+            "Be thorough but clinical."
+            + fmt_instruction
         ),
         "progress": (
-            base_data + "\nGenerate a clinical progress report with these sections:\n"
-            "1. **Current Status Summary** (brief overview of current brain health)\n"
-            "2. **Key Metrics** (brain age gap, most significant regional findings)\n"
-            "3. **Changes Since Baseline** (note this is the baseline scan if first visit)\n"
-            "4. **Areas of Concern** (any regions requiring monitoring)\n"
-            "5. **Positive Indicators** (regions within normal limits)\n"
-            "6. **Recommendations for Next Visit** (timeline, focus areas)\n"
-            "Use clear section headers. Be concise and actionable."
+            base_data +
+            "\nGenerate a clinical progress report with these sections:\n"
+            "## Current Status Summary\n(brief overview of current brain health)\n"
+            "## Key Metrics\n(brain age gap, most significant regional findings)\n"
+            "## Changes Since Baseline\n(note this is the baseline scan if first visit)\n"
+            "## Areas of Concern\n(any regions requiring monitoring)\n"
+            "## Positive Indicators\n(regions within normal limits)\n"
+            "## Recommendations for Next Visit\n(timeline, focus areas)\n"
+            "Be concise and actionable."
+            + fmt_instruction
         ),
         "care_plan": (
-            base_data + "\nGenerate a personalized brain health care plan with these sections:\n"
-            "1. **Patient Profile Summary** (brief clinical overview)\n"
-            "2. **Brain Health Assessment** (current status based on findings)\n"
-            "3. **Lifestyle Recommendations** (evidence-based interventions):\n"
-            "   - Cognitive training exercises\n"
-            "   - Physical activity plan\n"
-            "   - Nutrition recommendations\n"
-            "   - Sleep hygiene\n"
-            "   - Stress management\n"
-            "4. **Monitoring Plan** (what to track, when to re-scan)\n"
-            "5. **Risk Mitigation** (specific to any abnormal regions)\n"
-            "6. **Goals & Timeline** (3-month, 6-month, 12-month targets)\n"
+            base_data +
+            "\nGenerate a personalized brain health care plan with these sections:\n"
+            "## Patient Profile Summary\n(brief clinical overview)\n"
+            "## Brain Health Assessment\n(current status based on findings)\n"
+            "## Lifestyle Recommendations\n"
+            "### Cognitive Training Exercises\n"
+            "### Physical Activity Plan\n"
+            "### Nutrition Recommendations\n"
+            "### Sleep Hygiene\n"
+            "### Stress Management\n"
+            "## Monitoring Plan\n(what to track, when to re-scan)\n"
+            "## Risk Mitigation\n(specific to any abnormal regions)\n"
+            "## Goals & Timeline\n(3-month, 6-month, 12-month targets)\n"
             "Be evidence-based, specific, and actionable."
+            + fmt_instruction
         ),
         "executive": (
-            base_data + "\nGenerate a concise 1-page executive summary:\n"
-            "1. **Key Finding** (one sentence headline)\n"
-            "2. **Brain Age Result** (2 sentences)\n"
-            "3. **Notable Regions** (bullet list, max 5)\n"
-            "4. **Risk Assessment** (low/moderate/high with brief justification)\n"
-            "5. **Recommended Action** (2-3 actionable items)\n"
+            base_data +
+            "\nGenerate a concise 1-page executive summary:\n"
+            "## Key Finding\n(one sentence headline)\n"
+            "## Brain Age Result\n(2 sentences)\n"
+            "## Notable Regions\n(bullet list, max 5)\n"
+            "## Risk Assessment\n(low/moderate/high with brief justification)\n"
+            "## Recommended Action\n(2-3 actionable items)\n"
             "Keep everything extremely concise. This is for a busy clinician."
+            + fmt_instruction
         ),
     }
     return prompts.get(report_type, prompts["comprehensive"])
@@ -514,7 +584,7 @@ def generate_report_pdf(db: Session, scan_id: int,
         except Exception as e:
             narrative = f"Report generation error: {e}"
 
-    narrative_html = narrative.replace("**", "").replace("\n", "<br>")
+    narrative_html = _md_to_html(narrative)
 
     html = f"""<!DOCTYPE html>
 <html><head><meta charset="utf-8">
@@ -553,8 +623,16 @@ def generate_conversation_pdf(db: Session, scan_id: int,
     chat_html = ""
     for m in msgs:
         cls = "chat-user" if m.role == "user" else "chat-bot"
-        content = (m.content or "").replace("<", "&lt;").replace(">", "&gt;").replace("\n", "<br>")
-        chat_html += f'<div class="chat-msg {cls}">{content}</div>\n'
+        label_cls = "chat-user-label" if m.role == "user" else "chat-bot-label"
+        label_txt = "You" if m.role == "user" else "AI Assistant"
+        content_md = (m.content or "").replace("[REPORT_READY]", "")
+        content_html = _md_to_html(content_md)
+        chat_html += (
+            f'<div class="chat-msg {cls}">'
+            f'<span class="{label_cls}">{label_txt}</span>'
+            f'{content_html}'
+            f'</div>\n'
+        )
 
     if not chat_html:
         chat_html = '<div class="info-box">No messages in this conversation.</div>'

requirements.txt

@@ -16,3 +16,4 @@ nilearn>=0.10
 huggingface_hub>=0.23
 weasyprint==60.2
 pydyf==0.9.0
+markdown>=3.5