perfectionist

app/main.py

@@ -9,6 +9,7 @@ import os
 import shutil
 import tempfile
 import uuid
+from datetime import datetime
 from pathlib import Path
 
 from fastapi import FastAPI, File, Form, HTTPException, Request, UploadFile
@@ -109,7 +110,6 @@ async def upload_files(
     gender: str = Form(...),
     fat_percentage: float = Form(...),
     focus: str = Form(default="Endurance"),
-    session_id: str = Form(default="default"),
     next_testing_date: str = Form(...),
     report_type: str = Form(default="full"),
     spirometry_pdf: UploadFile = File(...),
@@ -179,6 +179,10 @@ async def upload_files(
         # Prepare patient information
         patient_name = f"{first_name} {last_name}"
         print(f"DEBUG: Received next_testing_date: '{next_testing_date}'")
+        
+        # Generate session_id internally using timestamp for unique identification
+        session_id = datetime.now().strftime("%Y%m%d_%H%M%S")
+        
         patient_info = {
             "patient_name": patient_name,
             "first_name": first_name,
@@ -290,8 +294,18 @@ async def upload_files(
 @app.get("/preview", response_class=HTMLResponse)
 async def preview(request: Request):
     """Preview generated report"""
+    # Check for required session data
     if not request.session.get("report_path"):
         return RedirectResponse(url="/", status_code=303)
+
+    # Ensure metrics exist in session, initialize if missing
+    if "metrics" not in request.session:
+        request.session["metrics"] = {"pnoe": {}, "spirometry": {}}
+
+    # Ensure patient_info exists
+    if "patient_info" not in request.session:
+        request.session["patient_info"] = {}
+
     return render_template(
         "preview.html", {"request": request, "session": request.session}
     )
@@ -309,8 +323,16 @@ async def serve_graph(filename: str):
 @app.get("/edit", response_class=HTMLResponse)
 async def edit_form(request: Request):
     """Display edit metrics form"""
-    if not request.session.get("metrics"):
+    # Check for required session data
+    if not request.session.get("report_path") or not request.session.get(
+        "patient_info"
+    ):
         return RedirectResponse(url="/", status_code=303)
+
+    # Ensure metrics exist in session, initialize if missing
+    if "metrics" not in request.session:
+        request.session["metrics"] = {"pnoe": {}, "spirometry": {}}
+
     return render_template(
         "edit.html", {"request": request, "session": request.session}
     )
@@ -325,69 +347,117 @@ async def edit_metrics(request: Request):
     # Get form data
     form_data = await request.form()
 
+    # Helper function to safely convert form values to float
+    def safe_float(value):
+        """Convert form value to float, return None if empty or invalid"""
+        if not value or value.strip() == "":
+            return None
+        try:
+            return float(value)
+        except (ValueError, TypeError):
+            return None
+
     # Build metric overrides
     metric_overrides = {"pnoe": {}, "spirometry": {}}
 
-    # Pnoe overrides
-    if form_data.get("vo2_max"):
-        metric_overrides["pnoe"]["vo2_max"] = float(form_data["vo2_max"])
-    if form_data.get("vo2_max_per_kg"):
-        metric_overrides["pnoe"]["vo2_max_per_kg"] = float(form_data["vo2_max_per_kg"])
-    if form_data.get("peak_vt"):
-        metric_overrides["pnoe"]["peak_vt"] = float(form_data["peak_vt"])
-    if form_data.get("peak_vt_hr"):
-        metric_overrides["pnoe"]["peak_vt_hr"] = float(form_data["peak_vt_hr"])
-    if form_data.get("fat_max_value"):
-        metric_overrides["pnoe"]["fat_max_value"] = float(form_data["fat_max_value"])
-    if form_data.get("fat_max_hr"):
-        metric_overrides["pnoe"]["fat_max_hr"] = float(form_data["fat_max_hr"])
+    # Pnoe overrides - only add if value is provided and valid
+    vo2_max_val = safe_float(form_data.get("vo2_max"))
+    if vo2_max_val is not None:
+        metric_overrides["pnoe"]["vo2_max"] = vo2_max_val
 
-    # VT1 and VT2 overrides
-    if (
-        form_data.get("vt1_hr")
-        or form_data.get("vt1_speed")
-        or form_data.get("vt1_time")
-    ):
-        metric_overrides["pnoe"]["vt1"] = {
-            "HeartRate": float(form_data.get("vt1_hr", 0)),
-            "Speed": float(form_data.get("vt1_speed", 0)),
-            "Time": float(form_data.get("vt1_time", 0)),
+    vo2_max_per_kg_val = safe_float(form_data.get("vo2_max_per_kg"))
+    if vo2_max_per_kg_val is not None:
+        metric_overrides["pnoe"]["vo2_max_per_kg"] = vo2_max_per_kg_val
+
+    peak_vt_val = safe_float(form_data.get("peak_vt"))
+    if peak_vt_val is not None:
+        metric_overrides["pnoe"]["peak_vt"] = peak_vt_val
+
+    peak_vt_hr_val = safe_float(form_data.get("peak_vt_hr"))
+    if peak_vt_hr_val is not None:
+        metric_overrides["pnoe"]["peak_vt_hr"] = peak_vt_hr_val
+
+    fat_max_value_val = safe_float(form_data.get("fat_max_value"))
+    if fat_max_value_val is not None:
+        metric_overrides["pnoe"]["fat_max_value"] = fat_max_value_val
+
+    fat_max_hr_val = safe_float(form_data.get("fat_max_hr"))
+    if fat_max_hr_val is not None:
+        metric_overrides["pnoe"]["fat_max_hr"] = fat_max_hr_val
+
+    # VT1 and VT2 overrides - use existing values if not provided
+    existing_metrics = request.session.get("metrics", {})
+    existing_pnoe = existing_metrics.get("pnoe", {})
+    existing_vt1 = existing_pnoe.get("vt1", {})
+    existing_vt2 = existing_pnoe.get("vt2", {})
+
+    vt1_hr_val = safe_float(form_data.get("vt1_hr"))
+    vt1_speed_val = safe_float(form_data.get("vt1_speed"))
+    vt1_time_val = safe_float(form_data.get("vt1_time"))
+
+    if vt1_hr_val is not None or vt1_speed_val is not None or vt1_time_val is not None:
+        vt1_dict = {
+            "HeartRate": vt1_hr_val
+            if vt1_hr_val is not None
+            else existing_vt1.get("HeartRate", 0),
+            "Speed": vt1_speed_val
+            if vt1_speed_val is not None
+            else existing_vt1.get("Speed", 0),
+            "Time": vt1_time_val
+            if vt1_time_val is not None
+            else existing_vt1.get("Time", 0),
         }
+        metric_overrides["pnoe"]["vt1"] = vt1_dict
 
-    if (
-        form_data.get("vt2_hr")
-        or form_data.get("vt2_speed")
-        or form_data.get("vt2_time")
-    ):
-        metric_overrides["pnoe"]["vt2"] = {
-            "HeartRate": float(form_data.get("vt2_hr", 0)),
-            "Speed": float(form_data.get("vt2_speed", 0)),
-            "Time": float(form_data.get("vt2_time", 0)),
+    vt2_hr_val = safe_float(form_data.get("vt2_hr"))
+    vt2_speed_val = safe_float(form_data.get("vt2_speed"))
+    vt2_time_val = safe_float(form_data.get("vt2_time"))
+
+    if vt2_hr_val is not None or vt2_speed_val is not None or vt2_time_val is not None:
+        vt2_dict = {
+            "HeartRate": vt2_hr_val
+            if vt2_hr_val is not None
+            else existing_vt2.get("HeartRate", 0),
+            "Speed": vt2_speed_val
+            if vt2_speed_val is not None
+            else existing_vt2.get("Speed", 0),
+            "Time": vt2_time_val
+            if vt2_time_val is not None
+            else existing_vt2.get("Time", 0),
         }
+        metric_overrides["pnoe"]["vt2"] = vt2_dict
 
-    # Heart rate zones
+    # Heart rate zones - only add if value is provided
     for i in range(1, 6):
         zone_key = f"zone{i}_bpm"
-        if form_data.get(zone_key):
-            metric_overrides["pnoe"][zone_key] = form_data[zone_key]
+        zone_val = form_data.get(zone_key)
+        if zone_val and zone_val.strip():
+            metric_overrides["pnoe"][zone_key] = zone_val.strip()
 
-    # Spirometry overrides
-    if form_data.get("fvc_best"):
-        metric_overrides["spirometry"]["fvc_best"] = float(form_data["fvc_best"])
-    if form_data.get("fvc_pred"):
-        metric_overrides["spirometry"]["fvc_pred"] = float(form_data["fvc_pred"])
-    if form_data.get("fev1_best"):
-        metric_overrides["spirometry"]["fev1_best"] = float(form_data["fev1_best"])
-    if form_data.get("fev1_pred"):
-        metric_overrides["spirometry"]["fev1_pred"] = float(form_data["fev1_pred"])
-    if form_data.get("fev1_fvc_pct_best"):
-        metric_overrides["spirometry"]["fev1_fvc_pct_best"] = float(
-            form_data["fev1_fvc_pct_best"]
-        )
-    if form_data.get("fev1_fvc_pct_pred"):
-        metric_overrides["spirometry"]["fev1_fvc_pct_pred"] = float(
-            form_data["fev1_fvc_pct_pred"]
-        )
+    # Spirometry overrides - only add if value is provided and valid
+    fvc_best_val = safe_float(form_data.get("fvc_best"))
+    if fvc_best_val is not None:
+        metric_overrides["spirometry"]["fvc_best"] = fvc_best_val
+
+    fvc_pred_val = safe_float(form_data.get("fvc_pred"))
+    if fvc_pred_val is not None:
+        metric_overrides["spirometry"]["fvc_pred"] = fvc_pred_val
+
+    fev1_best_val = safe_float(form_data.get("fev1_best"))
+    if fev1_best_val is not None:
+        metric_overrides["spirometry"]["fev1_best"] = fev1_best_val
+
+    fev1_pred_val = safe_float(form_data.get("fev1_pred"))
+    if fev1_pred_val is not None:
+        metric_overrides["spirometry"]["fev1_pred"] = fev1_pred_val
+
+    fev1_fvc_pct_best_val = safe_float(form_data.get("fev1_fvc_pct_best"))
+    if fev1_fvc_pct_best_val is not None:
+        metric_overrides["spirometry"]["fev1_fvc_pct_best"] = fev1_fvc_pct_best_val
+
+    fev1_fvc_pct_pred_val = safe_float(form_data.get("fev1_fvc_pct_pred"))
+    if fev1_fvc_pct_pred_val is not None:
+        metric_overrides["spirometry"]["fev1_fvc_pct_pred"] = fev1_fvc_pct_pred_val
 
     try:
         # Get file paths from session
@@ -468,6 +538,7 @@ async def edit_metrics(request: Request):
             "fat_percentage": patient_info.get("fat_percentage", 0),
             "gender": patient_info.get("gender", "female"),
         }
+        # Calculate fat_mass and lean_mass (extract_patient_info does this when no SECA file)
         context_gen.extract_patient_info(patient_info.get("last_name", ""))
 
         spirometry_overrides = metric_overrides.get("spirometry", {})
@@ -514,7 +585,6 @@ async def generate_report(
     height: str = Form(..., description="Patient height (e.g., 5'4\")"),
     weight: str = Form(..., description="Patient weight (e.g., 123lbs)"),
     focus: str = Form(default="Endurance", description="Training focus"),
-    session_id: str = Form(default="default", description="Session ID"),
     spirometry_pdf: UploadFile = File(..., description="Spirometry PDF file"),
     pnoe_csv: UploadFile = File(..., description="Pnoe CSV file"),
     seca_excel: UploadFile = File(..., description="SECA Excel file"),
@@ -534,7 +604,6 @@ async def generate_report(
         height: Patient height
         weight: Patient weight
         focus: Training focus (default: Endurance)
-        session_id: Session identifier (default: default)
 
     Returns:
         ReportResponse with report path, graphs generated, and analysis data
@@ -571,6 +640,9 @@ async def generate_report(
             with open(seca_path, "wb") as f:
                 shutil.copyfileobj(seca_excel.file, f)
 
+            # Generate session_id internally using timestamp for unique identification
+            session_id = datetime.now().strftime("%Y%m%d_%H%M%S")
+            
             # Prepare patient information
             patient_info = {
                 "patient_name": patient_name,

app/report_gen/page_19_20_minimal.html

@@ -471,3 +471,4 @@
 
 
 
+

app/report_gen/page_2_minimal.html

@@ -86,3 +86,4 @@
 
 
 
+

app/report_gen/page_6.html

@@ -34,7 +34,7 @@
                     <!-- Macro Body (fills to the bottom, cyan or white) -->
                     <div class="flex flex-col items-center py-1 px-2">
                         <div class="font-bold text-sm text-black mb-1">
-                            {{ deficit_calories | default('1725KCals') }}
+                            {{ deficit_calories | default('1725KCals') }} KCals
                         </div>
                         <div class="text-xs text-black leading-tight text-left">
                             <div>{{ deficit_protein | default('120g Protein') }}</div>

app/templates/preview.html

@@ -1,24 +1,32 @@
-{% extends "base.html" %}
-
-{% block title %}Report Preview - Report Generator{% endblock %}
-
-{% block content %}
+{% extends "base.html" %} {% block title %}Report Preview - Report Generator{%
+endblock %} {% block content %}
 <div class="px-4 py-6 sm:px-0">
     {% if not session.get('report_path') %}
     <div class="bg-yellow-50 border border-yellow-200 rounded-lg p-4 mb-6">
-        <p class="text-yellow-800">No report found. Please <a href="/" class="underline">upload files</a> first.</p>
+        <p class="text-yellow-800">
+            No report found. Please
+            <a href="/" class="underline">upload files</a> first.
+        </p>
     </div>
     {% else %}
 
     <div class="bg-white shadow rounded-lg mb-6">
         <div class="px-4 py-5 sm:p-6">
             <div class="flex justify-between items-center mb-6">
-                <h2 class="text-2xl font-bold text-gray-900">Generated Report Preview</h2>
+                <h2 class="text-2xl font-bold text-gray-900">
+                    Generated Report Preview
+                </h2>
                 <div class="flex space-x-3">
-                    <a href="/edit" class="inline-flex items-center px-4 py-2 border border-gray-300 shadow-sm text-sm font-medium rounded-md text-gray-700 bg-white hover:bg-gray-50">
+                    <a
+                        href="/edit"
+                        class="inline-flex items-center px-4 py-2 border border-gray-300 shadow-sm text-sm font-medium rounded-md text-gray-700 bg-white hover:bg-gray-50"
+                    >
                         Edit Metrics
                     </a>
-                    <a href="/download-report/{{ session.report_path.split('/')[-1] }}" class="inline-flex items-center px-4 py-2 border border-transparent shadow-sm text-sm font-medium rounded-md text-white bg-indigo-600 hover:bg-indigo-700">
+                    <a
+                        href="/download-report/{{ session.report_path.split('/')[-1] }}"
+                        class="inline-flex items-center px-4 py-2 border border-transparent shadow-sm text-sm font-medium rounded-md text-white bg-indigo-600 hover:bg-indigo-700"
+                    >
                         Download PDF
                     </a>
                 </div>
@@ -26,23 +34,33 @@
 
             <!-- Patient Information -->
             <div class="border-b border-gray-200 pb-6 mb-6">
-                <h3 class="text-lg font-medium text-gray-900 mb-4">Patient Information</h3>
+                <h3 class="text-lg font-medium text-gray-900 mb-4">
+                    Patient Information
+                </h3>
                 <div class="grid grid-cols-2 gap-4 sm:grid-cols-4">
                     <div>
                         <p class="text-sm text-gray-500">Name</p>
-                        <p class="text-base font-medium text-gray-900">{{ session.patient_info['patient_name'] }}</p>
+                        <p class="text-base font-medium text-gray-900">
+                            {{ session.patient_info['patient_name'] }}
+                        </p>
                     </div>
                     <div>
                         <p class="text-sm text-gray-500">Age</p>
-                        <p class="text-base font-medium text-gray-900">{{ session.patient_info['age'] }}</p>
+                        <p class="text-base font-medium text-gray-900">
+                            {{ session.patient_info['age'] }}
+                        </p>
                     </div>
                     <div>
                         <p class="text-sm text-gray-500">Height</p>
-                        <p class="text-base font-medium text-gray-900">{{ session.patient_info['height'] }}</p>
+                        <p class="text-base font-medium text-gray-900">
+                            {{ session.patient_info['height'] }}
+                        </p>
                     </div>
                     <div>
                         <p class="text-sm text-gray-500">Weight</p>
-                        <p class="text-base font-medium text-gray-900">{{ session.patient_info['weight'] }}</p>
+                        <p class="text-base font-medium text-gray-900">
+                            {{ session.patient_info['weight'] }}
+                        </p>
                     </div>
                 </div>
             </div>
@@ -52,56 +70,113 @@
             <div class="space-y-6">
                 <!-- Pnoe Metrics -->
                 <div>
-                    <h3 class="text-lg font-medium text-gray-900 mb-4">Pnoe Metrics</h3>
-                    <div class="grid grid-cols-1 gap-4 sm:grid-cols-2 lg:grid-cols-3">
+                    <h3 class="text-lg font-medium text-gray-900 mb-4">
+                        Pnoe Metrics
+                    </h3>
+                    <div
+                        class="grid grid-cols-1 gap-4 sm:grid-cols-2 lg:grid-cols-3"
+                    >
                         {% if session.metrics.pnoe.get('vo2_max') %}
                         <div class="bg-gray-50 p-4 rounded-lg">
                             <p class="text-sm text-gray-500">VO2 Max</p>
-                            <p class="text-2xl font-bold text-gray-900">{{ "%.2f"|format(session.metrics.pnoe['vo2_max']) }} ml/min</p>
+                            <p class="text-2xl font-bold text-gray-900">
+                                {{
+                                "%.2f"|format(session.metrics.pnoe['vo2_max'])
+                                }} ml/min
+                            </p>
                         </div>
-                        {% endif %}
-                        {% if session.metrics.pnoe.get('vo2_max_per_kg') %}
+                        {% endif %} {% if
+                        session.metrics.pnoe.get('vo2_max_per_kg') %}
                         <div class="bg-gray-50 p-4 rounded-lg">
                             <p class="text-sm text-gray-500">VO2 Max per kg</p>
-                            <p class="text-2xl font-bold text-gray-900">{{ "%.2f"|format(session.metrics.pnoe['vo2_max_per_kg']) }} ml/min/kg</p>
+                            <p class="text-2xl font-bold text-gray-900">
+                                {{
+                                "%.2f"|format(session.metrics.pnoe['vo2_max_per_kg'])
+                                }} ml/min/kg
+                            </p>
                         </div>
-                        {% endif %}
-                        {% if session.metrics.pnoe.get('peak_vt') %}
+                        {% endif %} {% if session.metrics.pnoe.get('peak_vt') %}
                         <div class="bg-gray-50 p-4 rounded-lg">
                             <p class="text-sm text-gray-500">Peak VT</p>
-                            <p class="text-2xl font-bold text-gray-900">{{ "%.2f"|format(session.metrics.pnoe['peak_vt']) }} L</p>
-                            <p class="text-sm text-gray-500 mt-1">HR: {{ "%.0f"|format(session.metrics.pnoe['peak_vt_hr']) }} bpm</p>
+                            <p class="text-2xl font-bold text-gray-900">
+                                {{
+                                "%.2f"|format(session.metrics.pnoe['peak_vt'])
+                                }} L
+                            </p>
+                            <p class="text-sm text-gray-500 mt-1">
+                                HR: {{
+                                "%.0f"|format(session.metrics.pnoe['peak_vt_hr'])
+                                }} bpm
+                            </p>
                         </div>
-                        {% endif %}
-                        {% if session.metrics.pnoe.get('fat_max_value') %}
+                        {% endif %} {% if
+                        session.metrics.pnoe.get('fat_max_value') %}
                         <div class="bg-gray-50 p-4 rounded-lg">
                             <p class="text-sm text-gray-500">Fat Max Value</p>
-                            <p class="text-2xl font-bold text-gray-900">{{ "%.2f"|format(session.metrics.pnoe['fat_max_value']) }} kcal/min</p>
-                            <p class="text-sm text-gray-500 mt-1">HR: {{ "%.0f"|format(session.metrics.pnoe['fat_max_hr']) }} bpm</p>
+                            <p class="text-2xl font-bold text-gray-900">
+                                {{
+                                "%.2f"|format(session.metrics.pnoe['fat_max_value'])
+                                }} kcal/min
+                            </p>
+                            <p class="text-sm text-gray-500 mt-1">
+                                HR: {{
+                                "%.0f"|format(session.metrics.pnoe['fat_max_hr'])
+                                }} bpm
+                            </p>
                         </div>
                         {% endif %}
                     </div>
                 </div>
 
                 <!-- VT1 and VT2 -->
-                {% if session.metrics.pnoe.get('vt1') or session.metrics.pnoe.get('vt2') %}
+                {% if session.metrics.pnoe.get('vt1') or
+                session.metrics.pnoe.get('vt2') %}
                 <div>
-                    <h3 class="text-lg font-medium text-gray-900 mb-4">Ventilatory Thresholds</h3>
+                    <h3 class="text-lg font-medium text-gray-900 mb-4">
+                        Ventilatory Thresholds
+                    </h3>
                     <div class="grid grid-cols-1 gap-4 sm:grid-cols-2">
                         {% if session.metrics.pnoe.get('vt1') %}
                         <div class="bg-blue-50 p-4 rounded-lg">
-                            <p class="text-sm font-medium text-blue-900 mb-2">VT1</p>
-                            <p class="text-sm text-blue-700">Heart Rate: {{ "%.0f"|format(session.metrics.pnoe['vt1']['HeartRate']) }} bpm</p>
-                            <p class="text-sm text-blue-700">Speed: {{ "%.2f"|format(session.metrics.pnoe['vt1']['Speed']) }} mph</p>
-                            <p class="text-sm text-blue-700">Time: {{ "%.0f"|format(session.metrics.pnoe['vt1']['Time']) }} sec</p>
+                            <p class="text-sm font-medium text-blue-900 mb-2">
+                                VT1
+                            </p>
+                            <p class="text-sm text-blue-700">
+                                Heart Rate: {{
+                                "%.0f"|format(session.metrics.pnoe['vt1']['HeartRate'])
+                                }} bpm
+                            </p>
+                            <p class="text-sm text-blue-700">
+                                Speed: {{
+                                "%.2f"|format(session.metrics.pnoe['vt1']['Speed'])
+                                }} mph
+                            </p>
+                            <p class="text-sm text-blue-700">
+                                Time: {{
+                                "%.0f"|format(session.metrics.pnoe['vt1']['Time'])
+                                }} sec
+                            </p>
                         </div>
-                        {% endif %}
-                        {% if session.metrics.pnoe.get('vt2') %}
+                        {% endif %} {% if session.metrics.pnoe.get('vt2') %}
                         <div class="bg-green-50 p-4 rounded-lg">
-                            <p class="text-sm font-medium text-green-900 mb-2">VT2</p>
-                            <p class="text-sm text-green-700">Heart Rate: {{ "%.0f"|format(session.metrics.pnoe['vt2']['HeartRate']) }} bpm</p>
-                            <p class="text-sm text-green-700">Speed: {{ "%.2f"|format(session.metrics.pnoe['vt2']['Speed']) }} mph</p>
-                            <p class="text-sm text-green-700">Time: {{ "%.0f"|format(session.metrics.pnoe['vt2']['Time']) }} sec</p>
+                            <p class="text-sm font-medium text-green-900 mb-2">
+                                VT2
+                            </p>
+                            <p class="text-sm text-green-700">
+                                Heart Rate: {{
+                                "%.0f"|format(session.metrics.pnoe['vt2']['HeartRate'])
+                                }} bpm
+                            </p>
+                            <p class="text-sm text-green-700">
+                                Speed: {{
+                                "%.2f"|format(session.metrics.pnoe['vt2']['Speed'])
+                                }} mph
+                            </p>
+                            <p class="text-sm text-green-700">
+                                Time: {{
+                                "%.0f"|format(session.metrics.pnoe['vt2']['Time'])
+                                }} sec
+                            </p>
                         </div>
                         {% endif %}
                     </div>
@@ -111,17 +186,20 @@
                 <!-- Heart Rate Zones -->
                 {% if session.metrics.pnoe.get('zone1_bpm') %}
                 <div>
-                    <h3 class="text-lg font-medium text-gray-900 mb-4">Heart Rate Zones</h3>
+                    <h3 class="text-lg font-medium text-gray-900 mb-4">
+                        Heart Rate Zones
+                    </h3>
                     <div class="grid grid-cols-1 gap-2 sm:grid-cols-5">
-                        {% for i in range(1, 6) %}
-                        {% set zone_key = "zone" + i|string + "_bpm" %}
-                        {% if session.metrics.pnoe.get(zone_key) %}
+                        {% for i in range(1, 6) %} {% set zone_key = "zone" +
+                        i|string + "_bpm" %} {% if
+                        session.metrics.pnoe.get(zone_key) %}
                         <div class="bg-gray-50 p-3 rounded-lg text-center">
                             <p class="text-xs text-gray-500">Zone {{ i }}</p>
-                            <p class="text-sm font-medium text-gray-900">{{ session.metrics.pnoe[zone_key] }}</p>
+                            <p class="text-sm font-medium text-gray-900">
+                                {{ session.metrics.pnoe[zone_key] }}
+                            </p>
                         </div>
-                        {% endif %}
-                        {% endfor %}
+                        {% endif %} {% endfor %}
                     </div>
                 </div>
                 {% endif %}
@@ -129,27 +207,53 @@
                 <!-- Spirometry Metrics -->
                 {% if session.metrics.spirometry %}
                 <div>
-                    <h3 class="text-lg font-medium text-gray-900 mb-4">Spirometry Metrics</h3>
+                    <h3 class="text-lg font-medium text-gray-900 mb-4">
+                        Spirometry Metrics
+                    </h3>
                     <div class="grid grid-cols-1 gap-4 sm:grid-cols-3">
                         {% if session.metrics.spirometry.get('fvc_best') %}
                         <div class="bg-gray-50 p-4 rounded-lg">
                             <p class="text-sm text-gray-500">FVC Best</p>
-                            <p class="text-2xl font-bold text-gray-900">{{ "%.2f"|format(session.metrics.spirometry['fvc_best']) }} L</p>
-                            <p class="text-sm text-gray-500 mt-1">{{ "%.1f"|format(session.metrics.spirometry['fvc_pred']) }}% predicted</p>
+                            <p class="text-2xl font-bold text-gray-900">
+                                {{
+                                "%.2f"|format(session.metrics.spirometry['fvc_best'])
+                                }} L
+                            </p>
+                            <p class="text-sm text-gray-500 mt-1">
+                                {{
+                                "%.1f"|format(session.metrics.spirometry['fvc_pred'])
+                                }}% predicted
+                            </p>
                         </div>
-                        {% endif %}
-                        {% if session.metrics.spirometry.get('fev1_best') %}
+                        {% endif %} {% if
+                        session.metrics.spirometry.get('fev1_best') %}
                         <div class="bg-gray-50 p-4 rounded-lg">
                             <p class="text-sm text-gray-500">FEV1 Best</p>
-                            <p class="text-2xl font-bold text-gray-900">{{ "%.2f"|format(session.metrics.spirometry['fev1_best']) }} L</p>
-                            <p class="text-sm text-gray-500 mt-1">{{ "%.1f"|format(session.metrics.spirometry['fev1_pred']) }}% predicted</p>
+                            <p class="text-2xl font-bold text-gray-900">
+                                {{
+                                "%.2f"|format(session.metrics.spirometry['fev1_best'])
+                                }} L
+                            </p>
+                            <p class="text-sm text-gray-500 mt-1">
+                                {{
+                                "%.1f"|format(session.metrics.spirometry['fev1_pred'])
+                                }}% predicted
+                            </p>
                         </div>
-                        {% endif %}
-                        {% if session.metrics.spirometry.get('fev1_fvc_pct_best') %}
+                        {% endif %} {% if
+                        session.metrics.spirometry.get('fev1_fvc_pct_best') %}
                         <div class="bg-gray-50 p-4 rounded-lg">
                             <p class="text-sm text-gray-500">FEV1/FVC%</p>
-                            <p class="text-2xl font-bold text-gray-900">{{ "%.2f"|format(session.metrics.spirometry['fev1_fvc_pct_best']) }}%</p>
-                            <p class="text-sm text-gray-500 mt-1">{{ "%.1f"|format(session.metrics.spirometry['fev1_fvc_pct_pred']) }}% predicted</p>
+                            <p class="text-2xl font-bold text-gray-900">
+                                {{
+                                "%.2f"|format(session.metrics.spirometry['fev1_fvc_pct_best'])
+                                }}%
+                            </p>
+                            <p class="text-sm text-gray-500 mt-1">
+                                {{
+                                "%.1f"|format(session.metrics.spirometry['fev1_fvc_pct_pred'])
+                                }}% predicted
+                            </p>
                         </div>
                         {% endif %}
                     </div>
@@ -157,24 +261,8 @@
                 {% endif %}
             </div>
             {% endif %}
-
-            <!-- Graphs Section -->
-            {% if session.graphs_generated %}
-            <div class="mt-8">
-                <h3 class="text-lg font-medium text-gray-900 mb-4">Generated Graphs</h3>
-                <div class="grid grid-cols-1 gap-4 sm:grid-cols-2">
-                    {% for graph in session.graphs_generated %}
-                    <div class="bg-gray-50 p-4 rounded-lg">
-                        <p class="text-sm font-medium text-gray-700 mb-2">{{ graph.name|replace('_', ' ')|title }}</p>
-                        <img src="/graphs/{{ graph.path.split('/')[-1] }}" alt="{{ graph.name }}" class="w-full h-auto rounded">
-                    </div>
-                    {% endfor %}
-                </div>
-            </div>
-            {% endif %}
         </div>
     </div>
     {% endif %}
 </div>
 {% endblock %}
-

app/templates/upload.html

@@ -132,20 +132,6 @@ Generator{% endblock %} {% block content %}
                                 class="mt-1 block w-full rounded-md border-gray-300 shadow-sm focus:border-indigo-500 focus:ring-indigo-500 sm:text-sm px-3 py-2 border"
                             />
                         </div>
-                        <div>
-                            <label
-                                for="session_id"
-                                class="block text-sm font-medium text-gray-700"
-                                >Session ID</label
-                            >
-                            <input
-                                type="text"
-                                name="session_id"
-                                id="session_id"
-                                value="default"
-                                class="mt-1 block w-full rounded-md border-gray-300 shadow-sm focus:border-indigo-500 focus:ring-indigo-500 sm:text-sm px-3 py-2 border"
-                            />
-                        </div>
                         <div>
                             <label
                                 class="block text-sm font-medium text-gray-700 mb-2"

notebooks/gemini_rer.py

@@ -0,0 +1,249 @@
+import pandas as pd
+
+
+def mifflin_st_jeor(weight_kg, height_cm, age_years, sex):
+    """
+    Compute predicted RMR with Mifflin St Jeor.
+    sex: 'male' or 'female'
+    """
+    base = 10.0 * weight_kg + 6.25 * height_cm - 5.0 * age_years
+    if sex.lower().startswith("m"):
+        return base + 5.0
+    else:
+        return base - 161.0
+
+
+def classify_metabolism(measured_kcal_day, predicted_kcal_day):
+    """
+    Classify metabolic rate relative to prediction.
+    Returns (label, ratio).
+    """
+    ratio = measured_kcal_day / predicted_kcal_day
+
+    if ratio < 0.70:
+        label = "very slow"
+    elif ratio < 0.90:
+        label = "slow"
+    elif ratio <= 1.10:
+        label = "average"
+    elif ratio <= 1.30:
+        label = "fast"
+    else:
+        label = "very fast"
+
+    return label, ratio
+
+
+def find_sampling_window(df):
+    """
+    Derive number of samples that represent about 2 minutes.
+    """
+    dt = df["T(sec)"].diff().median()
+    if dt is None or dt <= 0:
+        raise ValueError("Invalid time step in T(sec)")
+
+    samples = int(round(120.0 / dt))
+    if samples < 1:
+        samples = 1
+    return samples
+
+
+def rolling_stable_window(df, window_samples):
+    """
+    Find the most stable 2-minute window using rolling standard deviation.
+    Returns:
+        means_series, t_start, t_end
+    """
+    cols_mean = [
+        "VO2(ml/min)",
+        "VCO2(ml/min)",
+        "VE(l/min)",
+        "VT(l)",
+        "BF(bpm)",
+        "EE(kcal/min)",
+        "RER",
+        "CARBS(%)",
+        "FAT(%)",
+    ]
+
+    cols_std = [
+        "VO2(ml/min)",
+        "VCO2(ml/min)",
+        "VE(l/min)",
+        "VT(l)",
+        "BF(bpm)",
+    ]
+
+    roll_mean = df[cols_mean].rolling(window_samples, min_periods=window_samples).mean()
+    roll_std = df[cols_std].rolling(window_samples, min_periods=window_samples).std()
+
+    # Sum std devs to get stability score; use skipna=False to preserve NaN for incomplete windows
+    stability_score = roll_std.sum(axis=1, skipna=False)
+
+    # Find index with lowest stability score (dropna to ignore incomplete windows)
+    best_idx = stability_score.dropna().idxmin()
+
+    means_series = roll_mean.loc[best_idx].copy()
+
+    start_idx = max(best_idx - window_samples + 1, 0)
+    end_idx = best_idx
+
+    t_start = float(df["T(sec)"].iloc[start_idx])
+    t_end = float(df["T(sec)"].iloc[end_idx])
+
+    return means_series, t_start, t_end
+
+
+def manual_window_means(df, t_start, t_end):
+    """
+    Compute mean values inside a user-selected time window.
+    """
+    mask = (df["T(sec)"] >= t_start) & (df["T(sec)"] <= t_end)
+    slice_df = df.loc[mask].copy()
+
+    if slice_df.empty:
+        raise ValueError("Manual window has no rows inside T(sec) range")
+
+    cols = [
+        "VO2(ml/min)",
+        "VCO2(ml/min)",
+        "VE(l/min)",
+        "VT(l)",
+        "BF(bpm)",
+        "EE(kcal/min)",
+        "RER",
+        "CARBS(%)",
+        "FAT(%)",
+    ]
+
+    means = slice_df[cols].mean()
+    return means, float(t_start), float(t_end)
+
+
+def load_pnoe_csv(path):
+    """
+    Load and clean a PNOE CSV file.
+    """
+    df = pd.read_csv(path, sep=";")
+
+    numeric_cols = [
+        "T(sec)",
+        "VO2(ml/min)",
+        "VCO2(ml/min)",
+        "RER",
+        "VE(l/min)",
+        "VT(l)",
+        "BF(bpm)",
+        "EE(kcal/min)",
+        "CARBS(%)",
+        "FAT(%)",
+    ]
+
+    for col in numeric_cols:
+        df[col] = pd.to_numeric(df[col], errors="coerce")
+
+    df = df.dropna(subset=["VO2(ml/min)", "EE(kcal/min)"]).reset_index(drop=True)
+    return df
+
+
+def analyze_pnoe_rmr(
+    path,
+    weight_kg,
+    height_cm,
+    age_years,
+    sex,
+    subject_name=None,
+    test_date=None,
+    manual_window=None,
+):
+    """
+    Analyze resting RMR from a PNOE CSV file.
+
+    manual_window:
+        None for automatic stable window
+        or (t_start_sec, t_end_sec) for user-chosen window
+    """
+    df = load_pnoe_csv(path)
+    window_samples = find_sampling_window(df)
+
+    # Automatic stable window
+    auto_means, auto_t_start, auto_t_end = rolling_stable_window(df, window_samples)
+
+    # Manual override if provided
+    manual_means = None
+    manual_t_start = None
+    manual_t_end = None
+
+    if manual_window is not None:
+        t_start_manual, t_end_manual = manual_window
+        manual_means, manual_t_start, manual_t_end = manual_window_means(
+            df, t_start_manual, t_end_manual
+        )
+        chosen_source = "manual"
+        chosen_means = manual_means
+        chosen_t_start = manual_t_start
+        chosen_t_end = manual_t_end
+    else:
+        chosen_source = "auto"
+        chosen_means = auto_means
+        chosen_t_start = auto_t_start
+        chosen_t_end = auto_t_end
+
+    kcal_per_min = float(chosen_means["EE(kcal/min)"])
+    rmr_kcal_day = kcal_per_min * 1440.0
+
+    predicted_kcal_day = mifflin_st_jeor(weight_kg, height_cm, age_years, sex)
+    label, ratio = classify_metabolism(rmr_kcal_day, predicted_kcal_day)
+
+    def pack_metrics(prefix, means, t_start, t_end):
+        if means is None:
+            return {}
+        return {
+            f"{prefix}_window_start_sec": t_start,
+            f"{prefix}_window_end_sec": t_end,
+            f"{prefix}_VO2_L_min": float(means["VO2(ml/min)"]) / 1000.0,
+            f"{prefix}_VCO2_L_min": float(means["VCO2(ml/min)"]) / 1000.0,
+            f"{prefix}_VE_L_min": float(means["VE(l/min)"]),
+            f"{prefix}_VT_L": float(means["VT(l)"]),
+            f"{prefix}_BF_bpm": float(means["BF(bpm)"]),
+            f"{prefix}_RER": float(means["RER"]),
+            f"{prefix}_Fat_percent": float(means["FAT(%)"]),
+            f"{prefix}_Carb_percent": float(means["CARBS(%)"]),
+            f"{prefix}_kcal_per_min": float(means["EE(kcal/min)"]),
+        }
+
+    result = {
+        "subject_name": subject_name,
+        "test_date": test_date,
+        "sex": sex,
+        "weight_kg": weight_kg,
+        "height_cm": height_cm,
+        "age_years": age_years,
+        "chosen_window_source": chosen_source,
+        "chosen_window_start_sec": chosen_t_start,
+        "chosen_window_end_sec": chosen_t_end,
+        "RMR_kcal_day": rmr_kcal_day,
+        "Mifflin_kcal_day": predicted_kcal_day,
+        "Measured_to_Mifflin_ratio": ratio,
+        "Metabolic_classification": label,
+    }
+
+    result.update(pack_metrics("auto", auto_means, auto_t_start, auto_t_end))
+    result.update(pack_metrics("manual", manual_means, manual_t_start, manual_t_end))
+
+    return result
+
+
+result = analyze_pnoe_rmr(
+    path="/home/oluwasanmi/Documents/Work/MKD/report_generation/data/Pnoe_20250729_1550-Moran_Keirstyn.csv",
+    weight_kg=56,
+    height_cm=162,
+    age_years=34,
+    sex="female",
+    subject_name="Cullen Pacas",
+    test_date="2025-11-12",
+    manual_window=None,  # or (t_start_sec, t_end_sec)
+)
+
+for key, value in result.items():
+    print(f"{key}: {value}")