Checkpoint 3

app/main.py

@@ -179,10 +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,
@@ -642,7 +642,7 @@ async def generate_report(
 
             # 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_2.html

@@ -15,7 +15,8 @@
             <!-- Lung Analysis -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     3
                 </div>
@@ -35,7 +36,8 @@
             <!-- Cardio Metrics -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     4
                 </div>
@@ -52,7 +54,8 @@
             <!-- Fuel Utilization -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     5
                 </div>
@@ -66,7 +69,8 @@
             <!-- Local Muscle Activity -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     9
                 </div>
@@ -80,7 +84,8 @@
             <!-- Training Recommendations -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     10
                 </div>
@@ -94,7 +99,8 @@
             <!-- Next Steps -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     12
                 </div>
@@ -111,7 +117,8 @@
             <!-- Glossary -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     13
                 </div>

app/report_gen/page_2_minimal.html

@@ -15,7 +15,8 @@
             <!-- Nutrition Guidelines -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     3
                 </div>
@@ -35,7 +36,8 @@
             <!-- Nutrition Recommendations -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     4
                 </div>
@@ -49,7 +51,8 @@
             <!-- Next Steps -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     5
                 </div>
@@ -66,7 +69,8 @@
             <!-- Glossary -->
             <div class="flex items-start bg-gray-200 h-24">
                 <div
-                    class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
+                    class="bg-black text-white text-4xl font-extrabold w-24 h-24 flex items-center justify-center mr-8 flex-shrink-0"
+                    style="border-radius: 0;"
                 >
                     6
                 </div>
@@ -82,8 +86,3 @@
         </div>
     </div>
 </div>
-
-
-
-
-

app/report_gen/page_7.html

@@ -26,7 +26,7 @@
         <!-- Indications Box -->
         <div class="bg-gray-200 rounded-lg p-4 text-center mb-2">
             <h3 class="font-semibold text-lg mb-2">Indications</h3>
-            <p >{{ indication | default('No Respiratory Capacity Limitations')}}</p>
+            <p >{{ indication | default('No Respiratory Capacity Limitation')}}</p>
         </div>
     </div>
 

app/services/context_generator.py

@@ -232,10 +232,15 @@ class ContextGenerator:
                 if zone_key in metric_overrides:
                     metrics[zone_key] = metric_overrides[zone_key]
         else:
-            fat_max_idx = self.pnoe_df["FAT_smoothed"].idxmax()
+            # Use optimal fat burning zone (highest fat:carb ratio) - same as _calculate_zone_metrics
-            fat_max_row = self.pnoe_df.loc[fat_max_idx]
+            # This ensures consistency between zone calculations and zone metrics
+            self.pnoe_df["fat_carb_ratio"] = self.pnoe_df["FAT_smoothed"] / (
+                self.pnoe_df["CHO_smoothed"] + 0.00000001
+            )
+            optimal_fat_idx = self.pnoe_df["fat_carb_ratio"].idxmax()
+            optimal_row = self.pnoe_df.loc[optimal_fat_idx]
             zones = self._calculate_hr_zones(
-                metrics["vt1"], metrics["vt2"], fat_max_row
+                metrics["vt1"], metrics["vt2"], optimal_row
             )
             metrics.update(zones)
 
@@ -280,29 +285,46 @@ class ContextGenerator:
         return vt1, vt2
 
     def _calculate_hr_zones(
-        self, vt1: Optional[Dict], vt2: Optional[Dict], fat_max_row: pd.Series
+        self, vt1: Optional[Dict], vt2: Optional[Dict], optimal_row: pd.Series
     ) -> Dict:
-        """Calculate heart rate zones based on thresholds"""
+        """Calculate heart rate zones based on thresholds
+
+        Uses optimal fat burning zone (highest fat:carb ratio) to match _calculate_zone_metrics.
+        This ensures consistency between zone string calculations and zone metrics table.
+        """
+        import math
+
         zones = {}
         if vt1 and vt2:
-            zone_1_start = fat_max_row["HR(bpm)_smoothed"] - 15
+            # Use same zone boundary calculation as _calculate_zone_metrics
-            zone_2_start = fat_max_row["HR(bpm)_smoothed"]
+            zone_1_start = math.floor(optimal_row["HR(bpm)_smoothed"] - 15)
-            zone_3_start = vt1["HeartRate"]
+            zone_2_start = math.floor(optimal_row["HR(bpm)_smoothed"])
-            zone_4_start = vt2["HeartRate"] - 10
+            zone_3_start = math.floor(vt1["HeartRate"])
-            zone_5_start = vt2["HeartRate"] + 10
+            zone_4_start = math.floor(vt2["HeartRate"] - 10)
+            zone_5_start = math.floor(vt2["HeartRate"])
+            # zone_5_end is calculated for consistency with _calculate_zone_metrics
+            # (not used in string format since zone 5 is open-ended: "+bpm")
+            zone_5_end = math.floor(vt2["HeartRate"] + 10)  # noqa: F841
 
-            zones["zone1_bpm"] = f"{int(zone_1_start)}-{int(zone_2_start)}bpm"
+            # Calculate zone ends to match _calculate_zone_metrics exactly
-            zones["zone2_bpm"] = f"{int(zone_2_start)}-{int(vt1['HeartRate'])}bpm"
+            zone_1_end = zone_2_start
-            zones["zone3_bpm"] = f"{int(zone_3_start)}-{int(zone_4_start)}bpm"
+            zone_2_end = math.floor(vt1["HeartRate"])
-            zones["zone4_bpm"] = f"{int(zone_4_start)}-{int(zone_5_start)}bpm"
+            zone_3_end = zone_4_start
-            zones["zone5_bpm"] = f"{int(zone_5_start)}+bpm"
+            zone_4_end = zone_5_start
+
+            # Format zones to match _calculate_zone_metrics output
+            zones["zone1_bpm"] = f"{int(zone_1_start)}-{int(zone_1_end)}bpm"
+            zones["zone2_bpm"] = f"{int(zone_2_start)}-{int(zone_2_end)}bpm"
+            zones["zone3_bpm"] = f"{int(zone_3_start)}-{int(zone_3_end)}bpm"
+            zones["zone4_bpm"] = f"{int(zone_4_start)}-{int(zone_4_end)}bpm"
+            zones["zone5_bpm"] = f"{int(zone_5_start)}-{int(zone_5_end)}bpm"
         else:
             max_hr = 220 - self.patient_info["age"]
             zones["zone1_bpm"] = f"{int(max_hr * 0.55)}-{int(max_hr * 0.65)}bpm"
             zones["zone2_bpm"] = f"{int(max_hr * 0.65)}-{int(max_hr * 0.75)}bpm"
             zones["zone3_bpm"] = f"{int(max_hr * 0.75)}-{int(max_hr * 0.85)}bpm"
             zones["zone4_bpm"] = f"{int(max_hr * 0.85)}-{int(max_hr * 0.95)}bpm"
-            zones["zone5_bpm"] = f"{int(max_hr * 0.95)}+bpm"
+            zones["zone5_bpm"] = f"{int(max_hr * 0.95)}-{int(max_hr * 1.05)}bpm"
         return zones
 
     def _calculate_vo2_drop_points(self, pnoe_metrics: Dict) -> Dict:
@@ -1180,7 +1202,9 @@ class ContextGenerator:
                 "page_number": 4,
                 "fat_percentage": f"{self.patient_info['fat_percentage']:.1f}",
                 "body_composition_chart": graphs.get("body_composition", ""),
-                "body_fat_chart": graphs.get("body_fat_percent", ""),  # Alias for template
+                "body_fat_chart": graphs.get(
+                    "body_fat_percent", ""
+                ),  # Alias for template
                 "body_fat_percent_chart": graphs.get(
                     "body_fat_percent", ""
                 ),  # Keep for consistency
@@ -1199,29 +1223,29 @@ class ContextGenerator:
                 "weight_loss_rate": rmr_metrics.get("weight_loss_rate", 1.0),
                 "total_calories": rmr_metrics.get("total_calories", 1375),
             }
-            
+
             # For minimal reports, also generate resting heart rate table for page_5
             if report_type == "minimal" and graph_generator:
                 resting_hr_metrics = self._calculate_resting_heart_rate_metrics()
                 rhr_table_info = self._calculate_rhr_table_data(
                     self.patient_info["age"], self.patient_info["gender"]
                 )
-                
+
                 # Get resting heart rate value and determine category
                 rhr_value_str = resting_hr_metrics.get("resting_heart_rate", "0bpm")
                 rhr_value = float(rhr_value_str.replace("bpm", "").strip())
-                
+
                 category = self._determine_rhr_category(
                     rhr_value,
                     self.patient_info["age"],
                     self.patient_info["gender"],
                 )
-                
+
                 gender_label = (
                     "F" if self.patient_info["gender"].lower().startswith("f") else "M"
                 )
                 age_range_label = f"{rhr_table_info['age_range']} ({gender_label})"
-                
+
                 rhr_columns = [
                     "Age",
                     "Poor",
@@ -1244,7 +1268,7 @@ class ContextGenerator:
                         rhr_table_info["ranges"]["Athlete"],
                     ]
                 ]
-                
+
                 contexts["page_5"]["rhr_table"] = (
                     graph_generator.generate_resting_heart_rate_table(
                         data=rhr_data,
@@ -1265,12 +1289,16 @@ class ContextGenerator:
                 "deficit_carbs": f"{int(rmr_metrics.get('total_calories', 1600) * 0.39 / 4)}g Carbs",
                 "deficit_fat": f"{int(rmr_metrics.get('total_calories', 1600) * 0.39 / 9)}g Fat",
                 "deficit_fiber": "24g Fibre",
-                "refeed_weekday_calories": int(rmr_metrics.get("total_calories", 1600) * 0.85),
+                "refeed_weekday_calories": int(
+                    rmr_metrics.get("total_calories", 1600) * 0.85
+                ),
                 "refeed_weekday_protein": f"{int(rmr_metrics.get('total_calories', 1600) * 0.85 * 0.22 / 4)}g Protein",
                 "refeed_weekday_carbs": f"{int(rmr_metrics.get('total_calories', 1600) * 0.85 * 0.39 / 4)}g Carbs",
                 "refeed_weekday_fat": f"{int(rmr_metrics.get('total_calories', 1600) * 0.85 * 0.39 / 9)}g Fat",
                 "refeed_weekday_fiber": "20g Fibre",
-                "refeed_weekend_calories": int(rmr_metrics.get("total_calories", 1600) * 1.375),
+                "refeed_weekend_calories": int(
+                    rmr_metrics.get("total_calories", 1600) * 1.375
+                ),
                 "refeed_weekend_protein": f"{int(rmr_metrics.get('total_calories', 1600) * 1.375 * 0.22 / 4)}g Protein",
                 "refeed_weekend_carbs": f"{int(rmr_metrics.get('total_calories', 1600) * 1.375 * 0.39 / 4)}g Carbs",
                 "refeed_weekend_fat": f"{int(rmr_metrics.get('total_calories', 1600) * 1.375 * 0.39 / 9)}g Fat",
@@ -1291,12 +1319,12 @@ class ContextGenerator:
 
             # Page 7
             contexts["page_7"] = {
-            "peak_vt": f"{pnoe_metrics['peak_vt']:.2f}",
+                "peak_vt": f"{pnoe_metrics['peak_vt']:.2f}",
-            "peak_vt_bpm": f"{int(pnoe_metrics['peak_vt_hr'])}",
+                "peak_vt_bpm": f"{int(pnoe_metrics['peak_vt_hr'])}",
-            "fev1_percentage": f"{fev1_percentage:.1f}",
+                "fev1_percentage": f"{fev1_percentage:.1f}",
-            "lung_analysis_chart": graphs.get("spirometry_chart", ""),
+                "lung_analysis_chart": graphs.get("spirometry_chart", ""),
-            "respiratory_analysis_chart": graphs.get("respiratory", ""),
+                "respiratory_analysis_chart": graphs.get("respiratory", ""),
-        }
+            }
 
         # Page 8
         contexts["page_8"] = {
@@ -1562,7 +1590,11 @@ class ContextGenerator:
             }
 
         # For minimal reports, create combined context for page_19_20_minimal
-        if report_type == "minimal" and 19 in pages_to_generate and 20 in pages_to_generate:
+        if (
+            report_type == "minimal"
+            and 19 in pages_to_generate
+            and 20 in pages_to_generate
+        ):
             contexts["page_19_20_minimal"] = {
                 "patient_name": self.patient_info["name"],
                 "body_fat_percentage_chart": graphs.get(

notebooks/analysis.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "b18c1027",
    "metadata": {},
    "outputs": [],
@@ -88,7 +88,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "id": "56a9d655",
    "metadata": {},
    "outputs": [
@@ -104,7 +104,10 @@
    ],
    "source": [
     "import pandas as pd\n",
-    "spirometry_df = pd.read_csv(\"data/spirometry_data.csv\")\n",
+    "import os\n",
+    "\n",
+    "base_dir = os.path.dirname(os.path.abspath('.'))\n",
+    "spirometry_df = pd.read_csv(f\"{base_dir}/data/spirometry_data.csv\")\n",
     "\n",
     "fvc_best = spirometry_df.loc[spirometry_df['Parameters'] == 'FVC', 'Best'].values[0]\n",
     "fvc_pred = spirometry_df.loc[spirometry_df['Parameters'] == 'FVC', '%Pred.'].values[0]\n",
@@ -122,7 +125,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "990f4b4f",
    "metadata": {},
    "outputs": [
@@ -136,7 +139,7 @@
     }
    ],
    "source": [
-    "df = pd.read_csv('data/Pnoe_20250729_1550-Moran_Keirstyn.csv', delimiter=';')\n",
+    "df = pd.read_csv(f'{base_dir}/data/Pnoe_20250729_1550-Moran_Keirstyn.csv', delimiter=';')\n",
     "peak_vt = df['VT(l)'].max()\n",
     "max_vt_row = df.loc[df['VT(l)'].idxmax()]\n",
     "print(f\"Peak VT: {peak_vt}\")\n",
@@ -146,7 +149,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 19,
    "id": "041cbc3d",
    "metadata": {},
    "outputs": [
@@ -154,21 +157,21 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Peak VT: 2.3770000000000002\n",
+      "Peak VT: 2.3844444444444446\n",
-      "HR at Peak VT: 171.525\n"
+      "HR at Peak VT: 172.80555555555554\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/tmp/ipykernel_69398/4157056299.py:3: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead\n",
+      "/tmp/ipykernel_53922/361246798.py:3: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead\n",
       "  df = df.apply(pd.to_numeric, errors='ignore')\n"
      ]
     }
    ],
    "source": [
-    "df = pd.read_csv('data/Pnoe_20250729_1550-Moran_Keirstyn.csv', delimiter=';')\n",
+    "df = pd.read_csv(f'{base_dir}/data/Pnoe_20250729_1550-Moran_Keirstyn.csv', delimiter=';')\n",
     "# Convert all columns to numeric where possible, coercing errors to NaN\n",
     "df = df.apply(pd.to_numeric, errors='ignore')\n",
     "df['VO2 Pulse'] = df['VO2(ml/min)'] / df['HR(bpm)']  # VO2 Pulse in mL/beat\n",
@@ -176,7 +179,7 @@
     "df['CHO'] = df['EE(kcal/min)'] * df['CARBS(%)']/100\n",
     "df['FAT'] = df['EE(kcal/min)'] * df['FAT(%)']/100\n",
     "# Smooth key columns using rolling window\n",
-    "window_size = 10\n",
+    "window_size = 9\n",
     "\n",
     "# List of columns to smooth\n",
     "columns_to_smooth = ['VO2(ml/min)', 'VCO2(ml/min)', 'HR(bpm)', 'VT(l)', 'BF(bpm)', 'VE(l/min)', 'VO2 Pulse', 'VO2 Breath', 'CHO', 'FAT']\n",
@@ -195,7 +198,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 20,
    "id": "de7cadd1",
    "metadata": {},
    "outputs": [
@@ -203,7 +206,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Percent FEV: 72.91411042944786\n"
+      "Percent FEV: 73.14246762099523\n"
      ]
     }
    ],
@@ -214,7 +217,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 21,
    "id": "cb972ed3",
    "metadata": {},
    "outputs": [
@@ -311,13 +314,13 @@
        "[1 rows x 147 columns]"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 21,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "personal_df = pd.read_excel('data/SECA body comp for all patients.xlsx')\n",
+    "personal_df = pd.read_excel(f'{base_dir}/data/SECA body comp for all patients.xlsx')\n",
     "\n",
     "keirstyn_data = personal_df[personal_df['LastName'].str.contains('Moran', case=False, na=False)]\n",
     "keirstyn_data"
@@ -325,7 +328,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 22,
    "id": "98d9295a",
    "metadata": {},
    "outputs": [
@@ -333,7 +336,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "VO2 Max: 47.906290322580645\n"
+      "VO2 Max: 48.19062126642772\n"
      ]
     }
    ],
@@ -823,7 +826,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "report_generation",
+   "display_name": ".venv",
    "language": "python",
    "name": "python3"
   },
@@ -837,7 +840,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.12.6"
   }
  },
  "nbformat": 4,