feat: Enhance medical report generation with new features and improved data handling

- Added body fat percentage input and optional muscle oxygenation CSV upload in the upload form.
- Implemented TSI chart generation based on muscle oxygenation data.
- Updated report generation to include metabolism and fuel source charts.
- Refactored context generation to eliminate reliance on SECA data, using patient info directly instead.
- Improved error handling and logging for graph generation processes.
- Enhanced HTML templates for better user experience and functionality.

notebooks/page_context_gen.ipynb

@@ -18,13 +18,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": null,
    "id": "da5ac3c1",
    "metadata": {},
    "outputs": [],
    "source": [
     "pnoe_df = pd.read_csv('data/pnoe_data.csv', delimiter=';')\n",
-    "patients_info = pd.read_excel('data/patients_data.xlsx')\n",
     "spirometry_df = pd.read_csv('data/spirometry_data.csv')"
    ]
   },
@@ -254,7 +253,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "id": "2fa8ff13",
    "metadata": {},
    "outputs": [
@@ -270,15 +269,10 @@
     }
    ],
    "source": [
-    "def body_composition_chart(first_name='Keirstyn', last_name='Moran'):\n",
+    "def body_composition_chart(fat_percentage=22.4, weight_kg=70):\n",
     "\n",
     "    \n",
     "    #=========================== Body Composition Donut Chart ========================#\n",
-    "    patient_data = patients_info[(patients_info['FirstName'].str.contains(first_name, case=False, na=False)) & \n",
-    "                                  (patients_info['LastName'].str.contains(last_name, case=False, na=False))]\n",
-    "# Get the fat mass percentage for Keirstyn\n",
-    "    fat_percentage = patient_data['Adult_FMP'].iloc[0]\n",
-    "    weight_kg = patient_data['Weight'].iloc[0]\n",
     "    lean_percentage = 100 - fat_percentage\n",
     "\n",
     "# Create donut chart\n",