Update context for report: change patient name to Keirstyn; adjust execution count in analysis notebook

.gitignore

@@ -1,3 +1,5 @@
 .venv
 
-data/
+data/
+
+.env

analysis.ipynb

@@ -2,102 +2,93 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 6,
    "id": "b18c1027",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{'id': 'gen-1759135172-DIhs7TMuaaVY0h3T2ibV', 'provider': 'Google', 'model': 'google/gemini-2.5-flash-lite', 'object': 'chat.completion', 'created': 1759135172, 'choices': [{'logprobs': None, 'finish_reason': 'stop', 'native_finish_reason': 'STOP', 'index': 0, 'message': {'role': 'assistant', 'content': 'Parameters,Best,LLN,Pred.,%Pred.,ZScore,PRE#1,PRE#2,PRE#3\\nFVC,L,4.24,3.03,3.79,112.0,0.95,4.24,4.17,4.15\\nFEV1,L,3.26,2.53,3.16,103.3,0.28,3.26,3.21,3.14\\nFEV1/FVC%,76.89,72.47,83.78,91.8,-1.05,76.9,77.0,75.7\\nPEF,L/m,684,222,384,178.7,-,444,438,684\\nFEF2575,L/s,2.74,2.15,3.42,80.2,-0.84,2.74,2.68,2.48\\nFEF25,L/s,6.08,-,-,-,6.08,6.0,5.53\\nFEF50,L/s,3.06,-,-,-,3.06,3.1,2.77\\nFEF75,L/s,1.06,0.71,1.41,75.1,-0.72,1.06,1.12,0.94\\nPEFTime,ms,-,-,79,-,79,49,39\\nEvol,mL,-,-,78.0,-,78.0,77.0,197.0\\nFEV6,L,4.22,3.03,3.79,111.4,-,4.22,4.17,4.13', 'refusal': None, 'reasoning': None}}], 'usage': {'prompt_tokens': 1350, 'completion_tokens': 454, 'total_tokens': 1804, 'prompt_tokens_details': {'cached_tokens': 0}, 'completion_tokens_details': {'reasoning_tokens': 0, 'image_tokens': 0}}}\n",
-      "Content saved to extracted_table.csv\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "\n",
-    "import requests\n",
-    "import json\n",
-    "import base64\n",
-    "from pathlib import Path\n",
+    "# import requests\n",
+    "# import json\n",
+    "# import base64\n",
+    "# from pathlib import Path\n",
     "\n",
-    "API_KEY_REF = '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'\n",
-    "def encode_pdf_to_base64(pdf_path):\n",
-    "    with open(pdf_path, \"rb\") as pdf_file:\n",
-    "        return base64.b64encode(pdf_file.read()).decode('utf-8')\n",
+    "# API_KEY_REF = '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'\n",
+    "# def encode_pdf_to_base64(pdf_path):\n",
+    "#     with open(pdf_path, \"rb\") as pdf_file:\n",
+    "#         return base64.b64encode(pdf_file.read()).decode('utf-8')\n",
     "\n",
-    "url = \"https://openrouter.ai/api/v1/chat/completions\"\n",
-    "headers = {\n",
-    "    \"Authorization\": f\"Bearer {API_KEY_REF}\",\n",
-    "    \"Content-Type\": \"application/json\"\n",
-    "}\n",
+    "# url = \"https://openrouter.ai/api/v1/chat/completions\"\n",
+    "# headers = {\n",
+    "#     \"Authorization\": f\"Bearer {API_KEY_REF}\",\n",
+    "#     \"Content-Type\": \"application/json\"\n",
+    "# }\n",
     "\n",
-    "# Read and encode the PDF\n",
-    "pdf_path = \"data/~Moran~K~19910201~Spirometry Exam~20250729~20250729032843.pdf\"\n",
-    "base64_pdf = encode_pdf_to_base64(pdf_path)\n",
-    "data_url = f\"data:application/pdf;base64,{base64_pdf}\"\n",
+    "# # Read and encode the PDF\n",
+    "# pdf_path = \"data/~Moran~K~19910201~Spirometry Exam~20250729~20250729032843.pdf\"\n",
+    "# base64_pdf = encode_pdf_to_base64(pdf_path)\n",
+    "# data_url = f\"data:application/pdf;base64,{base64_pdf}\"\n",
     "\n",
-    "messages = [\n",
-    "    {\n",
-    "        \"role\": \"user\",\n",
-    "        \"content\": [\n",
-    "            {\n",
-    "                \"type\": \"text\",\n",
-    "                \"text\": \"Please extract the Spirometry table from the pdf and return the values in csv format, \"\n",
-    "                \"note that it is the unit of parameter that is beside it and it should not be a column. \"\n",
-    "                \"The '-' Should be treated as empty values.\"\n",
-    "                \"do not add 'csv' at the start or end of the response\"\n",
-    "            },\n",
-    "            {\n",
-    "                \"type\": \"file\",\n",
-    "                \"file\": {\n",
-    "                    \"filename\": \"document.pdf\",\n",
-    "                    \"file_data\": data_url\n",
-    "                }\n",
-    "            },\n",
-    "        ]\n",
-    "    }\n",
-    "]\n",
+    "# messages = [\n",
+    "#     {\n",
+    "#         \"role\": \"user\",\n",
+    "#         \"content\": [\n",
+    "#             {\n",
+    "#                 \"type\": \"text\",\n",
+    "#                 \"text\": \"Please extract the Spirometry table from the pdf and return the values in csv format, \"\n",
+    "#                 \"note that it is the unit of parameter that is beside it and it should not be a column. \"\n",
+    "#                 \"The '-' Should be treated as empty values.\"\n",
+    "#                 \"do not add 'csv' at the start or end of the response\"\n",
+    "#             },\n",
+    "#             {\n",
+    "#                 \"type\": \"file\",\n",
+    "#                 \"file\": {\n",
+    "#                     \"filename\": \"document.pdf\",\n",
+    "#                     \"file_data\": data_url\n",
+    "#                 }\n",
+    "#             },\n",
+    "#         ]\n",
+    "#     }\n",
+    "# ]\n",
     "\n",
-    "# Optional: Configure PDF processing engine\n",
-    "# PDF parsing will still work even if the plugin is not explicitly set\n",
-    "plugins = [\n",
-    "    {\n",
-    "        \"id\": \"file-parser\",\n",
-    "        \"pdf\": {\n",
-    "            \"engine\": \"pdf-text\"  # defaults to \"mistral-ocr\". See Pricing above\n",
-    "        }\n",
-    "    }\n",
-    "]\n",
+    "# # Optional: Configure PDF processing engine\n",
+    "# # PDF parsing will still work even if the plugin is not explicitly set\n",
+    "# plugins = [\n",
+    "#     {\n",
+    "#         \"id\": \"file-parser\",\n",
+    "#         \"pdf\": {\n",
+    "#             \"engine\": \"pdf-text\"  # defaults to \"mistral-ocr\". See Pricing above\n",
+    "#         }\n",
+    "#     }\n",
+    "# ]\n",
     "\n",
-    "payload = {\n",
-    "    \"model\": \"google/gemini-2.5-flash-lite\",\n",
-    "    \"messages\": messages,\n",
-    "}\n",
+    "# payload = {\n",
+    "#     \"model\": \"google/gemini-2.5-flash-lite\",\n",
+    "#     \"messages\": messages,\n",
+    "# }\n",
     "\n",
-    "response = requests.post(url, headers=headers, json=payload)\n",
-    "# Get the response content\n",
-    "response_data = response.json()\n",
-    "print(response_data)\n",
+    "# response = requests.post(url, headers=headers, json=payload)\n",
+    "# # Get the response content\n",
+    "# response_data = response.json()\n",
+    "# print(response_data)\n",
     "\n",
-    "# Extract the content from the response\n",
-    "if 'choices' in response_data and len(response_data['choices']) > 0:\n",
-    "    content = response_data['choices'][0]['message']['content']\n",
+    "# # Extract the content from the response\n",
+    "# if 'choices' in response_data and len(response_data['choices']) > 0:\n",
+    "#     content = response_data['choices'][0]['message']['content']\n",
     "    \n",
-    "    # Save to a CSV file\n",
-    "    output_file = \"extracted_table.csv\"\n",
-    "    with open(output_file, 'w', encoding='utf-8') as f:\n",
-    "        f.write(content)\n",
+    "#     # Save to a CSV file\n",
+    "#     output_file = \"extracted_table.csv\"\n",
+    "#     with open(output_file, 'w', encoding='utf-8') as f:\n",
+    "#         f.write(content)\n",
     "    \n",
-    "    print(f\"Content saved to {output_file}\")\n",
-    "else:\n",
-    "    print(\"No content found in response\")"
+    "#     print(f\"Content saved to {output_file}\")\n",
+    "# else:\n",
+    "#     print(\"No content found in response\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 7,
    "id": "56a9d655",
    "metadata": {},
    "outputs": [
@@ -107,13 +98,13 @@
      "text": [
       "FVC Best: 4.24, FVC Pred: 112.0\n",
       "FEV1 Best: 3.26, FEV1 Pred: 103.3\n",
-      "FEV1/FVC% Best: 76.89, FEV1/FVC% Pred: 91.8\n"
+      "FEV1/FVC% Best: 76.9, FEV1/FVC% Pred: 91.8\n"
      ]
     }
    ],
    "source": [
     "import pandas as pd\n",
-    "spirometry_df = pd.read_csv(\"extracted_table.csv\")\n",
+    "spirometry_df = pd.read_csv(\"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",
@@ -131,7 +122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 8,
    "id": "990f4b4f",
    "metadata": {},
    "outputs": [
@@ -155,7 +146,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 9,
    "id": "041cbc3d",
    "metadata": {},
    "outputs": [
@@ -171,7 +162,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/tmp/ipykernel_301535/4157056299.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_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",
       "  df = df.apply(pd.to_numeric, errors='ignore')\n"
      ]
     }
@@ -204,7 +195,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 10,
    "id": "de7cadd1",
    "metadata": {},
    "outputs": [
@@ -223,7 +214,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 11,
    "id": "cb972ed3",
    "metadata": {},
    "outputs": [
@@ -320,7 +311,7 @@
        "[1 rows x 147 columns]"
       ]
      },
-     "execution_count": 24,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -334,7 +325,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 12,
    "id": "98d9295a",
    "metadata": {},
    "outputs": [
@@ -354,7 +345,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 13,
    "id": "cdfeb309",
    "metadata": {},
    "outputs": [
@@ -418,7 +409,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 14,
    "id": "4420cfea",
    "metadata": {},
    "outputs": [
@@ -476,7 +467,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
+   "execution_count": 21,
    "id": "62803668",
    "metadata": {},
    "outputs": [
@@ -561,7 +552,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": 16,
    "id": "07593b56",
    "metadata": {},
    "outputs": [
@@ -572,8 +563,8 @@
       "Zone 1 (Active Recovery): 81.7 - 96.7 bpm\n",
       "Zone 2 (Aerobic Base): 96.7 - 100.5 bpm\n",
       "Zone 3 (Aerobic): 100.5 - 179.7 bpm\n",
-      "Zone 4 (Lactate Threshold): 179.7 - 199.7 bpm\n",
-      "Zone 5 (VO2 Max): 199.7+ bpm\n"
+      "Zone 4 (Lactate Threshold): 179.7 - 189.7 bpm\n",
+      "Zone 5 (VO2 Max): 189.7 - 199.7 bpm\n"
      ]
     }
    ],
@@ -582,7 +573,8 @@
     "zone_2_start = optimal_row['HR(bpm)_smoothed']\n",
     "zone_3_start = vt1\n",
     "zone_4_start = vt2['HeartRate'] - 10\n",
-    "zone_5_start = vt2['HeartRate'] + 10\n",
+    "zone_5_start = vt2['HeartRate']\n",
+    "zone_5_end = vt2['HeartRate'] + 10\n",
     "\n",
     "zone_1_end = zone_2_start\n",
     "zone_2_end = vt1['HeartRate']\n",
@@ -593,12 +585,12 @@
     "print(f\"Zone 2 (Aerobic Base): {zone_2_start:.1f} - {zone_2_end:.1f} bpm\")\n",
     "print(f\"Zone 3 (Aerobic): {zone_3_start['HeartRate']:.1f} - {zone_3_end:.1f} bpm\")\n",
     "print(f\"Zone 4 (Lactate Threshold): {zone_4_start:.1f} - {zone_4_end:.1f} bpm\")\n",
-    "print(f\"Zone 5 (VO2 Max): {zone_5_start:.1f}+ bpm\")"
+    "print(f\"Zone 5 (VO2 Max): {zone_5_start:.1f} - {zone_5_end:.1f} bpm\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 60,
+   "execution_count": 17,
    "id": "c90415b2",
    "metadata": {},
    "outputs": [
@@ -661,7 +653,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 66,
+   "execution_count": 18,
    "id": "c3b2cc59",
    "metadata": {},
    "outputs": [
@@ -750,7 +742,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 19,
    "id": "672d68f3",
    "metadata": {},
    "outputs": [

context.py

@@ -12,7 +12,7 @@ def image_to_base64(image_path):
 
 ### Defining Page Contexts ###
 page_1_context = {
-    "name": "John Doe",
+    "name": "Keirstyn",
     "surname": "Moran",
     "date": "July 29, 2025",
 }
@@ -32,17 +32,23 @@ page_4_context = {
     "body_fat_chart": image_to_base64(
         "/home/oluwasanmi/Documents/Work/MKD/report_generation/graphs/body_fat_percent_chart.png"
     ),
+
+    "fat_percentage": "22.4",
 }
 
 
 page_5_context = {
-    "metabolism_chart": "",
-    "fuel_source_chart": "",
-    "resting_calories": 1540,
-    "neat_calories": 310,
-    "weight_loss_calories": 1725,
+    "metabolism_chart": image_to_base64(
+        "/home/oluwasanmi/Documents/Work/MKD/report_generation/graphs/metabolism_chart.png"
+    ),
+    "fuel_source_chart": image_to_base64(
+        "/home/oluwasanmi/Documents/Work/MKD/report_generation/graphs/fuel_source_chart.png"
+    ),
+    "resting_calories": 1385,
+    "neat_calories": "null",
+    "weight_loss_calories": "null",
     "weight_loss_rate": "1lb/week",
-    "total_calories": 3575,
+    "total_calories": "null",
 }
 
 page_6_context = {
@@ -102,8 +108,8 @@ page_8_context = {
     "zone1_bpm": "81-96bpm",
     "zone2_bpm": "96-100bpm",
     "zone3_bpm": "100-178bpm",
-    "zone4_bpm": "178-188bpm",
-    "zone5_bpm": "188-198bpm",
+    "zone4_bpm": "178-189bpm",
+    "zone5_bpm": "189-199bpm",
     "zone1_speed": "3.5mph",
     "zone2_speed": "3.5-4.0mph",
     "zone3_speed": "4.0-6.5mph",
@@ -192,7 +198,12 @@ page_11_context = {
 }
 
 page_12_context = {
-    
+    "right_leg": image_to_base64(
+        "/home/oluwasanmi/Documents/Work/MKD/report_generation/graphs/right_leg.png"
+    ),
+    "left_leg": image_to_base64(
+        "/home/oluwasanmi/Documents/Work/MKD/report_generation/graphs/left_leg.png"
+    ),
 }
 
 page_13_context = {
@@ -308,7 +319,7 @@ page_17_context = {
 
 page_18_context = {
     "body_fat_percentage_chart": image_to_base64(
-        "/home/oluwasanmi/Documents/Work/MKD/report_generation/graphs/fat_percent_master_chart.png"
+        "/home/oluwasanmi/Documents/Work/MKD/report_generation/fat_percentage_master_chart.png"
     ),
 }
 

main.py

@@ -6,7 +6,12 @@ from context import context_list
 env = Environment(loader=FileSystemLoader("report_gen"))
 
 html_pages = []
-
+a = 1
+b = "string"
+c = [1,2,3,5]
+d = {
+    "key": "value"
+}
 header_context = {
     "patient_name": "Keirstyn Moran",
     "age": 34,
@@ -122,3 +127,4 @@ html_string_to_pdf(html_doc, "multi_page_report.pdf")
 # pdfkit.from_string(html_doc, "truth_report.pdf", options=options)
 
 print("✅ PDF generated: multi_page_report.pdf")
+

report_gen/page_12.html

@@ -15,7 +15,7 @@
         <div class="flex gap-8">
             <!-- Chart Image -->
             <div class="flex-1">
-                <img src="right-leg-chart.png" alt="Right Leg SMO2 Chart" class="w-full h-auto">
+                <img src= "data:image/png;base64,{{ right_leg }}" alt="Right Leg SMO2 Chart" class="w-full h-auto">
             </div>
             
             <!-- Right Side Info -->
@@ -48,7 +48,7 @@
         <div class="flex gap-8">
             <!-- Chart Image -->
             <div class="flex-1">
-                <img src="left-leg-chart.png" alt="Left Leg SMO2 Chart" class="w-full h-auto">
+                <img src= "data:image/png;base64,{{ left_leg }}" alt="Left Leg SMO2 Chart" class="w-full h-auto">
             </div>
             
             <!-- Right Side Info -->

report_gen/page_2.html

@@ -1,7 +1,7 @@
 <div class="bg-white w-full page m-0 px-10">
-    <div class="px-16 py-10">
+    <div class="px-16 pt-10">
         <!-- Table of Contents Header -->
-        <div class="mb-8">
+        <div class="mb-2">
             <h1
                 class="text-5xl font-bold text-black mb-6 tracking-wide border-b-4 border-blue-500 pb-2 text-center"
             >
@@ -12,12 +12,46 @@
 
         <!-- Table of Contents Items -->
         <div class="flex flex-col justify-between space-y-6 py-6">
+            <!-- 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"
+                >
+                    4
+                </div>
+                <div class="flex flex-col flex-1 py-1 justify-center h-full">
+                    <h2 class="text-2xl font-semibold text-black">
+                        Nutrition Guidelines
+                    </h2>
+                    <p class="text-gray-600 text-base">
+                        Ultrasound & Body Composition Assessment
+                    </p>
+                    <p class="text-gray-600 text-base">
+                        Resting Metabolic Rate Assessment
+                    </p>
+                </div>
+            </div>
+
+            <!-- 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"
+                >
+                    6
+                </div>
+                <div class="flex flex-col py-1 flex-1 justify-center h-full">
+                    <h2 class="text-2xl font-semibold text-black">
+                        Nutrition Recommendations
+                    </h2>
+                </div>
+            </div>
+
             <!-- 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"
                 >
-                    3
+                    7
                 </div>
                 <div class="flex flex-col flex-1 py-1 justify-center h-full">
                     <h2 class="text-2xl font-semibold text-black">
@@ -37,10 +71,10 @@
                 <div
                     class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
                 >
-                    4
+                    8
                 </div>
-                <div class="flex flex-col py-1  flex-1 justify-center h-full">
-                    <h2 class="text-2xl font-semibold text-black mb-3">
+                <div class="flex flex-col py-1 flex-1 justify-center h-full">
+                    <h2 class="text-2xl font-semibold text-black">
                         Cardio Metrics
                     </h2>
                     <p class="text-gray-600 text-base">
@@ -49,26 +83,12 @@
                 </div>
             </div>
 
-            <!-- 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"
-                >
-                    5
-                </div>
-                <div class="flex flex-col py-1 flex-1 justify-center flex-1 h-full">
-                    <h2 class="text-2xl font-semibold text-black">
-                        Fuel Utilization
-                    </h2>
-                </div>
-            </div>
-
             <!-- 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"
                 >
-                    9
+                    11
                 </div>
                 <div class="flex flex-col justify-center h-full flex-1">
                     <h2 class="text-2xl font-semibold text-black">
@@ -82,7 +102,7 @@
                 <div
                     class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
                 >
-                    10
+                    12
                 </div>
                 <div class="flex flex-col h-full justify-center flex-1">
                     <h2 class="text-2xl font-semibold text-black">
@@ -96,15 +116,12 @@
                 <div
                     class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
                 >
-                    12
+                    14
                 </div>
                 <div class="flex flex-col h-full justify-center flex-1">
                     <h2 class="text-2xl font-semibold text-black">
                         Next Steps
                     </h2>
-                    <div class="space-y-2">
-                        <!-- No sub-items -->
-                    </div>
                 </div>
             </div>
 
@@ -113,15 +130,12 @@
                 <div
                     class="bg-black text-white text-2xl font-bold w-16 h-full flex items-center justify-center mr-8 flex-shrink-0"
                 >
-                    13
+                    15
                 </div>
                 <div class="flex flex-col h-full justify-center flex-1">
                     <h2 class="text-2xl font-semibold text-black">
                         Glossary
                     </h2>
-                    <div class="space-y-2">
-                        <!-- No sub-items -->
-                    </div>
                 </div>
             </div>
         </div>