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bolade
2025-11-28 16:19:32 +01:00
parent fc62b64624
commit 35ea522283
10 changed files with 113 additions and 72 deletions
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notebooks/analysis.ipynb
+23 -20
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@@ -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",
"HR at Peak VT: 171.525\n"
"Peak VT: 2.3844444444444446\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,