| from pathlib import Path |
| import sys |
|
|
| sys.path.insert(0, str(Path(__file__).resolve().parent / "tools")) |
|
|
| import json |
|
|
| import pandas as pd |
|
|
| from harmonize import normalize_frame |
|
|
| with open('/root/environment/data/respiratory_panel.json') as handle: |
| raw = json.load(handle)['panels'] |
|
|
| rows = [] |
| for entry in raw: |
| if entry['status'] != 'final': |
| continue |
| rows.append({ |
| 'sample_id': entry['sample_id'], |
| 'pH_Arterial': entry['measurements']['acid_base']['pH_Arterial'], |
| 'pCO2_Arterial': entry['measurements']['acid_base']['pCO2_Arterial'], |
| 'pO2_Arterial': entry['measurements']['acid_base']['pO2_Arterial'], |
| 'Bicarbonate': entry['measurements']['acid_base']['Bicarbonate'], |
| 'Lactate': entry['measurements']['metabolic']['Lactate'], |
| 'Glucose': entry['measurements']['metabolic']['Glucose'], |
| 'Magnesium': entry['measurements']['metabolic']['Magnesium'], |
| }) |
|
|
| df = pd.DataFrame(rows) |
| specs = {'pH_Arterial': ('same', 1.0, 6.8, 7.8), 'pCO2_Arterial': ('single', 0.133, 15, 100), 'pO2_Arterial': ('single', 0.133, 30, 500), 'Bicarbonate': ('same', 1.0, 5, 40), 'Lactate': ('single-reverse', 9.01, 0.3, 20), 'Glucose': ('single', 0.0555, 20, 800), 'Magnesium': ('single', 0.411, 0.5, 10)} |
| clean = normalize_frame(df, specs, id_column='sample_id') |
| clean[['pH_Arterial', 'pCO2_Arterial', 'pO2_Arterial', 'Bicarbonate', 'Lactate', 'Glucose', 'Magnesium']].to_csv('/root/respiratory_panel_harmonized.csv', index=False) |
|
|
