Add compiled Python bytecode for report generator and spirometry table extractor services
- Generated bytecode for report_generator.py and spirometry_table_extractor.py - These changes include the compiled .pyc files in the __pycache__ directory - The report generator service handles the generation of medical reports from uploaded files - The spirometry table extractor service extracts data from PDF files and processes it for further analysis
This commit is contained in:
bolade
@@ -1,319 +1,180 @@
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import base64
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"""
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Context Generator Service
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This service processes all data files and generates context dictionaries for each page
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of the medical report. It performs analysis on Pnoe, Spirometry, and SECA data.
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"""
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from datetime import datetime
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from pathlib import Path
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from typing import Dict, List, Optional, Tuple
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import matplotlib.pyplot as plt
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import pandas as pd
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class ReportGenerator:
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class ContextGenerator:
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"""Generate context data for report pages"""
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def __init__(self):
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self.pnoe_df = None
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self.patient_df = None
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self.spirometry_df = None
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self.seca_df = None
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self.patient_info = {}
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self.charts_dir = Path("graphs")
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self.charts_dir.mkdir(exist_ok=True)
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def load_data(
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self,
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pnoe_path: str,
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patient_path: str,
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spirometry_path: str,
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seca_path: str = None,
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seca_path: str,
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):
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"""Load all required datasets"""
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self.pnoe_df = pd.read_csv(pnoe_path, delimiter=";")
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self.patient_df = pd.read_csv(patient_path)
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self.spirometry_df = pd.read_csv(spirometry_path)
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if seca_path:
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self.seca_df = pd.read_excel(seca_path)
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self.seca_df = pd.read_excel(seca_path)
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self._preprocess_pnoe_data()
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# Apply preprocessing
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self._preprocess_data()
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def _preprocess_data(self):
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"""Apply preprocessing steps from your notebook"""
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# Convert to numeric
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def _preprocess_pnoe_data(self):
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"""Apply preprocessing steps to Pnoe data"""
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self.pnoe_df = self.pnoe_df.apply(pd.to_numeric, errors="ignore")
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# Calculate derived columns
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self.pnoe_df["VO2 Pulse"] = (
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self.pnoe_df["VO2(ml/min)"] / self.pnoe_df["HR(bpm)"]
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)
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self.pnoe_df["VO2 Breath"] = (
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self.pnoe_df["VO2(ml/min)"] / self.pnoe_df["BF(bpm)"]
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)
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self.pnoe_df["CHO"] = (
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self.pnoe_df["EE(kcal/min)"] * self.pnoe_df["CARBS(%)"] / 100
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)
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self.pnoe_df["FAT"] = (
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self.pnoe_df["EE(kcal/min)"] * self.pnoe_df["FAT(%)"] / 100
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)
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# Apply smoothing
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self.pnoe_df["VO2 Pulse"] = self.pnoe_df["VO2(ml/min)"] / self.pnoe_df["HR(bpm)"]
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self.pnoe_df["VO2 Breath"] = self.pnoe_df["VO2(ml/min)"] / self.pnoe_df["BF(bpm)"]
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self.pnoe_df["CHO"] = self.pnoe_df["EE(kcal/min)"] * self.pnoe_df["CARBS(%)"] / 100
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self.pnoe_df["FAT"] = self.pnoe_df["EE(kcal/min)"] * self.pnoe_df["FAT(%)"] / 100
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window_size = 10
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columns_to_smooth = [
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"VO2(ml/min)",
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"VCO2(ml/min)",
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"HR(bpm)",
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"VT(l)",
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"BF(bpm)",
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"VE(l/min)",
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"VO2 Pulse",
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"VO2 Breath",
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"CHO",
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"FAT",
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]
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columns_to_smooth = ["VO2(ml/min)", "VCO2(ml/min)", "HR(bpm)", "VT(l)", "BF(bpm)", "VE(l/min)", "VO2 Pulse", "VO2 Breath", "CHO", "FAT"]
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for col in columns_to_smooth:
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if col in self.pnoe_df.columns:
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self.pnoe_df[f"{col}_smoothed"] = (
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self.pnoe_df[col].rolling(window=window_size, min_periods=1).mean()
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)
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self.pnoe_df[f"{col}_smoothed"] = self.pnoe_df[col].rolling(window=window_size, min_periods=1).mean()
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def extract_patient_info(self, last_name: str) -> Dict:
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"""Extract patient information from datasets"""
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def extract_patient_info(self, patient_name: str) -> Dict:
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"""Extract patient information from SECA dataset"""
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if self.seca_df is not None:
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patient_data = self.seca_df[
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self.seca_df["LastName"].str.contains(last_name, case=False, na=False)
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]
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patient_data = self.seca_df[self.seca_df["LastName"].str.contains(patient_name, case=False, na=False)]
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if not patient_data.empty:
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row = patient_data.iloc[0]
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weight_kg = float(row.get("Weight", 0))
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fat_pct = float(row.get("Adult_FMP", 0))
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self.patient_info = {
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"name": f"{row.get('FirstName', '')} {last_name}",
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"name": f"{row.get('FirstName', '')} {row.get('LastName', '')}",
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"first_name": row.get("FirstName", ""),
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"last_name": row.get("LastName", ""),
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"age": int(row.get("Age", 0)),
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"height": f"{row.get('Height', '')}",
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"weight": float(row.get("Weight", 0)),
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"weight": weight_kg,
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"gender": row.get("Gender", "").lower(),
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"fat_percentage": float(row.get("Adult_FMP", 0)),
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"fat_percentage": fat_pct,
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"fat_mass_lbs": weight_kg * fat_pct / 100 * 2.20462,
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"lean_mass_lbs": weight_kg * (1 - fat_pct / 100) * 2.20462,
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}
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return self.patient_info
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def calculate_spirometry_metrics(self) -> Dict:
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"""Calculate spirometry-related metrics"""
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metrics = {}
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# Extract key spirometry values
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for param in ["FVC", "FEV1", "FEV1/FVC%"]:
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row = self.spirometry_df.loc[self.spirometry_df["Parameters"] == param]
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row = self.spirometry_df.loc[self.spirometry_df["Parameters"].str.strip() == param]
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if not row.empty:
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metrics[
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f"{param.lower().replace('/', '_').replace('%', '_pct')}_best"
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] = row["Best"].values[0]
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metrics[
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f"{param.lower().replace('/', '_').replace('%', '_pct')}_pred"
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] = row["%Pred."].values[0]
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param_key = param.lower().replace('/', '_').replace('%', '_pct')
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metrics[f"{param_key}_best"] = row["Best"].values[0]
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metrics[f"{param_key}_pred"] = row["%Pred."].values[0]
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return metrics
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def calculate_pnoe_metrics(self) -> Dict:
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"""Calculate all Pnoe-derived metrics"""
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metrics = {}
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# Basic metrics
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metrics["vo2_max"] = self.pnoe_df["VO2(ml/min)_smoothed"].max()
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metrics["vo2_max_per_kg"] = metrics["vo2_max"] / self.patient_info["weight"]
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# Peak VT
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peak_vt_idx = self.pnoe_df["VT(l)_smoothed"].idxmax()
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peak_vt_row = self.pnoe_df.loc[peak_vt_idx]
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metrics["peak_vt"] = peak_vt_row["VT(l)_smoothed"]
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metrics["peak_vt_hr"] = peak_vt_row["HR(bpm)_smoothed"]
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# Fat burning metrics
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fat_max_idx = self.pnoe_df["FAT_smoothed"].idxmax()
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fat_max_row = self.pnoe_df.loc[fat_max_idx]
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metrics["fat_max_value"] = fat_max_row["FAT_smoothed"]
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metrics["fat_max_hr"] = fat_max_row["HR(bpm)_smoothed"]
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# Calculate zones (simplified from your logic)
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metrics.update(self._calculate_hr_zones())
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# VT1/VT2 detection
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vt1, vt2 = self._detect_thresholds()
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metrics["vt1"] = vt1
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metrics["vt2"] = vt2
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zones = self._calculate_hr_zones(vt1, vt2, fat_max_row)
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metrics.update(zones)
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return metrics
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def _detect_thresholds(self) -> Tuple[Optional[Dict], Optional[Dict]]:
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"""Detect VT1 and VT2 thresholds"""
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# VT1: First crossover where carbs > fat
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condition = self.pnoe_df["CHO_smoothed"] > self.pnoe_df["FAT_smoothed"]
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crossover_indices = condition[condition].index
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vt1 = None
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if len(crossover_indices) > 0:
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vt1_idx = crossover_indices[0]
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vt1_row = self.pnoe_df.loc[vt1_idx]
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vt1 = {
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"HeartRate": vt1_row["HR(bpm)_smoothed"],
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"Speed": vt1_row["Speed"],
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"Time": vt1_row["T(sec)"],
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}
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# VT2: Ventilation inflection (simplified)
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vt1 = {"HeartRate": vt1_row["HR(bpm)_smoothed"], "Speed": vt1_row["Speed"], "Time": vt1_row["T(sec)"]}
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ve_slope = self.pnoe_df["VE(l/min)_smoothed"].diff()
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second_derivative = ve_slope.diff()
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vt2_idx = second_derivative.idxmax()
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vt2 = None
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if pd.notna(vt2_idx):
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vt2_row = self.pnoe_df.loc[vt2_idx]
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vt2 = {
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"HeartRate": vt2_row["HR(bpm)_smoothed"],
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"Speed": vt2_row["Speed"],
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"Time": vt2_row["T(sec)"],
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}
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vt2 = {"HeartRate": vt2_row["HR(bpm)_smoothed"], "Speed": vt2_row["Speed"], "Time": vt2_row["T(sec)"]}
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return vt1, vt2
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def _calculate_hr_zones(self) -> Dict:
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"""Calculate heart rate zones"""
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max_hr = 220 - self.patient_info["age"]
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# Simplified zone calculation - you can make this more sophisticated
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zones = {
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"zone1_bpm": f"{int(max_hr * 0.55)}-{int(max_hr * 0.65)}bpm",
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"zone2_bpm": f"{int(max_hr * 0.65)}-{int(max_hr * 0.75)}bpm",
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"zone3_bpm": f"{int(max_hr * 0.75)}-{int(max_hr * 0.85)}bpm",
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"zone4_bpm": f"{int(max_hr * 0.85)}-{int(max_hr * 0.95)}bpm",
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"zone5_bpm": f"{int(max_hr * 0.95)}+bpm",
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}
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def _calculate_hr_zones(self, vt1: Optional[Dict], vt2: Optional[Dict], fat_max_row: pd.Series) -> Dict:
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"""Calculate heart rate zones based on thresholds"""
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zones = {}
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if vt1 and vt2:
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zone_1_start = fat_max_row["HR(bpm)_smoothed"] - 15
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zone_2_start = fat_max_row["HR(bpm)_smoothed"]
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zone_3_start = vt1["HeartRate"]
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zone_4_start = vt2["HeartRate"] - 10
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zone_5_start = vt2["HeartRate"] + 10
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zones["zone1_bpm"] = f"{int(zone_1_start)}-{int(zone_2_start)}bpm"
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zones["zone2_bpm"] = f"{int(zone_2_start)}-{int(vt1['HeartRate'])}bpm"
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zones["zone3_bpm"] = f"{int(zone_3_start)}-{int(zone_4_start)}bpm"
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zones["zone4_bpm"] = f"{int(zone_4_start)}-{int(zone_5_start)}bpm"
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zones["zone5_bpm"] = f"{int(zone_5_start)}+bpm"
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else:
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max_hr = 220 - self.patient_info["age"]
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zones["zone1_bpm"] = f"{int(max_hr * 0.55)}-{int(max_hr * 0.65)}bpm"
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zones["zone2_bpm"] = f"{int(max_hr * 0.65)}-{int(max_hr * 0.75)}bpm"
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zones["zone3_bpm"] = f"{int(max_hr * 0.75)}-{int(max_hr * 0.85)}bpm"
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zones["zone4_bpm"] = f"{int(max_hr * 0.85)}-{int(max_hr * 0.95)}bpm"
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zones["zone5_bpm"] = f"{int(max_hr * 0.95)}+bpm"
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return zones
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def generate_charts(self) -> Dict[str, str]:
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"""Generate all charts and return base64 encoded versions"""
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charts = {}
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# Generate fuel utilization chart
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charts["fuel_utilization_chart"] = self._create_fuel_chart()
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# Generate VO2 pulse chart
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charts["vo2_pulse_chart"] = self._create_vo2_pulse_chart()
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# Generate body composition chart
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charts["body_composition_chart"] = self._create_body_comp_chart()
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# Add more chart generation methods...
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return charts
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def _create_fuel_chart(self) -> str:
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"""Create and save fuel utilization chart"""
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# Use your existing chart code but make it dynamic
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speed_groups = self.pnoe_df.groupby("Speed").mean(numeric_only=True).round(1)
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speed_groups = speed_groups.iloc[1:-1]
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filtered_data = speed_groups[
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(speed_groups.index >= 3.5) & (speed_groups.index <= 7.5)
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]
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plt.figure(figsize=(15, 8))
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# ... your chart code here ...
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chart_path = self.charts_dir / "fuel_utilization_chart.png"
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plt.savefig(chart_path, dpi=300)
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plt.close()
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return self._image_to_base64(chart_path)
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def _create_vo2_pulse_chart(self) -> str:
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"""Create VO2 pulse chart"""
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# Your VO2 pulse chart code here
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chart_path = self.charts_dir / "vo2_pulse_chart.png"
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# ... chart generation code ...
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return self._image_to_base64(chart_path)
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def _create_body_comp_chart(self) -> str:
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"""Create body composition chart"""
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# Your body composition chart code here
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chart_path = self.charts_dir / "body_composition_chart.png"
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# ... chart generation code ...
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return self._image_to_base64(chart_path)
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def _image_to_base64(self, image_path: Path) -> str:
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"""Convert image to base64"""
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try:
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with open(image_path, "rb") as image_file:
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return base64.b64encode(image_file.read()).decode("utf-8")
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except FileNotFoundError:
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return ""
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def generate_all_contexts(self, last_name: str = "Moran") -> List[Dict]:
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def generate_all_contexts(self, patient_name: str, graphs: Dict[str, str]) -> List[Dict]:
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"""Main method to generate all page contexts"""
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# Extract patient info
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self.extract_patient_info(last_name)
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# Calculate metrics
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self.extract_patient_info(patient_name)
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spirometry_metrics = self.calculate_spirometry_metrics()
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pnoe_metrics = self.calculate_pnoe_metrics()
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# Generate charts
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charts = self.generate_charts()
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# Build contexts for each page
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contexts = []
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# Page 1
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contexts.append(
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{
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"name": self.patient_info["name"],
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"surname": last_name,
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"date": "July 29, 2025",
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}
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)
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# Page 2-6 (add as needed)
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for i in range(5):
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contexts.append({})
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# Page 7 - Spirometry
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contexts.append(
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{
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"peak_vt": pnoe_metrics["peak_vt"],
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"peak_vt_bpm": pnoe_metrics["peak_vt_hr"],
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"fev1_percentage": (
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pnoe_metrics["peak_vt"] / spirometry_metrics["fvc_best"]
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)
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* 100,
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"lung_analysis_chart": charts.get("spirometry_chart", ""),
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"respiratory_analysis_chart": charts.get("respiratory_chart", ""),
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}
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)
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# Page 8 - VO2 Max and Zones
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contexts.append(
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{
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"vo2_max_value": f"{pnoe_metrics['vo2_max_per_kg']:.1f}",
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"age_range": f"{self.patient_info['age'] // 10 * 10}-{self.patient_info['age'] // 10 * 10 + 9}",
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**pnoe_metrics, # Include all zone calculations
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}
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)
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# Continue for all pages...
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# Add remaining pages as needed
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contexts.append({"name": self.patient_info["name"], "surname": self.patient_info["last_name"], "date": datetime.now().strftime("%B %d, %Y")})
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contexts.append({"patient_name": self.patient_info["name"], "test_date": datetime.now().strftime("%B %d, %Y")})
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for i in range(4):
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contexts.append({"patient_name": self.patient_info["name"], "page_number": i + 3})
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fev1_percentage = 0
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if spirometry_metrics.get("fvc_best"):
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fev1_percentage = (pnoe_metrics["peak_vt"] / spirometry_metrics["fvc_best"]) * 100
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contexts.append({"peak_vt": f"{pnoe_metrics['peak_vt']:.2f}", "peak_vt_bpm": f"{int(pnoe_metrics['peak_vt_hr'])}", "fev1_percentage": f"{fev1_percentage:.1f}", "lung_analysis_chart": graphs.get("spirometry_chart", ""), "respiratory_analysis_chart": graphs.get("respiratory", "")})
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contexts.append({"vo2_max_value": f"{pnoe_metrics['vo2_max_per_kg']:.1f}", "age_range": f"{self.patient_info['age'] // 10 * 10}-{self.patient_info['age'] // 10 * 10 + 9}", "zone1_bpm": pnoe_metrics.get("zone1_bpm", ""), "zone2_bpm": pnoe_metrics.get("zone2_bpm", ""), "zone3_bpm": pnoe_metrics.get("zone3_bpm", ""), "zone4_bpm": pnoe_metrics.get("zone4_bpm", ""), "zone5_bpm": pnoe_metrics.get("zone5_bpm", ""), "vo2_pulse_chart": graphs.get("vo2_pulse", "")})
|
||||
contexts.append({"fat_max_value": f"{pnoe_metrics['fat_max_value']:.2f}", "fat_max_hr": f"{int(pnoe_metrics['fat_max_hr'])}", "fuel_utilization_chart": graphs.get("fuel_utilization", ""), "fat_metabolism_chart": graphs.get("fat_metabolism", "")})
|
||||
contexts.append({"fat_percentage": f"{self.patient_info['fat_percentage']:.1f}", "fat_mass_lbs": f"{self.patient_info['fat_mass_lbs']:.1f}", "lean_mass_lbs": f"{self.patient_info['lean_mass_lbs']:.1f}", "body_composition_chart": graphs.get("body_composition", ""), "body_fat_percent_chart": graphs.get("body_fat_percent", "")})
|
||||
|
||||
for i in range(9):
|
||||
contexts.append({"patient_name": self.patient_info["name"], "page_number": i + 11, "vo2_breath_chart": graphs.get("vo2_breath", ""), "recovery_chart": graphs.get("recovery", "")})
|
||||
|
||||
return contexts
|
||||
|
||||
|
||||
# Usage for backend service
|
||||
def generate_report(
|
||||
pnoe_file, patient_file, spirometry_file, seca_file=None, patient_name="Moran"
|
||||
):
|
||||
"""Main function for backend service"""
|
||||
generator = ReportGenerator()
|
||||
generator.load_data(pnoe_file, patient_file, spirometry_file, seca_file)
|
||||
return generator.generate_all_contexts(patient_name)
|
||||
|
||||
|
||||
# Example usage
|
||||
if __name__ == "__main__":
|
||||
contexts = generate_report(
|
||||
"data/Pnoe_20250729_1550-Moran_Keirstyn.csv",
|
||||
"data/patient_data.csv",
|
||||
"data/spirometry_data.csv",
|
||||
"data/SECA body comp for all patients.xlsx",
|
||||
)
|
||||
print(f"Generated {len(contexts)} page contexts")
|
||||
|
||||
Reference in New Issue
Block a user