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bio-performx/app/services/graph_generator.py
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"""
Graph Generator Service
This service generates all the charts and visualizations required for the medical report.
Based on the analysis notebooks in services_dfdf/.
"""
import base64
from pathlib import Path
import matplotlib
matplotlib.use("Agg") # Use non-interactive backend
import matplotlib.pyplot as plt
import matplotlib.transforms as mtransforms
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib.patches import FancyBboxPatch
class GraphGenerator:
"""Generate all charts for medical reports"""
def __init__(self, charts_dir: str = "graphs"):
"""
Initialize the graph generator.
Args:
charts_dir: Directory to save generated charts
"""
self.charts_dir = Path(charts_dir)
self.charts_dir.mkdir(exist_ok=True)
def _image_to_base64(self, image_path: Path) -> str:
"""
Convert image file to base64 string.
Args:
image_path: Path to image file
Returns:
Base64 encoded string
"""
try:
with open(image_path, "rb") as image_file:
return base64.b64encode(image_file.read()).decode("utf-8")
except FileNotFoundError:
return ""
def generate_respiratory_chart(
self, df: pd.DataFrame, save_as_base64: bool = True
) -> str:
"""
Generate respiratory chart (VT and Speed over time).
Args:
df: Processed DataFrame with smoothed columns
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
first_unique_phase = df.drop_duplicates(subset="PHASE")
phase_times = first_unique_phase["T(sec)"].tolist()
plt.figure(figsize=(18, 5))
ax1 = plt.subplot()
# Plot VT
sns.lineplot(data=df, x="T(sec)", y="VT(l)_smoothed", label="VT (L)")
ax1.set_xlabel("Time (sec)")
ax1.set_ylabel("VT (L)")
ax1.grid(True, alpha=0.1)
ax1.set_ylim(0, min(8, df["VT(l)_smoothed"].max()))
# Plot speed on secondary y-axis
ax2 = ax1.twinx()
ax1.set_xticks(np.arange(0, df["T(sec)"].max() + 200, 200))
sns.lineplot(
data=df,
x="T(sec)",
y="Speed",
color="green",
ax=ax2,
drawstyle="steps-post",
linewidth=2,
label="Speed",
)
ax2.set_ylabel("Speed")
ax2.set_ylim(0, min(30, df["Speed"].max()) + 1)
# Combine legends
ax1.get_legend().remove()
ax2.get_legend().remove()
lines1, labels1 = ax1.get_legend_handles_labels()
lines2, labels2 = ax2.get_legend_handles_labels()
ax1.legend(lines1 + lines2, labels1 + labels2, loc="upper left")
# Add colored background regions
if len(phase_times) >= 4:
ax1.axvspan(0, phase_times[1], alpha=0.2, color="lightblue")
ax1.axvspan(phase_times[1], phase_times[2], alpha=0.2, color="purple")
ax1.axvspan(phase_times[2], phase_times[3], alpha=0.2, color="lightgreen")
ax1.axvspan(phase_times[3], df["T(sec)"].max(), alpha=0.2, color="blue")
chart_path = self.charts_dir / "respiratory.png"
plt.savefig(chart_path, dpi=300, bbox_inches="tight")
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_fuel_utilization_chart(
self, df: pd.DataFrame, save_as_base64: bool = True
) -> str:
"""
Generate fuel utilization chart (CHO vs FAT by stage).
Args:
df: Processed DataFrame with smoothed columns
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
# Group by speed and calculate mean
speed_groups = df.groupby("Speed").mean(numeric_only=True).round(1)
speed_groups = speed_groups.iloc[1:-1]
# Filter data
filtered_data = speed_groups[
(speed_groups.index >= 3.5) & (speed_groups.index <= 7.5)
]
plt.figure(figsize=(15, 8))
plt.style.use("default")
stage_labels = [f"Stage {i}" for i in range(1, len(filtered_data) + 1)]
x_positions = np.arange(len(filtered_data))
# Calculate fat and carbs energy expenditure
fat_ee = filtered_data["EE(kcal/min)"] * filtered_data["FAT(%)"] / 100
carbs_ee = filtered_data["EE(kcal/min)"] * filtered_data["CARBS(%)"] / 100
ax1 = plt.gca()
# Create stacked bar chart
ax1.bar(
x_positions,
fat_ee,
color="#1f77b4",
alpha=0.8,
width=0.6,
label="Fat",
)
ax1.bar(
x_positions,
carbs_ee,
bottom=fat_ee,
color="#ff7f0e",
alpha=0.8,
width=0.6,
label="Carbs",
)
ax1.set_xlabel("", fontsize=12)
ax1.set_ylabel("Fuel (kcal/min)", fontsize=12)
ax1.set_ylim(0, 20)
# Add values on bars
for i, (fat_val, carb_val, total_val) in enumerate(
zip(fat_ee, carbs_ee, filtered_data["EE(kcal/min)"])
):
if fat_val > 0.3:
ax1.text(
i,
fat_val / 2,
f"{fat_val:.1f}",
ha="center",
va="center",
fontsize=9,
fontweight="bold",
color="white",
)
if carb_val > 0.3:
ax1.text(
i,
fat_val + carb_val / 2,
f"{carb_val:.1f}",
ha="center",
va="center",
fontsize=9,
fontweight="bold",
color="white",
)
ax1.text(
i,
total_val + 0.5,
f"{total_val:.1f} kcal",
ha="center",
va="bottom",
fontsize=10,
fontweight="bold",
color="black",
)
# Add speed labels
for i, speed in enumerate(filtered_data.index):
ax1.text(i, -1.5, f"{speed:.1f} mph", ha="center", va="top", fontsize=9)
ax1.text(
i,
-2.8,
f"{speed * 1.609:.1f} min/km",
ha="center",
va="top",
fontsize=8,
color="gray",
)
# Create secondary y-axis for heart rate
ax2 = ax1.twinx()
ax2.plot(
x_positions,
filtered_data["HR(bpm)"],
marker="o",
linewidth=3,
markersize=8,
color="red",
label="Heart Rate",
)
ax2.set_ylabel("Heart Rate (bpm)", fontsize=12, color="red")
ax2.tick_params(axis="y", labelcolor="red")
ax2.set_ylim(0, 220)
# Add HR values
for i, hr in enumerate(filtered_data["HR(bpm)"]):
ax2.text(
i,
hr + 10,
f"{int(hr)}bpm",
ha="center",
va="bottom",
fontsize=10,
fontweight="bold",
color="red",
)
ax1.set_xticks(x_positions)
ax1.set_xticklabels(stage_labels, fontsize=11)
# Create legend
lines1, labels1 = ax1.get_legend_handles_labels()
lines2, labels2 = ax2.get_legend_handles_labels()
ax1.legend(
lines1 + lines2,
labels1 + labels2,
loc="upper left",
frameon=True,
fancybox=True,
shadow=True,
)
ax1.grid(True, alpha=0.3, linestyle="-", linewidth=0.5)
ax1.set_axisbelow(True)
plt.tight_layout()
plt.subplots_adjust(bottom=0.1, top=0.9)
chart_path = self.charts_dir / "fuel_utilization_chart.png"
plt.savefig(chart_path, dpi=300)
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_vo2_pulse_chart(
self, df: pd.DataFrame, save_as_base64: bool = True
) -> str:
"""
Generate VO2 Pulse chart with HR and Speed.
Args:
df: Processed DataFrame with smoothed columns
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
first_unique_phase = df.drop_duplicates(subset="PHASE")
phase_times = first_unique_phase["T(sec)"].tolist()
plt.figure(figsize=(18, 5))
ax1 = plt.subplot()
# Plot VO2 Pulse
sns.lineplot(
data=df,
x="T(sec)",
y="VO2 Pulse_smoothed",
label="VO2 Pulse (mL/beat)",
color="blue",
)
ax1.set_xlabel("Time (sec)")
ax1.set_ylabel("VO2 Pulse (mL/beat)")
ax1.set_ylim(0, df["VO2 Pulse_smoothed"].max())
ax1.grid(True, alpha=0.1)
# Create second y-axis for heart rate
ax2 = ax1.twinx()
sns.lineplot(
data=df,
x="T(sec)",
y="HR(bpm)_smoothed",
color="red",
ax=ax2,
linewidth=2,
label="Heart Rate (bpm)",
)
ax2.set_ylabel("Heart Rate (bpm)", color="red")
ax2.tick_params(axis="y", labelcolor="red")
ax2.set_ylim(0, df["HR(bpm)_smoothed"].max() + 1)
# Create third y-axis for speed
ax3 = ax1.twinx()
ax3.spines["right"].set_position(("outward", 60))
sns.lineplot(
data=df,
x="T(sec)",
y="Speed",
color="green",
ax=ax3,
drawstyle="steps-post",
linewidth=2,
label="Speed",
)
ax3.set_ylabel("Speed", color="green")
ax3.tick_params(axis="y", labelcolor="green")
ax3.set_ylim(0, df["Speed"].max() + 1)
ax1.set_xticks(np.arange(0, df["T(sec)"].max() + 200, 200))
# Combine legends
if ax1.get_legend():
ax1.get_legend().remove()
if ax2.get_legend():
ax2.get_legend().remove()
if ax3.get_legend():
ax3.get_legend().remove()
lines1, labels1 = ax1.get_legend_handles_labels()
lines2, labels2 = ax2.get_legend_handles_labels()
lines3, labels3 = ax3.get_legend_handles_labels()
ax1.legend(
lines1 + lines2 + lines3, labels1 + labels2 + labels3, loc="upper left"
)
# Add colored background regions
if len(phase_times) >= 4:
ax1.axvspan(0, phase_times[1], alpha=0.2, color="lightblue")
ax1.axvspan(phase_times[1], phase_times[2], alpha=0.2, color="purple")
ax1.axvspan(phase_times[2], phase_times[3], alpha=0.2, color="lightgreen")
ax1.axvspan(phase_times[3], df["T(sec)"].max(), alpha=0.2, color="blue")
chart_path = self.charts_dir / "vo2_pulse_chart.png"
plt.savefig(chart_path, bbox_inches="tight", dpi=300)
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_vo2_breath_chart(
self, df: pd.DataFrame, save_as_base64: bool = True
) -> str:
"""
Generate VO2 per Breath chart.
Args:
df: Processed DataFrame with smoothed columns
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
first_unique_phase = df.drop_duplicates(subset="PHASE")
phase_times = first_unique_phase["T(sec)"].tolist()
plt.figure(figsize=(18, 5))
ax1 = plt.subplot()
sns.lineplot(
data=df,
x="T(sec)",
y="VO2 Breath_smoothed",
label="VO2 per Breath (mL/breath)",
)
ax1.set_xlabel("Time (sec)")
ax1.set_ylabel("VO2 per Breath (mL/breath)")
ax1.set_ylim(0, df["VO2 Breath_smoothed"].max() + 1)
ax1.grid(True, alpha=0.1)
# Plot speed on secondary y-axis
ax2 = ax1.twinx()
ax1.set_xticks(np.arange(0, df["T(sec)"].max() + 200, 200))
sns.lineplot(
data=df,
x="T(sec)",
y="Speed",
color="green",
ax=ax2,
drawstyle="steps-post",
linewidth=2,
label="Speed",
)
ax2.set_ylim(0, df["Speed"].max() + 1)
ax2.set_ylabel("Speed")
# Combine legends
ax1.get_legend().remove()
ax2.get_legend().remove()
lines1, labels1 = ax1.get_legend_handles_labels()
lines2, labels2 = ax2.get_legend_handles_labels()
ax1.legend(lines1 + lines2, labels1 + labels2, loc="upper left")
# Add colored background regions
if len(phase_times) >= 4:
ax1.axvspan(0, phase_times[1], alpha=0.2, color="lightblue")
ax1.axvspan(phase_times[1], phase_times[2], alpha=0.2, color="purple")
ax1.axvspan(phase_times[2], phase_times[3], alpha=0.2, color="lightgreen")
ax1.axvspan(phase_times[3], df["T(sec)"].max(), alpha=0.2, color="blue")
chart_path = self.charts_dir / "vo2_breath_chart.png"
plt.savefig(chart_path, bbox_inches="tight", dpi=300)
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_fat_metabolism_chart(
self, df: pd.DataFrame, save_as_base64: bool = True
) -> str:
"""
Generate fat metabolism chart (CHO vs FAT over time).
Args:
df: Processed DataFrame with smoothed columns
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
first_unique_phase = df.drop_duplicates(subset="PHASE")
phase_times = first_unique_phase["T(sec)"].tolist()
plt.figure(figsize=(18, 5))
ax1 = plt.subplot()
# Plot CHO
sns.lineplot(data=df, x="T(sec)", y="CHO_smoothed", label="CHO (kcal/min)")
ax1.set_xlabel("Time (sec)")
ax1.set_ylabel("CHO (g/min)")
ax1.grid(True, alpha=0.1)
# Plot FAT on secondary y-axis
ax2 = ax1.twinx()
ax1.set_xticks(np.arange(0, df["T(sec)"].max() + 200, 200))
sns.lineplot(
data=df,
x="T(sec)",
y="FAT_smoothed",
color="green",
ax=ax2,
label="FAT (kcal/min)",
)
ax2.set_ylabel("FAT (kcal/min)")
ax2.set_ylim(0, 15)
# Combine legends
ax1.get_legend().remove()
ax2.get_legend().remove()
lines1, labels1 = ax1.get_legend_handles_labels()
lines2, labels2 = ax2.get_legend_handles_labels()
ax1.legend(lines1 + lines2, labels1 + labels2, loc="upper left")
# Add colored background regions
if len(phase_times) >= 4:
ax1.axvspan(0, phase_times[1], alpha=0.2, color="lightblue")
ax1.axvspan(phase_times[1], phase_times[2], alpha=0.2, color="purple")
ax1.axvspan(phase_times[2], phase_times[3], alpha=0.2, color="lightgreen")
ax1.axvspan(phase_times[3], df["T(sec)"].max(), alpha=0.2, color="blue")
chart_path = self.charts_dir / "fat_metabolism_chart.png"
plt.savefig(chart_path, bbox_inches="tight", dpi=300)
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_recovery_chart(
self, df: pd.DataFrame, save_as_base64: bool = True
) -> str:
"""
Generate recovery chart (VCO2, HR, and BF).
Args:
df: Processed DataFrame with smoothed columns
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
first_unique_phase = df.drop_duplicates(subset="PHASE")
phase_times = first_unique_phase["T(sec)"].tolist()
plt.figure(figsize=(18, 5))
ax1 = plt.subplot()
# Plot VCO2
sns.lineplot(
data=df,
x="T(sec)",
y="VCO2(ml/min)_smoothed",
label="VCO2 (ml/min)",
color="blue",
)
ax1.set_xlabel("Time (sec)")
ax1.set_ylabel("VO2 Pulse (mL/beat)")
ax1.set_ylim(0, df["VCO2(ml/min)"].max())
ax1.grid(True, alpha=0.1)
# Create second y-axis for heart rate
ax2 = ax1.twinx()
sns.lineplot(
data=df,
x="T(sec)",
y="HR(bpm)_smoothed",
color="red",
ax=ax2,
linewidth=2,
label="Heart Rate (bpm)",
)
ax2.set_ylabel("Heart Rate (bpm)", color="red")
ax2.set_ylim(df["HR(bpm)_smoothed"].min(), df["HR(bpm)_smoothed"].max() + 1)
ax2.tick_params(axis="y", labelcolor="red")
# Create third y-axis for BF
ax3 = ax1.twinx()
ax3.spines["right"].set_position(("outward", 60))
sns.lineplot(
data=df,
x="T(sec)",
y="BF(bpm)_smoothed",
color="green",
ax=ax3,
linewidth=2,
label="BF (bpm)",
)
ax3.set_ylabel("BF (bpm)", color="green")
ax3.tick_params(axis="y", labelcolor="green")
ax3.set_ylim(0, df["BF(bpm)_smoothed"].max() + 1)
ax1.set_xticks(np.arange(0, df["T(sec)"].max() + 200, 200))
# Combine legends
if ax1.get_legend():
ax1.get_legend().remove()
if ax2.get_legend():
ax2.get_legend().remove()
if ax3.get_legend():
ax3.get_legend().remove()
lines1, labels1 = ax1.get_legend_handles_labels()
lines2, labels2 = ax2.get_legend_handles_labels()
lines3, labels3 = ax3.get_legend_handles_labels()
ax1.legend(
lines1 + lines2 + lines3, labels1 + labels2 + labels3, loc="upper left"
)
# Add colored background regions
if len(phase_times) >= 4:
ax1.axvspan(0, phase_times[1], alpha=0.2, color="lightblue")
ax1.axvspan(phase_times[1], phase_times[2], alpha=0.2, color="purple")
ax1.axvspan(phase_times[2], phase_times[3], alpha=0.2, color="lightgreen")
ax1.axvspan(phase_times[3], df["T(sec)"].max(), alpha=0.2, color="blue")
chart_path = self.charts_dir / "recovery_chart.png"
plt.savefig(chart_path, bbox_inches="tight", dpi=300)
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_tsi_chart(
self, oxygenation_df: pd.DataFrame, save_as_base64: bool = True
) -> str:
"""
Generate TSI (Tissue Saturation Index) chart with trend lines per stage.
Args:
oxygenation_df: DataFrame with Time, TSI, and TSI-second columns
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
from numpy.polynomial.polynomial import Polynomial
plt.figure(figsize=(12, 5.5))
# Plot TSI (Left Leg)
plt.plot(
oxygenation_df["Time"],
oxygenation_df["TSI"],
label="TSI (Left Leg)",
color="steelblue",
linewidth=2,
)
# Plot TSI2 (Right Leg)
plt.plot(
oxygenation_df["Time"],
oxygenation_df["TSI-second"],
label="TSI2 (Right Leg)",
color="orange",
linewidth=2,
)
# Define time intervals for stages (adjust these based on your test protocol)
max_time = oxygenation_df["Time"].max()
intervals = [
(0, 250),
(250, 500),
(500, 750),
(750, 1000),
(1000, 1250),
(1250, 1500),
(1500, max_time),
]
# Calculate and plot trend lines for each interval
for start_time, end_time in intervals:
# Filter data for this interval
mask_interval = (oxygenation_df["Time"] >= start_time) & (
oxygenation_df["Time"] <= end_time
)
# TSI (Left Leg) trend for this interval
mask_left = mask_interval & ~oxygenation_df["TSI"].isna()
if mask_left.sum() > 1: # Need at least 2 points for a line
x_left = oxygenation_df.loc[mask_left, "Time"]
y_left = oxygenation_df.loc[mask_left, "TSI"]
coefs_left = Polynomial.fit(x_left, y_left, 1).convert().coef
trend_left = coefs_left[0] + coefs_left[1] * x_left
plt.plot(
x_left,
trend_left,
color="black",
linestyle="--",
linewidth=2,
alpha=0.8,
)
# TSI-second (Right Leg) trend for this interval
mask_right = mask_interval & ~oxygenation_df["TSI-second"].isna()
if mask_right.sum() > 1: # Need at least 2 points for a line
x_right = oxygenation_df.loc[mask_right, "Time"]
y_right = oxygenation_df.loc[mask_right, "TSI-second"]
coefs_right = Polynomial.fit(x_right, y_right, 1).convert().coef
trend_right = coefs_right[0] + coefs_right[1] * x_right
plt.plot(
x_right,
trend_right,
color="black",
linestyle="--",
linewidth=2,
alpha=0.8,
)
plt.xlabel("Time (s)")
plt.ylabel("TSI (%)")
plt.title("TSI (Left) and TSI2 (Right) with Black Slope Lines per Stage")
plt.legend(fontsize=10, loc="upper right")
plt.grid(alpha=0.25)
plt.tight_layout()
chart_path = self.charts_dir / "tsi_chart.png"
plt.savefig(chart_path, bbox_inches="tight", dpi=160)
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_body_composition_chart(
self, fat_mass_lbs: float, lean_mass_lbs: float, save_as_base64: bool = True
) -> str:
"""
Generate body composition donut chart.
Args:
fat_mass_lbs: Fat mass in pounds
lean_mass_lbs: Lean mass in pounds
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
# Calculate percentages
total_weight = fat_mass_lbs + lean_mass_lbs
fat_percentage = (fat_mass_lbs / total_weight) * 100
lean_percentage = (lean_mass_lbs / total_weight) * 100
sizes = [fat_percentage, lean_percentage]
colors = ["#fde3ac", "#ff9966"]
plt.figure(figsize=(8, 8))
# Create donut chart
plt.pie(
sizes,
autopct="",
startangle=90,
wedgeprops=dict(width=0.5, edgecolor="w"),
colors=colors,
labels=["", ""],
)
# Add custom text annotations
plt.text(
-1,
1,
f"Fat Mass ({fat_mass_lbs:.1f}lbs)\n{fat_percentage:.1f}%",
fontsize=14,
fontweight="bold",
ha="center",
va="center",
bbox=dict(boxstyle="round,pad=0.3", facecolor="white", alpha=0.8),
)
plt.text(
1,
-1,
f"Lean Mass ({lean_mass_lbs:.1f}lbs)\n{lean_percentage:.1f}%",
fontsize=14,
fontweight="bold",
ha="center",
va="center",
bbox=dict(boxstyle="round,pad=0.3", facecolor="white", alpha=0.8),
)
plt.axis("equal")
chart_path = self.charts_dir / "body_composition_chart.png"
plt.savefig(chart_path, bbox_inches="tight", dpi=600)
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_body_fat_percent_chart(
self,
fat_percentage: float,
age: int,
gender: str,
save_as_base64: bool = True,
) -> str:
"""
Generate body fat percentage chart.
Args:
fat_percentage: Body fat percentage
age: Patient age
gender: Patient gender ('male' or 'female')
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
# Determine age group
if 20 <= age <= 39:
age_group = "20-39"
elif 40 <= age <= 59:
age_group = "40-59"
elif 60 <= age <= 79:
age_group = "60-79"
else:
age_group = "20-39" # Default
gender_abbrev = "M" if gender.lower() == "male" else "F"
demographic = f"{age_group}\n({gender_abbrev})"
# Define segments based on gender and age group
if gender.lower() == "female":
if age_group == "20-39":
segments = [
("#F8A8A8", 0, 15), # Bad: 0-15%
("#FFEECC", 15, 5), # Okay: 15-20%
("#D0F0C0", 20, 15), # Good: 20-35%
("#FFEECC", 35, 5), # Okay: 35-40%
("#F8A8A8", 40, 10), # Bad: 40-50%
]
else: # 40-59 and 60-79 have same ranges for females
segments = [
("#F8A8A8", 0, 20), # Bad: 0-20%
("#FFEECC", 20, 5), # Okay: 20-25%
("#D0F0C0", 25, 10), # Good: 25-35%
("#FFEECC", 35, 5), # Okay: 35-40%
("#F8A8A8", 40, 10), # Bad: 40-50%
]
else: # male
if age_group == "20-39":
segments = [
("#F8A8A8", 0, 5), # Bad: 0-5%
("#FFEECC", 5, 5), # Okay: 5-10%
("#D0F0C0", 10, 10), # Good: 10-20%
("#FFEECC", 20, 5), # Okay: 20-25%
("#F8A8A8", 25, 25), # Bad: 25-50%
]
elif age_group == "40-59":
segments = [
("#F8A8A8", 0, 5), # Bad: 0-5%
("#FFEECC", 5, 5), # Okay: 5-10%
("#D0F0C0", 10, 10), # Good: 10-20%
("#FFEECC", 20, 10), # Okay: 20-30%
("#F8A8A8", 30, 20), # Bad: 30-50%
]
else: # 60-79
segments = [
("#F8A8A8", 0, 5), # Bad: 0-5%
("#FFEECC", 5, 5), # Okay: 5-10%
("#D0F0C0", 10, 15), # Good: 10-25%
("#FFEECC", 25, 5), # Okay: 25-30%
("#F8A8A8", 30, 20), # Bad: 30-50%
]
fig, ax = plt.subplots(figsize=(10, 2))
# Create the segmented bar
for color, start, length in segments:
ax.barh(
y=0,
width=length,
left=start,
height=1,
color=color,
edgecolor="black",
linewidth=0.5,
)
# Add the indicator (triangle)
ax.plot(
fat_percentage,
1.05,
marker="v",
color="black",
markersize=10,
clip_on=False,
transform=ax.get_xaxis_transform(),
)
# Set axis properties
ax.set_xlim(0, 50)
ax.set_xticks(range(0, 51, 5))
ax.set_yticks([])
ax.text(
-0.05,
0,
demographic,
transform=ax.get_yaxis_transform(),
va="center",
ha="right",
fontsize=12,
)
ticks = range(0, 51, 5)
ax.set_xticks(ticks)
labels = [f"{t}%" for t in ticks]
ax.set_xticklabels(labels)
# Clean up spines
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
ax.spines["left"].set_visible(False)
ax.spines["bottom"].set_visible(True)
# Add tick marks
for x in range(0, 51, 5):
ax.plot(
[x, x],
[-0.05, -0.01],
color="black",
transform=ax.get_xaxis_transform(),
clip_on=False,
)
plt.tight_layout()
chart_path = self.charts_dir / "body_fat_percent_chart.png"
plt.savefig(chart_path, bbox_inches="tight", dpi=300)
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_spirometry_chart(
self, spirometry_df: pd.DataFrame, save_as_base64: bool = True
) -> str:
"""
Generate spirometry chart with Z-scores.
Args:
spirometry_df: Spirometry DataFrame with parameters
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
# Coerce numeric columns - handle various column name formats
# Map standard column names to possible variations
column_aliases = {
"Best": ["Best", "best", "BEST"],
"LLN": ["LLN", "lln"],
"Pred.": ["Pred.", "Pred", "pred", "Predicted", "predicted"],
"%Pred.": [
"%Pred.",
"%Pred",
"%pred",
"% Pred.",
"% Pred",
"Pred %",
"Pred%",
],
"ZScore": ["ZScore", "Z-Score", "z-score", "Zscore", "zscore", "Z Score"],
}
# Find and normalize column names
column_mapping = {}
for target_col, possible_names in column_aliases.items():
for col_name in possible_names:
if col_name in spirometry_df.columns:
column_mapping[target_col] = col_name
# Convert to numeric
spirometry_df[col_name] = pd.to_numeric(
spirometry_df[col_name], errors="coerce"
)
break
# If standard columns don't exist, create aliases
for target_col, source_col in column_mapping.items():
if target_col not in spirometry_df.columns and source_col != target_col:
spirometry_df[target_col] = spirometry_df[source_col]
# Select rows of interest
rows_map = {
"Lung Volume": "FVC",
"Lung Power": "FEV1",
"Power/Volume": "FEV1/FVC%",
}
records = []
for label, param in rows_map.items():
# Try exact match first
row = spirometry_df.loc[spirometry_df["Parameters"].str.strip() == param]
if row.empty:
# Try case-insensitive match
row = spirometry_df.loc[
spirometry_df["Parameters"].str.strip().str.upper() == param.upper()
]
if row.empty:
# Try matching without % sign
if "%" in param:
param_no_pct = param.replace("%", "")
row = spirometry_df.loc[
spirometry_df["Parameters"].str.strip() == param_no_pct
]
if row.empty:
print(f"Warning: Could not find parameter '{param}' in spirometry data")
print(f"Available parameters: {spirometry_df['Parameters'].tolist()}")
continue
row = row.iloc[0]
# Get values with fallbacks for column name variations
best_val = row.get("Best", row.get("best", pd.NA))
pct_val = row.get(
"%Pred.", row.get("%Pred", row.get("Pred %", row.get("Pred%", pd.NA)))
)
z_val = row.get("ZScore", row.get("Z-Score", row.get("Zscore", pd.NA)))
records.append(
{
"label": label,
"param": param,
"best": best_val,
"pct": pct_val,
"z": z_val,
}
)
# Validate we have exactly 3 records
if len(records) != 3:
raise ValueError(
f"Expected 3 spirometry parameters (FVC, FEV1, FEV1/FVC%), "
f"but found {len(records)}. Found: {[r['param'] for r in records]}"
)
# Figure setup
fig, axes = plt.subplots(
nrows=3,
ncols=1,
figsize=(11.5, 3.6),
sharex=True,
gridspec_kw={"hspace": 0.65},
)
x_min, x_max = -5, 3
# Segment colors
segments = [
(-5, -4, "#f4a7a7"), # red-ish
(-4, -3, "#f7c49a"), # orange-ish
(-3, -1.7, "#f6e3a3"), # yellow-ish
(-1.7, 3, "#c9f0cc"), # green-ish
]
ticks = np.arange(x_min, x_max + 1, 1)
labels = [str(i) for i in ticks]
# Plot each row
for ax, rec in zip(axes, records):
# Background segments
for a, b, color in segments:
ax.barh(
0, width=b - a, left=a, height=0.6, color=color, edgecolor="none"
)
# LLN and Predicted markers
ax.axvline(0, color="black", lw=1)
# Z-score pointer
if pd.notna(rec["z"]):
trans = mtransforms.blended_transform_factory(
ax.transData, ax.transAxes
)
ax.plot(
float(rec["z"]),
1.2,
marker="v",
markersize=12,
color="dimgray",
transform=trans,
clip_on=False,
)
# Labels and styling
ax.set_title(
rec["label"], loc="left", fontsize=11, fontweight="bold", pad=2
)
ax.set_xlim(x_min, x_max)
ax.set_yticks([])
ax.set_xticks(ticks)
ax.set_xticklabels(labels, fontsize=8)
ax.set_xlabel("")
# Top annotations
axes[0].text(-1.7, 0.45, "LLN", ha="center", va="bottom", fontsize=9)
axes[0].text(0, 0.45, "Predicted", ha="center", va="bottom", fontsize=9)
# Right-side summary boxes
fig.subplots_adjust(right=0.78)
box_ax = fig.add_axes([0.805, 0.06, 0.18, 0.90])
box_ax.axis("off")
def pill(ax, xy, text):
x, y = xy
bbox = FancyBboxPatch(
(x - 0.48, y - 0.09),
0.96,
0.18,
boxstyle="round,pad=0.02,rounding_size=0.08",
ec="#dddddd",
fc="#f3f3f3",
linewidth=1.0,
)
ax.add_patch(bbox)
ax.text(
x,
y + 0.025,
text,
ha="center",
va="center",
fontsize=11,
fontweight="bold",
)
ax.text(
x,
y - 0.055,
"of predicted",
ha="center",
va="center",
fontsize=9,
color="#555555",
)
box_ax.set_xlim(0, 1)
box_ax.set_ylim(0, 1)
# Prepare display strings
right_items = []
for rec in records:
name = (
"FVC"
if rec["param"] == "FVC"
else ("FEV1" if rec["param"] == "FEV1" else "FEV1/FVC")
)
unit = "L" if rec["param"] in ("FVC", "FEV1") else "%"
value_fmt = f"{rec['best']:.2f}{unit}"
pct_fmt = f"{rec['pct']:.1f}%"
right_items.append((name, value_fmt, pct_fmt))
# Sort to match order
order = ["FVC", "FEV1", "FEV1/FVC"]
right_items_sorted = [
next(item for item in right_items if item[0] == k) for k in order
]
ys = [0.82, 0.48, 0.15]
for (name, value_fmt, pct_fmt), y in zip(right_items_sorted, ys):
main_line = f"{name}\n{value_fmt}{pct_fmt}"
pill(box_ax, (0.5, y), main_line)
chart_path = self.charts_dir / "spirometry_chart.png"
plt.savefig(chart_path, dpi=300, bbox_inches="tight")
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_metabolism_chart(
self, rmr_kcal: float, save_as_base64: bool = True
) -> str:
"""
Generate metabolism chart (Slow vs Fast Metabolism).
Args:
rmr_kcal: Resting metabolic rate in kcal/day
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
from matplotlib.patches import FancyBboxPatch
fig, ax = plt.subplots(figsize=(10, 2.5))
# Chart data and positions
categories = ["Very Slow", "Slow", "Average", "Fast", "Very Fast"]
positions = [1500, 3000, 4500, 6000, 7500]
indicator_pos = rmr_kcal
highlight_end = rmr_kcal
# Main Bar (Background)
main_bar = FancyBboxPatch(
(0, 0.4),
9000,
0.2,
boxstyle="round,pad=0,rounding_size=0.1",
ec="none",
fc="#E0E0E0",
)
ax.add_patch(main_bar)
# Highlighted Bar
highlight_bar = FancyBboxPatch(
(0, 0.4),
highlight_end,
0.2,
boxstyle="round,pad=0,rounding_size=0.1",
ec="none",
fc="#B2FFC8",
)
ax.add_patch(highlight_bar)
# Text and Labels
ax.text(
highlight_end / 2,
0.5,
f"{rmr_kcal:.0f}kCals",
ha="center",
va="center",
color="#006400",
fontsize=14,
weight="bold",
)
# Indicator Triangle
ax.plot(indicator_pos, 0.65, "v", markersize=15, color="#606060", clip_on=False)
# Ticks and Labels
for pos, label in zip(positions, categories):
ax.text(
pos, 0.15, label, ha="center", va="center", fontsize=12, color="#333333"
)
ax.plot([pos, pos], [0.35, 0.39], color="grey", lw=5)
# Chart Styling
ax.set_title("Slow vs Fast Metabolism", fontsize=18, weight="bold", loc="left")
ax.set_xlim(0, 9000)
ax.set_ylim(0, 1)
ax.axis("off")
plt.tight_layout()
chart_path = self.charts_dir / "metabolism_chart.png"
plt.savefig(chart_path, bbox_inches="tight", dpi=300)
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
def generate_fuel_source_chart(
self, fat_percentage: float, save_as_base64: bool = True
) -> str:
"""
Generate fuel source chart (Fats vs Carbs).
Args:
fat_percentage: Fat percentage at rest
save_as_base64: If True, return base64 string, else return file path
Returns:
Base64 string or file path
"""
from matplotlib.patches import FancyBboxPatch
fig, ax = plt.subplots(figsize=(10, 2.5))
carb_percentage = 100 - fat_percentage
optimal_point = 75
# Main Bars (Fats and Carbs)
# Fats bar (yellow)
fats_bar = FancyBboxPatch(
(0, 0.4),
fat_percentage,
0.2,
boxstyle="round,pad=0,rounding_size=0.1",
ec="none",
fc="#FEEAAB",
)
ax.add_patch(fats_bar)
# Carbs bar (blue) - starts where the fats bar ends
carbs_bar = FancyBboxPatch(
(fat_percentage, 0.4),
carb_percentage,
0.2,
boxstyle="round,pad=0,rounding_size=0.1",
ec="none",
fc="#A7F5FF",
)
ax.add_patch(carbs_bar)
# Text and Labels
ax.text(
fat_percentage / 2,
0.5,
f"Fats\n{fat_percentage:.1f}%",
ha="center",
va="center",
color="#333333",
fontsize=12,
weight="bold",
)
ax.text(
fat_percentage + carb_percentage / 2,
0.5,
f"Carbs\n{carb_percentage:.1f}%",
ha="center",
va="center",
color="#333333",
fontsize=12,
weight="bold",
)
# Add 'Optimal' label
ax.text(optimal_point, 0.75, "Optimal", ha="center", va="center", fontsize=12)
# Indicator Triangle
ax.plot(
fat_percentage, 0.65, "v", markersize=15, color="#606060", clip_on=False
)
# Ticks and Labels
positions = [0, 25, 50, 75, 100]
for pos in positions:
ax.text(
pos,
0.15,
str(pos),
ha="center",
va="center",
fontsize=12,
color="#333333",
)
ax.plot([pos, pos], [0.35, 0.39], color="grey", lw=5)
# Add a special tick for the 'Optimal' point
ax.plot([optimal_point, optimal_point], [0.6, 0.7], color="black", lw=2)
# Chart Styling
ax.set_title("Fuel Source", fontsize=18, weight="bold", loc="left")
ax.set_ylim(0, 1)
ax.axis("off")
plt.tight_layout()
chart_path = self.charts_dir / "fuel_source_chart.png"
plt.savefig(chart_path, bbox_inches="tight", dpi=300)
plt.close()
return self._image_to_base64(chart_path) if save_as_base64 else str(chart_path)
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def generate_vo2_max_table(
self,
data: list[list],
columns: list[str],
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vo2_max_value: float = None,
category: str = None,
cell_colors: list[list[str]] = None,
save_as_base64: bool = True,
) -> str:
"""
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Generate VO2 Max table as an image with optimized sizing, highlighting the patient's category.
Args:
data: List of rows (each row is a list of values)
columns: List of column headers
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vo2_max_value: Patient's VO2 max value (for title and arrow)
category: Category that the patient falls into (e.g., 'Good', 'Excellent')
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cell_colors: Optional matrix of cell colors
save_as_base64: If True, return base64 string
Returns:
Base64 string or file path
"""
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import io
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from matplotlib.patches import FancyArrowPatch, RegularPolygon
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# Fixed optimal sizing for VO2 Max table (7 columns, 1 data row)
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fig, ax = plt.subplots(figsize=(14, 2.2))
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ax.axis("off")
# Create table
table = ax.table(
cellText=data,
colLabels=columns,
cellLoc="center",
loc="center",
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bbox=[0, 0, 1, 1],
)
# Style the table
table.auto_set_font_size(False)
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table.set_fontsize(11)
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table.scale(1, 1.8)
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# Header row styling (cyan background)
for i in range(len(columns)):
cell = table[(0, i)]
cell.set_facecolor("#7dd3fc") # cyan-300 equivalent
cell.set_text_props(weight="bold", color="black", fontsize=12)
cell.set_edgecolor("#9ca3af") # gray-400
cell.set_linewidth(1)
# Find the column index for the category (if provided)
category_index = None
if category and category in columns:
category_index = columns.index(category)
# Data row styling
for i in range(len(data[0])):
cell = table[(1, i)]
if i == 0: # Age column
cell.set_facecolor("#a5f3fc") # cyan-200
cell.set_text_props(weight="semibold", color="black", fontsize=11)
else:
cell.set_facecolor("#f3f4f6") # gray-100
cell.set_text_props(color="black", fontsize=10)
# Bold the cell that corresponds to the patient's category
if category_index is not None and i == category_index:
cell.set_text_props(weight="bold", color="black", fontsize=11)
cell.set_edgecolor("#9ca3af") # gray-400
cell.set_linewidth(1)
# Add arrow indicator below the category column
if category_index is not None:
# Calculate position
cell_width = 1.0 / len(columns)
arrow_x = (category_index + 0.5) * cell_width
# Draw arrow pointing up
arrow = FancyArrowPatch(
(arrow_x, -0.15),
(arrow_x, -0.05),
arrowstyle="->",
mutation_scale=20,
linewidth=2,
color="black",
transform=ax.transAxes,
)
ax.add_patch(arrow)
# Add triangle at the top
triangle = RegularPolygon(
(arrow_x, -0.05),
3,
radius=0.02,
orientation=np.pi / 2,
color="black",
transform=ax.transAxes,
)
ax.add_patch(triangle)
# Set title - calculate approximate percentile
if vo2_max_value is not None:
if category == "Superior":
percentile = "100th percentile"
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else:
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percentile_map = {
"Very Poor": "1st-10th percentile",
"Poor": "10th-20th percentile",
"Fair": "20th-40th percentile",
"Good": "40th-60th percentile",
"Excellent": "60th-80th percentile",
}
percentile = percentile_map.get(category, "N/A")
title = f"VO2 Max - {vo2_max_value:.1f} ({percentile})"
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ax.set_title(title, fontsize=14, fontweight="bold", pad=10)
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if save_as_base64:
buf = io.BytesIO()
plt.savefig(
buf,
format="png",
bbox_inches="tight",
dpi=300,
facecolor="white",
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pad_inches=0.05,
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)
plt.close(fig)
buf.seek(0)
return base64.b64encode(buf.read()).decode("utf-8")
else:
output_path = (
self.charts_dir / f"vo2_max_table_{pd.Timestamp.now().timestamp()}.png"
)
plt.savefig(
output_path,
bbox_inches="tight",
dpi=300,
facecolor="white",
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pad_inches=0.05,
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)
plt.close(fig)
return str(output_path)
def generate_heart_rate_zones_table(
self,
data: list[list],
columns: list[str],
cell_colors: list[list[str]] = None,
save_as_base64: bool = True,
) -> str:
"""
Generate Heart Rate Zones table as an image with optimized sizing.
Args:
data: List of rows (each row is a list of values)
columns: List of column headers (Zone 1-5)
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cell_colors: Optional matrix of cell colors (IGNORED - using notebook colors)
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save_as_base64: If True, return base64 string
Returns:
Base64 string or file path
"""
import io
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# Optimal sizing for HR Zones table (5 columns, 8 rows) - match notebook exactly
fig, ax = plt.subplots(figsize=(12, 8))
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ax.axis("off")
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# Data comes pre-formatted with newlines from context_generator - use as-is
# No text wrapping needed
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# Create table without rowLabels - match notebook exactly
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table = ax.table(
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cellText=data,
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colLabels=columns,
loc="center",
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cellLoc="center",
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)
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# Style the table - match notebook exactly
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table.auto_set_font_size(False)
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table.set_fontsize(10)
table.scale(1, 3.5) # Increased vertical scale for multi-line text
# Header row styling
for j, label in enumerate(columns):
cell = table[(0, j)]
cell.set_facecolor("#7dd3fc") # cyan-300
cell.set_text_props(weight="bold")
# Row specific styling - match notebook colors exactly
colors = ["#fecaca", "#fecaca", "#fef08a", "#bbf7d0", "#bbf7d0"]
# HR BPM row is at index 2 (0-based in data) -> row 3 in table (0 is header)
for j in range(len(columns)):
cell = table[(3, j)]
cell.set_facecolor(colors[j])
cell.set_text_props(weight="bold")
# Breathing row is at index 7 -> row 8 in table
for j in range(len(columns)):
cell = table[(8, j)]
cell.set_facecolor(colors[j])
cell.set_text_props(weight="bold")
# Add title matching notebook
plt.title(
"Personalized Heart Rate Zones", fontsize=16, fontweight="bold", pad=5
)
plt.tight_layout()
if save_as_base64:
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buf = io.BytesIO()
plt.savefig(
buf,
format="png",
bbox_inches="tight",
dpi=300,
facecolor="white",
)
plt.close(fig)
buf.seek(0)
return base64.b64encode(buf.read()).decode("utf-8")
else:
output_path = (
self.charts_dir / f"hr_zones_table_{pd.Timestamp.now().timestamp()}.png"
)
plt.savefig(
output_path,
bbox_inches="tight",
dpi=300,
facecolor="white",
)
plt.close(fig)
return str(output_path)
def generate_resting_heart_rate_table(
self,
data: list[list],
columns: list[str],
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rhr_value: float = None,
category: str = None,
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cell_colors: list[list[str]] = None,
save_as_base64: bool = True,
) -> str:
"""
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Generate Resting Heart Rate table as an image with optimized sizing, highlighting the patient's category.
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Args:
data: List of rows (each row is a list of values)
columns: List of column headers
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rhr_value: Patient's resting heart rate value in bpm (for title and arrow)
category: Category that the patient falls into (e.g., 'Good', 'Excellent')
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cell_colors: Optional matrix of cell colors
save_as_base64: If True, return base64 string
Returns:
Base64 string or file path
"""
import io
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from matplotlib.patches import FancyArrowPatch, RegularPolygon
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# Optimal sizing for RHR table (8 columns, 1 data row)
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fig, ax = plt.subplots(figsize=(16, 2.2))
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ax.axis("off")
# Create table
table = ax.table(
cellText=data,
colLabels=columns,
cellLoc="center",
loc="center",
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bbox=[0, 0, 1, 1],
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)
# Style the table
table.auto_set_font_size(False)
table.set_fontsize(11)
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table.scale(1, 1.8)
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# Header row styling (cyan background)
for i in range(len(columns)):
cell = table[(0, i)]
cell.set_facecolor("#7dd3fc") # cyan-300 equivalent
cell.set_text_props(weight="bold", color="black", fontsize=12)
cell.set_edgecolor("#9ca3af") # gray-400
cell.set_linewidth(1)
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# Find the column index for the category (if provided)
category_index = None
if category and category in columns:
category_index = columns.index(category)
# Data row styling
for i in range(len(data[0])):
cell = table[(1, i)]
if i == 0: # Age column
cell.set_facecolor("#a5f3fc") # cyan-200
cell.set_text_props(weight="semibold", color="black", fontsize=11)
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else:
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# Highlight the category cell with light green background
if category_index is not None and i == category_index:
cell.set_facecolor("#d1fae5") # green-200 equivalent
cell.set_text_props(weight="bold", color="black", fontsize=11)
else:
cell.set_facecolor("#f3f4f6") # gray-100
cell.set_text_props(color="black", fontsize=10)
cell.set_edgecolor("#9ca3af") # gray-400
cell.set_linewidth(1)
# Add arrow indicator below the category column
if category_index is not None:
# Calculate position
cell_width = 1.0 / len(columns)
arrow_x = (category_index + 0.5) * cell_width
# Draw arrow pointing up
arrow = FancyArrowPatch(
(arrow_x, -0.15),
(arrow_x, -0.05),
arrowstyle="->",
mutation_scale=20,
linewidth=2,
color="black",
transform=ax.transAxes,
)
ax.add_patch(arrow)
# Add triangle at the top
triangle = RegularPolygon(
(arrow_x, -0.05),
3,
radius=0.02,
orientation=np.pi / 2,
color="black",
transform=ax.transAxes,
)
ax.add_patch(triangle)
# Set title
if rhr_value is not None:
title = f"Resting Heart Rate - {rhr_value:.0f}bpm"
ax.set_title(title, fontsize=14, fontweight="bold", pad=10)
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if save_as_base64:
buf = io.BytesIO()
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plt.savefig(
buf,
format="png",
bbox_inches="tight",
dpi=300,
facecolor="white",
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pad_inches=0.05,
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)
plt.close(fig)
buf.seek(0)
return base64.b64encode(buf.read()).decode("utf-8")
else:
output_path = (
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self.charts_dir / f"rhr_table_{pd.Timestamp.now().timestamp()}.png"
)
plt.savefig(
output_path,
bbox_inches="tight",
dpi=300,
facecolor="white",
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pad_inches=0.05,
)
plt.close(fig)
return str(output_path)