feat: add functionality to plot time series of steps

Author: chanshing

setup.py

@@ -62,7 +62,8 @@ def get_string(string, rel_path="src/stepcount/__init__.py"):
         "torch==1.13.*",
         "torchvision==0.14.*",
         "transforms3d==0.4.*",
-        "numba==0.58.*"
+        "numba==0.58.*",
+        "matplotlib==3.7.*",
     ],
     extras_require={
         "dev": [

src/stepcount/stepcount.py

@@ -11,6 +11,8 @@
 import numpy as np
 import pandas as pd
 import joblib
+import matplotlib.pyplot as plt
+import matplotlib.dates as mdates
 from numba import njit
 
 from stepcount import utils
@@ -388,6 +390,10 @@ def main():
     print(daily_adj.set_index('Date').drop(columns='Filename'))
     print("\nOutput files saved in:", outdir)
 
+    print("\nPlotting...")
+    fig = plot(Y, title=basename)
+    fig.savefig(f"{outdir}/{basename}-Steps.png", bbox_inches='tight', pad_inches=0)
+
     after = time.time()
     print(f"Done! ({round(after - before,2)}s)")
 
@@ -1085,6 +1091,73 @@ def numba_detect_bouts(
     return bouts
 
 
+def plot(Y, title=None):
+    """
+    Plot time series of steps per minute for each day.
+
+    Parameters:
+    - Y: pandas Series or DataFrame with a 'Steps' column. Must have a DatetimeIndex.
+
+    Returns:
+    - fig: matplotlib figure object
+    """
+
+    MAX_STEPS_PER_MINUTE = 180
+
+    if isinstance(Y, pd.DataFrame):
+        Y = Y['Steps']
+
+    assert isinstance(Y, pd.Series), "Y must be a pandas Series, or a DataFrame with a 'Steps' column"
+
+    # Resample to 1 minute intervals
+    # Note: .sum() returns 0 when all values are NaN, so we need to use a custom function
+    def _sum(x):
+        if x.isna().all():
+            return np.nan
+        return x.sum()
+
+    Y = Y.resample('1T').agg(_sum)
+
+    dates_index = Y.index.normalize()
+    unique_dates = dates_index.unique()
+
+    # Set the plot figure and size
+    fig = plt.figure(figsize=(10, len(unique_dates) * 2))
+
+    # Group by each day
+    for i, (day, y) in enumerate(Y.groupby(dates_index)):
+        ax = fig.add_subplot(len(unique_dates), 1, i + 1)
+
+        # Plot steps
+        ax.plot(y.index, y, label='steps/min')
+
+        # Grey shading where NA
+        ax.fill_between(y.index, 0, MAX_STEPS_PER_MINUTE, where=y.isna(), color='grey', alpha=0.3, interpolate=True, label='missing')
+
+        # Formatting the x-axis to show hours and minutes
+        ax.xaxis.set_major_locator(mdates.HourLocator(interval=1))
+        ax.xaxis.set_minor_locator(mdates.MinuteLocator(interval=15))
+        ax.xaxis.set_major_formatter(mdates.DateFormatter("%H:%M"))
+
+        # Set x-axis limits to start at 00:00 and end at 24:00
+        ax.set_xlim(day, day + pd.DateOffset(days=1))
+        # Set y-axis limits
+        ax.set_ylim(-10, MAX_STEPS_PER_MINUTE)
+
+        ax.tick_params(axis='x', rotation=45)
+        ax.set_ylabel('steps/min')
+        ax.set_title(day.strftime('%Y-%m-%d'))
+        ax.grid(True)
+        ax.legend(loc='upper left')
+
+    if title:
+        fig.suptitle(title)
+
+    fig.tight_layout()
+
+    return fig
+
+
 
 if __name__ == '__main__':
     main()