- Docstrings, README and examples

Author: Nicolas Legrand

README.rst

@@ -43,92 +43,25 @@ The following packages are required to use Systole:
 * Pandas (>=0.24)
 * Matplotlib (>=3.0.2)
 * Seaborn (>=0.9.0)
+* py-ecg-detectors (>=1.0.2)
 
-Recording
-=========
-
-Systole natively supports the recording of PPG signals through the `Nonin 3012LP Xpod USB pulse oximeter <https://www.nonin.com/products/xpod/>`_ together with the `Nonin 8000SM 'soft-clip' fingertip sensors <https://www.nonin.com/products/8000s/>`_.
-It can easily interface with `PsychoPy <https://www.psychopy.org/>`_ to record PPG signal during psychological experiments, and to synchronize stimulus deliver to e.g., systole or diastole.
-
-For example, you can record and plot data in less than 6 lines of code:
-
-.. code-block:: python
-
-  import serial
-  from systole.recording import Oximeter
-  ser = serial.Serial('COM4')  # Add your USB port here
-
-  # Open serial port, initialize and plot recording for Oximeter
-  oxi = Oximeter(serial=ser).setup().read(duration=10)
-
-
-Interfacing with PsychoPy
--------------------------
-
-The ``Oximeter`` class can be used together with a stimulus presentation software to record cardiac activity during psychological experiments.
-
-* The ``read()`` method
-
-will record for a predefined amount of time (specified by the ``duration`` parameter, in seconds). This 'serial mode' is the easiest and most robust method, but it does not allow the execution of other instructions in the meantime.
-
-.. code-block:: python
-
-  # Code 1 {}
-  oximeter.read(duration=10)
-  # Code 2 {}
-
-* The ``readInWaiting()`` method
+Interactive plotting functions and reports generation will also require the following packages to be installed:
 
-will only read the bytes temporally stored in the USB buffer. For the Nonin device, this represents up to 10 seconds of recording (this procedure should be executed at least one time every 10 seconds for a continuous recording). When inserted into a while loop, it can record PPG signal in parallel with other commands.
+* plotly (>=4.8.0)
+* plotly_express (>=0.4.1)
 
-.. code-block:: python
-
-  import time
-  tstart = time.time()
-  while time.time() - tstart < 10:
-      oximeter.readInWaiting()
-      # Insert code here {...}
-
-Online detection
-----------------
-
-Online heart beat detection, for cardiac-stimulus synchrony:
-
-.. code-block:: python
-
-  import serial
-  import time
-  from systole.recording import Oximeter
-
-  # Open serial port
-  ser = serial.Serial('COM4')  # Change this value according to your setup
-
-  # Create an Oxymeter instance and initialize recording
-  oxi = Oximeter(serial=ser, sfreq=75, add_channels=4).setup()
+For an overview of all the recording functionalities, you can refer to the following tutorials:
 
-  # Online peak detection for 10 seconds
-  tstart = time.time()
-  while time.time() - tstart < 10:
-      while oxi.serial.inWaiting() >= 5:
-          paquet = list(oxi.serial.read(5))
-          oxi.add_paquet(paquet[2])  # Add new data point
-          if oxi.peaks[-1] == 1:
-            print('Heartbeat detected')
+* Recording
+* Artefacts detection and artefacts correction
+* Heart rate variability
 
-Peaks detection
-===============
-
-Heartbeats can be detected in the PPG signal either online or offline.
-
-Methods from clipping correction and peak detection algorithm is adapted from [#]_.
-
-.. code-block:: python
-
-  # Plot data
-  oxi.plot_oximeter()
+Recording
+=========
 
-.. figure::  https://github.com/embodied-computation-group/systole/raw/master/Images/recording.png
-   :align:   center
+Systole natively supports recording of physiological signals from the following setups:
+* `Nonin 3012LP Xpod USB pulse oximeter <https://www.nonin.com/products/xpod/>`_ together with the `Nonin 8000SM 'soft-clip' fingertip sensors <https://www.nonin.com/products/8000s/>`_ (USB).
+* Remote Data Access (RDA) via BrainVision Recorder together with Brain product ExG amplifier `<https://www.brainproducts.com/>`_ (Ethernet).
 
 Artefact correction
 ===================

examples/Tutorial_HRV.py

@@ -0,0 +1,54 @@
+"""
+Recording
+=========
+
+
+"""
+
+# Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>
+# Licence: GPL v3
+
+# It can easily interface with `PsychoPy <https://www.psychopy.org/>`_ to
+# record PPG signal during psychological experiments, and to synchronize
+# stimulus deliver to e.g., systole or diastole.
+
+# For example, you can record and plot data in less than 6 lines of code:
+
+
+#%%
+# Event related cardiac deceleration
+# ----------------------------------
+import serial
+from systole.recording import Oximeter
+ser = serial.Serial('COM4')  # Add your USB port here
+
+# Open serial port, initialize and plot recording for Oximeter
+oxi = Oximeter(serial=ser).setup().read(duration=10)
+
+
+Interfacing with PsychoPy
+-------------------------
+
+The ``Oximeter`` class can be used together with a stimulus presentation software to record cardiac activity during psychological experiments.
+
+* The ``read()`` method
+
+will record for a predefined amount of time (specified by the ``duration`` parameter, in seconds). This 'serial mode' is the easiest and most robust method, but it does not allow the execution of other instructions in the meantime.
+
+.. code-block:: python
+
+  # Code 1 {}
+  oximeter.read(duration=10)
+  # Code 2 {}
+
+* The ``readInWaiting()`` method
+
+will only read the bytes temporally stored in the USB buffer. For the Nonin device, this represents up to 10 seconds of recording (this procedure should be executed at least one time every 10 seconds for a continuous recording). When inserted into a while loop, it can record PPG signal in parallel with other commands.
+
+.. code-block:: python
+
+  import time
+  tstart = time.time()
+  while time.time() - tstart < 10:
+      oximeter.readInWaiting()
+      # Insert code here {...}

examples/Tutorial_recording.py

@@ -0,0 +1,87 @@
+"""
+Recording PPG signal
+====================
+"""
+
+# Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>
+# Licence: GPL v3
+
+# The py:class:systole.recording.Oximeter class can be used to read incoming
+# PPG signal from `Nonin 3012LP Xpod USB pulse oximeter
+# <https://www.nonin.com/products/xpod/>`_ together with the `Nonin 8000SM
+# 'soft-clip' fingertip sensors <https://www.nonin.com/products/8000s/>`_.
+# This function can easily be integrated with other stimulus presentation
+# software lie `PsychoPy <https://www.psychopy.org/>`_ to record cardiac
+# activity during psychological experiments, or to synchronize stimulus
+# delivery with cardiac phases (e.g. systole or diastole).
+
+
+#%%
+# Reading
+# -------
+# Recording and plotting your first time-series will only require 5 lines
+# of code:
+
+import serial
+from systole.recording import Oximeter
+ser = serial.Serial('COM4')  # Add your USB port here
+
+# Open serial port, initialize and plot recording for Oximeter
+oxi = Oximeter(serial=ser).setup().read(duration=10)
+
+# The signal can be directly plotted using built-in functions.
+oxi.plot_oximeter()
+
+##############################################################################
+# .. figure::  https://github.com/embodied-computation-group/systole/raw/master/Images/recording.png
+#    :align:   center
+##############################################################################
+
+#%%
+# Interfacing with PsychoPy
+# -------------------------
+
+# * The ``read()`` method will record for a predefined amount of time
+# (specified by the ``duration`` parameter, in seconds). This 'serial mode'
+# is the easiest and most robust method, but it does not allow the execution
+# of other instructions in the meantime.
+
+# Code 1 {}
+oximeter.read(duration=10)
+# Code 2 {}
+
+# * The ``readInWaiting()`` method will only read the bytes temporally stored
+# in the USB buffer. For the Nonin device, this represents up to 10 seconds of
+# recording (this procedure should be executed at least one time every 10
+# seconds for a continuous recording). When inserted into a while loop, it can
+# record PPG signal in parallel with other commands.
+
+import time
+tstart = time.time()
+while time.time() - tstart < 10:
+    oximeter.readInWaiting()
+    # Insert code here {...}
+
+#%%
+# Online detection
+# ----------------
+# Online heart beat detection, for cardiac-stimulus synchrony
+
+import serial
+import time
+from systole.recording import Oximeter
+
+# Open serial port
+ser = serial.Serial('COM4')  # Change this value according to your setup
+
+# Create an Oxymeter instance and initialize recording
+oxi = Oximeter(serial=ser, sfreq=75, add_channels=4).setup()
+
+# Online peak detection for 10 seconds
+tstart = time.time()
+while time.time() - tstart < 10:
+    while oxi.serial.inWaiting() >= 5:
+        paquet = list(oxi.serial.read(5))
+        oxi.add_paquet(paquet[2])  # Add new data point
+        if oxi.peaks[-1] == 1:
+            print('Heartbeat detected')

examples/plot_ECGProcessing.py

@@ -27,7 +27,7 @@
 # ---------------
 # The peaks detection algorithms are imported from the py-ecg-detectors module:
 # https://github.com/berndporr/py-ecg-detectors
-signal, peaks = ecg_peaks(signal_df.ecg, method='hamilton', sfreq=2000,
+signal, peaks = ecg_peaks(signal_df.ecg, method='hamilton', sfreq=1000,
                           find_local=True)
 
 #%%
@@ -50,10 +50,12 @@
 neutral[
     np.round(np.where(signal_df.stim.to_numpy() == 3)[0]).astype(int)] = 1
 
+#%%
 # Event related plot
+# ------------------
 sns.set_context('talk')
 fig, ax = plt.subplots(figsize=(8, 5))
-for cond, col, data in zip(
+for cond, data, col in zip(
         ['Neutral', 'Disgust'], [neutral, disgust],
         [sns.xkcd_rgb["denim blue"], sns.xkcd_rgb["pale red"]]):
 
@@ -72,6 +74,7 @@
 ax.set_ylabel('Heart Rate (BPM)')
 ax.set_title('Instantaneous heart rate after neutral and disgusting images')
 sns.despine()
+plt.tight_layout()
 
 
 #%%

source/api.rst

@@ -17,6 +17,7 @@ Detection
  :toctree: generated/
 
   oxi_peaks
+  ecg_peaks
   rr_artefacts
   interpolate_clipping
 
@@ -72,6 +73,7 @@ Recording
   :toctree: generated/
 
    recording.Oximeter
+   recording.BrainVisionExG
 
 Utils
 -----
@@ -86,3 +88,4 @@ Utils
   heart_rate
   to_angles
   to_epochs
+  to_rr

systole/detection.py

@@ -49,17 +49,16 @@ def oxi_peaks(x, sfreq=75, win=1, new_sfreq=1000, clipping=True,
     >>> df = import_ppg()  # Import PPG recording
     >>> signal, peaks = oxi_peaks(df.ppg.to_numpy())
     >>> print(f'{sum(peaks)} peaks detected.')
+    378 peaks detected.
 
     References
     ----------
-    Some of the processing steps were adapted from the HeartPy toolbox:
-    https://python-heart-rate-analysis-toolkit.readthedocs.io/en/latest/index.html
-
     .. [1] van Gent, P., Farah, H., van Nes, N. and van Arem, B., 2019.
     Analysing Noisy Driver Physiology Real-Time Using Off-the-Shelf Sensors:
     Heart Rate Analysis Software from the Taking the Fast Lane Project. Journal
     of Open Research Software, 7(1), p.32. DOI: http://doi.org/10.5334/jors.241
     """
+
     if isinstance(x, list):
         x = np.asarray(x)
 
@@ -151,12 +150,14 @@ def ecg_peaks(x, sfreq=1000, new_sfreq=1000, method='pan-tompkins',
     >>> signal, peaks = ecg_peaks(signal_df.ecg.to_numpy(), method='hamilton',
     >>>                           sfreq=2000, find_local=True)
     >>> print(f'{sum(peaks)} peaks detected.')
+    24 peaks detected.
 
     References
     ----------
     .. [#] Howell, L., Porr, B. Popular ECG R peak detectors written in
     python. DOI: 10.5281/zenodo.3353396
     """
+
     if isinstance(x, list):
         x = np.asarray(x)
 
@@ -256,6 +257,8 @@ def rr_artefacts(rr, c1=0.13, c2=0.17, alpha=5.2):
     >>> rr = simulate_rr()  # Simulate RR time series
     >>> artefacts = rr_artefacts(rr)
     >>> print(artefacts.keys())
+    dict_keys(['subspace1', 'subspace2', 'subspace3', 'mRR', 'ectopic', 'long',
+    'short', 'missed', 'extra', 'threshold1', 'threshold2'])
 
     References
     ----------
@@ -388,14 +391,14 @@ def interpolate_clipping(signal, threshold=255):
     Examples
     --------
     .. plot::
+
        >>> import matplotlib.pyplot as plt
        >>> from systole import import_ppg
        >>> from systole.detection import interpolate_clipping
        >>> df = import_ppg()
-       >>> clean_signal = interpolate_clipping(df.ppg.to_numpy(),
-       >>>                                     threshold=255)
+       >>> clean_signal = interpolate_clipping(df.ppg.to_numpy())
        >>> plt.plot(df.time, clean_signal, color='#F15854')
-       >>> plt.plot(df.time, ppg, color='#5DA5DA')
+       >>> plt.plot(df.time, df.ppg, color='#5DA5DA')
        >>> plt.axhline(y=255, linestyle='--', color='k')
        >>> plt.xlabel('Time (s)')
        >>> plt.ylabel('PPG level (a.u)')