- Remove install folder

- Docs
embodied-computation-group · Jan 16, 2020 · 0598629 · 0598629
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diff --git a/README.rst b/README.rst
@@ -25,6 +25,8 @@
 In particular, the package provides tools to pre-process, analyze, and synchronize cardiac data from psychophysiology research.
 This includes tools for data epoching, heart-rate variability, and synchronizing stimulus presentation with different cardiac phases via psychopy.
 
+The documentation can be found under the following `links <https://embodied-computation-group.github.io/>`_.
+
 Installation
 ============
 

diff --git a/dist/systole-0.0.1-py3-none-any.whl b/dist/systole-0.0.1-py3-none-any.whl
diff --git a/dist/systole-0.0.1-py3.7.egg b/dist/systole-0.0.1-py3.7.egg
diff --git a/dist/systole-0.0.1.tar.gz b/dist/systole-0.0.1.tar.gz
diff --git a/examples/plot_RRSubspacesDetection.py b/examples/plot_RRSubspacesDetection.py
@@ -16,7 +16,7 @@
 
 #%%
 # Simulate RR time series
-# ----------------------
+# -----------------------
 
 rr = import_rr().rr[:100]
 

diff --git a/source/auto_examples/auto_examples_jupyter.zip b/source/auto_examples/auto_examples_jupyter.zip
diff --git a/source/auto_examples/auto_examples_python.zip b/source/auto_examples/auto_examples_python.zip
diff --git a/source/auto_examples/images/sphx_glr_plot_HeartBeatEvokedArpeggios_001.png b/source/auto_examples/images/sphx_glr_plot_HeartBeatEvokedArpeggios_001.png
diff --git a/source/auto_examples/images/sphx_glr_plot_HeartBeatEvokedArpeggios_002.png b/source/auto_examples/images/sphx_glr_plot_HeartBeatEvokedArpeggios_002.png
diff --git a/source/auto_examples/images/sphx_glr_plot_InstantaneousHeartRate_001.png b/source/auto_examples/images/sphx_glr_plot_InstantaneousHeartRate_001.png
diff --git a/source/auto_examples/images/thumb/sphx_glr_plot_HeartBeatEvokedArpeggios_thumb.png b/source/auto_examples/images/thumb/sphx_glr_plot_HeartBeatEvokedArpeggios_thumb.png
diff --git a/source/auto_examples/images/thumb/sphx_glr_plot_InstantaneousHeartRate_thumb.png b/source/auto_examples/images/thumb/sphx_glr_plot_InstantaneousHeartRate_thumb.png
diff --git a/source/auto_examples/index.rst b/source/auto_examples/index.rst
@@ -9,7 +9,7 @@
 Tutorials
 =========
 
-This section shows off some of the basic functionality of **systole**.
+This section demonstrates some of the basic functionality of **systole**.
 If you want to see the tutorials in action, you can also click on the link below and navigate to the ``tutorials/`` folder to launch one of the interactive Jupyter notebooks.
 
 .. contents:: Contents
@@ -20,7 +20,7 @@ If you want to see the tutorials in action, you can also click on the link below
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to detect ectobeat extra, missed and ectobeats from RR time series using...">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to detect extra ectobeats, missed and ectobeats from RR time series usin...">
 
 .. only:: html
 
@@ -40,7 +40,7 @@ If you want to see the tutorials in action, you can also click on the link below
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="This example show how to record PPG signal through the `Nonin 3012LP Xpod USB pulse oximeter &lt;h...">
+    <div class="sphx-glr-thumbcontainer" tooltip="This example show how to record PPG signals using the `Nonin 3012LP Xpod USB pulse oximeter &lt;ht...">
 
 .. only:: html
 
@@ -60,7 +60,7 @@ If you want to see the tutorials in action, you can also click on the link below
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial illustrates how to use the Oximeter class to trigger stimuli at different cardiac...">
+    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial illustrates how to use the Oximeter class to trigger stimuli at different phases ...">
 
 .. only:: html
 

diff --git a/source/auto_examples/plot_HeartBeatEvokedArpeggios.ipynb b/source/auto_examples/plot_HeartBeatEvokedArpeggios.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nHeart Beats Evoked Arpeggios\n============================\n\nThis tutorial illustrates how to use the ``Oximeter`` class to trigger stimuli\nat different cardiac cycles using the [Psychopy](https://www.psychopy.org/)\ntoolbox. The PPG signal is recorded for 30 seconds and peaks are detected\nonline. Four notes ('C', 'E', 'G', 'Bfl') are played in synch with peak\ndetection with various delay: no delay,  1/4, 2/4 or 3/4 of the previous\ncardiac cycle length. While R-R intervals are prone to large changes in the\nlong term, such changes are physiologically limited for heartbeat, thus\nlimiting the variability of phase in which the note is played.\n"
+        "\nHeartbeat Evoked Arpeggios\n============================\n\nThis tutorial illustrates how to use the ``Oximeter`` class to trigger stimuli\nat different phases of the cardiac cycle using the [Psychopy](https://www.psychopy.org/)\ntoolbox. The PPG signal is recorded for 30 seconds and peaks are detected\nonline. Four notes ('C', 'E', 'G', 'Bfl') are played in synch with peak\ndetection with various delays: no delay,  1/4, 2/4 or 3/4 of the previous\ncardiac cycle length. While R-R intervals are prone to large changes over longer\ntimescales, such changes are physiologically limited from one heartbeat to the next,\nlimiting variance in the onset synchrony between the tones and the cardiac cycle.\nOn this basis, each presentation time is calibrated based on the previous RR-interval.\nThis procedure can easily be adapted to create a standard interoception task, e.g. by either presenting\ntones at no delay (systole, s+) or at a fixed offset (diastole, s-).\n"
       ]
     },
     {
@@ -51,7 +51,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "If you want to allow online data acquisition, you should uncomment the\nfollowing lines and provide the reference of the COM port where the pulse\noximeter is plugged.\n\n"
+        "If you want to allow online data acquisition, you should uncomment the\nfollowing lines and provide the reference of the COM port where the pulse\noximeter is plugged in.\n\n"
       ]
     },
     {
@@ -65,7 +65,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Create an Oxymeter instance, initialize recording and record for 10 seconds\n\n"
+        "Create an Oximeter instance, initialize recording and record for 10 seconds\n\n"
       ]
     },
     {

diff --git a/source/auto_examples/plot_HeartBeatEvokedArpeggios.py b/source/auto_examples/plot_HeartBeatEvokedArpeggios.py
@@ -1,15 +1,18 @@
 """
-Heart Beats Evoked Arpeggios
+Heartbeat Evoked Arpeggios
 ============================
 
 This tutorial illustrates how to use the ``Oximeter`` class to trigger stimuli
-at different cardiac cycles using the [Psychopy](https://www.psychopy.org/)
+at different phases of the cardiac cycle using the [Psychopy](https://www.psychopy.org/)
 toolbox. The PPG signal is recorded for 30 seconds and peaks are detected
 online. Four notes ('C', 'E', 'G', 'Bfl') are played in synch with peak
-detection with various delay: no delay,  1/4, 2/4 or 3/4 of the previous
-cardiac cycle length. While R-R intervals are prone to large changes in the
-long term, such changes are physiologically limited for heartbeat, thus
-limiting the variability of phase in which the note is played.
+detection with various delays: no delay,  1/4, 2/4 or 3/4 of the previous
+cardiac cycle length. While R-R intervals are prone to large changes over longer
+timescales, such changes are physiologically limited from one heartbeat to the next,
+limiting variance in the onset synchrony between the tones and the cardiac cycle.
+On this basis, each presentation time is calibrated based on the previous RR-interval.
+This procedure can easily be adapted to create a standard interoception task, e.g. by either presenting
+tones at no delay (systole, s+) or at a fixed offset (diastole, s-).
 """
 
 # Author: Nicolas Legrand <[email protected]>
@@ -39,7 +42,7 @@
 #%%
 # If you want to allow online data acquisition, you should uncomment the
 # following lines and provide the reference of the COM port where the pulse
-# oximeter is plugged.
+# oximeter is plugged in.
 
 ###############################################################################
 # .. code-block:: python
@@ -48,7 +51,7 @@
 #   ser = serial.Serial('COM4')  # Change this value according to your setup
 
 #%%
-# Create an Oxymeter instance, initialize recording and record for 10 seconds
+# Create an Oximeter instance, initialize recording and record for 10 seconds
 
 oxi = Oximeter(serial=ser, sfreq=75, add_channels=4).setup()
 

diff --git a/source/auto_examples/plot_HeartBeatEvokedArpeggios.py.md5 b/source/auto_examples/plot_HeartBeatEvokedArpeggios.py.md5
@@ -1 +1 @@
-cb7354c44dcefa6f0a93a45d8ad9fad7
+694cbbf3348bf43e6b6f5f00d4315a8d
diff --git a/source/auto_examples/plot_HeartBeatEvokedArpeggios.rst b/source/auto_examples/plot_HeartBeatEvokedArpeggios.rst
@@ -7,17 +7,20 @@
 .. _sphx_glr_auto_examples_plot_HeartBeatEvokedArpeggios.py:
 
 
-Heart Beats Evoked Arpeggios
+Heartbeat Evoked Arpeggios
 ============================
 
 This tutorial illustrates how to use the ``Oximeter`` class to trigger stimuli
-at different cardiac cycles using the [Psychopy](https://www.psychopy.org/)
+at different phases of the cardiac cycle using the [Psychopy](https://www.psychopy.org/)
 toolbox. The PPG signal is recorded for 30 seconds and peaks are detected
 online. Four notes ('C', 'E', 'G', 'Bfl') are played in synch with peak
-detection with various delay: no delay,  1/4, 2/4 or 3/4 of the previous
-cardiac cycle length. While R-R intervals are prone to large changes in the
-long term, such changes are physiologically limited for heartbeat, thus
-limiting the variability of phase in which the note is played.
+detection with various delays: no delay,  1/4, 2/4 or 3/4 of the previous
+cardiac cycle length. While R-R intervals are prone to large changes over longer
+timescales, such changes are physiologically limited from one heartbeat to the next,
+limiting variance in the onset synchrony between the tones and the cardiac cycle.
+On this basis, each presentation time is calibrated based on the previous RR-interval.
+This procedure can easily be adapted to create a standard interoception task, e.g. by either presenting
+tones at no delay (systole, s+) or at a fixed offset (diastole, s-).
 
 
 .. code-block:: default
@@ -66,14 +69,14 @@ the pulse oximeter using pre-recorded signal.
 
 If you want to allow online data acquisition, you should uncomment the
 following lines and provide the reference of the COM port where the pulse
-oximeter is plugged.
+oximeter is plugged in.
 
 .. code-block:: python
 
   import serial
   ser = serial.Serial('COM4')  # Change this value according to your setup
 
-Create an Oxymeter instance, initialize recording and record for 10 seconds
+Create an Oximeter instance, initialize recording and record for 10 seconds
 
 
 .. code-block:: default
@@ -216,7 +219,7 @@ Cardiac cycle
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  32.338 seconds)
+   **Total running time of the script:** ( 0 minutes  31.752 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_HeartBeatEvokedArpeggios.py:

diff --git a/source/auto_examples/plot_HeartBeatEvokedArpeggios_codeobj.pickle b/source/auto_examples/plot_HeartBeatEvokedArpeggios_codeobj.pickle
diff --git a/source/auto_examples/plot_InstantaneousHeartRate.ipynb b/source/auto_examples/plot_InstantaneousHeartRate.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nInstantaneous Heart Rate\n========================\n\nThis example show how to record PPG signal through the `Nonin 3012LP\nXpod USB pulse oximeter <https://www.nonin.com/products/xpod/>`_ and the `Nonin\n8000SM 'soft-clip' fingertip sensors <https://www.nonin.com/products/8000s/>`_.\nPeaks are automatically labelled online and the instantaneous heart rate is\nplotted.\n"
+        "\nInstantaneous Heart Rate\n========================\n\nThis example show how to record PPG signals using the `Nonin 3012LP\nXpod USB pulse oximeter <https://www.nonin.com/products/xpod/>`_ and the `Nonin\n8000SM 'soft-clip' fingertip sensors <https://www.nonin.com/products/8000s/>`_.\nPeaks are automatically labelled online and the instantaneous heart rate is\nplotted.\n"
       ]
     },
     {
@@ -33,7 +33,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Recording\n---------\nFor the purpose of demonstration, here we simulate data acquisition through\nthe pulse oximeter using pre-recorded signal.\n\n"
+        "Recording\n---------\nFor the demonstration purpose, here we simulate data acquisition through\nthe pulse oximeter using pre-recorded signal.\n\n"
       ]
     },
     {
@@ -51,7 +51,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "If you want to allow online data acquisition, you should uncomment the\nfollowing lines and provide the reference of the COM port where the pulse\noximeter is plugged.\n\n"
+        "If you want to enable online data acquisition, you should uncomment the\nfollowing lines and provide the reference of the COM port where the pulse\noximeter is plugged in.\n\n"
       ]
     },
     {

diff --git a/source/auto_examples/plot_InstantaneousHeartRate.py b/source/auto_examples/plot_InstantaneousHeartRate.py
@@ -2,7 +2,7 @@
 Instantaneous Heart Rate
 ========================
 
-This example show how to record PPG signal through the `Nonin 3012LP
+This example show how to record PPG signals using the `Nonin 3012LP
 Xpod USB pulse oximeter <https://www.nonin.com/products/xpod/>`_ and the `Nonin
 8000SM 'soft-clip' fingertip sensors <https://www.nonin.com/products/8000s/>`_.
 Peaks are automatically labelled online and the instantaneous heart rate is
@@ -21,15 +21,15 @@
 #%%
 # Recording
 # ---------
-# For the purpose of demonstration, here we simulate data acquisition through
+# For the demonstration purpose, here we simulate data acquisition through
 # the pulse oximeter using pre-recorded signal.
 
 ser = serialSim()
 
 #%%
-# If you want to allow online data acquisition, you should uncomment the
+# If you want to enable online data acquisition, you should uncomment the
 # following lines and provide the reference of the COM port where the pulse
-# oximeter is plugged.
+# oximeter is plugged in.
 
 ###############################################################################
 # .. code-block:: python

diff --git a/source/auto_examples/plot_InstantaneousHeartRate.py.md5 b/source/auto_examples/plot_InstantaneousHeartRate.py.md5
@@ -1 +1 @@
-30d323223ddfc8eb8292956cc89bcb09
+2e5f5defbd94632a635de74bc150aaa1
diff --git a/source/auto_examples/plot_InstantaneousHeartRate.rst b/source/auto_examples/plot_InstantaneousHeartRate.rst
@@ -10,7 +10,7 @@
 Instantaneous Heart Rate
 ========================
 
-This example show how to record PPG signal through the `Nonin 3012LP
+This example show how to record PPG signals using the `Nonin 3012LP
 Xpod USB pulse oximeter <https://www.nonin.com/products/xpod/>`_ and the `Nonin
 8000SM 'soft-clip' fingertip sensors <https://www.nonin.com/products/8000s/>`_.
 Peaks are automatically labelled online and the instantaneous heart rate is
@@ -38,7 +38,7 @@ plotted.
 
 Recording
 ---------
-For the purpose of demonstration, here we simulate data acquisition through
+For the demonstration purpose, here we simulate data acquisition through
 the pulse oximeter using pre-recorded signal.
 
 
@@ -54,9 +54,9 @@ the pulse oximeter using pre-recorded signal.
 
 
 
-If you want to allow online data acquisition, you should uncomment the
+If you want to enable online data acquisition, you should uncomment the
 following lines and provide the reference of the COM port where the pulse
-oximeter is plugged.
+oximeter is plugged in.
 
 .. code-block:: python
 
@@ -83,7 +83,7 @@ oximeter is plugged.
 
     Reset input buffer
 
-    <systole.recording.Oximeter object at 0x00000267906F90B8>
+    <systole.recording.Oximeter object at 0x0000027EC53A2B70>
 
 
 
@@ -124,7 +124,7 @@ Plotting
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  31.409 seconds)
+   **Total running time of the script:** ( 0 minutes  31.257 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_InstantaneousHeartRate.py:

diff --git a/source/auto_examples/plot_InstantaneousHeartRate_codeobj.pickle b/source/auto_examples/plot_InstantaneousHeartRate_codeobj.pickle
diff --git a/source/auto_examples/plot_RRSubspacesDetection.ipynb b/source/auto_examples/plot_RRSubspacesDetection.ipynb
@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\nOutliers and ectobeats detection\n================================\n\nThis example shows how to detect ectobeat extra, missed and ectobeats from RR\ntime series using the method proposed by Lipponen & Tarvainen (2019) [#]_.\n"
+        "\nOutliers and ectobeats detection\n================================\n\nThis example shows how to detect extra ectobeats, missed and ectobeats from RR\ntime series using the method proposed by Lipponen & Tarvainen (2019) [#]_.\n"
       ]
     },
     {
@@ -44,7 +44,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Simulate RR time serie\n----------------------\n\n"
+        "Simulate RR time series\n-----------------------\n\n"
       ]
     },
     {

diff --git a/source/auto_examples/plot_RRSubspacesDetection.py b/source/auto_examples/plot_RRSubspacesDetection.py
@@ -2,7 +2,7 @@
 Outliers and ectobeats detection
 ================================
 
-This example shows how to detect ectobeat extra, missed and ectobeats from RR
+This example shows how to detect extra ectobeats, missed and ectobeats from RR
 time series using the method proposed by Lipponen & Tarvainen (2019) [#]_.
 """
 
@@ -15,8 +15,8 @@
 from systole import import_rr
 
 #%%
-# Simulate RR time serie
-# ----------------------
+# Simulate RR time series
+# -----------------------
 
 rr = import_rr().rr[:100]
 

diff --git a/source/auto_examples/plot_RRSubspacesDetection.py.md5 b/source/auto_examples/plot_RRSubspacesDetection.py.md5
@@ -1 +1 @@
-27ff66cbe2240503c8708a57adde3792
+4a7b14e5a0b10cc5d10d5c633997826c
diff --git a/source/auto_examples/plot_RRSubspacesDetection.rst b/source/auto_examples/plot_RRSubspacesDetection.rst
@@ -10,7 +10,7 @@
 Outliers and ectobeats detection
 ================================
 
-This example shows how to detect ectobeat extra, missed and ectobeats from RR
+This example shows how to detect extra ectobeats, missed and ectobeats from RR
 time series using the method proposed by Lipponen & Tarvainen (2019) [#]_.
 
 
@@ -41,8 +41,8 @@ time series using the method proposed by Lipponen & Tarvainen (2019) [#]_.
 
 
 
-Simulate RR time serie
-----------------------
+Simulate RR time series
+-----------------------
 
 
 .. code-block:: default
@@ -112,8 +112,8 @@ too long or too short (right pannel).
  .. code-block:: none
 
 
-    array([<matplotlib.axes._subplots.AxesSubplot object at 0x000001790F5ADF98>,
-           <matplotlib.axes._subplots.AxesSubplot object at 0x000001790FA577F0>],
+    array([<matplotlib.axes._subplots.AxesSubplot object at 0x0000027EC4DE8A90>,
+           <matplotlib.axes._subplots.AxesSubplot object at 0x0000027EC50C9048>],
           dtype=object)
 
 
@@ -143,7 +143,7 @@ We can then plot back the labelled outliers in the RR interval time course
  .. code-block:: none
 
 
-    <matplotlib.axes._subplots.AxesSubplot object at 0x000001790FDB61D0>
+    <matplotlib.axes._subplots.AxesSubplot object at 0x0000027EC5436EB8>
 
 
 
@@ -157,7 +157,7 @@ References
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  0.511 seconds)
+   **Total running time of the script:** ( 0 minutes  0.500 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_RRSubspacesDetection.py:

diff --git a/source/auto_examples/plot_RRSubspacesDetection_codeobj.pickle b/source/auto_examples/plot_RRSubspacesDetection_codeobj.pickle
diff --git a/source/auto_examples/sg_execution_times.rst b/source/auto_examples/sg_execution_times.rst
@@ -5,12 +5,12 @@
 
 Computation times
 =================
-**00:32.849** total execution time for **auto_examples** files:
+**00:31.758** total execution time for **auto_examples** files:
 
 +-------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_plot_HeartBeatEvokedArpeggios.py` (``plot_HeartBeatEvokedArpeggios.py``) | 00:32.338 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_plot_InstantaneousHeartRate.py` (``plot_InstantaneousHeartRate.py``)     | 00:31.257 | 0.0 MB |
 +-------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_plot_RRSubspacesDetection.py` (``plot_RRSubspacesDetection.py``)         | 00:00.511 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_plot_RRSubspacesDetection.py` (``plot_RRSubspacesDetection.py``)         | 00:00.500 | 0.0 MB |
 +-------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_plot_InstantaneousHeartRate.py` (``plot_InstantaneousHeartRate.py``)     | 00:00.000 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_plot_HeartBeatEvokedArpeggios.py` (``plot_HeartBeatEvokedArpeggios.py``) | 00:00.000 | 0.0 MB |
 +-------------------------------------------------------------------------------------------------------+-----------+--------+
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		cb7354c44dcefa6f0a93a45d8ad9fad7
		694cbbf3348bf43e6b6f5f00d4315a8d
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		30d323223ddfc8eb8292956cc89bcb09
		2e5f5defbd94632a635de74bc150aaa1
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		27ff66cbe2240503c8708a57adde3792
		4a7b14e5a0b10cc5d10d5c633997826c