Documentation and tests

Author: LegrandNico

.coverage

@@ -114,8 +114,8 @@ The package integrates a set of functions for interactive or non interactive dat
   plot_raw(signal[60000 : 120000], modality="ecg", backend="bokeh", 
               show_heart_rate=True, show_artefacts=True, figsize=300)
 
-.. raw:: html
-   :file: source/images/raw.html
+.. figure::  https://github.com/embodied-computation-group/systole/raw/master/source/images/raw.png
+   :align:   center
 
 
 Artefacts detection and rejection
@@ -132,8 +132,8 @@ Artefacts can be detected and corrected in the RR interval time series or the pe
 
   plot_subspaces(peaks, input_type="peaks", backend="bokeh")
 
-.. raw:: html
-   :file: source/images/subspaces.html
+.. figure::  https://github.com/embodied-computation-group/systole/raw/master/source/images/subspaces.png
+   :align:   center
 
 Instantaneous and evoked heart rate
 ===================================
@@ -153,8 +153,8 @@ Systole implemetns basic time-domain, frequency-domain and non-linear HRV indice
       plot_pointcare(peaks, input_type="peaks", backend="bokeh", figsize=(400, 400)),
       )
 
-.. raw:: html
-   :file: source/images/hrv.html
+.. figure::  https://github.com/embodied-computation-group/systole/raw/master/source/images/hrv.png
+   :align:   center
 
 
 Online systolic peak detection, cardiac-stimulus synchrony, and cardiac circular analysis

README.rst

@@ -52,7 +52,7 @@
 # panel plot subspaces that will be more sensitive to long or short beats,
 # comprizing the extra and missed beats.
 
-plot_subspaces(rr)
+plot_subspaces(rr, figsize=(12, 6))
 
 #%%
 # References

examples/Artefacts/plot_ArtefactsDetection.py

@@ -2,7 +2,7 @@
 Recording PPG signal
 ====================
 
-The py:class:systole.recording.Oximeter class can be used to read incoming PPG signal 
+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 

examples/plot_HeartBeatrpeggios.py renamed to examples/Recording/plot_HeartBeatrpeggios.py

@@ -45,7 +45,7 @@ The package integrates a set of functions for interactive or non interactive dat
               show_heart_rate=True, show_artefacts=True, figsize=300)
 
 .. raw:: html
-   :file: source/images/raw.html
+   :file: ./images/raw.html
 
 
 Artefacts detection and rejection
@@ -63,7 +63,7 @@ Artefacts can be detected and corrected in the RR interval time series or the pe
   plot_subspaces(peaks, input_type="peaks", backend="bokeh")
 
 .. raw:: html
-   :file: source/images/subspaces.html
+   :file: ./images/subspaces.html
 
 Instantaneous and evoked heart rate
 ===================================
@@ -79,12 +79,12 @@ Systole implemetns basic time-domain, frequency-domain and non-linear HRV indice
   from systole.plots plot_frequency, plot_pointcare
 
   row(
-      plot_frequency(peaks, input_type="peaks", backend="bokeh", figsize=(600, 400)),
-      plot_pointcare(peaks, input_type="peaks", backend="bokeh", figsize=(400, 400)),
+      plot_frequency(peaks, input_type="peaks", backend="bokeh", figsize=(300, 200)),
+      plot_pointcare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
       )
 
 .. raw:: html
-   :file: source/images/hrv.html
+   :file: ./images/hrv.html
 
 
 Online systolic peak detection, cardiac-stimulus synchrony, and cardiac circular analysis

examples/Recording/plot_RecordingPPG.py

@@ -46,8 +46,8 @@
 #%% As HTML
 save(
     row(
-        plot_frequency(peaks, input_type="peaks", backend="bokeh", figsize=(600, 400)),
-        plot_pointcare(peaks, input_type="peaks", backend="bokeh", figsize=(400, 400)),
+        plot_frequency(peaks, input_type="peaks", backend="bokeh", figsize=(300, 200)),
+        plot_pointcare(peaks, input_type="peaks", backend="bokeh", figsize=(200, 200)),
     ),filename="hrv.html"
 )