Test functions

Author: Nicolas Marc Simon Legrand

systole/tests/test_hrv.py

@@ -4,7 +4,7 @@
 import matplotlib
 import unittest
 from unittest import TestCase
-from systole.hrv import nnX, pnnX, rmssd, time_domain, hrv_psd,\
+from systole.hrv import nnX, pnnX, rmssd, time_domain,\
     frequency_domain, nonlinear
 from systole import import_rr
 
@@ -34,13 +34,6 @@ def test_time_domain(self):
         assert isinstance(stats, pd.DataFrame)
         assert stats.size == 24
 
-    def test_hrv_psd(self):
-        """Test hrv_psd function"""
-        ax = hrv_psd(rr)
-        assert isinstance(ax, matplotlib.axes.Axes)
-        freq, psd = hrv_psd(rr, show=False)
-        assert len(freq) == len(psd)
-
     def test_frequency_domain(self):
         """Test frequency_domain function"""
         stats = frequency_domain(rr)

systole/tests/test_plotting.py

@@ -6,9 +6,8 @@
 import matplotlib
 from unittest import TestCase
 
-from systole import import_rr
 from systole.plotting import plot_hr, plot_events, plot_oximeter,\
-    plot_subspaces, circular, plot_circular, plot_subspaces
+    plot_subspaces, circular, plot_circular, plot_psd
 from systole import import_ppg, import_rr
 from systole.recording import Oximeter
 from systole.detection import hrv_subspaces
@@ -38,6 +37,10 @@ class TestPlotting(TestCase):
     def test_plot_hr(self):
         ax = plot_hr(oxi)
         assert isinstance(ax, matplotlib.axes.Axes)
+        ax = plot_hr(oxi.peaks)
+        assert isinstance(ax, matplotlib.axes.Axes)
+        ax = plot_hr(np.asarray(oxi.peaks))
+        assert isinstance(ax, matplotlib.axes.Axes)
 
     def test_plot_events(self):
         ax = plot_events(oxi)
@@ -47,13 +50,21 @@ def test_plot_oximeter(self):
         ax = plot_oximeter(oxi)
         assert isinstance(ax, matplotlib.axes.Axes)
 
-    def plot_subspaces(self):
+    def test_plot_subspaces(self):
         rr = import_rr()
         s1, s2, s3 = hrv_subspaces(rr)
         ax = plot_subspaces(s1, s2, s3)
         assert isinstance(ax[0], matplotlib.axes.Axes)
         assert isinstance(ax[1], matplotlib.axes.Axes)
 
+    def test_plot_psd(self):
+        """Test plot_psd function"""
+        rr = import_rr().rr.values
+        ax = plot_psd(rr)
+        assert isinstance(ax, matplotlib.axes.Axes)
+        freq, psd = plot_psd(rr, show=False)
+        assert len(freq) == len(psd)
+
     def test_circular(self):
         """Tests _circular function"""
         ax = circular(x)

systole/tests/test_recording.py

@@ -1,11 +1,10 @@
 # Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>
 
 import unittest
-import time
 import matplotlib
 import numpy as np
 from unittest import TestCase
-from systole import import_ppg, serialSim
+from systole import serialSim
 from systole.recording import Oximeter
 
 
@@ -17,7 +16,7 @@ class TestRecording(TestCase):
 
     def test_oximeter(self):
         oxi.setup()
-        oxi.read(5)
+        oxi.read(10)
         oxi.find_peaks()
 
         # Simulate events in recording

systole/utils.py

@@ -105,8 +105,10 @@ def heart_rate(x, sfreq=1000, unit='rr', kind='cubic'):
     before the first peak anf after the last peak will be filled with the
     adjacent heartrate.
     """
-    if np.any((np.abs(np.diff(x)) > 1)):
+    if not ((x == 1) | (x == 0)).all():
         raise ValueError('Input vector should only contain 0 and 1')
+    if isinstance(x, list):
+        x = np.asarray(x)
 
     # Find peak indexes
     peaks_idx = np.where(x)[0]
@@ -128,7 +130,7 @@ def heart_rate(x, sfreq=1000, unit='rr', kind='cubic'):
     if kind is not None:
         # Interpolate
         f = interp1d(time, heartrate, kind=kind, bounds_error=False,
-                     fill_value=(heartrate[0], heartrate[-1]))
+                     fill_value=(np.nan, np.nan))
         heartrate = f(new_time)
 
     return heartrate, new_time