update test data loading from tutorials folder

bycycle/tests/test_burst.py

@@ -9,13 +9,17 @@
 import numpy as np
 from bycycle import burst, filt, features
 import itertools
+import os
+
+# Set data path
+data_path = '/'.join(os.path.dirname(bycycle.__file__).split('/')[:-1]) + '/tutorials/data/'
 
 
 def test_detect_bursts_cycles():
     """Test amplitude and period consistency burst detection"""
 
     # Load signal
-    signal = np.load('data/sim_bursting.npy')
+    signal = np.load(data_path + 'sim_bursting.npy')
     Fs = 1000  # Sampling rate
     f_range = (6, 14)  # Frequency range
 
@@ -43,7 +47,7 @@ def test_detect_bursts_df_amp():
     """Test amplitde-threshold burst detection"""
 
     # Load signal
-    signal = np.load('data/sim_bursting.npy')
+    signal = np.load(data_path + 'sim_bursting.npy')
     Fs = 1000  # Sampling rate
     f_range = (6, 14)  # Frequency range
     signal = filt.lowpass_filter(signal, Fs, 30, N_seconds=.3,

bycycle/tests/test_cyclepoints.py

@@ -9,13 +9,17 @@
 from bycycle import cyclepoints
 import numpy as np
 from scipy.signal import argrelextrema
+import os
+
+# Set data path
+data_path = '/'.join(os.path.dirname(bycycle.__file__).split('/')[:-1]) + '/tutorials/data/'
 
 
 def test_find_extrema():
     """Test ability to find peaks and troughs"""
 
     # Load signal
-    signal = np.load('data/sim_stationary.npy')
+    signal = np.load(data_path + 'sim_stationary.npy')
     Fs = 1000  # Sampling rate
     f_range = (6, 14)  # Frequency range
 
@@ -42,7 +46,7 @@ def test_find_zerox():
     """Test ability to find peaks and troughs"""
 
     # Load signal
-    signal = np.load('data/sim_stationary.npy')
+    signal = np.load(data_path + 'sim_stationary.npy')
     Fs = 1000  # Sampling rate
     f_range = (6, 14)  # Frequency range
 
@@ -64,7 +68,7 @@ def test_extrema_interpolated_phase():
     """Test waveform phase estimate"""
 
     # Load signal
-    signal = np.load('data/sim_stationary.npy')
+    signal = np.load(data_path + 'sim_stationary.npy')
     Fs = 1000  # Sampling rate
     f_range = (6, 14)  # Frequency range
 

bycycle/tests/test_features.py

@@ -4,42 +4,21 @@
 -----
 The tests here are not strong tests for accuracy.
     They serve rather as 'smoke tests', for if anything fails completely.
-
-Code to generate data from bycycle v.0.1.0 before sim module was removed:
-
-from bycycle import sim
-import numpy as np
-
-# Stationary oscillator
-np.random.seed(0)
-cf = 10 # Oscillation center frequency
-T = 10 # Recording duration (seconds)
-Fs = 1000 # Sampling rate
-
-rdsym = .3
-signal = sim.sim_oscillator(T, Fs, cf, rdsym=rdsym)
-np.save('sim_stationary.npy', signal)
-
-# Bursting oscillator
-np.random.seed(0)
-cf = 10 # Oscillation center frequency
-T = 10 # Recording duration (seconds)
-Fs = 1000 # Sampling rate
-
-signal = sim.sim_noisy_bursty_oscillator(T, Fs, cf, prob_enter_burst=.1,
-                                         prob_leave_burst=.1, SNR=5)
-np.save('sim_bursting.npy', signal)
 """
 
 import numpy as np
 from bycycle import features
+import os
+
+# Set data path
+data_path = '/'.join(os.path.dirname(bycycle.__file__).split('/')[:-1]) + '/tutorials/data/'
 
 
 def test_compute_features():
     """Test cycle-by-cycle feature computation"""
 
     # Load signal
-    signal = np.load('data/sim_stationary.npy')
+    signal = np.load(data_path + 'sim_stationary.npy')
     Fs = 1000  # Sampling rate
     f_range = (6, 14)  # Frequency range
 

bycycle/tests/test_filt.py

@@ -8,13 +8,17 @@
 
 from bycycle import filt
 import numpy as np
+import os
+
+# Set data path
+data_path = '/'.join(os.path.dirname(bycycle.__file__).split('/')[:-1]) + '/tutorials/data/'
 
 
 def test_bandpass():
     """Test bandpass filter functionality"""
 
     # Load signal
-    signal = np.load('data/sim_bursting.npy')
+    signal = np.load(data_path + 'sim_bursting.npy')
     Fs = 1000  # Sampling rate
 
     # Test output same length as input
@@ -56,7 +60,7 @@ def test_lowpass():
     """Test lowpass filter functionality"""
 
     # Load signal
-    signal = np.load('data/sim_bursting.npy')
+    signal = np.load(data_path + 'sim_bursting.npy')
     Fs = 1000  # Sampling rate
 
     # Test output same length as input
@@ -86,7 +90,7 @@ def test_amp():
     """Test phase time series functionality"""
 
     # Load signal
-    signal = np.load('data/sim_bursting.npy')
+    signal = np.load(data_path + 'sim_bursting.npy')
     Fs = 1000  # Sampling rate
     f_range = (6, 14)  # Frequency range
 
@@ -123,7 +127,7 @@ def test_phase():
     """Test phase time series functionality"""
 
     # Load signal
-    signal = np.load('data/sim_bursting.npy')
+    signal = np.load(data_path + 'sim_bursting.npy')
     Fs = 1000  # Sampling rate
     f_range = (6, 14)  # Frequency range
 

tutorials/Untitled.ipynb

@@ -0,0 +1,62 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import bycycle\n",
+    "import os"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'/gh/bv/bycycle/tutorials/data/'"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "'/'.join(os.path.dirname(bycycle.__file__).split('/')[:-1]) + '/tutorials/data/'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}