clean up test syntax and fix an import. fixes #99

tests/test_processing.py

@@ -1,7 +1,9 @@
 import numpy
+
 import wfdb
 from wfdb import processing
 
+
 class test_processing():
 
     def test_1(self):
@@ -65,7 +67,7 @@ def test_6(self):
         assert numpy.array_equal(peaks, expecting)
 
     def test_7(self):
-        sig, fields = wfdb.rdsamp('sample-data/100', channels = [0, 1])
+        sig, fields = wfdb.rdsamp('sample-data/100')
         ann = wfdb.rdann('sample-data/100', 'atr')
         fs = fields['fs']
         min_bpm = 10
@@ -89,9 +91,6 @@ class test_qrs():
     def test_xqrs_1(self):
         sig, fields = wfdb.rdsamp('sample-data/100', channels=[0])
         ann_reference = wfdb.rdann('sample-data/100','atr')
-        conf = Conf()
-        xqrs = XQRS(sig=sig[:,0], fs=fields['fs'], conf=conf)
+        conf = processing.Conf()
+        xqrs = processing.XQRS(sig=sig[:,0], fs=fields['fs'], conf=conf)
         xqrs.detect()
-
-
-

wfdb/plot/plot.py

@@ -297,10 +297,7 @@ def label_figure(axes, n_subplots, sig_units, time_units, chan_name, title):
 
 
 def plot_wfdb(record=None, annotation=None, time_units='samples',
-              plot_physical=True, plot_ann_sym=False, 
-
-
-    title=None, sig_style=[''], ann_style=['r*'],
+              plot_physical=True, plot_ann_sym=False,  title=None, sig_style=[''], ann_style=['r*'],
 
 
 

wfdb/processing/basic.py

@@ -1,7 +1,7 @@
 import numpy
 from scipy import signal
 
-from wfdb import Annotation
+from ..io.annotation import Annotation
 
 
 def resample_ann(resampled_t, ann_sample):

wfdb/processing/gqrs.py

@@ -1,6 +1,6 @@
 import numpy
 import copy
-import matplotlib.pyplot as plt
+
 
 def time_to_sample_number(seconds, frequency):
     return seconds * frequency + 0.5
@@ -188,7 +188,7 @@ def qfv_at(self, t):
     def qfv_put(self, t, v):
         self.qfv[t & (self.c._BUFLN - 1)] = v
 
-    def sm(self, at_t):  # CHECKED!
+    def sm(self, at_t):
         # implements a trapezoidal low pass (smoothing) filter
         # (with a gain of 4*smdt) applied to input signal sig
         # before the QRS matched filter qf().
@@ -199,9 +199,6 @@ def sm(self, at_t):  # CHECKED!
         smt = self.c.smt
         smdt = int(self.c.smdt)
 
-
-        #print('in sm: smt == %d, at_t == %d' % (smt, at_t))
-
         v = 0
         while at_t > smt:
             smt += 1
@@ -248,9 +245,6 @@ def qf(self):  # CHECKED!
         self.SIG_QRS.append(v0 ** 2)
 
     def gqrs(self, from_sample, to_sample):
-
-        print('gqrs in state: %s' % self.state)
-        print('dt == smt0 == %d' % self.c.dt)
         q0 = None
         q1 = 0
         q2 = 0
@@ -364,7 +358,6 @@ def find_missing(r, p):
             q0 = self.qfv_at(self.t)
             q1 = self.qfv_at(self.t - 1)
             q2 = self.qfv_at(self.t - 2)
-            print(self.c.qthr)
             # state == RUNNING only
             if q1 > self.c.pthr and q2 < q1 and q1 >= q0 and self.t > self.c.dt4:
                 add_peak(self.t - 1, q1, 0)
@@ -536,14 +529,5 @@ def gqrs_detect(x, fs, adc_gain, adc_zero, threshold=1.0,
                 thresh=threshold)
     gqrs = GQRS()
     annotations = gqrs.detect(x=x, conf=conf, adc_zero=adc_zero)
-    fig = plt.plot(numpy.array(gqrs.SIG_SMOOTH), 'b')
-    plt.show()
-
-    fig2 = plt.plot(numpy.array(gqrs.SIG_QRS), 'r')
-
-    fig3 = plt.plot(x, 'k')
 
-    print('\nSmoothed signal head and tail:')
-    print(gqrs.SIG_SMOOTH[:12])
-    print(gqrs.SIG_SMOOTH[-12:])
     return numpy.array([a.time for a in annotations])

wfdb/processing/qrs.py

@@ -3,9 +3,6 @@
 from sklearn.cluster import KMeans
 from sklearn.preprocessing import normalize
 
-import matplotlib.pyplot as plt
-import pdb
-
 from .peaks import find_local_peaks