Merge d3b4ef1 into 2c1ca56

tests/test_bestwindow.py

@@ -1,5 +1,7 @@
 from nose.tools import assert_true, assert_equal, assert_almost_equal
+import os
 import numpy as np
+import matplotlib.pyplot as plt
 import thunderfish.bestwindow as bw
 
 
@@ -22,7 +24,7 @@ def test_best_window():
     # compute best window:
     print("call bestwindow() function...")
     idx0, idx1, clipped = bw.best_window_indices(data, rate, single=False,
-                                                 win_size=1.0, win_shift=0.1, thresh_ampl_fac=2.0,
+                                                 win_size=1.0, win_shift=0.1,
                                                  min_clip=-clip, max_clip=clip,
                                                  w_cv_ampl=10.0, tolerance=0.5)
 
@@ -40,3 +42,23 @@ def test_best_window():
                 'clip_amplitudes() failed to detect minimum clip amplitude')
     assert_true(max_clip >= 0.8 * clip and max_clip <= clip,
                 'clip_amplitudes() failed to detect maximum clip amplitude')
+
+    # plotting 1:
+    fig = plt.figure()
+    ax = fig.add_subplot(1, 1, 1)
+    bw.plot_best_data(data, rate, 'a.u.', idx0, idx1, clipped, ax)
+    fig.savefig('bestwindow.png')
+    assert_true(os.path.exists('bestwindow.png'), 'plotting failed')
+    os.remove('bestwindow.png')
+
+    # plotting 2:
+    fig, ax = plt.subplots(5, sharex=True)
+    bw.best_window_indices(data, rate, single=False,
+                           win_size=1.0, win_shift=0.1,
+                           min_clip=-clip, max_clip=clip,
+                           w_cv_ampl=10.0, tolerance=0.5,
+                           plot_data_func=bw.plot_best_window, ax=ax)
+    fig.savefig('bestdata.png')
+    assert_true(os.path.exists('bestdata.png'), 'plotting failed')
+    os.remove('bestdata.png')
+

tests/test_eodanalysis.py

@@ -0,0 +1,31 @@
+from nose.tools import assert_true, assert_equal, assert_almost_equal
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+import thunderfish.fakefish as ff
+import thunderfish.eodanalysis as ea
+
+
+def test_pulsefish():
+    samplerate = 44100.0
+    data = ff.generate_biphasic_pulses(200.0, samplerate, 5.0, noise_std=0.02)
+    mean_eod, eod_times = ea.eod_waveform(data, samplerate)
+    mean_eod, props, peaks, power, intervals = ea.analyze_pulse(mean_eod, eod_times)
+    fig = plt.figure()
+    ax = fig.add_subplot(1, 1, 1)
+    ea.pulse_spectrum_plot(power, props, ax)
+    fig.savefig('pulse.png')
+    assert_true(os.path.exists('pulse.png'), 'plotting failed')
+    os.remove('pulse.png')
+
+def test_wavefish():
+    samplerate = 44100.0
+    data = ff.generate_alepto(800.0, samplerate, duration=10.0, noise_std=0.01)
+    mean_eod, eod_times = ea.eod_waveform(data, samplerate)
+    mean_eod, props, power = ea.analyze_wave(mean_eod, 800.0)
+    fig = plt.figure()
+    ax = fig.add_subplot(1, 1, 1)
+    ea.eod_waveform_plot(mean_eod, [], ax)
+    fig.savefig('wave.png')
+    assert_true(os.path.exists('wave.png'), 'plotting failed')
+    os.remove('wave.png')

thunderfish/checkpulse.py

@@ -28,7 +28,7 @@
     pass
 
 
-def check_pulse_width(data, samplerate, th_factor=2.0, percentile=25.0,
+def check_pulse_width(data, samplerate, th_factor=0.8, percentile=1.0,
                       pulse_thresh=0.1, verbose=0, plot_data_func=None, **kwargs):
     """Detects if a fish is pulse- or wave-type based on the proportion of the time distance
     between a peak and its following trough, relative to the time between consecutive peaks.
@@ -272,7 +272,7 @@ def plot_peak_trough_hist(vals, ax, hist_color, plot_label, label_size):
     # Cosmetics
     ax[0].set_title('Raw-data with peak detection', fontsize=fs + 2)
     ax[0].set_xlabel('Time [sec]', fontsize=fs)
-    ax[0].set_ylabel('Amplitude [a.u.]', fontsize=fs)
+    ax[0].set_ylabel('Amplitude', fontsize=fs)
     ax[0].tick_params(axis='both', which='major', labelsize=fs - 2)
 
     # Second Plot: Window inset
@@ -282,7 +282,7 @@ def plot_peak_trough_hist(vals, ax, hist_color, plot_label, label_size):
     f_type = 'pulse' if pulse_fish else 'wave'
     ax[1].set_title('Inset of plot above. Suggested fish-type is %s' % f_type, fontsize=fs + 2)
     ax[1].set_xlabel('Time [sec]', fontsize=fs)
-    ax[1].set_ylabel('Amplitude [a.u.]', fontsize=fs)
+    ax[1].set_ylabel('Amplitude', fontsize=fs)
     ax[1].tick_params(axis='both', which='major', labelsize=fs - 2)
     ax[1].legend(frameon=False, loc='best')
 
@@ -339,7 +339,7 @@ def plot_psd_proportion(freqs, power, proportions, percentiles, pulse_fish,
     ax.set_ylabel('Power [dB]', fontsize=fs)
 
 
-def add_check_pulse_width_config(cfg, th_factor=2.0, percentile=25.0, pulse_thresh=0.1):
+def add_check_pulse_width_config(cfg, th_factor=0.8, percentile=1.0, pulse_thresh=0.1):
     """ Add parameter needed for check_pulse_width() as
     a new section to a configuration.