Coverage for src / thunderfish / fishfinder.py: 0%
635 statements
« prev ^ index » next coverage.py v7.13.1, created at 2026-01-15 17:50 +0000
« prev ^ index » next coverage.py v7.13.1, created at 2026-01-15 17:50 +0000
1import sys
2import os
3import warnings
4import argparse
5import numpy as np
6import matplotlib.pyplot as plt
7import matplotlib.mlab as ml
9from audioio import PlayAudio, fade, write_audio
10from thunderlab.configfile import ConfigFile
11from thunderlab.dataloader import DataLoader
12from thunderlab.powerspectrum import nfft, decibel, psd, spectrogram
13from thunderlab.powerspectrum import add_multi_psd_config, multi_psd_args
15from .version import __version__, __year__
16from .harmonics import harmonic_groups, harmonic_groups_args, psd_peak_detection_args
17from .harmonics import add_psd_peak_detection_config, add_harmonic_groups_config, colors_markers
18from .bestwindow import clip_amplitudes, clip_args, best_window_indices
19from .bestwindow import best_window_args
20from .thunderfish import configuration, save_configuration
21# check: import logging https://docs.python.org/2/howto/logging.html#logging-basic-tutorial
24class SignalPlot:
25 def __init__(self, data, samplingrate, unit, filename, channel, verbose, cfg):
26 self.filename = filename
27 self.channel = channel
28 self.rate = samplingrate
29 self.data = data
30 self.unit = unit
31 self.cfg = cfg
32 self.verbose = verbose
33 self.tmax = (len(self.data)-1)/self.rate
34 self.toffset = 0.0
35 self.twindow = 8.0
36 if self.twindow > self.tmax:
37 self.twindow = np.round(2 ** (np.floor(np.log(self.tmax) / np.log(2.0)) + 1.0))
38 self.ymin = -1.0
39 self.ymax = +1.0
40 self.trace_artist = None
41 self.spectrogram_artist = None
42 self.fmin = 0.0
43 self.fmax = 0.0
44 self.decibel = True
45 self.freq_resolution = self.cfg.value('frequencyResolution')
46 self.deltaf = 1.0
47 self.mains_freq = self.cfg.value('mainsFreq')
48 self.power_label = None
49 self.all_peaks_artis = None
50 self.good_peaks_artist = None
51 self.power_artist = None
52 self.power_frequency_label = None
53 self.peak_artists = []
54 self.legend = True
55 self.legendhandle = None
56 self.help = False
57 self.helptext = []
58 self.allpeaks = []
59 self.fishlist = []
60 self.mains = []
61 self.peak_specmarker = []
62 self.peak_annotation = []
63 self.min_clip = self.cfg.value('minClipAmplitude')
64 self.max_clip = self.cfg.value('maxClipAmplitude')
65 self.colorrange, self.markerrange = colors_markers()
67 # audio output:
68 self.audio = PlayAudio()
70 # set key bindings:
71 plt.rcParams['keymap.fullscreen'] = 'ctrl+f'
72 plt.rcParams['keymap.pan'] = 'ctrl+m'
73 plt.rcParams['keymap.quit'] = 'ctrl+w, alt+q, q'
74 plt.rcParams['keymap.yscale'] = ''
75 plt.rcParams['keymap.xscale'] = ''
76 plt.rcParams['keymap.grid'] = ''
77 #plt.rcParams['keymap.all_axes'] = ''
79 # the figure:
80 plt.ioff()
81 self.fig = plt.figure(figsize=(15, 9))
82 self.fig.canvas.manager.set_window_title(self.filename + ' channel {0:d}'.format(self.channel))
83 self.fig.canvas.mpl_connect('key_press_event', self.keypress)
84 self.fig.canvas.mpl_connect('button_press_event', self.buttonpress)
85 self.fig.canvas.mpl_connect('pick_event', self.onpick)
86 self.fig.canvas.mpl_connect('resize_event', self.resize)
87 # trace plot:
88 self.axt = self.fig.add_axes([0.1, 0.7, 0.87, 0.25])
89 self.axt.set_ylabel('Amplitude [{:s}]'.format(self.unit))
90 ht = self.axt.text(0.98, 0.05, '(ctrl+) page and arrow up, down, home, end: scroll', ha='right',
91 transform=self.axt.transAxes)
92 self.helptext.append(ht)
93 ht = self.axt.text(0.98, 0.15, '+, -, X, x: zoom in/out', ha='right', transform=self.axt.transAxes)
94 self.helptext.append(ht)
95 ht = self.axt.text(0.98, 0.25, 'y,Y,v,V: zoom amplitudes', ha='right', transform=self.axt.transAxes)
96 self.helptext.append(ht)
97 ht = self.axt.text(0.98, 0.35, 'p,P: play audio (display,all)', ha='right', transform=self.axt.transAxes)
98 self.helptext.append(ht)
99 ht = self.axt.text(0.98, 0.45, 'ctrl-f: full screen', ha='right', transform=self.axt.transAxes)
100 self.helptext.append(ht)
101 ht = self.axt.text(0.98, 0.55, 'w: plot waveform into png file', ha='right', transform=self.axt.transAxes)
102 self.helptext.append(ht)
103 ht = self.axt.text(0.98, 0.65, 's: save figure', ha='right', transform=self.axt.transAxes)
104 self.helptext.append(ht)
105 ht = self.axt.text(0.98, 0.75, 'S: save audiosegment', ha='right', transform=self.axt.transAxes)
106 self.helptext.append(ht)
107 ht = self.axt.text(0.98, 0.85, 'q: quit', ha='right', transform=self.axt.transAxes)
108 self.helptext.append(ht)
109 ht = self.axt.text(0.98, 0.95, 'h: toggle this help', ha='right', transform=self.axt.transAxes)
110 self.helptext.append(ht)
111 self.axt.set_xticklabels([])
112 # spectrogram:
113 self.axs = self.fig.add_axes([0.1, 0.45, 0.87, 0.25])
114 self.axs.set_xlabel('Time [seconds]')
115 self.axs.set_ylabel('Frequency [Hz]')
116 # power spectrum:
117 self.axp = self.fig.add_axes([0.1, 0.1, 0.87, 0.25])
118 ht = self.axp.text(0.98, 0.9, 'r, R: frequency resolution', ha='right', transform=self.axp.transAxes)
119 self.helptext.append(ht)
120 ht = self.axp.text(0.98, 0.8, 'f, F: zoom', ha='right', transform=self.axp.transAxes)
121 self.helptext.append(ht)
122 ht = self.axp.text(0.98, 0.7, '(ctrl+) left, right: move', ha='right', transform=self.axp.transAxes)
123 self.helptext.append(ht)
124 ht = self.axp.text(0.98, 0.6, 'l: toggle legend', ha='right', transform=self.axp.transAxes)
125 self.helptext.append(ht)
126 ht = self.axp.text(0.98, 0.5, 'd: toggle decibel', ha='right', transform=self.axp.transAxes)
127 self.helptext.append(ht)
128 ht = self.axp.text(0.98, 0.4, 'm: toggle mains filter', ha='right', transform=self.axp.transAxes)
129 self.helptext.append(ht)
130 ht = self.axp.text(0.98, 0.3, 'left mouse: show peak properties', ha='right', transform=self.axp.transAxes)
131 self.helptext.append(ht)
132 ht = self.axp.text(0.98, 0.2, 'shift/ctrl + left/right mouse: goto previous/next harmonic', ha='right',
133 transform=self.axp.transAxes)
134 self.helptext.append(ht)
135 # plot:
136 for ht in self.helptext:
137 ht.set_visible(self.help)
138 self.update_plots(False)
139 plt.show()
141 def __del__(self):
142 self.audio.close()
144 def remove_peak_annotation(self):
145 for fm in self.peak_specmarker:
146 fm.remove()
147 self.peak_specmarker = []
148 for fa in self.peak_annotation:
149 fa.remove()
150 self.peak_annotation = []
152 def annotate_peak(self, peak, harmonics=-1, inx=-1):
153 # marker:
154 if inx >= 0:
155 m, = self.axs.plot([self.toffset + 0.01 * self.twindow], [peak[0]], linestyle='None',
156 color=self.colorrange[inx % len(self.colorrange)],
157 marker=self.markerrange[inx], ms=10.0, mec=None, mew=0.0, zorder=2)
158 else:
159 m, = self.axs.plot([self.toffset + 0.01 * self.twindow], [peak[0]], linestyle='None',
160 color='k', marker='o', ms=10.0, mec=None, mew=0.0, zorder=2)
161 self.peak_specmarker.append(m)
162 # annotation:
163 fwidth = self.fmax - self.fmin
164 pl = []
165 pl.append(r'$f=$%.1f Hz' % peak[0])
166 pl.append(r'$h=$%d' % harmonics)
167 pl.append(r'$p=$%g' % peak[1])
168 pl.append(r'$c=$%.0f' % peak[2])
169 self.peak_annotation.append(self.axp.annotate('\n'.join(pl), xy=(peak[0], peak[1]),
170 xytext=(peak[0] + 0.03 * fwidth, peak[1]),
171 bbox=dict(boxstyle='round', facecolor='white'),
172 arrowprops=dict(arrowstyle='-')))
174 def annotate_fish(self, fish, inx=-1):
175 self.remove_peak_annotation()
176 for harmonic, freq in enumerate(fish[:, 0]):
177 peak = self.allpeaks[np.abs(self.allpeaks[:, 0] - freq) < 0.8 * self.deltaf, :]
178 if len(peak) > 0:
179 self.annotate_peak(peak[0, :], harmonic, inx)
180 self.fig.canvas.draw()
182 def update_plots(self, draw=True):
183 self.remove_peak_annotation()
184 # trace:
185 self.axt.set_xlim(self.toffset, self.toffset + self.twindow)
186 t0 = int(np.round(self.toffset * self.rate))
187 t1 = int(np.round((self.toffset + self.twindow) * self.rate))
188 if t1>len(self.data):
189 t1 = len(self.data)
190 time = np.arange(t0, t1) / self.rate
191 if self.trace_artist == None:
192 self.trace_artist, = self.axt.plot(time, self.data[t0:t1,self.channel])
193 else:
194 self.trace_artist.set_data(time, self.data[t0:t1,self.channel])
195 self.axt.set_ylim(self.ymin, self.ymax)
197 # compute power spectrum:
198 n_fft = nfft(self.rate, self.freq_resolution)
199 t00 = t0
200 t11 = t1
201 w = t11 - t00
202 minw = n_fft * (self.cfg.value('minPSDAverages') + 1) // 2
203 if t11 - t00 < minw:
204 w = minw
205 t11 = t00 + w
206 if t11 >= len(self.data):
207 t11 = len(self.data)
208 t00 = t11 - w
209 if t00 < 0:
210 t00 = 0
211 t11 = w
212 freqs, power = psd(self.data[t00:t11,self.channel], self.rate,
213 self.freq_resolution, detrend=ml.detrend_mean)
214 self.deltaf = freqs[1] - freqs[0]
215 # detect fish:
216 h_kwargs = psd_peak_detection_args(self.cfg)
217 h_kwargs.update(harmonic_groups_args(self.cfg))
218 self.fishlist, fzero_harmonics, self.mains, self.allpeaks, peaks, lowth, highth, center = harmonic_groups(freqs, power, verbose=self.verbose, **h_kwargs)
219 highth = center + highth - 0.5 * lowth
220 lowth = center + 0.5 * lowth
222 # spectrogram:
223 t2 = t1 + n_fft
224 freqs, bins, specpower = spectrogram(self.data[t0:t2,self.channel],
225 self.rate,
226 self.freq_resolution,
227 detrend=ml.detrend_mean)
228 z = decibel(specpower)
229 z = np.flipud(z)
230 extent = self.toffset, self.toffset + np.amax(bins), freqs[0], freqs[-1]
231 self.axs.set_xlim(self.toffset, self.toffset + self.twindow)
232 if self.spectrogram_artist == None:
233 self.fmax = np.round((freqs[-1] / 4.0) / 100.0) * 100.0
234 min = highth
235 min = np.percentile(z, 70.0)
236 max = np.percentile(z, 99.9) + 30.0
237 # cm = plt.get_cmap( 'hot_r' )
238 cm = plt.get_cmap('jet')
239 self.spectrogram_artist = self.axs.imshow(z, aspect='auto',
240 extent=extent, vmin=min, vmax=max,
241 cmap=cm, zorder=1)
242 else:
243 self.spectrogram_artist.set_data(z)
244 self.spectrogram_artist.set_extent(extent)
245 self.axs.set_ylim(self.fmin, self.fmax)
247 # power spectrum:
248 self.axp.set_xlim(self.fmin, self.fmax)
249 if self.deltaf >= 1000.0:
250 dfs = '%.3gkHz' % 0.001 * self.deltaf
251 else:
252 dfs = '%.3gHz' % self.deltaf
253 tw = float(w) / self.rate
254 if tw < 1.0:
255 tws = '%.3gms' % (1000.0 * tw)
256 else:
257 tws = '%.3gs' % (tw)
258 a = 2 * w // n_fft - 1 # number of ffts
259 m = ''
260 if self.cfg.value('mainsFreq') > 0.0:
261 m = ', mains=%.0fHz' % self.cfg.value('mainsFreq')
262 if self.power_frequency_label == None:
263 self.power_frequency_label = self.axp.set_xlabel(
264 r'Frequency [Hz] (nfft={:d}, $\Delta f$={:s}: T={:s}/{:d}{:s})'.format(n_fft, dfs, tws, a, m))
265 else:
266 self.power_frequency_label.set_text(
267 r'Frequency [Hz] (nfft={:d}, $\Delta f$={:s}: T={:s}/{:d}{:s})'.format(n_fft, dfs, tws, a, m))
268 self.axp.set_xlim(self.fmin, self.fmax)
269 if self.power_label == None:
270 self.power_label = self.axp.set_ylabel('Power')
271 if self.decibel:
272 if len(self.allpeaks) > 0:
273 self.allpeaks[:, 1] = decibel(self.allpeaks[:, 1])
274 power = decibel(power)
275 pmin = np.min(power[freqs < self.fmax])
276 pmin = np.floor(pmin / 10.0) * 10.0
277 pmax = np.max(power[freqs < self.fmax])
278 pmax = np.ceil(pmax / 10.0) * 10.0
279 doty = pmax - 5.0
280 self.power_label.set_text('Power [dB]')
281 self.axp.set_ylim(pmin, pmax)
282 else:
283 pmax = np.max(power[freqs < self.fmax])
284 doty = pmax
285 pmax *= 1.1
286 self.power_label.set_text('Power')
287 self.axp.set_ylim(0.0, pmax)
288 if self.all_peaks_artis == None:
289 self.all_peaks_artis, = self.axp.plot(self.allpeaks[:, 0],
290 np.zeros(len(self.allpeaks[:, 0])) + doty,
291 'o', color='#ffffff')
292 self.good_peaks_artist, = self.axp.plot(peaks, np.zeros(len(peaks)) + doty,
293 'o', color='#888888')
294 else:
295 self.all_peaks_artis.set_data(self.allpeaks[:, 0],
296 np.zeros(len(self.allpeaks[:, 0])) + doty)
297 self.good_peaks_artist.set_data(peaks, np.zeros(len(peaks)) + doty)
298 labels = []
299 fsizes = [np.sqrt(np.sum(self.fishlist[k][:, 1])) for k in range(len(self.fishlist))]
300 fmaxsize = np.max(fsizes) if len(fsizes) > 0 else 1.0
301 for k in range(len(self.peak_artists)):
302 self.peak_artists[k].remove()
303 self.peak_artists = []
304 for k in range(len(self.fishlist)):
305 if k >= len(self.markerrange):
306 break
307 fpeaks = self.fishlist[k][:, 0]
308 fpeakinx = [int(np.round(fp / self.deltaf)) for fp in fpeaks if fp < freqs[-1]]
309 fsize = 7.0 + 10.0 * (fsizes[k] / fmaxsize) ** 0.5
310 fishpoints, = self.axp.plot(fpeaks[:len(fpeakinx)], power[fpeakinx], linestyle='None',
311 color=self.colorrange[k % len(self.colorrange)],
312 marker=self.markerrange[k], ms=fsize,
313 mec=None, mew=0.0, zorder=1)
314 self.peak_artists.append(fishpoints)
315 if self.deltaf < 0.1:
316 labels.append('%4.2f Hz' % fpeaks[0])
317 elif self.deltaf < 1.0:
318 labels.append('%4.1f Hz' % fpeaks[0])
319 else:
320 labels.append('%4.0f Hz' % fpeaks[0])
321 if len(self.mains) > 0:
322 fpeaks = self.mains[:, 0]
323 fpeakinx = np.array([np.round(fp / self.deltaf) for fp in fpeaks if fp < freqs[-1]], dtype=int)
324 fishpoints, = self.axp.plot(fpeaks[:len(fpeakinx)],
325 power[fpeakinx], linestyle='None',
326 marker='.', color='k', ms=10, mec=None, mew=0.0, zorder=2)
327 self.peak_artists.append(fishpoints)
328 labels.append('%3.0f Hz mains' % self.cfg.value('mainsFreq'))
329 ncol = (len(labels)-1) // 8 + 1
330 self.legendhandle = self.axs.legend(self.peak_artists[:len(labels)], labels, loc='upper right', ncol=ncol)
331 self.legenddict = dict()
332 for legpoints, (finx, fish) in zip(self.legendhandle.get_lines(), enumerate(self.fishlist)):
333 legpoints.set_picker(8)
334 self.legenddict[legpoints] = [finx, fish]
335 self.legendhandle.set_visible(self.legend)
336 if self.power_artist == None:
337 self.power_artist, = self.axp.plot(freqs, power, 'b', zorder=3)
338 else:
339 self.power_artist.set_data(freqs, power)
340 if draw:
341 self.fig.canvas.draw()
343 def keypress(self, event):
344 # print('pressed', event.key)
345 if event.key in '+=X':
346 if self.twindow * self.rate > 20:
347 self.twindow *= 0.5
348 self.update_plots()
349 elif event.key in '-x':
350 if self.twindow < len(self.data) / self.rate:
351 self.twindow *= 2.0
352 self.update_plots()
353 elif event.key == 'pagedown':
354 if self.toffset + 0.5 * self.twindow < len(self.data) / self.rate:
355 self.toffset += 0.5 * self.twindow
356 self.update_plots()
357 elif event.key == 'pageup':
358 if self.toffset > 0:
359 self.toffset -= 0.5 * self.twindow
360 if self.toffset < 0.0:
361 self.toffset = 0.0
362 self.update_plots()
363 elif event.key == 'a':
364 if self.min_clip == 0.0 or self.max_clip == 0.0:
365 self.min_clip, self.max_clip = clip_amplitudes(
366 self.data[:,self.channel],
367 **clip_args(self.cfg, self.rate))
368 try:
369 if self.cfg.value('windowSize') <= 0.0:
370 self.cfg.set('windowSize', (len(self.data)-1)/self.rate)
371 idx0, idx1, clipped = best_window_indices(
372 self.data[:,self.channel], self.rate,
373 min_clip=self.min_clip, max_clip=self.max_clip,
374 **best_window_args(self.cfg))
375 if idx1 > 0:
376 self.toffset = idx0 / self.rate
377 self.twindow = (idx1 - idx0) / self.rate
378 self.twindow *= 2.0/(self.cfg.value('numberPSDWindows')+1.0)
379 self.update_plots()
380 except UserWarning as e:
381 if self.verbose > 0:
382 print(str(e))
383 elif event.key == 'ctrl+pagedown':
384 if self.toffset + 5.0 * self.twindow < len(self.data) / self.rate:
385 self.toffset += 5.0 * self.twindow
386 self.update_plots()
387 elif event.key == 'ctrl+pageup':
388 if self.toffset > 0:
389 self.toffset -= 5.0 * self.twindow
390 if self.toffset < 0.0:
391 self.toffset = 0.0
392 self.update_plots()
393 elif event.key == 'down':
394 if self.toffset + self.twindow < len(self.data) / self.rate:
395 self.toffset += 0.05 * self.twindow
396 self.update_plots()
397 elif event.key == 'up':
398 if self.toffset > 0.0:
399 self.toffset -= 0.05 * self.twindow
400 if self.toffset < 0.0:
401 self.toffset = 0.0
402 self.update_plots()
403 elif event.key == 'home':
404 if self.toffset > 0.0:
405 self.toffset = 0.0
406 self.update_plots()
407 elif event.key == 'end':
408 toffs = np.floor(len(self.data) / self.rate / self.twindow) * self.twindow
409 if self.toffset < toffs:
410 self.toffset = toffs
411 self.update_plots()
412 elif event.key == 'y':
413 h = self.ymax - self.ymin
414 c = 0.5 * (self.ymax + self.ymin)
415 self.ymin = c - h
416 self.ymax = c + h
417 self.axt.set_ylim(self.ymin, self.ymax)
418 self.fig.canvas.draw()
419 elif event.key == 'Y':
420 h = 0.25 * (self.ymax - self.ymin)
421 c = 0.5 * (self.ymax + self.ymin)
422 self.ymin = c - h
423 self.ymax = c + h
424 self.axt.set_ylim(self.ymin, self.ymax)
425 self.fig.canvas.draw()
426 elif event.key == 'v':
427 t0 = int(np.round(self.toffset * self.rate))
428 t1 = int(np.round((self.toffset + self.twindow) * self.rate))
429 min = np.min(self.data[t0:t1,self.channel])
430 max = np.max(self.data[t0:t1,self.channel])
431 h = 0.5 * (max - min)
432 c = 0.5 * (max + min)
433 self.ymin = c - h
434 self.ymax = c + h
435 self.axt.set_ylim(self.ymin, self.ymax)
436 self.fig.canvas.draw()
437 elif event.key == 'V':
438 self.ymin = -1.0
439 self.ymax = +1.0
440 self.axt.set_ylim(self.ymin, self.ymax)
441 self.fig.canvas.draw()
442 elif event.key == 'left':
443 if self.fmin > 0.0:
444 fwidth = self.fmax - self.fmin
445 self.fmin -= 0.5 * fwidth
446 self.fmax -= 0.5 * fwidth
447 if self.fmin < 0.0:
448 self.fmin = 0.0
449 self.fmax = fwidth
450 self.axs.set_ylim(self.fmin, self.fmax)
451 self.axp.set_xlim(self.fmin, self.fmax)
452 self.fig.canvas.draw()
453 elif event.key == 'right':
454 if self.fmax < 0.5 * self.rate:
455 fwidth = self.fmax - self.fmin
456 self.fmin += 0.5 * fwidth
457 self.fmax += 0.5 * fwidth
458 self.axs.set_ylim(self.fmin, self.fmax)
459 self.axp.set_xlim(self.fmin, self.fmax)
460 self.fig.canvas.draw()
461 elif event.key == 'ctrl+left':
462 if self.fmin > 0.0:
463 fwidth = self.fmax - self.fmin
464 self.fmin = 0.0
465 self.fmax = fwidth
466 self.axs.set_ylim(self.fmin, self.fmax)
467 self.axp.set_xlim(self.fmin, self.fmax)
468 self.fig.canvas.draw()
469 elif event.key == 'ctrl+right':
470 if self.fmax < 0.5 * self.rate:
471 fwidth = self.fmax - self.fmin
472 fm = 0.5 * self.rate
473 self.fmax = np.ceil(fm / fwidth) * fwidth
474 self.fmin = self.fmax - fwidth
475 if self.fmin < 0.0:
476 self.fmin = 0.0
477 self.fmax = fwidth
478 self.axs.set_ylim(self.fmin, self.fmax)
479 self.axp.set_xlim(self.fmin, self.fmax)
480 self.fig.canvas.draw()
481 elif event.key in 'f':
482 if self.fmax < 0.5 * self.rate or self.fmin > 0.0:
483 fwidth = self.fmax - self.fmin
484 if self.fmax < 0.5 * self.rate:
485 self.fmax = self.fmin + 2.0 * fwidth
486 elif self.fmin > 0.0:
487 self.fmin = self.fmax - 2.0 * fwidth
488 if self.fmin < 0.0:
489 self.fmin = 0.0
490 self.fmax = 2.0 * fwidth
491 self.axs.set_ylim(self.fmin, self.fmax)
492 self.axp.set_xlim(self.fmin, self.fmax)
493 self.fig.canvas.draw()
494 elif event.key in 'F':
495 if self.fmax - self.fmin > 1.0:
496 fwidth = self.fmax - self.fmin
497 self.fmax = self.fmin + 0.5 * fwidth
498 self.axs.set_ylim(self.fmin, self.fmax)
499 self.axp.set_xlim(self.fmin, self.fmax)
500 self.fig.canvas.draw()
501 elif event.key in 'r':
502 if self.freq_resolution < 1000.0:
503 self.freq_resolution *= 2.0
504 self.update_plots()
505 elif event.key in 'R':
506 if 1.0 / self.freq_resolution < self.tmax:
507 self.freq_resolution *= 0.5
508 self.update_plots()
509 elif event.key in 'd':
510 self.decibel = not self.decibel
511 self.update_plots()
512 elif event.key in 'm':
513 if self.cfg.value('mainsFreq') == 0.0:
514 self.cfg.set('mainsFreq', self.mains_freq)
515 else:
516 self.cfg.set('mainsFreq', 0.0)
517 self.update_plots()
518 elif event.key in 't':
519 t_diff = self.cfg.value('highThresholdFactor') - self.cfg.value('lowThresholdFactor')
520 self.cfg.set('lowThresholdFactor', self.cfg.value('lowThresholdFactor') - 0.1)
521 if self.cfg.value('lowThresholdFactor') < 0.1:
522 self.cfg.set('lowThresholdFactor', 0.1)
523 self.cfg.set('highThresholdFactor', self.cfg.value('lowThresholdFactor') + t_diff)
524 print('lowThresholdFactor =', self.cfg.value('lowThresholdFactor'))
525 self.update_plots()
526 elif event.key in 'T':
527 t_diff = self.cfg.value('highThresholdFactor') - self.cfg.value('lowThresholdFactor')
528 self.cfg.set('lowThresholdFactor', self.cfg.value('lowThresholdFactor') + 0.1)
529 if self.cfg.value('lowThresholdFactor') > 20.0:
530 self.cfg.set('lowThresholdFactor', 20.0)
531 self.cfg.set('highThresholdFactor', self.cfg.value('lowThresholdFactor') + t_diff)
532 print('lowThresholdFactor =', self.cfg.value('lowThresholdFactor'))
533 self.update_plots()
534 elif event.key == 'escape':
535 self.remove_peak_annotation()
536 self.fig.canvas.draw()
537 elif event.key in 'h':
538 self.help = not self.help
539 for ht in self.helptext:
540 ht.set_visible(self.help)
541 self.fig.canvas.draw()
542 elif event.key in 'l':
543 self.legend = not self.legend
544 self.legendhandle.set_visible(self.legend)
545 self.fig.canvas.draw()
546 elif event.key in 'w':
547 self.plot_waveform()
548 elif event.key in 'p':
549 self.play_segment()
550 elif event.key in 'P':
551 self.play_all()
552 elif event.key in '1' :
553 self.play_tone('c3')
554 elif event.key in '2' :
555 self.play_tone('a3')
556 elif event.key in '3' :
557 self.play_tone('e4')
558 elif event.key in '4' :
559 self.play_tone('a4')
560 elif event.key in '5' :
561 self.play_tone('c5')
562 elif event.key in '6' :
563 self.play_tone('e5')
564 elif event.key in '7' :
565 self.play_tone('g5')
566 elif event.key in '8' :
567 self.play_tone('a5')
568 elif event.key in '9' :
569 self.play_tone('c6')
570 elif event.key in 'S':
571 self.save_segment()
573 def buttonpress( self, event ) :
574 # print('mouse pressed', event.button, event.key, event.step)
575 if event.inaxes == self.axp:
576 if event.key == 'shift' or event.key == 'control':
577 # show next or previous harmonic:
578 if event.key == 'shift':
579 if event.button == 1:
580 ftarget = event.xdata / 2.0
581 elif event.button == 3:
582 ftarget = event.xdata * 2.0
583 else:
584 if event.button == 1:
585 ftarget = event.xdata / 1.5
586 elif event.button == 3:
587 ftarget = event.xdata * 1.5
588 foffs = event.xdata - self.fmin
589 fwidth = self.fmax - self.fmin
590 self.fmin = ftarget - foffs
591 self.fmax = self.fmin + fwidth
592 self.axs.set_ylim(self.fmin, self.fmax)
593 self.axp.set_xlim(self.fmin, self.fmax)
594 self.fig.canvas.draw()
595 else:
596 # put label on peak
597 self.remove_peak_annotation()
598 # find closest peak:
599 fwidth = self.fmax - self.fmin
600 peakdist = np.abs(self.allpeaks[:, 0] - event.xdata)
601 inx = np.argmin(peakdist)
602 if peakdist[inx] < 0.005 * fwidth:
603 peak = self.allpeaks[inx, :]
604 # find fish:
605 foundfish = False
606 for finx, fish in enumerate(self.fishlist):
607 if np.min(np.abs(fish[:, 0] - peak[0])) < 0.8 * self.deltaf:
608 self.annotate_fish(fish, finx)
609 foundfish = True
610 break
611 if not foundfish:
612 self.annotate_peak(peak)
613 self.fig.canvas.draw()
614 else:
615 self.fig.canvas.draw()
617 def onpick(self, event):
618 # print('pick')
619 legendpoint = event.artist
620 finx, fish = self.legenddict[legendpoint]
621 self.annotate_fish(fish, finx)
623 def resize(self, event):
624 # print('resized', event.width, event.height)
625 leftpixel = 80.0
626 rightpixel = 20.0
627 xaxispixel = 50.0
628 toppixel = 20.0
629 timeaxis = 0.42
630 left = leftpixel / event.width
631 width = 1.0 - left - rightpixel / event.width
632 xaxis = xaxispixel / event.height
633 top = toppixel / event.height
634 height = (1.0 - timeaxis - top) / 2.0
635 if left < 0.5 and width < 1.0 and xaxis < 0.3 and top < 0.2:
636 self.axt.set_position([left, timeaxis + height, width, height])
637 self.axs.set_position([left, timeaxis, width, height])
638 self.axp.set_position([left, xaxis, width, timeaxis - 2.0 * xaxis])
640 def plot_waveform(self):
641 fig = plt.figure()
642 ax = fig.add_subplot(1, 1, 1)
643 name = self.filename.split('.')[0]
644 if self.channel > 0:
645 ax.set_title('{filename} channel={channel:d}'.format(
646 filename=self.filename, channel=self.channel))
647 figfile = '{name}-{channel:d}-{time:.4g}s-waveform.png'.format(
648 name=name, channel=self.channel, time=self.toffset)
649 else:
650 ax.set_title(self.filename)
651 figfile = '{name}-{time:.4g}s-waveform.png'.format(
652 name=name, time=self.toffset)
653 t0 = int(np.round(self.toffset * self.rate))
654 t1 = int(np.round((self.toffset + self.twindow) * self.rate))
655 if t1>len(self.data):
656 t1 = len(self.data)
657 time = np.arange(t0, t1) / self.rate
658 if self.twindow < 1.0:
659 ax.set_xlabel('Time [ms]')
660 ax.set_xlim(1000.0 * self.toffset,
661 1000.0 * (self.toffset + self.twindow))
662 ax.plot(1000.0 * time, self.data[t0:t1,self.channel])
663 else:
664 ax.set_xlabel('Time [s]')
665 ax.set_xlim(self.toffset, self.toffset + self.twindow)
666 ax.plot(time, self.data[t0:t1,self.channel])
667 ax.set_ylabel('Amplitude [{:s}]'.format(self.unit))
668 fig.tight_layout()
669 fig.savefig(figfile)
670 fig.clear()
671 plt.close(fig)
672 print('saved waveform figure to', figfile)
674 def play_segment(self):
675 t0 = int(np.round(self.toffset * self.rate))
676 t1 = int(np.round((self.toffset + self.twindow) * self.rate))
677 playdata = 1.0 * self.data[t0:t1,self.channel]
678 fade(playdata, self.rate, 0.1)
679 self.audio.play(playdata, self.rate, blocking=False)
681 def save_segment(self):
682 t0s = int(np.round(self.toffset))
683 t1s = int(np.round(self.toffset + self.twindow))
684 t0 = int(np.round(self.toffset * self.rate))
685 t1 = int(np.round((self.toffset + self.twindow) * self.rate))
686 savedata = 1.0 * self.data[t0:t1,self.channel]
687 filename = self.filename.split('.')[0]
688 segmentfilename = '{name}-{time0:.4g}s-{time1:.4g}s.wav'.format(
689 name=filename, time0=t0s, time1 = t1s)
690 write_audio(segmentfilename, savedata, self.data.rate)
691 print('saved segment to: ' , segmentfilename)
693 def play_all(self):
694 self.audio.play(self.data[:,self.channel], self.rate,
695 blocking=False)
697 def play_tone( self, frequency ) :
698 self.audio.beep(1.0, frequency)
701def short_user_warning(message, category, filename, lineno, file=None, line=''):
702 if file is None:
703 file = sys.stderr
704 if category == UserWarning:
705 file.write('%s line %d: %s\n' % ('/'.join(filename.split('/')[-2:]), lineno, message))
706 else:
707 s = warnings.formatwarning(message, category, filename, lineno, line)
708 file.write(s)
711def main(cargs=None):
712 warnings.showwarning = short_user_warning
714 # config file name:
715 cfgfile = __package__ + '.cfg'
717 # command line arguments:
718 if cargs is None:
719 cargs = sys.argv[1:]
720 parser = argparse.ArgumentParser(
721 description='Display waveform, and power spectrum with detected fundamental frequencies of EOD recordings.',
722 epilog='version %s by Jan Benda (2015-%s)' % (__version__, __year__))
723 parser.add_argument('--version', action='version', version=__version__)
724 parser.add_argument('-v', action='count', dest='verbose')
725 parser.add_argument('-c', '--save-config', nargs='?', default='', const=cfgfile,
726 type=str, metavar='cfgfile',
727 help='save configuration to file cfgfile (defaults to {0})'.format(cfgfile))
728 parser.add_argument('file', nargs='?', default='', type=str,
729 help='name of the file with the time series data')
730 parser.add_argument('channel', nargs='?', default=0, type=int,
731 help='channel to be displayed')
732 args = parser.parse_args(cargs)
733 filepath = args.file
735 # set verbosity level from command line:
736 verbose = 0
737 if args.verbose != None:
738 verbose = args.verbose
740 if len(args.save_config):
741 # save configuration:
742 cfg = configuration()
743 cfg.load_files(cfgfile, filepath, 4, verbose)
744 save_configuration(cfg, cfgfile)
745 return
746 elif len(filepath) == 0:
747 parser.error('you need to specify a file containing some data')
749 # load configuration:
750 cfg = configuration()
751 cfg.load_files(cfgfile, filepath, 4, verbose-1)
753 # load data:
754 filename = os.path.basename(filepath)
755 channel = args.channel
756 # TODO: add blocksize and backsize as configuration parameter!
757 with DataLoader(filepath, 60.0, 10.0, verbose) as data:
758 SignalPlot(data, data.rate, data.unit, filename, channel, verbose, cfg)
761if __name__ == '__main__':
762 main()
765# 50301L02.WAV t=9 bis 9.15 sec
768## 1 fish:
769# simple aptero (clipped):
770# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L14.WAV
771# nice sterno:
772# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L31.WAV
773# sterno (clipped) with a little bit of background:
774# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L26.WAV
775# simple brachy (clipped, with a very small one in the background): still difficult, but great with T=4s
776# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L30.WAV
777# eigenmannia (very nice): EN086.MP3
778# single, very nice brachy, with difficult psd:
779# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L19.WAV
780# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L2[789].WAV
782## 2 fish:
783# 2 aptero:
784# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L10.WAV
785# EN098.MP3 and in particular EN099.MP3 nice 2Hz beat!
786# 2 brachy beat:
787# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L08.WAV
788# >= 2 brachys:
789# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L2[12789].WAV
791## one sterno with weak aptero:
792# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L11.WAV
793# EN144.MP3
795## 2 and 2 fish:
796# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L12.WAV
798## one aptero with brachy:
799# EN148
801## lots of fish:
802# python fishfinder.py ~/data/fishgrid/Panama2014/MP3_1/20140517_RioCanita/40517L07.WAV
803# EN065.MP3 EN066.MP3 EN067.MP3 EN103.MP3 EN104.MP3
804# EN109: 1Hz beat!!!!
805# EN013: doppel detection of 585 Hz
806# EN015,30,31: noise estimate problem
808# EN083.MP3 aptero glitch
809# EN146 sek 4 sterno frequency glitch
811# EN056.MP3 EN080.MP3 difficult low frequencies
812# EN072.MP3 unstable low and high freq
813# EN122.MP3 background fish detection difficulties at low res
815# problems: EN088, EN089, 20140524_RioCanita/EN055 sterno not catched, EN056, EN059