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trackingGUI.py
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import sys
import os
import time
import datetime
import numpy as np
import matplotlib.pyplot as plt
from thunderfish.version import __version__
from thunderfish.powerspectrum import decibel, next_power_of_two, spectrogram
from thunderfish.dataloader import fishgrid_grids, fishgrid_spacings
from thunderfish.dataloader import DataLoader as open_data
from thunderfish.harmonics import harmonic_groups, fundamental_freqs
from signal_tracker import freq_tracking_v5, plot_tracked_traces, Emit_progress
from thunderfish.eventdetection import hist_threshold
import multiprocessing
from functools import partial
from IPython import embed
from PyQt5.QtWidgets import *
from PyQt5.QtCore import *
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
class SettingsHarmonicGroup(QMainWindow):
def __init__(self):
super().__init__()
self.cfg = None
self.verbose=0
self.low_threshold=0.0
self.low_threshold_G = 0.0
self.low_thresh_factor=6.0
self.high_threshold=0.0
self.high_threshold_G=0.0
self.high_thresh_factor=10.0
self.freq_tol_fac=1.0
self.mains_freq=50.0
self.mains_freq_tol=1.0
self.max_divisor=2
self.min_group_size=2
self.max_rel_power_weight=2.0
self.max_rel_power=0.0
self.setGeometry(350, 200, 600, 600)
self.setWindowTitle('Harminic groups settings')
self.central_widget = QWidget(self)
self.gridLayout = QGridLayout()
self.gridLayout.setColumnStretch(0, 1)
self.gridLayout.setColumnStretch(1, 1)
self.gridLayout.setColumnStretch(2, 1)
self.gridLayout.setRowStretch(0, 1)
self.gridLayout.setRowStretch(1, 1)
self.gridLayout.setRowStretch(2, 1)
self.gridLayout.setRowStretch(3, 1)
self.gridLayout.setRowStretch(4, 1)
self.gridLayout.setRowStretch(5, 1)
self.gridLayout.setRowStretch(6, 1)
self.gridLayout.setRowStretch(7, 1)
self.init_widgets()
self.central_widget.setLayout(self.gridLayout)
self.setCentralWidget(self.central_widget)
self.write_cfg_dict()
def init_widgets(self):
self.verboseW = QLineEdit(str(0), self.central_widget)
self.verboseL = QLabel('Verbose', self.central_widget)
self.gridLayout.addWidget(self.verboseW, 0, 0)
self.gridLayout.addWidget(self.verboseL, 0, 1)
self.lowTH_W = QLineEdit(str(self.low_threshold), self.central_widget)
self.lowTH_L = QLabel('low threshold [dB]', self.central_widget)
self.gridLayout.addWidget(self.lowTH_W, 1, 0)
self.gridLayout.addWidget(self.lowTH_L, 1, 1)
self.lowTH_fac_W = QLineEdit(str(self.low_thresh_factor), self.central_widget)
self.lowTH_fac_L = QLabel('low threshold factor', self.central_widget)
self.gridLayout.addWidget(self.lowTH_fac_W, 2, 0)
self.gridLayout.addWidget(self.lowTH_fac_L, 2, 1)
self.highTH_W = QLineEdit(str(self.high_threshold), self.central_widget)
self.highTH_L = QLabel('high threshold [dB]', self.central_widget)
self.gridLayout.addWidget(self.highTH_W, 3, 0)
self.gridLayout.addWidget(self.highTH_L, 3, 1)
self.highTH_fac_W = QLineEdit(str(self.high_thresh_factor), self.central_widget)
self.highTH_fac_L = QLabel('high threshold factor', self.central_widget)
self.gridLayout.addWidget(self.highTH_fac_W, 4, 0)
self.gridLayout.addWidget(self.highTH_fac_L, 4, 1)
self.freq_tol_fac_W = QLineEdit(str(self.freq_tol_fac), self.central_widget)
self.freq_tol_fac_L = QLabel('freq tollerance factor', self.central_widget)
self.gridLayout.addWidget(self.freq_tol_fac_W, 5, 0)
self.gridLayout.addWidget(self.freq_tol_fac_L, 5, 1)
self.mains_freq_W = QLineEdit(str(self.mains_freq), self.central_widget)
self.mains_freq_L = QLabel('Main frequencies [Hz]', self.central_widget)
self.gridLayout.addWidget(self.mains_freq_W, 6, 0)
self.gridLayout.addWidget(self.mains_freq_L, 6, 1)
self.mains_freq_tol_W = QLineEdit(str(self.mains_freq_tol), self.central_widget)
self.mains_freq_tol_L = QLabel('Main frequencies tollerance [Hz]', self.central_widget)
self.gridLayout.addWidget(self.mains_freq_tol_W, 7, 0)
self.gridLayout.addWidget(self.mains_freq_tol_L, 7, 1)
self.max_divisor_W = QLineEdit(str(self.max_divisor), self.central_widget)
self.max_divisor_L = QLabel('Max divisor', self.central_widget)
self.gridLayout.addWidget(self.max_divisor_W, 8, 0)
self.gridLayout.addWidget(self.max_divisor_L, 8, 1)
self.min_group_size_W = QLineEdit(str(self.min_group_size), self.central_widget)
self.min_group_size_L = QLabel('min. harmonic group size', self.central_widget)
self.gridLayout.addWidget(self.min_group_size_W, 9, 0)
self.gridLayout.addWidget(self.min_group_size_L, 9, 1)
self.max_rel_power_weight_W = QLineEdit(str(self.max_rel_power_weight), self.central_widget)
self.max_rel_power_weight_L = QLabel('max. rel. power weight', self.central_widget)
self.gridLayout.addWidget(self.max_rel_power_weight_W, 10, 0)
self.gridLayout.addWidget(self.max_rel_power_weight_L, 10, 1)
self.max_rel_power_W = QLineEdit(str(self.max_rel_power), self.central_widget)
self.max_rel_power_L = QLabel('max. rel. power', self.central_widget)
self.gridLayout.addWidget(self.max_rel_power_W, 11, 0)
self.gridLayout.addWidget(self.max_rel_power_L, 11, 1)
space = QLabel('', self.central_widget)
self.gridLayout.addWidget(space, 12, 0)
Apply = QPushButton('&Apply', self.central_widget)
Apply.clicked.connect(self.apply_settings)
self.gridLayout.addWidget(Apply, 13, 1)
Cancel = QPushButton('&Cancel', self.central_widget)
Cancel.clicked.connect(self.close)
self.gridLayout.addWidget(Cancel, 13, 2)
def apply_settings(self):
self.verbose = int(self.verboseW.text())
self.low_threshold = float(self.lowTH_W.text())
self.low_thresh_factor = float(self.lowTH_fac_W.text())
self.high_threshold = float(self.highTH_W.text())
self.high_thresh_factor = float(self.highTH_fac_W.text())
self.freq_tol_fac = float(self.freq_tol_fac_W.text())
self.mains_freq = float(self.mains_freq_W.text())
self.mains_freq_tol = float(self.mains_freq_tol_W.text())
self.max_divisor = int(self.max_divisor_W.text())
self.min_group_size = int(self.min_group_size_W.text())
self.max_rel_power_weight = float(self.max_rel_power_weight_W.text())
self.max_rel_power = float(self.max_rel_power_W.text())
self.write_cfg_dict()
def write_cfg_dict(self):
self.cfg = {}
self.cfg.update({'verbose': self.verbose})
self.cfg.update({'low_thresh_factor': self.low_thresh_factor})
self.cfg.update({'high_thresh_factor': self.high_thresh_factor})
self.cfg.update({'freq_tol_fac': self.freq_tol_fac})
self.cfg.update({'mains_freq': self.mains_freq})
self.cfg.update({'mains_freq_tol': self.mains_freq_tol})
self.cfg.update({'max_divisor': self.max_divisor})
self.cfg.update({'min_group_size': self.min_group_size})
self.cfg.update({'max_rel_power_weight': self.max_rel_power_weight})
self.cfg.update({'max_rel_power': self.max_rel_power})
class SettingsSpectrogram(QMainWindow):
def __init__(self):
super().__init__()
# ToDo: get samplerate in here !!!
self.samplerate = None
self.start_time = 0
self.end_time = -1
self.data_snippet_sec = 15.
self.data_snippet_idxs = 15 * 20000
self.fresolution = 1.5
self.overlap_frac = 0.85
self.nffts_per_psd = 1
self.setGeometry(350, 200, 600, 600)
self.setWindowTitle('Harminic groups settings')
self.central_widget = QWidget(self)
self.gridLayout = QGridLayout()
self.gridLayout.setColumnStretch(0, 1)
self.gridLayout.setColumnStretch(1, 1)
self.gridLayout.setColumnStretch(2, 1)
self.gridLayout.setRowStretch(0, 1)
self.gridLayout.setRowStretch(1, 1)
self.gridLayout.setRowStretch(2, 1)
self.gridLayout.setRowStretch(3, 1)
self.gridLayout.setRowStretch(4, 1)
self.gridLayout.setRowStretch(5, 1)
self.gridLayout.setRowStretch(6, 1)
self.gridLayout.setRowStretch(7, 1)
self.init_widgets()
self.central_widget.setLayout(self.gridLayout)
self.setCentralWidget(self.central_widget)
def init_widgets(self):
self.StartTime = QLineEdit('%.2f' % (self.start_time / 60), self.central_widget)
self.gridLayout.addWidget(self.StartTime, 0, 0)
t0 = QLabel('start time [min]', self.central_widget)
self.gridLayout.addWidget(t0, 0, 1)
self.EndTime = QLineEdit('%.2f' % (self.end_time / 60), self.central_widget)
self.gridLayout.addWidget(self.EndTime, 1, 0)
t1 = QLabel('end time [min]', self.central_widget)
self.gridLayout.addWidget(t1, 1, 1)
self.SnippetSize = QLineEdit(str(self.data_snippet_sec), self.central_widget)
self.gridLayout.addWidget(self.SnippetSize, 2, 0)
snip_size = QLabel('data snippet size [sec]', self.central_widget)
self.gridLayout.addWidget(snip_size, 2, 1)
self.FreqResolution = QLineEdit(str(self.fresolution), self.central_widget)
self.gridLayout.addWidget(self.FreqResolution, 3, 0)
freqres = QLabel('frequency resolution [Hz]', self.central_widget)
self.gridLayout.addWidget(freqres, 3, 1)
self.Overlap = QLineEdit(str(self.overlap_frac), self.central_widget)
self.gridLayout.addWidget(self.Overlap, 4, 0)
overlap = QLabel('overlap fraction', self.central_widget)
self.gridLayout.addWidget(overlap, 4, 1)
self.NfftPerPsd = QLineEdit(str(self.nffts_per_psd), self.central_widget)
self.gridLayout.addWidget(self.NfftPerPsd, 5, 0)
overlap = QLabel('nffts per PSD [n]', self.central_widget)
self.gridLayout.addWidget(overlap, 5, 1)
if self.samplerate:
self.real_nfft = QLineEdit('%.0f' % next_power_of_two(self.samplerate / self.fresolution),
self.central_widget)
self.temp_res = QLineEdit(
'%.3f' % (next_power_of_two(self.samplerate / self.fresolution) * (1. - self.overlap_frac)),
self.central_widget)
print('%.3f' % (
next_power_of_two(self.samplerate / self.fresolution) * (1. - self.overlap_frac) / self.samplerate))
else:
self.real_nfft = QLineEdit('~', self.central_widget)
self.temp_res = QLineEdit('~', self.central_widget)
self.real_nfft.setReadOnly(True)
self.temp_res.setReadOnly(True)
self.real_nfftL = QLabel('real nfft [n]', self.central_widget)
self.temp_resL = QLabel('temp. resolution [s]', self.central_widget)
self.gridLayout.addWidget(self.real_nfft, 6, 1)
self.gridLayout.addWidget(self.real_nfftL, 6, 2)
self.gridLayout.addWidget(self.temp_res, 7, 1)
self.gridLayout.addWidget(self.temp_resL, 7, 2)
space = QLabel('', self.central_widget)
self.gridLayout.addWidget(space, 8, 0)
Apply = QPushButton('&Apply', self.central_widget)
Apply.clicked.connect(self.apply_settings)
self.gridLayout.addWidget(Apply, 9, 1)
Cancel = QPushButton('&Cancel', self.central_widget)
Cancel.clicked.connect(self.close)
self.gridLayout.addWidget(Cancel, 9, 2)
def apply_settings(self):
self.start_time = float(self.StartTime.text()) * 60
self.end_time = float(self.EndTime.text()) * 60
self.data_snippet_sec = float(self.SnippetSize.text())
self.fresolution = float(self.FreqResolution.text())
self.overlap_frac = float(self.Overlap.text())
self.nffts_per_psd = int(self.NfftPerPsd.text())
self.real_nfft.setText('%.0f' % next_power_of_two(20000. / self.fresolution))
self.temp_res.setText('%.3f' % (next_power_of_two(20000. / self.fresolution) * (1. - self.overlap_frac) / 20000.))
if self.samplerate:
self.data_snippet_idxs = int(self.data_snippet_sec * self.samplerate)
self.real_nfft.setText('%.0f' % next_power_of_two(self.samplerate / self.fresolution))
self.temp_res.setText('%.3f' % (next_power_of_two(self.samplerate / self.fresolution) * (1. - self.overlap_frac) / self.samplerate))
class EOD_extraxt(QThread):
finished = pyqtSignal()
progress = pyqtSignal(float)
# tracking_progress = pyqtSignal(float)
return_spec = pyqtSignal()
return_EODf = pyqtSignal()
def __init__(self):
super(QThread, self).__init__()
self.HGSettings = SettingsHarmonicGroup()
self.SpecSettings = SettingsSpectrogram()
self.single_chennel_analysis=False
# self.TrackingProgress = Emit_progress()
# self.TrackingProgress.progress.connect(self.emit_tracking_progress)
self.params()
def params(self):
self.current_tast = None
self.samplerate = None
self.channels = None
self.channel_list = []
self.data = None
self.fundamentals_SCH = []
self.signatures_SCH = []
self.fundamentals = []
self.signatures = []
self.times = []
self.tmp_spectra_SCH = None
self.tmp_spectra = None
self.tmp_times = None
self.life_plotting = False
self.folder = None
self.all_fund_v = []
self.all_ident_v = []
self.all_idx_v = []
self.all_original_sign_v = []
def run(self):
self.SpecSettings.apply_settings()
self.HGSettings.apply_settings()
if self.current_tast == 'fill_spec':
self.fill_spec()
else:
self.snippet_spectrogram()
def fill_spec(self):
start_idx = int(self.SpecSettings.start_time * self.samplerate)
if self.SpecSettings.end_time < 0.0:
end_time = len(self.data) / self.samplerate
end_idx = int(len(self.data) - 1)
self.SpecSettings.end_time = end_time
else:
end_idx = int(self.SpecSettings.end_time * self.samplerate)
if end_idx >= int(len(self.data) - 1):
end_idx = int(len(self.data) - 1)
last_run = False
get_spec_plot_matrix = False
p0 = start_idx
pn = end_idx
first_run = True
pre_save_spectra = np.array([])
while start_idx <= end_idx:
self.progress.emit((start_idx - p0) / (end_idx - p0) * 100)
# self.progress.setValue((start_idx - p0) / (end_idx - p0) * 100)
if start_idx >= end_idx - self.SpecSettings.data_snippet_idxs:
last_run = True
core_count = multiprocessing.cpu_count()
pool = multiprocessing.Pool(core_count - 1)
nfft = next_power_of_two(self.samplerate / self.SpecSettings.fresolution)
func = partial(spectrogram, ratetime=self.samplerate, freq_resolution=self.SpecSettings.fresolution, overlap_frac=self.SpecSettings.overlap_frac)
if len(np.shape(self.data)) == 1:
a = pool.map(func, [self.data[start_idx: start_idx + self.SpecSettings.data_snippet_idxs]])
else:
a = pool.map(func, [self.data[start_idx: start_idx + self.SpecSettings.data_snippet_idxs, channel] for channel in
self.channel_list]) # ret: spec, freq, time
self.spectra = [a[channel][0] for channel in range(len(a))]
self.spec_freqs = a[0][1]
self.spec_times = a[0][2]
pool.terminate()
self.comb_spectra = np.sum(self.spectra, axis=0)
self.tmp_times = self.spec_times + (start_idx / self.samplerate)
############################################
fill_spec_str = os.path.join('/home/raab/analysis/fine_specs', os.path.split(self.folder)[-1], 'fill_spec.npy')
if first_run:
first_run = False
if not os.path.exists(os.path.join('/home/raab/analysis/fine_specs', os.path.split(self.folder)[-1])):
os.mkdir(os.path.join('/home/raab/analysis/fine_specs', os.path.split(self.folder)[-1]))
fill_spec = np.memmap(fill_spec_str, dtype='float', mode='w+',
shape=(len(self.comb_spectra), len(self.tmp_times)), order='F')
fill_spec[:, :] = self.comb_spectra
else:
if len(pre_save_spectra) == 0:
pre_save_spectra = self.comb_spectra
else:
pre_save_spectra = np.append(pre_save_spectra, self.comb_spectra, axis=1)
if np.shape(pre_save_spectra)[1] >= 500:
old_len = np.shape(fill_spec)[1]
fill_spec = np.memmap(fill_spec_str, dtype='float', mode='r+', shape=(
np.shape(pre_save_spectra)[0], np.shape(pre_save_spectra)[1] + old_len), order='F')
fill_spec[:, old_len:] = pre_save_spectra
pre_save_spectra = np.array([])
non_overlapping_idx = (1 - self.SpecSettings.overlap_frac) * nfft
start_idx += int(len(self.spec_times) * non_overlapping_idx)
self.times = np.concatenate((self.times, self.tmp_times))
if start_idx >= end_idx or last_run:
break
file_str = os.path.split(self.folder)[-1]
np.save(os.path.join('/home/raab/analysis/fine_specs', file_str, 'fill_spec_shape.npy'), np.array(np.shape(fill_spec)))
np.save(os.path.join('/home/raab/analysis/fine_specs', file_str, 'fill_times.npy'), self.times)
np.save(os.path.join('/home/raab/analysis/fine_specs', file_str, 'fill_freqs.npy'), self.spec_freqs)
print('')
print('### ###')
print('')
print('fill spec completed')
print('')
print('### ###')
print('')
self.quit()
def snippet_spectrogram(self):
start_idx = int(self.SpecSettings.start_time * self.samplerate)
if self.SpecSettings.end_time < 0.0:
end_time = len(self.data) / self.samplerate
end_idx = int(len(self.data) - 1)
self.SpecSettings.end_time = end_time
else:
end_idx = int(self.SpecSettings.end_time * self.samplerate)
if end_idx >= int(len(self.data) - 1):
end_idx = int(len(self.data) - 1)
last_run = False
get_spec_plot_matrix = False
p0 = start_idx
pn = end_idx
for ch in self.channel_list:
self.fundamentals_SCH.append([])
self.signatures_SCH.append([])
while start_idx <= end_idx:
self.progress.emit((start_idx - p0) / (end_idx - p0) * 100)
# self.progress.setValue((start_idx - p0) / (end_idx - p0) * 100)
if start_idx >= end_idx - self.SpecSettings.data_snippet_idxs:
last_run = True
core_count = multiprocessing.cpu_count()
pool = multiprocessing.Pool(core_count - 1)
nfft = next_power_of_two(self.samplerate / self.SpecSettings.fresolution)
func = partial(spectrogram, ratetime=self.samplerate, freq_resolution=self.SpecSettings.fresolution, overlap_frac=self.SpecSettings.overlap_frac)
if len(np.shape(self.data)) == 1:
a = pool.map(func, [self.data[start_idx: start_idx + self.SpecSettings.data_snippet_idxs]]) # ret: spec, freq, time
else:
a = pool.map(func, [self.data[start_idx: start_idx + self.SpecSettings.data_snippet_idxs, channel] for channel in
self.channel_list]) # ret: spec, freq, time
self.spectra = [a[channel][0] for channel in range(len(a))]
self.spec_freqs = a[0][1]
self.spec_times = a[0][2]
pool.terminate()
self.comb_spectra = np.sum(self.spectra, axis=0)
self.tmp_times = self.spec_times + (start_idx / self.samplerate)
comp_max_freq = 2000
comp_min_freq = 0
create_plotable_spectrogram = True
if create_plotable_spectrogram:
plot_freqs = self.spec_freqs[self.spec_freqs < comp_max_freq]
plot_spectra = np.sum(self.spectra, axis=0)[self.spec_freqs < comp_max_freq]
if self.life_plotting:
self.spec_ret = plot_spectra[(plot_freqs < 1200) & (plot_freqs > 400)]
self.freq_ret = plot_freqs[(plot_freqs < 1200) & (plot_freqs > 400)]
self.times_ret = self.tmp_times
self.return_spec.emit()
# if not checked_xy_borders:
if not get_spec_plot_matrix:
fig_xspan = 20.
fig_yspan = 12.
fig_dpi = 80.
no_x = fig_xspan * fig_dpi
no_y = fig_yspan * fig_dpi
min_x = self.SpecSettings.start_time
max_x = self.SpecSettings.end_time
min_y = comp_min_freq
max_y = comp_max_freq
x_borders = np.linspace(min_x, max_x, int(no_x * 2))
y_borders = np.linspace(min_y, max_y, int(no_y * 2))
self.tmp_spectra = np.zeros((len(y_borders) - 1, len(x_borders) - 1))
self.tmp_spectra_SCH = np.array([np.zeros((len(y_borders) - 1, len(x_borders) - 1)) for ch in self.channel_list])
recreate_matrix = False
if (self.tmp_times[1] - self.tmp_times[0]) > (x_borders[1] - x_borders[0]):
try:
print('da')
x_borders = np.linspace(min_x, max_x, int((max_x - min_x) // (self.tmp_times[1] - self.tmp_times[0]) + 1))
except:
embed()
quit()
recreate_matrix = True
if (self.spec_freqs[1] - self.spec_freqs[0]) > (y_borders[1] - y_borders[0]):
recreate_matrix = True
y_borders = np.linspace(min_y, max_y, (max_y - min_y) // (self.spec_freqs[1] - self.spec_freqs[0]) + 1)
if recreate_matrix:
self.tmp_spectra = np.zeros((len(y_borders) - 1, len(x_borders) - 1))
self.tmp_spectra_SCH = np.array([np.zeros((len(y_borders) - 1, len(x_borders) - 1)) for ch in self.channel_list])
get_spec_plot_matrix = True
# checked_xy_borders = True
for i in range(len(y_borders) - 1):
# print(i/len(y_borders))
for j in range(len(x_borders) - 1):
if x_borders[j] > self.tmp_times[-1]:
break
if x_borders[j + 1] < self.tmp_times[0]:
continue
t_mask = np.arange(len(self.tmp_times))[(self.tmp_times >= x_borders[j]) & (self.tmp_times < x_borders[j + 1])]
f_mask = np.arange(len(plot_spectra))[(plot_freqs >= y_borders[i]) & (plot_freqs < y_borders[i + 1])]
if len(t_mask) == 0 or len(f_mask) == 0:
continue
# print('yay')
self.tmp_spectra[i, j] = np.max(plot_spectra[f_mask[:, None], t_mask])
for ch in self.channel_list:
self.tmp_spectra_SCH[ch, i, j] = np.max(self.spectra[ch][f_mask[:, None], t_mask])
# if self.CBgroup_analysis.isChecked():
if self.single_chennel_analysis == True:
# self.power = self.spectra
####
for ch in self.channel_list:
# self.fundamentals_SCH.append([])
# self.signatures_SCH.append([])
# ToDo: error here !!!
self.power = [np.array([]) for i in range(len(self.spec_times))]
for t in range(len(self.spec_times)):
self.power[t] = np.mean(self.spectra[ch][:, t:t + 1], axis=1)
# self.power[t] = np.mean(self.comb_spectra[:, t:t + 1], axis=1)
self.extract_fundamentals_and_signatures(channel=ch)
####
else:
self.power = [np.array([]) for i in range(len(self.spec_times))]
for t in range(len(self.spec_times)):
self.power[t] = np.mean(self.comb_spectra[:, t:t + 1], axis=1)
self.extract_fundamentals_and_signatures()
# if self.single_chennel_analysis == True:
# for i in range(len(a)):
# self.extract_fundamentals_and_signatures(channel=i)
non_overlapping_idx = (1 - self.SpecSettings.overlap_frac) * nfft
start_idx += int((len(self.spec_times) - self.SpecSettings.nffts_per_psd + 1) * non_overlapping_idx)
self.times = np.concatenate((self.times, self.tmp_times))
# print('check 4')
if start_idx >= end_idx or last_run:
# self.progress.setValue(100)
self.progress.emit(100)
# print('done')
print(np.shape(self.data))
print(self.channels)
if self.single_chennel_analysis == True:
self.all_fund_v = []
self.all_ident_v = []
self.all_idx_v = []
self.all_sign_v = []
self.all_a_error_distribution = []
self.all_f_error_distribution = []
self.all_idx_of_origin_v = []
self.all_original_sign_v = []
for it in range(len(self.fundamentals_SCH)):
print('### tracking Ch: %.0f of %.0f' % (it, len(self.fundamentals_SCH)) )
self.fund_v, self.ident_v, self.idx_v, self.sign_v, self.a_error_distribution, \
self.f_error_distribution, self.idx_of_origin_v, self.original_sign_v = \
freq_tracking_v5(self.fundamentals_SCH[it], self.signatures_SCH[it], self.times,
freq_tolerance=self.HGSettings.freq_tol_fac, n_channels=self.channels)
self.all_fund_v.append(self.fund_v)
self.all_ident_v.append(self.ident_v)
self.all_idx_v.append(self.idx_v)
self.all_sign_v.append(self.sign_v)
self.all_a_error_distribution.append(self.a_error_distribution)
self.all_f_error_distribution.append(self.f_error_distribution)
self.all_idx_of_origin_v.append(self.idx_of_origin_v)
self.all_original_sign_v.append(self.original_sign_v)
# embed()
# quit()
else:
self.fund_v, self.ident_v, self.idx_v, self.sign_v, self.a_error_distribution, \
self.f_error_distribution, self.idx_of_origin_v, self.original_sign_v = \
freq_tracking_v5(self.fundamentals, self.signatures, self.times, freq_tolerance=self.HGSettings.freq_tol_fac, n_channels=self.channels)
self.finished.emit()
break
def extract_fundamentals_and_signatures(self, channel = None):
core_count = multiprocessing.cpu_count()
pool = multiprocessing.Pool(core_count - 1)
if channel == None:
func = partial(harmonic_groups, self.spec_freqs, low_threshold = self.HGSettings.low_threshold_G,
high_threshold = self.HGSettings.high_threshold_G, min_freq = 400, max_freq=2000, **self.HGSettings.cfg)
a = pool.map(func, self.power)
else:
func = partial(harmonic_groups, self.spec_freqs, low_threshold = self.HGSettings.low_threshold,
high_threshold = self.HGSettings.high_threshold, min_freq = 400, max_freq=2000, **self.HGSettings.cfg)
a = pool.map(func, self.power)
# print(a[0][5], a[0][6])
if channel == None:
if self.HGSettings.low_threshold_G <= 0 or self.HGSettings.high_threshold_G <= 0:
self.HGSettings.low_threshold_G = a[0][5]
self.HGSettings.high_threshold_G = a[0][6]
else:
if self.HGSettings.low_threshold <= 0 or self.HGSettings.high_threshold <= 0:
self.HGSettings.low_threshold = a[0][5]
self.HGSettings.high_threshold = a[0][6]
log_spectra = decibel(np.array(self.spectra))
if self.life_plotting:
self.EODf_ret = []
for p in range(len(self.power)):
tmp_fundamentals = fundamental_freqs(a[p][0])
if self.life_plotting:
self.EODf_ret.append(tmp_fundamentals)
if channel != None:
self.fundamentals_SCH[channel].append(tmp_fundamentals)
else:
self.fundamentals.append(tmp_fundamentals)
if len(tmp_fundamentals) >= 1:
f_idx = np.array([np.argmin(np.abs(self.spec_freqs - f)) for f in tmp_fundamentals])
tmp_signatures = log_spectra[:, np.array(f_idx), p].transpose()
else:
tmp_signatures = np.array([])
if channel != None:
self.signatures_SCH[channel].append(tmp_signatures)
else:
self.signatures.append(tmp_signatures)
if self.life_plotting:
self.return_EODf.emit()
pool.terminate()
class MainWindow(QMainWindow):
def __init__(self, parent=None):
super(MainWindow, self).__init__(parent)
self.EodEctractThread = EOD_extraxt()
self.EodEctractThread.finished.connect(self.thread_finished)
self.EodEctractThread.progress.connect(self.show_progress)
self.EodEctractThread.return_spec.connect(self.life_spec)
self.EodEctractThread.return_EODf.connect(self.life_eodf)
#
# self.EodEctractThread.tracking_progress.connect(self.show_progress)
self.life_plot = LifePlot()
# self.test_thread = Test_thread()
# self.test_thread.finished.connect(self.thread_finished)
# self.test_thread.progress.connect(self.show_progress)
self.setGeometry(300, 150, 600, 300) # set window proportion
self.setWindowTitle('Fish Tracking') # set window title
self.central_widget = QWidget(self)
self.gridLayout = QGridLayout()
self.params()
self.create_widgets()
self.gridLayout.setColumnStretch(0, 1)
self.gridLayout.setColumnStretch(1, 1)
self.gridLayout.setColumnStretch(2, 1)
self.gridLayout.setRowStretch(0, 1)
self.gridLayout.setRowStretch(1, 1)
self.gridLayout.setRowStretch(2, 1)
self.gridLayout.setRowStretch(3, 1)
self.gridLayout.addWidget(self.open_B, 0, 0)
self.gridLayout.addWidget(self.open_fileL, 0, 1)
self.gridLayout.addWidget(self.save_B, 0, 2)
self.gridLayout.addWidget(self.auto_save_cb, 1, 2)
self.gridLayout.addWidget(self.single_trace_cb, 1, 0)
self.gridLayout.addWidget(self.HG_B, 3, 0)
self.gridLayout.addWidget(self.fill_spec_B, 3, 1)
self.gridLayout.addWidget(self.Spec_B, 4, 0)
self.gridLayout.addWidget(self.run_B, 3, 2)
self.gridLayout.addWidget(self.life_plot_B, 4, 2)
self.gridLayout.addWidget(self.progress, 5, 0, 1, 3)
self.central_widget.setLayout(self.gridLayout)
self.setCentralWidget(self.central_widget)
self.filenames = []
self.total_file_count = 0
self.finisched_count = 0
def params(self):
self.filename = None
self.folder = None
self.rec_datetime = None
self.data = None
self.samplerate = None
self.channels = None
self.elecs_y, self.elecs_x = None, None
self.elecs_y_spacing, self.elecs_x_spacing = None, None
self.fund_v = None
self.ident_v = None
self.idx_v = None
self.original_sign_v = None
self.start_time = None
self.end_time = None
def create_widgets(self):
self.open_B = QPushButton('open', self.central_widget)
self.open_B.clicked.connect(self.open)
self.open_fileL = QLabel('N.a.', self.central_widget)
self.HG_B = QPushButton('Harmonic groups', self.central_widget)
self.HG_B.clicked.connect(self.HG_main)
self.Spec_B = QPushButton('Spectrogram', self.central_widget)
self.Spec_B.clicked.connect(self.Spec_main)
self.progress = QProgressBar(self)
self.run_B = QPushButton('Run', self.central_widget)
self.run_B.clicked.connect(self.run_main)
self.fill_spec_B = QPushButton('Calc. fine spec', self.central_widget)
self.fill_spec_B.clicked.connect(self.run_fill_spec)
self.save_B = QPushButton('Save', self.central_widget)
self.save_B.clicked.connect(self.save)
self.save_B.setEnabled(False)
self.auto_save_cb = QCheckBox('Auto Save', self.central_widget)
self.single_trace_cb = QCheckBox('Single Trace', self.central_widget)
self.life_plot_B = QPushButton('Life Plot', self.central_widget)
self.life_plot_B.clicked.connect(self.life_dialog)
def life_dialog(self):
if self.life_plot.running == False:
self.life_plot.show()
self.EodEctractThread.life_plotting = True
self.life_plot.running = True
else:
self.life_plot.close()
self.EodEctractThread.life_plotting = False
self.life_plot.running = False
def life_spec(self):
life_spec = np.copy(self.EodEctractThread.spec_ret)
life_freq = np.copy(self.EodEctractThread.freq_ret)
life_times = np.copy(self.EodEctractThread.tmp_times)
self.life_plot.update.spec = life_spec
self.life_plot.update.freq = life_freq
self.life_plot.update.times = life_times
# self.life_plot.show()
self.life_plot.update.start()
def life_eodf(self):
life_eodf = np.copy(self.EodEctractThread.EODf_ret)
life_times = np.copy(self.EodEctractThread.tmp_times)
self.life_plot.update_eodf.eodf = life_eodf
self.life_plot.update_eodf.times = life_times
self.life_plot.update_eodf.start()
def show_progress(self, e):
self.progress.setValue(e)
@pyqtSlot()
def thread_finished(self):
# self.test_thread.wait()
self.finisched_count += 1
self.open_B.setText('open (%.0f/%.0f)' % (self.finisched_count, self.total_file_count))
self.EodEctractThread.wait()
self.HG_B.setEnabled(True)
self.Spec_B.setEnabled(True)
self.fund_v = self.EodEctractThread.fund_v
self.ident_v = self.EodEctractThread.ident_v
self.idx_v = self.EodEctractThread.idx_v
self.original_sign_v = self.EodEctractThread.original_sign_v
self.all_fund_v = self.EodEctractThread.all_fund_v
self.all_ident_v = self.EodEctractThread.all_ident_v
self.all_idx_v = self.EodEctractThread.all_idx_v
self.all_original_sign_v = self.EodEctractThread.all_original_sign_v
self.tmp_spectra_SCH = self.EodEctractThread.tmp_spectra_SCH
self.times = self.EodEctractThread.times
self.tmp_spectra = self.EodEctractThread.tmp_spectra
self.save_B.setEnabled(True)
if self.auto_save_cb.isChecked():
self.save()
self.filenames.pop(0)
if len(self.filenames) == 0:
print('all files analysed')
self.close()
quit()
else:
self.params()
self.EodEctractThread.params()
# self.filename, ok = self.filenames[0]
self.run_main()
def run_fill_spec(self):
self.EodEctractThread.current_tast = 'fill_spec'
self.run_main()
@pyqtSlot()
def run_main(self):
def get_datetime(folder):
rec_year, rec_month, rec_day, rec_time = \
os.path.split(os.path.split(folder)[-1])[-1].split('-')
rec_year = int(rec_year)
rec_month = int(rec_month)
rec_day = int(rec_day)
try:
rec_time = [int(rec_time.split('_')[0]), int(rec_time.split('_')[1]), 0]
except:
rec_time = [int(rec_time.split(':')[0]), int(rec_time.split(':')[1]), 0]
rec_datetime = datetime.datetime(year=rec_year, month=rec_month, day=rec_day, hour=rec_time[0],
minute=rec_time[1], second=rec_time[2])
return rec_datetime
self.filename, ok = self.filenames[0]
if ok:
self.open_fileL.setText(os.path.join('...', os.path.split(os.path.split(self.filename)[0])[-1]))
self.folder = os.path.split(self.filename)[0]
self.EodEctractThread.folder = self.folder
self.rec_datetime = get_datetime(self.folder)
self.data = open_data(self.filename, 60.0, 10.0, channel=-1)
self.EodEctractThread.data = self.data
self.samplerate= self.data.samplerate
self.EodEctractThread.samplerate = self.samplerate
self.EodEctractThread.SpecSettings.samplerate = self.samplerate
# ToDo: delete this after again... error analysis
self.channels = self.data.channels - 1
# self.channels = self.data.channels
self.EodEctractThread.channels = self.data.channels - 1
self.EodEctractThread.channel_list = np.arange(self.data.channels)
self.open_fileL.setText(os.path.join('...', os.path.split(os.path.split(self.filename)[0])[-1]))
if os.path.exists(os.path.join(os.path.split(self.filename)[0], 'fishgrid.cfg')):
self.elecs_y, self.elecs_x = fishgrid_grids(self.filename)[0]
self.elecs_y_spacing, self.elecs_x_spacing = fishgrid_spacings(self.filename)[0]
self.HG_B.setEnabled(False)
self.Spec_B.setEnabled(False)
# self.test_thread.start()
if self.single_trace_cb.isChecked():
self.EodEctractThread.single_chennel_analysis = True
self.EodEctractThread.start()
else:
print('error in data')
self.filenames.pop(0)
if len(self.filenames) == 0:
quit()
else:
self.params()
self.run_main()
@pyqtSlot()
def HG_main(self):
self.EodEctractThread.HGSettings.show()
@pyqtSlot()
def Spec_main(self):
self.EodEctractThread.SpecSettings.show()
@pyqtSlot()
def open(self):
def get_datetime(folder):
rec_year, rec_month, rec_day, rec_time = \
os.path.split(os.path.split(folder)[-1])[-1].split('-')
rec_year = int(rec_year)
rec_month = int(rec_month)
rec_day = int(rec_day)
try:
rec_time = [int(rec_time.split('_')[0]), int(rec_time.split('_')[1]), 0]
except:
rec_time = [int(rec_time.split(':')[0]), int(rec_time.split(':')[1]), 0]
rec_datetime = datetime.datetime(year=rec_year, month=rec_month, day=rec_day, hour=rec_time[0],
minute=rec_time[1], second=rec_time[2])
return rec_datetime
fd = QFileDialog()
self.filename, ok = fd.getOpenFileName(self, 'Open File', '/', 'Select Raw-File (*.raw)')
self.filenames.append((self.filename, ok))
self.total_file_count += 1
self.open_B.setText('open (%.0f/%.0f)' % (self.finisched_count, self.total_file_count))
# if os.path.exists('/home/raab/data/'):
# self.filename, ok = fd.getOpenFileName(self, 'Open File', '/home/raab/data/', 'Select Raw-File (*.raw)')
# else:
# self.filename, ok = fd.getOpenFileName(self, 'Open File', '/home/', 'Select Raw-File (*.raw)')
# if ok:
# self.folder = os.path.split(self.filename)[0]
# self.rec_datetime = get_datetime(self.folder)
#
# self.data = open_data(self.filename, -1, 60.0, 10.0)
# self.EodEctractThread.data = self.data
#
# self.samplerate= self.data.samplerate
# self.EodEctractThread.samplerate = self.samplerate
# self.EodEctractThread.SpecSettings.samplerate = self.samplerate
#
# self.channels = self.data.channels
# self.EodEctractThread.channels = self.data.channels
# self.EodEctractThread.channel_list = np.arange(self.channels)
#
# self.open_fileL.setText(os.path.join('...', os.path.split(os.path.split(self.filename)[0])[-1]))
#
# if os.path.exists(os.path.join(os.path.split(self.filename)[0], 'fishgrid.cfg')):
# self.elecs_y, self.elecs_x = fishgrid_grids(self.filename)[0]
# self.elecs_y_spacing, self.elecs_x_spacing = fishgrid_spacings(self.filename)[0]
@pyqtSlot()