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signal_tracker_GUI.py
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signal_tracker_GUI.py
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import sys
import os
import time
import datetime
import numpy as np
import matplotlib.pyplot as plt
from .version import __version__
from .powerspectrum import decibel, next_power_of_two, spectrogram
from .dataloader import open_data, fishgrid_grids, fishgrid_spacings
from .harmonics import harmonic_groups, fundamental_freqs
from .eventdetection import hist_threshold
import multiprocessing
from functools import partial
from IPython import embed
from PyQt5.QtWidgets import *
from PyQt5.QtGui import *
from PyQt5 import QtCore
from PyQt5.QtCore import *
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.widgets import RectangleSelector, EllipseSelector
def position_tracking(sign_v, ident_v, elecs, elecs_spacing, n = 6, id = None):
def get_elec_pos(elecs_y, elecs_x, elecs_y_spacing, elecs_x_spacing ):
elec_pos = np.zeros((2, elecs_y * elecs_x))
elec_pos[0] = (np.arange(elecs_y * elecs_x) % elecs_x) * elecs_x_spacing
elec_pos[1] = (np.arange(elecs_y * elecs_x) // elecs_x) * elecs_y_spacing
return elec_pos.T
elecs_y, elecs_x = elecs
elecs_y_spacing, elecs_x_spacing = elecs_spacing
if np.max(sign_v[0]) != 1:
sqr_sign = np.sqrt(0.1 * 10.**sign_v)
else:
sqr_sign = sign_v
# ToDo: check in goettingen stuff how i calculate distance there !!!
x_v = np.zeros(len(sign_v))
y_v = np.zeros(len(sign_v))
elec_pos = get_elec_pos(elecs_y, elecs_x, elecs_y_spacing, elecs_x_spacing )
max_power_electrodes = np.argsort(sign_v, axis = 1)[:, -n:][:, ::-1]
max_power = list(map(lambda x, y: x[y], sign_v, max_power_electrodes))
x_pos = list(map(lambda x, y: np.sum(elec_pos[x][:, 0] * y) / np.sum(y), max_power_electrodes, max_power ))
y_pos = list(map(lambda x, y: np.sum(elec_pos[x][:, 1] * y) / np.sum(y), max_power_electrodes, max_power ))
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=60.0
self.mains_freq_tol=1.0
self.max_divisor=4
self.min_group_size=4
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 * 60
self.end_time = .1 * 60
self.data_snippet_sec = 15.
self.data_snippet_idxs = 15 * 20.000
self.fresolution = 0.5
self.overlap_frac = 0.95
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(str(self.start_time), 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(str(self.end_time), 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.data_snippet_idxs = int(self.data_snippet_sec * self.samplerate)
self.fresolution = float(self.FreqResolution.text())
self.overlap_frac = float(self.Overlap.text())
self.nffts_per_psd = int(self.NfftPerPsd.text())
if 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 AnalysisDialog(QMainWindow):
def __init__(self):
super().__init__()
self.HGSettings = SettingsHarmonicGroup()
self.SpecSettings = SettingsSpectrogram()
self.initMe()
def initMe(self):
# self.setGeometry(300, 150, 200, 200) # set window proportion
self.got_changed = False
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.setGeometry(300, 150, 600, 300)
self.setWindowTitle('EODf and signature extraction')
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.init_widgets()
self.central_widget.setLayout(self.gridLayout)
self.setCentralWidget(self.central_widget)
def init_widgets(self):
# self.StartTime = QLineEdit(str(self.start_time), 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(str(self.end_time), 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)
HGsettings_B = QPushButton('&Harmonic Group settings', self.central_widget)
HGsettings_B.clicked.connect(self.MHGsettings)
self.gridLayout.addWidget(HGsettings_B, 0, 0)
self.CBgroup_analysis = QCheckBox('Multi-Channel', self.central_widget)
self.gridLayout.addWidget(self.CBgroup_analysis, 1, 0)
self.CB_SCH_analysis = QCheckBox('Single-Channel', self.central_widget)
self.gridLayout.addWidget(self.CB_SCH_analysis, 2, 0)
self.CB_SCH_analysis.setChecked(True)
SpecSettings_B = QPushButton('&Spectrogram Settings', self.central_widget)
SpecSettings_B.clicked.connect(self.MSpecSettings)
self.gridLayout.addWidget(SpecSettings_B, 0, 1)
space = QLabel('', self.central_widget)
self.gridLayout.addWidget(space, 3, 0)
self.progress = QProgressBar(self)
self.gridLayout.addWidget(self.progress, 4, 0, 1, 3)
Run = QPushButton('&Run', self.central_widget)
Run.clicked.connect(self.snippet_spectrogram)
self.gridLayout.addWidget(Run, 5, 0)
Cancel = QPushButton('&Cancel', self.central_widget)
Cancel.clicked.connect(self.close)
self.gridLayout.addWidget(Cancel, 5, 2)
def MHGsettings(self):
self.HGSettings.show()
def MSpecSettings(self):
self.SpecSettings.show()
def snippet_spectrogram(self):
# self.apply_settings()
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)
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
while start_idx <= end_idx:
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 // 2)
nfft = next_power_of_two(self.samplerate / self.SpecSettings.fresolution)
func = partial(spectrogram, samplerate=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
# print('check 1')
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
# print('check 2')
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 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, no_x * 2)
y_borders = np.linspace(min_y, max_y, no_y * 2)
# checked_xy_borders = False
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]):
x_borders = np.linspace(min_x, max_x, (max_x - min_x) // (self.tmp_times[1] - self.tmp_times[0]) + 1)
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])
####
# print('check 3')
if self.CBgroup_analysis.isChecked():
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.CB_SCH_analysis.isChecked():
for self.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[self.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 = self.ch)
##########
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)
# print('done')
break
self.got_changed = True
# print('done')
self.close()
def extract_fundamentals_and_signatures(self, channel = None):
core_count = multiprocessing.cpu_count()
pool = multiprocessing.Pool(core_count // 2)
# ToDo the kwarg problem ....
# if True:
# #psd_freqs
# #psd
# self.verbose=0
# #check_freqs=[]
# self.low_threshold=0.0
# self.high_threshold=0.0
# #thresh_bins=100
# self.low_thresh_factor=6.0
# self.high_thresh_factor=10.0
# self.freq_tol_fac=1.0
# self.mains_freq=60.0
# self.mains_freq_tol=1.0
# #min_freq=0.0
# #max_freq=2000.0
# self.max_divisor=4
# self.min_group_size=4
# self.max_rel_power_weight=2.0
# self.max_rel_power=0.0
# #max_harmonics=0
# #max_groups=0
if channel == None:
func = partial(harmonic_groups, self.spec_freqs, low_threshold = self.HGSettings.low_threshold_G,
high_threshold = self.HGSettings.high_threshold_G, **self.HGSettings.cfg)
else:
func = partial(harmonic_groups, self.spec_freqs, low_threshold = self.HGSettings.low_threshold,
high_threshold = self.HGSettings.high_threshold, **self.HGSettings.cfg)
a = pool.map(func, self.power)
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))
for p in range(len(self.power)):
tmp_fundamentals = fundamental_freqs(a[p][0])
self.fundamentals.append(tmp_fundamentals)
if channel != None:
self.fundamentals_SCH[channel].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([])
self.signatures.append(tmp_signatures)
if channel != None:
self.signatures_SCH[channel].append(tmp_signatures)
pool.terminate()
class GridDialog(QMainWindow):
def __init__(self):
super().__init__()
self.initMe()
def initMe(self):
# self.setGeometry(300, 150, 200, 200) # set window proportion
self.setGeometry(300, 150, 300, 450)
self.setWindowTitle('Grid Layout')
print('init dialig grid')
self.channels = 1
self.elecs_x = 1
self.elecs_x_spacing = 1
self.elecs_y = 1
self.elecs_y_spacing = 1
self.grid_handle = None
self.e0_handle = None
self.en_handle = None
self.elec_TL = 1
self.elec_BR = 'n'
self.central_widget = QWidget(self)
self.gridLayout = QGridLayout()
self.gridLayout.setColumnStretch(0, 2)
self.gridLayout.setColumnStretch(1, 1)
self.gridLayout.setColumnStretch(2, 2)
self.gridLayout.setColumnStretch(3, 5)
self.gridLayout.setRowStretch(0, 1)
self.gridLayout.setRowStretch(1, 1)
self.gridLayout.setRowStretch(2, 1)
self.gridLayout.setRowStretch(3, 2)
self.gridLayout.setRowStretch(4, 1)
# self.gridLayout.setColumnStretch(1, 1)
self.layout_plot()
self.init_widgets()
self.update_grid()
self.central_widget.setLayout(self.gridLayout)
self.setCentralWidget(self.central_widget)
# self.show()
def init_widgets(self):
self.layout_xW = QLineEdit(str(self.elecs_x), self.central_widget)
self.layout_xW.setValidator(QIntValidator(0, 10))
self.gridLayout.addWidget(self.layout_xW, 0, 0)
x = QLabel('x', self.central_widget)
self.gridLayout.addWidget(x, 0, 1)
self.layout_yW = QLineEdit(str(self.elecs_y), self.central_widget)
self.layout_yW.setValidator(QIntValidator(0, 10))
self.gridLayout.addWidget(self.layout_yW, 0, 2)
layout_textW = QLabel('grid_layout [x, y]', self.central_widget)
self.gridLayout.addWidget(layout_textW, 0, 3)
self.x_spaceW = QLineEdit(str(self.elecs_x_spacing), self.central_widget)
self.x_spaceW.setValidator(QIntValidator(0, 1000))
self.gridLayout.addWidget(self.x_spaceW, 1, 0, 1, 3)
x_space_textW = QLabel('x-spacing [cm]', self.central_widget)
self.gridLayout.addWidget(x_space_textW, 1, 3)
self.y_spaceW = QLineEdit(str(self.elecs_y_spacing), self.central_widget)
self.y_spaceW.setValidator(QIntValidator(0, 1000))
self.gridLayout.addWidget(self.y_spaceW, 2, 0, 1, 3)
y_space_textW = QLabel('y-spacing [cm]', self.central_widget)
self.gridLayout.addWidget(y_space_textW, 2, 3)
self.gridLayout.addWidget(self.canvas, 3, 0, 1, 4)
Apply = QPushButton('&Apply', self.central_widget)
Apply.clicked.connect(self.apply_settings)
self.gridLayout.addWidget(Apply, 4, 0, 1, 3)
Cancel = QPushButton('&Cancel', self.central_widget)
Cancel.clicked.connect(self.close)
self.gridLayout.addWidget(Cancel, 4, 3)
def update_widgets(self):
self.layout_xW.setText(str(self.elecs_x))
self.layout_yW.setText(str(self.elecs_y))
self.x_spaceW.setText(str(self.elecs_x_spacing))
self.y_spaceW.setText(str(self.elecs_y_spacing))
self.update_grid()
def layout_plot(self):
self.figure = plt.figure()
self.canvas = FigureCanvas(self.figure)
self.ax = self.figure.add_axes([0, 0, 1, 1])
self.ax.axis('off')
self.ax.invert_yaxis()
def update_grid(self):
if self.grid_handle:
self.grid_handle.remove()
if self.e0_handle:
self.e0_handle.remove()
if self.en_handle:
self.en_handle.remove()
X, Y = np.meshgrid(np.arange(int(self.layout_xW.text())), np.arange(int(self.layout_yW.text())))
x = np.hstack(X) * int(self.x_spaceW.text())
y = np.hstack(Y) * int(self.y_spaceW.text())
max_lim = np.max(np.hstack([x, y]))
self.grid_handle, = self.ax.plot(x[1:-1], y[1:-1], 'o', color='k')
self.e0_handle = self.ax.text(x[0], y[0], str(self.elec_TL), color='red', va='center', ha='center')
if len(x) + len(y) > 2:
self.en_handle = self.ax.text(x[-1], y[-1], str(self.elec_BR), color='red', va='center', ha='center')
self.ax.set_xlim(-10, max_lim+10)
self.ax.set_ylim(-10, max_lim+10)
self.ax.invert_yaxis()
self.canvas.draw()
def apply_settings(self):
self.update_grid()
print(int(self.layout_xW.text()))
def keyPressEvent(self, e):
# print(e.key())
if e.key() == Qt.Key_Return:
self.update_grid()
class PlotWidget():
def __init__(self):
self.figure = plt.figure()
self.canvas = FigureCanvas(self.figure)
self.ax = self.figure.add_subplot(111)
self.xlim = None
self.ylim = None
self.init_xlim = None
self.init_ylim = None
self.fundamentals_handle = None
self.spec_img_handle = None
self.trace_handles = []
self.active_id_handle0 = None
self.active_id_handle1 = None
self.active_cut_handle = None
self.active_group_handle = None
self.current_task = None
self.rec_datetime = None
self.fundamentals = None
self.fundamentals_SCH = None
self.times = None
def plot_fundamentals(self, ch = None):
flat_fundamentals = []
flat_t = []
if ch == None:
for f, t in zip(self.fundamentals, self.times):
flat_fundamentals.extend(f)
flat_t.extend(np.ones(len(f)) * t)
else:
for f, t in zip(self.fundamentals_SCH[ch], self.times):
flat_fundamentals.extend(f)
flat_t.extend(np.ones(len(f)) * t)
if self.fundamentals_handle:
self.fundamentals_handle.remove()
self.fundamentals_handle = None
self.fundamentals_handle, = self.ax.plot(flat_t, flat_fundamentals, '.', color='k')
self.canvas.draw()
def remove_fundamentals(self):
if self.fundamentals_handle:
self.fundamentals_handle.remove()
self.fundamentals_handle = None
self.canvas.draw()
def plot_traces(self, ident_v, times, idx_v, fund_v, task = 'init', active_id = None, active_id2 = None, active_ids = None):
if task == 'init':
for handle in self.trace_handles:
handle[0].remove()
self.trace_handles = []
possible_identities = np.unique(ident_v[~np.isnan(ident_v)])
for i, ident in enumerate(np.array(possible_identities)):
c = np.random.rand(3)
h, = self.ax.plot(times[idx_v[ident_v == ident]], fund_v[ident_v == ident], marker='.', color=c)
self.trace_handles.append((h, ident))
self.xlim = self.ax.get_xlim()
self.ylim = self.ax.get_ylim()
self.init_xlim = self.xlim
self.init_ylim = self.ylim
elif task == 'post cut':
handle_idents = np.array([x[1] for x in self.trace_handles])
refresh_handle = np.array(self.trace_handles)[handle_idents == active_id][0]
refresh_handle[0].remove()
c = np.random.rand(3)
h, = self.ax.plot(times[idx_v[ident_v == active_id]], fund_v[ident_v == active_id], marker='.', color=c)
self.trace_handles[np.arange(len(self.trace_handles))[handle_idents == active_id][0]] = (h, active_id)
new_ident = np.max(ident_v[~np.isnan(ident_v)])
c = np.random.rand(3)
h, = self.ax.plot(times[idx_v[ident_v == new_ident]], fund_v[ident_v == new_ident], marker='.', color=c)
self.trace_handles.append((h, new_ident))
elif task == 'post_connect':
handle_idents = np.array([x[1] for x in self.trace_handles])
remove_handle = np.array(self.trace_handles)[handle_idents == active_id2][0]
remove_handle[0].remove()
joined_handle = np.array(self.trace_handles)[handle_idents == active_id][0]
joined_handle[0].remove()
c = np.random.rand(3)
# sorter = np.argsort(self.times[self.idx_v[self.ident_v == self.active_ident0]])
h, = self.ax.plot(times[idx_v[ident_v == active_id]], fund_v[ident_v == active_id], marker='.', color=c)
self.trace_handles[np.arange(len(self.trace_handles))[handle_idents == active_id][0]] = (h, active_id)
# self.trace_handles.append((h, self.active_ident0))
self.trace_handles.pop(np.arange(len(self.trace_handles))[handle_idents == active_id2][0])
elif task == 'post_delete':
handle_idents = np.array([x[1] for x in self.trace_handles])
delete_handle_idx = np.arange(len(self.trace_handles))[handle_idents == active_id][0]
delete_handle = np.array(self.trace_handles)[handle_idents == active_id][0]
delete_handle[0].remove()
self.trace_handles.pop(delete_handle_idx)
elif task == 'post_group_connect' or task == 'post_group_delete':
handle_idents = np.array([x[1] for x in self.trace_handles])
effected_idents = active_ids
mask = np.array([x in effected_idents for x in handle_idents], dtype=bool)
delete_handle_idx = np.arange(len(self.trace_handles))[mask]
delete_handle = np.array(self.trace_handles)[mask]
delete_afterwards = []
for dhi, dh in zip(delete_handle_idx, delete_handle):
dh[0].remove()
if len(ident_v[ident_v == dh[1]]) >= 1:
c = np.random.rand(3)
h, = self.ax.plot(times[idx_v[ident_v == dh[1]]], fund_v[ident_v == dh[1]], marker='.', color=c)
self.trace_handles[dhi] = (h, dh[1])
else:
delete_afterwards.append(dhi)
for i in reversed(sorted(delete_afterwards)):
self.trace_handles.pop(i)
def highlight_group(self, active_idx, ident_v, times, idx_v, fund_v):
if self.active_group_handle:
self.active_group_handle.remove()
self.active_group_handle, = self.ax.plot(times[idx_v[active_idx]], fund_v[active_idx], 'o', color='orange', markersize=4)
def highlight_id(self, active_id, ident_v, times, idx_v, fund_v, no):
if no == 'first':
if self.active_id_handle0:
self.active_id_handle0.remove()
self.active_id_handle0, = self.ax.plot(times[idx_v[ident_v == active_id]], fund_v[ident_v == active_id], color='orange', alpha=0.7, linewidth=4)
elif no == 'second':
if self.active_id_handle1:
self.active_id_handle1.remove()
self.active_id_handle1, = self.ax.plot(times[idx_v[ident_v == active_id]], fund_v[ident_v == active_id], color='red', alpha=0.7, linewidth=4)
def highlight_cut(self, active_idx_in_trace, times, idx_v, fund_v):
if self.active_cut_handle:
self.active_cut_handle.remove()
self.active_cut_handle, = self.ax.plot(times[idx_v[active_idx_in_trace]], fund_v[active_idx_in_trace] , 'o', color='red', alpha = 0.7, markersize=5)
def clock_time(self, rec_datetime, times):
xlim = self.xlim
dx = np.diff(xlim)[0]
label_idx0 = 0
if dx <= 20:
res = 1
elif dx > 20 and dx <= 120:
res = 10
elif dx > 120 and dx <=1200:
res = 60
elif dx > 1200 and dx <= 3600:
res = 600 # 10 min
elif dx > 3600 and dx <= 7200:
res = 1800 # 30 min
else:
res = 3600 # 60 min
if dx > 1200:
if rec_datetime.minute % int(res / 60) != 0:
dmin = int(res / 60) - rec_datetime.minute % int(res / 60)
label_idx0 = dmin * 60
xtick = np.arange(label_idx0, times[-1], res)
datetime_xlabels = list(map(lambda x: rec_datetime + datetime.timedelta(seconds= x), xtick))
if dx > 120:
xlabels = list(map(lambda x: ('%2s:%2s' % (str(x.hour), str(x.minute))).replace(' ', '0'), datetime_xlabels))