Update EStiMo_GUI.py
updated comments
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1 changed files with 8 additions and 65 deletions
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@ -30,10 +30,8 @@ import datetime
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import ctypes
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import scipy
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import pywt
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# import queue
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from cycler import cycler
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# from matplotlib.backend_bases import MouseButton
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from PyQt5.QtCore import QTimer, Qt
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from PyQt5.QtGui import QImage, QPixmap, QIcon, QFont
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from PyQt5.QtWidgets import (QMainWindow, QFileDialog, QMessageBox, QCheckBox, QLineEdit, QWidget, QPushButton,
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@ -154,19 +152,13 @@ class NeurOneOffline():
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eeg_chn = np.arange(0,num_electr,1)
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hdr = mne.io.read_raw_brainvision(tmp_path)
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# hdr.set_channel_types({'EMGleft': 'emg', 'EOGright': 'eog'})
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# hdr.set_montage(mne.channels.read_custom_montage('easycap-M10_63_NO.txt'))
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# mrk_fullpath = tmp_path[:-4]+'vmrk'
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# eeg_fullpath = tmp_path[:-4]+'eeg' #this two are made by hand instead of function.
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#Maybe there is some func for this
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# Annotations returns all events - stimA, stimB, stopA, stopB, start of experiment etc... We chose only stim
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stim = hdr.annotations.onset[np.logical_or(hdr.annotations.description=="Stimulus/A",
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hdr.annotations.description=="Stimulus/B")]
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# Separate stimA and stimB
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stimA = hdr.annotations.onset[hdr.annotations.description=="Stimulus/A"]
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stimB = hdr.annotations.onset[hdr.annotations.description=="Stimulus/B"]
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#divide for stim A and B
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#stimR = hdr.annotations.onset[hdr.annotations.description=='Response/R 16']
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npts = hdr.n_times
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nfft = int(hdr.info['sfreq']) # Sampling rate [Hz]
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fs = int(hdr.info['sfreq']) # Sampling rate [Hz]
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@ -335,8 +327,7 @@ class AppForm(QMainWindow):
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10: 7.812 - 15.625 Hz
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11: 15.625 - 31.25 Hz
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"""
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band = band - 9 #weird way, but then call from function works well for particular band
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#but works correctly only for this set of features!
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band = band - 9
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dwt_pw1, dwt_pw2, dwt_pw3, dwt_pw4 = self.dwt[:4]
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#sum of squares
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dwt_pw1 = np.sum(dwt_pw1**2)
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@ -380,8 +371,7 @@ class AppForm(QMainWindow):
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'High Gamma FFT Power', 'Spectral entropy', 'Temporal entropy',
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'Line length', 'DWT Power 0-4 Hz', 'DWT 4-8 Hz',
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'DWT 8-16 Hz', 'DWT 16-31 Hz','Variance','Correlation']
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# One last thing to use your new function is to add string with its name
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# to the other First_window.py: variable features_names in class First_window
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def all_params(self, passed_params = None, restarted=''):
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#reads values from TMS_protocol.txt file
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@ -562,10 +552,6 @@ class AppForm(QMainWindow):
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self.last_sec = ss.filtfilt(A, B, self.last_sec)
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self.last_sec = ss.detrend(self.last_sec, axis=1)
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# plt.figure()
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# plt.plot(self.last_sec[self.included_ch].T)
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# plt.plot(eog)
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#that's stupid, move channel selection before!!!!!!!!!!!!!
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if self.use_regression:
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self.last_sec = eye_reg(self.last_sec[self.included_ch], eog)
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return self.last_sec
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@ -592,9 +578,7 @@ class AppForm(QMainWindow):
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self.results[idx] = self.functions[feature](feature)
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else:
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self.results[idx] = self.functions[feature]()
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#Checks how many fields were filled already, so we know what stage are we on
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#and where to save the data
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x = np.where(self.feature1==None)[0][0]
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y = np.where(self.feature1==None)[1][0]
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@ -616,9 +600,6 @@ class AppForm(QMainWindow):
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print("Calculation of features: {}".format(times1-times))
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#if value is not within threshold values then background color is red (salmon), otherwise green
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#checks if there is a need to change a color of the background
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old_prv_state = self.previous_state.copy()
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if not all(np.isnan(self.thr_1)):
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if self.results[0]>=self.thr_1[0] and self.results[0]<=self.thr_1[1]:
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@ -724,9 +705,7 @@ class AppForm(QMainWindow):
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#If there is a need to redraw we do that. draw() option is slower, but more robust
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if need_redraw:
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self.canvasMap.draw()
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#otherwise we can just update the line, or to be precise, I think it just
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#draws the line on the old one. In this application it's fine. Faster than previous method.
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#I can think about blitting, so it could be even faster...
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#otherwise we can just update the line, or to be precise,
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else:
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for i in range(3):
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for j in range(2):
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@ -740,8 +719,7 @@ class AppForm(QMainWindow):
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def update(self):
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"""Updates data, checks if something should be plotted"""
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time_start = time.time()
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# There were some problems with delay. This way it works, but probably it can be done better
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# If the queue with data timer is sped up.
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if self.q.qsize()>0:
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self.timer.setInterval(int(1*self.speed_general*0.97))
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if self.q.qsize()<1 and self.timer.interval()!= int(self.speed_general*1.1):
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@ -827,13 +805,6 @@ class AppForm(QMainWindow):
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if len(stim)>0:
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for ind in stim[::-1]:
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size = self.data_len - (od+ind-int(int_from*self.Fs))
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# print('size:', size)
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# print(len(self.loaded))
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# Interpolation - pretty long line, but basically it chooses ranges and
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# assign boundary value as a baseline and does that in (I guess) more optimal way than using loops
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# self.loaded[:, od+ind-int(int_from*self.Fs):od+ind+int(int_to*self.Fs)] = np.outer(
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# self.loaded[:,min(od+ind+int(int_to*self.Fs), 30000-1)], np.ones(min(size, int((int_from+int_to)*self.Fs))))
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# this way is even easier...
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self.loaded[:, od+ind-int(int_from*self.Fs):od+ind+int(int_to*self.Fs)] = self.loaded[:,min(od+ind+int(int_to*self.Fs), 30000-1)].reshape(-1, 1)
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# for i in range(self.loaded.shape[0]):
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# self.loaded[i, od+ind-int(int_from*self.Fs):od+ind+int(int_to*self.Fs)] = np.linspace(
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@ -861,8 +832,6 @@ class AppForm(QMainWindow):
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step9 = time.time()-time_start
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# If do_calibration is True and there were trigger recently then stop calibration
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# TODO: THAT'S CONDITION REQUIRED FOR STARTING MEASURMENTS. PROBABLY IT WON'T WORK FOR SOME MORE EXTREME SETTINGS
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# if self.do_calibration and len(stim_where[stim_where>(self.data_len-max(
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# 2000, round(self.Fs*self.time_between_bursts*0.7, -3)))])>0:
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if self.do_calibration and len(stim_where[stim_where>(self.data_len-max(2000, self.exp_time+1500))])>0:
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@ -876,7 +845,6 @@ class AppForm(QMainWindow):
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return 0 #ends run of this function so nothing else happens
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step10 = time.time()-time_start
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# If set number of stimuli is detected
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# doit --> set length of the measurment between bursts
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# if self.doit==0 and sum(stim_where>self.data_len-max(
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# 2000, round(self.Fs*self.time_between_bursts*0.7, -3)))==10:
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print(sum(stim_where>self.data_len-max(2000, self.exp_time+1500)))
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@ -900,9 +868,6 @@ class AppForm(QMainWindow):
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elif self.doit>0:
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print(self.doit)
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self.last_stim = stim_where[-1]
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# In some situations last stimuli might be already from another train, while
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# First 100ms of loaded signal belong to previous one. That is why this exception exists
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# EDIT: not sure if it's still needed after other changes I made
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if any(np.diff(stim_where[stim_where>self.data_len-max(
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2000, round(self.Fs*self.time_between_bursts*1.2, -3))])>1000):
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print('UWAGA NA TO')
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@ -1015,7 +980,6 @@ class AppForm(QMainWindow):
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self.button4.setText("Start calibration")
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self.button4.setStyleSheet('')
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#par = self.thr_parameter
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#Need to clean the figure to prepare is for a different type of plot
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for i in range(6):
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self.axesMap[i//2,i%2].cla()
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@ -1120,8 +1084,7 @@ class AppForm(QMainWindow):
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#calculate fft
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self.S = abs(np.fft.rfft(self.second_to_analyze))
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#this is a bit shady, but should work. check it out if doesn't!
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#do dwt only if any features requires it
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if any(feature_num in self.used_features for feature_num in [8,9,10,11]):
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self.dwt = pywt.wavedec(self.second_to_analyze, 'db1', level=8)
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@ -1152,8 +1115,7 @@ class AppForm(QMainWindow):
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self.cals = [self.f1_cal, self.f2_cal, self.f3_cal, self.f4_cal, self.f5_cal,
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self.f6_cal]
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#!!! Temporary, it's wrong but it's overwritten later. It's needed to check if all features are used,
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#but there could be more optimal solution. Remove it at some point!
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self.thr_1 = [np.min(self.f1_cal)-0.1*np.min(self.f1_cal),
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np.max(self.f1_cal)+0.1*np.max(self.f1_cal)]
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self.thr_2 = [np.min(self.f2_cal)-0.1*np.min(self.f2_cal),
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@ -1245,12 +1207,6 @@ class AppForm(QMainWindow):
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tick.tick2line.set_visible(False)
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tick.label1.set_visible(False)
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tick.label2.set_visible(False)
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# for tick in self.axes.yaxis.get_major_ticks():
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# tick.tick1line.set_visible(False)
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# tick.tick2line.set_visible(False)
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# tick.label1.set_visible(False)
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# tick.label2.set_visible(False)
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self.axes.set_yticks(np.arange(1, (self.num_of_ch)*1.01, 1))
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self.axes.set_yticklabels(self.ch_names[::-1])
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@ -1304,14 +1260,6 @@ class AppForm(QMainWindow):
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self.canvas.draw()
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self.canvasMap.draw() #update canvas
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#NOT NEEDED
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# for i in range(self.num_of_ch):
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# self.axbackground = self.canvas.copy_from_bbox(self.axes.bbox)
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# texts = []
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# for ind,name in enumerate(self.ch_names):
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# texts.append(self.axes.text(-0.03,1-(ind+1)/(len(self.ch_names)+1),
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# name, transform=self.axes.transAxes, color='r', fontsize=13))
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self.button1 = QPushButton("&Settings")
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self.button1.setCheckable(False)
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@ -1416,8 +1364,3 @@ if __name__ == '__main__':
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form = First_window(AppForm) #AppForm()
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form.show()
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sys.exit(app.exec_())
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# cut time different from both sides
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# some deafult settings. Maybe remember last configuration?
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# EMG and EOG - none, more than one?
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# change names to final names
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