Update EStiMo_GUI.py

updated comments

EStiMo_GUI.py

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