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analysis.py
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analysis.py
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from ast import arguments
import datetime
import numpy as npy
import scipy as scy
from scipy import signal as ssy
import matplotlib as mpl
from matplotlib import pyplot as plt
import os
import sys
from datetime import date
import pyabf as abf
import threading
import thingies.io
import thingies.tp
from thingies.mainwindow import Ui_MainWindow
from PyQt5 import QtWidgets as qtw
from PyQt5 import QtCore as qtc
from PyQt5.QtCore import Qt, QThread, pyqtSignal
from PyQt5.QtWidgets import QListWidget, QDoubleSpinBox
import thingies.protocols as prot_module
mpl.use('agg')
class mwin(qtw.QMainWindow):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.mwinui = Ui_MainWindow()
self.mwinui.setupUi(self)
self.mwinui.startbutton.setDisabled(False)
self.mwinui.HEKAfmt.setDisabled(False)
self.mwinui.ABFfmt.setDisabled(False)
self.mwinui.iclamptp.setDisabled(True)
self.mwinui.io_switch.setDisabled(False)
self.mwinui.tab_3.setDisabled(False)
self.mwinui.tab_4.setDisabled(True)
self.template_file = ''
self.template_file_2 = ''
self.mwinui.startbutton.clicked.connect(self.cleared)
self.mwinui.scanfolder.clicked.connect(self.scan_folder)
def update1(self,updatetext):
self.mwinui.textInfo1.setText(updatetext)
def update2(self,updatetext):
self.mwinui.textInfo2.setText(updatetext)
def get_tp_check(self):
det_check = self.mwinui.tp_switch.isChecked()
return det_check
def get_io_check(self):
det_check = self.mwinui.io_switch.isChecked()
return det_check
def getformat(self):
if self.mwinui.HEKAfmt.isChecked():
formatselection = 'HEKA'
if self.mwinui.ABFfmt.isChecked():
formatselection = 'ABF'
return(formatselection)
def scan_folder(self):
protocol_names = []
channel_names = []
selected_format = 'HEKA'
file_filter = '.inf'
selected_format = str(self.getformat())
if selected_format == 'HEKA':
file_filter = '.inf'
if selected_format == 'ABF':
file_filter = '.abf'
askfiledlg = qtw.QFileDialog()
askfiledlg.directory()
askfolder = askfiledlg.getExistingDirectory()
expfiles = []
currentexpfile = 0
for file in os.scandir(str(askfolder)):
if (str(file.path)[-4:]) == file_filter :
ch = []
protocol = []
try:
expfiles.append(str(file.path))
currentexpfile += 1
if selected_format == 'HEKA':
inffy = open(file, 'r', newline='\n')
allfile = inffy.readlines()
inffy.close()
numlines = npy.size(allfile) - 1
ch=[]
protocol=[]
for i in range(int(npy.size(allfile)/17)-1):
temp1,junkstr=allfile[17*i + 4].split(';')
ch.append(temp1.strip())
temp2,junkstr=allfile[17*i + 5].split(';')
protocol.append(temp2.strip())
if selected_format == 'ABF':
allfile = abf.ABF(file.path)
ch=[]
protocol=[]
protocol.append(allfile.protocol.strip())
for temp_ch in allfile.adcNames:
ch.append(temp_ch.strip())
except:
continue
for channel in ch:
if not (channel in channel_names):
channel_names.append(channel)
for prot in protocol:
if not (prot in protocol_names):
protocol_names.append(prot)
self.mwinui.prot_list_2.addItems(protocol_names)
self.mwinui.ch_list_2.addItems(channel_names)
self.mwinui.prot_list_3.addItems(protocol_names)
self.mwinui.ch_list_3.addItems(channel_names)
def selectprots(self,caller):
selected_p = []
if caller == 'tp':
selected_pi = self.mwinui.prot_list_2.selectedItems()
if caller == 'io':
selected_pi = self.mwinui.prot_list_3.selectedItems()
for i in selected_pi:
selected_p.append(i.text())
return(selected_p)
def selectch(self,caller):
selected_c = []
if caller == 'tp':
selected_ci = self.mwinui.ch_list_2.selectedItems()
if caller == 'io':
selected_ci = self.mwinui.ch_list_3.selectedItems()
for i in selected_ci:
selected_c.append(i.text())
return(selected_c)
def get_start_of_testpulse(self):
start_of_tp = self.mwinui.stepstartbox.value()
return(start_of_tp)
def get_end_of_testpulse(self):
end_of_tp = self.mwinui.stependbox.value()
return(end_of_tp)
def get_start_of_io(self):
start_of_io = self.mwinui.stepstartbox_2.value()
return(start_of_io)
def get_end_of_io(self):
end_of_io = self.mwinui.stependbox_2.value()
return(end_of_io)
def notch(self):
selected_freqs = [False, False, False, False, False]
notch_freq = self.mwinui.doubleSpinBox.value()
if self.mwinui.checkBox.isChecked():
selected_freqs[0] = True
if self.mwinui.checkBox_2.isChecked():
selected_freqs[1] = True
if self.mwinui.checkBox_3.isChecked():
selected_freqs[2] = True
if self.mwinui.checkBox_4.isChecked():
selected_freqs[3] = True
if self.mwinui.checkBox_6.isChecked():
selected_freqs[4] = True
return(notch_freq, selected_freqs)
def get_naming_setting(self):
if self.mwinui.default_naming.isChecked():
naming_setting = ''
if self.mwinui.custom_naming.isChecked():
naming_setting = self.mwinui.folder_identifier.text()
return naming_setting
def get_timestamp_setting(self):
if self.mwinui.add_timestamp.isChecked():
timestampstring = datetime.datetime.now().strftime('%Y%m%d%H%M%S')
else:
timestampstring = ''
return timestampstring
def get_log_setting(self):
if self.mwinui.Log_active.isChecked():
log_flag = True
user_comment = self.mwinui.log_comment.toPlainText()
else:
log_flag = False
user_comment = ''
return log_flag, user_comment
def cleared(self):
self.mwinui.scanfolder.setDisabled(True)
self.mwinui.HEKAfmt.setDisabled(True)
self.mwinui.ABFfmt.setDisabled(True)
self.mwinui.tab_2.setDisabled(True)
self.mwinui.tab_3.setDisabled(True)
self.mwinui.groupBox_2.setDisabled(True)
self.mwinui.groupBox_3.setDisabled(True)
self.mwinui.tab_4.setDisabled(True)
askfiledlg = qtw.QFileDialog()
askfiledlg.directory()
askfolder = askfiledlg.getExistingDirectory()
self.mwinui.startbutton.setDisabled(True)
self.mwinui.startbutton.setText('running')
self.analysisthread = analysisloop()
#self.analysisthread.__init__()
self.analysisthread.setup(askfolder)
self.analysisthread.start()
class analysisloop(QThread):
def __init__(self, *args, **kwargs):
super(analysisloop, self).__init__(*args, **kwargs)
self.recfolder = str()
self.fir = npy.array([])
self.fir2 = npy.array([])
self.sampling_rate = float()
self.protocol_list = []
self.ch_list = []
self.template_selection = str()
self.template_sampling_rate = float()
self.fmtselection = str()
self.prots_instance = object()
def setup(self,askfolder):
self.fir = ssy.remez(2799,[0,400,420,5000],[1,0],[1,10],10000,'bandpass',2048,256)
self.fir = npy.convolve(self.fir,self.fir,'full')
self.fir2 = ssy.remez(2799,[0,2200,2213,5000],[1,0],[1,10],10000,'bandpass',2048,256)
self.fir2 = npy.convolve(self.fir2,self.fir2,'full')
#presets:
self.sampling_rate = 10000.0
self.fmtselection = 'HEKA'
try:
self.fmtselection = str(mwi.getformat())
except:
self.protocol_list = []
self.ch_list = []
self.fmtselection = 'HEKA'
print(self.protocol_list)
print(self.ch_list)
self.recfolder = askfolder
def run(self):
selected_modules = []
if mwi.get_tp_check() == True:
selected_modules.append('tp')
if mwi.get_io_check() == True:
selected_modules.append('io')
print('selected modules: ' + str(selected_modules))
current_module = str()
logcheck, logcomment = mwi.get_log_setting()
if logcheck == True:
logfile = open(self.recfolder+ '/log.txt', 'a')
logfile.write('# '+ datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S')+ '\r')
logfile.write('analysis folder: ' + str(self.recfolder) + '\r')
logfile.write('selected analyses: ' + str(selected_modules)+ '\r')
logfile.write('/ user comment / : '+ str(logcomment) +'\r/end user comment/\r')
logfile.write('format: '+ self.fmtselection +'\r')
logfile.write('custom output name: '+ mwi.get_naming_setting() + '\t' + mwi.get_timestamp_setting() +'\r')
for current_module in selected_modules:
print('currently in ' + str(current_module))
self.protocol_list = mwi.selectprots(caller=current_module)
self.ch_list = mwi.selectch(caller=current_module)
print('protocols for '+ str(current_module) + ' : '+ str(self.protocol_list))
if current_module == 'tp':
#logging
if logcheck == True:
logfile.write('*tp settings\r')
protocol_list_2 = mwi.selectprots(caller='tp')
ch_list_2 = mwi.selectch(caller='tp')
logfile.write('protocols: '+ str(protocol_list_2) +'\r')
logfile.write('channels: '+ str(ch_list_2) +'\r')
logfile.write(' >- processing start - '+ datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +'\r')
#call
thingies.tp.main(recfolder=self.recfolder, prot_list=self.protocol_list,ch_list=self.ch_list,fir=self.fir,fir2=self.fir2,fmtselection=self.fmtselection,window_reference=mwi)
if logcheck == True:
logfile.write(' <- processing end - '+ datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +'\r')
if current_module == 'io':
#logging
if logcheck == True:
logfile.write('*io settings\r')
protocol_list_3 = mwi.selectprots(caller='io')
ch_list_3 = mwi.selectch(caller='io')
logfile.write('protocols: '+ str(protocol_list_3) +'\r')
logfile.write('channels: '+ str(ch_list_3) +'\r')
logfile.write(' >- processing start - '+ datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +'\r')
#call
thingies.io.main(recfolder=self.recfolder, prot_list=self.protocol_list,ch_list=self.ch_list,fir=self.fir,fir2=self.fir2,fmtselection=self.fmtselection,window_reference=mwi)
if logcheck == True:
logfile.write(' <- processing end - '+ datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S') +'\r')
if logcheck == True:
logfile.write('[session end]\r\r')
logfile.close()
if __name__ == "__main__":
app = qtw.QApplication([])
mwi = mwin()
mwi.show()
app.exec_()