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Nanopore-tools/EventDetectorUI.py
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EventDetectorUI.py
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import sys
import os
from PyQt5.QtWidgets import *
from PyQt5 import QtCore
from PyQt5.QtGui import QColor, QIntValidator
import matplotlib
matplotlib.use('QT5Agg')
import numpy as np
import matplotlib.pylab as plt
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
font = {'weight' : 'regular',
'size' : 4}
matplotlib.rc('font', **font) # pass in the font dict as kwargs
matplotlib.rc('lines', linewidth = 0.5)
from EventDetection import *
from Plotting.EventPlots import *
from LoadData import *
class AnalysisUI(QWidget):
def __init__(self):
super().__init__()
self.initUI()
def AllVariable(self):
# Let's dump all the variable we will need here...
self.importedFiles = []
self.selectedFiles = []
self.analyzedFiles = []
self.rawtrace = []
self.rawtracesamplerate = 0
self.AllEvents = NC.AllEvents()
self.wholetracedrawnforthefirsttime = True
self.dsrawtrace = []
self.dssamplerate = 0
# Defining the plots
self.TurnToolbarsOn = True
self.fig_singleEvent = plt.figure(1, figsize=(10, 10))
self.ax_singleEvent = self.fig_singleEvent.add_subplot(111)
self.ax_singleEvent.plot(np.arange(1, 10), np.arange(1, 10))
self.fig_wholeTrace = plt.figure(2, figsize=(16, 9))
self.ax_wholeTrace = self.fig_wholeTrace.add_subplot(111)
self.line_wholeTrace, = self.ax_wholeTrace.plot(np.arange(1, 10), -np.arange(1, 10))
self.figure_singleEvent = FigureCanvas(figure=self.fig_singleEvent)
self.figure_wholeTrace = FigureCanvas(figure=self.fig_wholeTrace)
if self.TurnToolbarsOn:
self.toolbarWholeTrace = NavigationToolbar(self.figure_wholeTrace, self)
self.toolbarSingleEvent = NavigationToolbar(self.figure_singleEvent, self)
def initUI(self):
# Main Window
self.AllVariable()
self.setGeometry(0, 0, 1200, 600)
self.setWindowTitle('A user interface is like a joke...')
# Assemble the different layout pieces
self.MakeFileImportLayout()
self.MakeAnalysisParametersAndRunLayout()
self.MakeEventNavigatorLayout()
windowLayout = QHBoxLayout()
windowLayout.addWidget(self.FileImportLayout)
windowLayout.addWidget(self.AnalysisParameters)
windowLayout.addWidget(self.EventNavigatorLayout)
self.setLayout(windowLayout)
## All Actions go here:
self.button_fileimport.clicked.connect(self.ImportButtonPushed)
self.button_clearfilelist.clicked.connect(self.ClearListButtonPushed)
self.list_filelist.clicked.connect(self.SelectionInFileListChanged)
self.list_filelist.doubleClicked.connect(self.FileDoubleClicked)
self.button_startAnalysis.clicked.connect(self.AnalysisButtonPressed)
self.text_eventNumber.returnPressed.connect(self.EventNumberChanged)
self.button_eventForward.clicked.connect(self.ForwardButtonPushed)
self.button_eventBackward.clicked.connect(self.BackwardButtonPushed)
self.setting_LPForWholeTracePlot.editingFinished.connect(self.LPForWholeTracePlotChanged)
self.show()
def MakeFileImportLayout(self):
self.FileImportLayout = QGroupBox("File Import")
self.FileImportLayout.setFixedWidth(200)
layout = QGridLayout()
self.button_fileimport = QPushButton('Open Files')
self.button_fileimport.setToolTip('Select the files you want to import into the list. You can do multiple selections.')
self.button_clearfilelist = QPushButton('Clear List')
self.button_clearfilelist.setToolTip('This deletes your current list of files.')
self.list_filelist = QListWidget()
self.list_filelist.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.list_filelist.setToolTip('This is the list of current files. Entries in green are already analyzed. Your selection defines which files are used in the analysis.')
layout.addWidget(self.button_fileimport, 0, 0)
layout.addWidget(self.list_filelist, 1, 0)
layout.addWidget(self.button_clearfilelist, 2, 0)
self.FileImportLayout.setLayout(layout)
def MakeAnalysisParametersAndRunLayout(self):
self.AnalysisParameters = QGroupBox("Analysis")
self.AnalysisParameters.setSizePolicy(QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum))
self.LowPassSettings = QGroupBox("Low Pass Settings")
self.LowPassSettings.setSizePolicy(QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum))
self.CusumSettings = QGroupBox("Cusum Settings")
self.CusumSettings.setSizePolicy(QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)) #This allows this part to remain small in vertical position when the UI resizes.
self.OtherSettings = QGroupBox("Other Settings")
self.OtherSettings.setSizePolicy(QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)) #This allows this part to remain small in vertical position when the UI resizes.
self.button_startAnalysis = QPushButton('Start Analysis')
self.button_startAnalysis.setToolTip('This button will provoke your computer to sel-destruct. Use at your own risk!!!!!')
## Low Pass Settings
self.settings_LP_a = QComboBox()
availableoptions = [0.99, 0.999, 0.9999]
for i in availableoptions:
self.settings_LP_a.addItem(str(i))
self.settings_LP_a.setToolTip('How strong should the filter be? Higher number is stronger filtering, which means less found events...')
## EndValueE
self.settings_LP_E = QDoubleSpinBox()
self.settings_LP_E.setValue(0)
self.settings_LP_E.setSingleStep(0.1)
self.settings_LP_E.setToolTip('The current needs to go above mean + E*std to terminate the event')
## StartValueS
self.settings_LP_S = QDoubleSpinBox()
self.settings_LP_S.setValue(5)
self.settings_LP_S.setSingleStep(0.1)
self.settings_LP_S.setToolTip('The current needs to go below mean + S*std to initiate an event')
layout1 = QGridLayout()
layout1.addWidget(QLabel('Filter Coefficient (a)'), 0, 0)
layout1.addWidget(self.settings_LP_a, 0, 1)
layout1.addWidget(QLabel('Start Coefficient (S)'), 1, 0)
layout1.addWidget(self.settings_LP_S, 1, 1)
layout1.addWidget(QLabel('End Coefficient (E)'), 3, 0)
layout1.addWidget(self.settings_LP_E, 3, 1)
self.LowPassSettings.setLayout(layout1)
##Cusum Settings
self.settings_cusum_hBook = QDoubleSpinBox()
self.settings_cusum_hBook.setValue(1)
self.settings_cusum_hBook.setSingleStep(0.1)
self.settings_cusum_hBook.setToolTip('Some random stupid parameter')
self.settings_cusum_dI = QDoubleSpinBox()
self.settings_cusum_dI.setValue(1)
self.settings_cusum_dI.setSuffix(' nA')
self.settings_cusum_dI.setSingleStep(0.1)
self.settings_cusum_dI.setToolTip('The most probable current drop')
layoutCusum = QGridLayout()
layoutCusum.addWidget(QLabel('h-Book'), 0, 0)
layoutCusum.addWidget(self.settings_cusum_hBook, 0, 1)
layoutCusum.addWidget(QLabel('Delta I'), 1, 0)
layoutCusum.addWidget(self.settings_cusum_dI, 1, 1)
self.CusumSettings.setLayout(layoutCusum)
## Other Settings
self.settings_other_ChimeraLP = QDoubleSpinBox()
self.settings_other_ChimeraLP.setValue(10)
self.settings_other_ChimeraLP.setSingleStep(10)
self.settings_other_ChimeraLP.setSuffix(' kHz')
self.settings_other_ChimeraLP.setToolTip('Low pass setting for high-bandwidth Chimera Data')
self.settings_other_MaxEventLength = QDoubleSpinBox()
self.settings_other_MaxEventLength.setValue(0.2)
self.settings_other_MaxEventLength.setSingleStep(0.05)
self.settings_other_MaxEventLength.setSuffix(' s')
self.settings_other_MaxEventLength.setToolTip('maximal event length to be considered an event')
self.settings_other_MinEventLength = QDoubleSpinBox()
self.settings_other_MinEventLength.setValue(600)
self.settings_other_MinEventLength.setSingleStep(100)
self.settings_other_MinEventLength.setSuffix(' us')
self.settings_other_MinEventLength.setToolTip('maximal event length to be considered an impulse')
self.settings_other_fitLength = QDoubleSpinBox()
self.settings_other_fitLength.setValue(3)
self.settings_other_fitLength.setSingleStep(0.5)
self.settings_other_fitLength.setSuffix(' ms')
self.settings_other_fitLength.setToolTip('minimal event length to be fitted for impulses')
layoutOther = QGridLayout()
layoutOther.addWidget(QLabel('Chimera LP'), 0, 0)
layoutOther.addWidget(self.settings_other_ChimeraLP, 0, 1)
layoutOther.addWidget(QLabel('Max event length'), 1, 0)
layoutOther.addWidget(self.settings_other_MaxEventLength, 1, 1)
layoutOther.addWidget(QLabel('Min event length'), 2, 0)
layoutOther.addWidget(self.settings_other_MinEventLength, 2, 1)
layoutOther.addWidget(QLabel('Fit length'), 3, 0)
layoutOther.addWidget(self.settings_other_fitLength, 3, 1)
self.OtherSettings.setLayout(layoutOther)
##Final Assembly
layout = QGridLayout()
layout.addWidget(self.LowPassSettings, 0, 0)
layout.addWidget(self.CusumSettings, 1, 0)
layout.addWidget(self.OtherSettings, 2, 0)
layout.addWidget(self.button_startAnalysis, 3, 0)
self.AnalysisParameters.setLayout(layout)
def MakeEventNavigatorLayout(self):
self.EventNavigatorLayout = QGroupBox("Event Navigator")
self.navigation_buttons =QButtonGroup()
self.button_eventForward = QPushButton('Forward')
self.button_eventForward.setToolTip('Advance one event forward')
self.button_eventBackward = QPushButton('Backward')
self.button_eventBackward.setToolTip('Go one event back')
self.setting_LPForWholeTracePlot = QDoubleSpinBox()
self.setting_LPForWholeTracePlot.setValue(10)
self.setting_LPForWholeTracePlot.setSingleStep(0.5)
self.setting_LPForWholeTracePlot.setSuffix(' kHz')
self.text_eventNumber = QLineEdit('0')
self.text_eventNumber.setValidator(QIntValidator(0, 100000))
self.text_eventNumber.setToolTip('This is the number of the current event. You can edit this field to jump directly to an event.')
self.text_eventNumber.setAlignment(QtCore.Qt.AlignCenter)
layout = QGridLayout()
layout.addWidget(self.figure_singleEvent, 0, 0, 1, 5)
self.figure_singleEvent.setFixedHeight(250)
self.figure_singleEvent.setFixedWidth(600)
layout.addWidget(self.button_eventForward, 2, 4)
layout.addWidget(self.text_eventNumber, 2, 3)
layout.addWidget(self.button_eventBackward, 2, 2)
layout.addWidget(self.setting_LPForWholeTracePlot, 2, 1)
layout.addWidget(QLabel('Downsample plot below: '), 2, 0)
layout.addWidget(self.figure_wholeTrace, 3, 0, 1, 5)
self.figure_wholeTrace.setFixedHeight(250)
self.figure_wholeTrace.setFixedWidth(600)
if self.TurnToolbarsOn:
layout.addWidget(self.toolbarSingleEvent, 1, 0, 1, 5)
layout.addWidget(self.toolbarWholeTrace, 4, 0, 1, 5)
self.EventNavigatorLayout.setLayout(layout)
## Button Actions
def ImportButtonPushed(self, event):
files = QFileDialog.getOpenFileNames(self, 'Select Files to Add to list', filter = "Images (*.dat *.log)")
## Add to file list if unique:
for i in files[0]:
if i not in self.importedFiles:
self.importedFiles.append(i)
self.UpdateFileList()
def ClearListButtonPushed(self, event):
self.importedFiles = []
self.UpdateFileList()
def UpdateFileList(self):
self.list_filelist.clear()
for ind, i in enumerate(self.importedFiles):
self.list_filelist.addItem(os.path.split(i)[1])
folder = os.path.dirname(i) + os.sep + 'analysisfiles'
filename, file_extension = os.path.splitext(os.path.basename(i))
potentialanalysisfile = folder + os.sep + filename + 'data'
print(potentialanalysisfile)
print(os.path.exists(potentialanalysisfile))
if os.path.isfile(potentialanalysisfile + '.dat') or os.path.isfile(potentialanalysisfile + '.db'):
## If file is present, make the row green. This means analysis was done on it.
self.list_filelist.item(ind).setBackground(QColor('green'))
def SelectionInFileListChanged(self, event):
items = self.list_filelist.selectedItems()
x = []
for i in range(len(items)):
x.append(str(self.list_filelist.selectedItems()[i].text()))
self.selectedFiles = x
print('The following files are selected in the list:')
print(x)
def GetFullFilePath(self, listoffiles):
fullfilepaths = []
for i in listoffiles:
for j in self.importedFiles:
if i in j:
fullfilepaths.append(j)
return fullfilepaths
def AnalysisButtonPressed(self):
# Get Full File Paths:
fullfilepaths = self.GetFullFilePath(self.selectedFiles)
print(fullfilepaths)
# Fill coefficient dictionary from the user inputs
coefficients = {}
coefficients['maxEventLength'] = self.settings_other_MaxEventLength.value()
coefficients['minEventLength'] = self.settings_other_MinEventLength.value()
coefficients['fitLength'] = self.settings_other_fitLength.value()
coefficients['delta'] = self.settings_cusum_dI.value()
coefficients['hbook'] = self.settings_cusum_hBook.value()
coefficients['a'] = np.float(self.settings_LP_a.currentText())
coefficients['S'] = self.settings_LP_S.value()
coefficients['E'] = self.settings_LP_E.value()
coefficients['ChimeraLowPass'] = self.settings_other_ChimeraLP.value()
coefficients['dt'] = 25
coefficients['deltaRel'] = None
for i in fullfilepaths:
eventdetectionwithfilegeneration(i, coefficients, forceRun=True, verboseLevel=1)
self.UpdateFileList()
def BackwardButtonPushed(self):
if (int(self.text_eventNumber.text())-1) < 0:
self.text_eventNumber.setText('0')
else:
self.text_eventNumber.setText(str(int(self.text_eventNumber.text())-1))
self.EventNumberChanged()
def ForwardButtonPushed(self):
if (int(self.text_eventNumber.text())+1) >= len(self.AllEvents.events):
self.text_eventNumber.setText(str(len(self.AllEvents.events)-1))
else:
self.text_eventNumber.setText(str(int(self.text_eventNumber.text())+1))
self.EventNumberChanged()
def EventNumberChanged(self):
print(int(self.text_eventNumber.text()))
if len(self.AllEvents.events):
self.DrawEvent(int(self.text_eventNumber.text()))
self.DrawWholeTrace(int(self.text_eventNumber.text()))
def DrawEvent(self, number):
self.ax_singleEvent.clear()
PlotEvent(self.AllEvents.events[number], ax=self.ax_singleEvent, savefile=os.getcwd(), showCUSUM=True,
showCurrent=False, showButtons=False, axisFormatter=False, plotTitleBool=False)
self.figure_singleEvent.draw()
def DrawWholeTrace(self, number):
ShowEventInTrace_SignalPreloaded(self.dsrawtrace, self.AllEvents, number, self.ax_wholeTrace, line=self.line_wholeTrace, firstCall=self.wholetracedrawnforthefirsttime, dscorrection=self.dssamplerate/self.rawtracesamplerate)
self.wholetracedrawnforthefirsttime = False
#self.ax_wholeTrace.autoscale(enable=True)
self.figure_wholeTrace.draw()
#self.figure_wholeTrace.flush_events()
def FileDoubleClicked(self, event):
DoubleclickedFile = self.list_filelist.selectedItems()[0].text()
# Get Analysis file
fullfilepath = self.GetFullFilePath([DoubleclickedFile])[0]
filename, file_extension = os.path.splitext(os.path.basename(fullfilepath))
folder = os.path.dirname(fullfilepath) + os.sep + 'analysisfiles'
analysisfilepath = folder + os.sep + filename + 'data'
print('Analysis File Path: {}'.format(analysisfilepath))
if os.path.isfile(analysisfilepath + '.dat') or os.path.isfile(analysisfilepath + '.db'):
## Display the analysis
print('Lets show the analysis')
## Load the analysis file
self.AllEvents = LoadEvents(analysisfilepath)
self.text_eventNumber.setValidator(QIntValidator(0, len(self.AllEvents.events)-1))
inputfile = LoadData.OpenFile(self.AllEvents.events[0].filename, ChimeraLowPass = 10e3, approxImpulseResponse = True, Split = True, verbose = False)
self.rawtrace = inputfile['i1']
self.rawtracesamplerate = inputfile['samplerate']
self.LPForWholeTracePlotChanged()
self.DrawEvent(int(self.text_eventNumber.text()))
self.DrawWholeTrace(int(self.text_eventNumber.text()))
print(self.AllEvents)
else:
error = QMessageBox.critical(self, 'Important Message', 'Please select a file that has been analyzed (turned green).', QMessageBox.Retry)
self.wholetracedrawnforthefirsttime = True
def LPForWholeTracePlotChanged(self):
print(self.setting_LPForWholeTracePlot.value())
self.dsrawtrace, self.dssamplerate = LowPassAndResample(self.rawtrace, self.rawtracesamplerate, self.setting_LPForWholeTracePlot.value() * 1e3, LPtoSR=2)
def closeEvent(self, event):
'''
reply = QMessageBox.question(self, 'Message',
"Are you sure to quit? Don't make me sad... :( :( :(", QMessageBox.Yes |
QMessageBox.No, QMessageBox.No)
if reply == QMessageBox.Yes:
event.accept()
else:
event.ignore()
'''
## Execution
if __name__ == '__main__':
app = QApplication(sys.argv)
ex = AnalysisUI()
sys.exit(app.exec_())
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