def pbEst_Callback(self):
from SourceRun import Ui_FormSourceRun
self.FormSourceRun = QtWidgets.QWidget()
self.uiEst = Ui_FormSourceRun()
self.uiEst.setupUi(self.FormSourceRun)
self.FormSourceRun.show()
return #sden
def pbEst_Callback(self):
from SourceRun import Ui_FormSourceRun
self.FormSourceRun = QtWidgets.QWidget()
self.uiEst = Ui_FormSourceRun()
self.uiEst.setupUi(self.FormSourceRun)
self.FormSourceRun.show()
return #sden
class Ui_FormGS(object):
def setupUi(self, FormGS):
FormGS.setObjectName("FormGS")
FormGS.resize(790, 373)
self.pbEEG = QtWidgets.QPushButton(FormGS)
self.pbEEG.setGeometry(QtCore.QRect(20, 20, 180, 60))
self.pbEEG.setObjectName("pbEEG")
self.pbHM = QtWidgets.QPushButton(FormGS)
self.pbHM.setGeometry(QtCore.QRect(210, 20, 180, 60))
self.pbHM.setObjectName("pbHM")
self.pbEst = QtWidgets.QPushButton(FormGS)
self.pbEst.setGeometry(QtCore.QRect(400, 20, 180, 60))
self.pbEst.setObjectName("pbEst")
self.pbStat = QtWidgets.QPushButton(FormGS)
self.pbStat.setGeometry(QtCore.QRect(590, 20, 180, 60))
self.pbStat.setObjectName("pbStat")
self.pbVis = QtWidgets.QPushButton(FormGS)
self.pbVis.setGeometry(QtCore.QRect(590, 88, 180, 150))
self.pbVis.setObjectName("pbVis")
self.pbQuit = QtWidgets.QPushButton(FormGS)
self.pbQuit.setGeometry(QtCore.QRect(590, 245, 180, 110))
self.pbQuit.setObjectName("pbQuit")
self.pbTopo = QtWidgets.QPushButton(FormGS)
self.pbTopo.setGeometry(QtCore.QRect(400, 245, 180, 110))
self.pbTopo.setObjectName("pbTopo")
self.frame = QtWidgets.QFrame(FormGS)
self.frame.setGeometry(QtCore.QRect(25, 90, 170, 140))
self.frame.setFrameShape(QtWidgets.QFrame.StyledPanel)
self.frame.setFrameShadow(QtWidgets.QFrame.Raised)
self.frame.setObjectName("frame")
self.cbTrial = QtWidgets.QComboBox(self.frame)
self.cbTrial.setGeometry(QtCore.QRect(50, 30, 110, 26))
self.cbTrial.setObjectName("cbTrial")
self.labelTrial = QtWidgets.QLabel(self.frame)
self.labelTrial.setGeometry(QtCore.QRect(10, 35, 40, 16))
self.labelTrial.setObjectName("labelTrial")
self.labelThreshold = QtWidgets.QLabel(self.frame)
self.labelThreshold.setGeometry(QtCore.QRect(10, 80, 80, 16))
self.labelThreshold.setObjectName("labelThreshold")
self.sliderThreshold = QtWidgets.QSlider(self.frame)
self.sliderThreshold.setGeometry(QtCore.QRect(15, 105, 141, 22))
self.sliderThreshold.setMaximum(100)
self.sliderThreshold.setOrientation(QtCore.Qt.Horizontal)
self.sliderThreshold.setObjectName("sliderThreshold")
self.listThreshold = QtWidgets.QSpinBox(self.frame)
self.listThreshold.setGeometry(QtCore.QRect(100, 77, 57, 26))
self.listThreshold.setObjectName("listThreshold")
self.txtEpoch = QtWidgets.QFrame(FormGS)
self.txtEpoch.setGeometry(QtCore.QRect(215, 90, 170, 140))
self.txtEpoch.setFrameShape(QtWidgets.QFrame.StyledPanel)
self.txtEpoch.setFrameShadow(QtWidgets.QFrame.Raised)
self.txtEpoch.setObjectName("txtEpoch")
self.labelStart = QtWidgets.QLabel(self.txtEpoch)
self.labelStart.setGeometry(QtCore.QRect(20, 35, 40, 16))
self.labelStart.setObjectName("labelStart")
self.labelEnd = QtWidgets.QLabel(self.txtEpoch)
self.labelEnd.setGeometry(QtCore.QRect(20, 85, 40, 16))
self.labelEnd.setObjectName("labelEnd")
self.editStart = QtWidgets.QLineEdit(self.txtEpoch)
self.editStart.setGeometry(QtCore.QRect(80, 30, 70, 23))
self.editStart.setObjectName("editStart")
self.editEnd = QtWidgets.QLineEdit(self.txtEpoch)
self.editEnd.setGeometry(QtCore.QRect(80, 80, 70, 23))
self.editEnd.setObjectName("editEnd")
# self.editEnd.setReadOnly(True)
self.txtMovie = QtWidgets.QFrame(FormGS)
self.txtMovie.setGeometry(QtCore.QRect(405, 90, 170, 140))
self.txtMovie.setFrameShape(QtWidgets.QFrame.StyledPanel)
self.txtMovie.setFrameShadow(QtWidgets.QFrame.Raised)
self.txtMovie.setObjectName("txtMovie")
self.rbMovie = QtWidgets.QRadioButton(self.txtMovie)
self.rbMovie.setGeometry(QtCore.QRect(20, 20, 102, 20))
self.rbMovie.setChecked(True)
self.rbMovie.setObjectName("rbMovie")
self.rbAveragEpoch = QtWidgets.QRadioButton(self.txtMovie)
self.rbAveragEpoch.setGeometry(QtCore.QRect(20, 90, 120, 20))
self.rbAveragEpoch.setObjectName("rbAveragEpoch")
self.cbColor = QtWidgets.QCheckBox(self.txtMovie)
self.cbColor.setGeometry(QtCore.QRect(40, 50, 90, 20))
self.cbColor.setObjectName("cbColor")
self.txtTopomap = QtWidgets.QFrame(FormGS)
self.txtTopomap.setGeometry(QtCore.QRect(25, 250, 360, 100))
self.txtTopomap.setFrameShape(QtWidgets.QFrame.StyledPanel)
self.txtTopomap.setFrameShadow(QtWidgets.QFrame.Raised)
self.txtTopomap.setObjectName("txtTopomap")
self.rbEEG = QtWidgets.QRadioButton(self.txtTopomap)
self.rbEEG.setGeometry(QtCore.QRect(10, 40, 50, 20))
self.rbEEG.setChecked(True)
self.rbEEG.setObjectName("rbEEG")
self.rbAllForward = QtWidgets.QRadioButton(self.txtTopomap)
self.rbAllForward.setGeometry(QtCore.QRect(100, 20, 100, 20))
self.rbAllForward.setObjectName("rbAllForward")
self.rbAllResidual = QtWidgets.QRadioButton(self.txtTopomap)
self.rbAllResidual.setGeometry(QtCore.QRect(100, 60, 100, 20))
self.rbAllResidual.setObjectName("rbAllResidual")
self.rbPartForward = QtWidgets.QRadioButton(self.txtTopomap)
self.rbPartForward.setGeometry(QtCore.QRect(225, 20, 102, 20))
self.rbPartForward.setObjectName("rbPartForward")
self.rbPartResidual = QtWidgets.QRadioButton(self.txtTopomap)
self.rbPartResidual.setGeometry(QtCore.QRect(225, 60, 102, 20))
self.rbPartResidual.setObjectName("rbPartResidual")
self.retranslateUi(FormGS)
self.pbEEG.clicked.connect(self.pbEEG_Callback)
self.pbHM.clicked.connect(self.pbHM_Callback)
self.pbEst.clicked.connect(self.pbEst_Callback)
self.pbStat.clicked.connect(self.pbStat_Callback)
self.sliderThreshold.valueChanged['int'].connect(self.listThreshold.setValue)
self.listThreshold.valueChanged['int'].connect(self.sliderThreshold.setValue)
self.listThreshold.editingFinished.connect(self.editTH_Callback)
self.editStart.editingFinished.connect(self.editStart_Callback)
self.editEnd.editingFinished.connect(self.editEnd_Callback)
self.pbVis.clicked.connect(self.pbVis_Callback)
self.pbQuit.clicked.connect(FormGS.close)
# import HeadModelOpen
# self.pbQuit.clicked.connect(self.FormHM.close)
# self.pbQuit.clicked.connect(self.FormSourceRun.close)
QtCore.QMetaObject.connectSlotsByName(FormGS)
FormGS.setTabOrder(self.pbEEG, self.pbHM)
FormGS.setTabOrder(self.pbHM, self.pbEst)
FormGS.setTabOrder(self.pbEst, self.pbStat)
FormGS.setTabOrder(self.pbStat, self.cbTrial)
FormGS.setTabOrder(self.cbTrial, self.listThreshold)
FormGS.setTabOrder(self.listThreshold, self.sliderThreshold)
FormGS.setTabOrder(self.sliderThreshold, self.editStart)
FormGS.setTabOrder(self.editStart, self.editEnd)
FormGS.setTabOrder(self.editEnd, self.rbMovie)
FormGS.setTabOrder(self.rbMovie, self.cbColor)
FormGS.setTabOrder(self.cbColor, self.rbAveragEpoch)
FormGS.setTabOrder(self.rbAveragEpoch, self.pbVis)
FormGS.setTabOrder(self.pbVis, self.rbEEG)
FormGS.setTabOrder(self.rbEEG, self.rbAllForward)
FormGS.setTabOrder(self.rbAllForward, self.rbAllResidual)
FormGS.setTabOrder(self.rbAllResidual, self.rbPartForward)
FormGS.setTabOrder(self.rbPartForward, self.rbPartResidual)
FormGS.setTabOrder(self.rbPartResidual, self.pbTopo)
FormGS.setTabOrder(self.pbTopo, self.pbQuit)
def retranslateUi(self, FormGS):
_translate = QtCore.QCoreApplication.translate
FormGS.setWindowTitle(_translate("FormGS", "GeoSource"))
self.pbEEG.setText(_translate("FormGS", "EEG"))
self.pbHM.setText(_translate("FormGS", "Head Model"))
self.pbEst.setText(_translate("FormGS", "Estimate"))
self.pbStat.setText(_translate("FormGS", "Stat"))
self.pbVis.setText(_translate("FormGS", "Visualize"))
self.pbQuit.setText(_translate("FormGS", "Quit"))
self.pbTopo.setText(_translate("FormGS", "Topomap"))
self.labelTrial.setText(_translate("FormGS", "Trial"))
self.labelThreshold.setText(_translate("FormGS", "Threshold(%)"))
# self.listThreshold.setText(_translate("FormGS", "0"))
self.labelStart.setText(_translate("FormGS", "Start"))
self.labelEnd.setText(_translate("FormGS", "End"))
self.editStart.setText(_translate("FormGS", "0"))
self.editEnd.setText(_translate("FormGS", "0"))
self.rbMovie.setText(_translate("FormGS", "Movie"))
self.rbAveragEpoch.setText(_translate("FormGS", "Average Epoch"))
self.cbColor.setText(_translate("FormGS", "Color Lock"))
self.rbEEG.setText(_translate("FormGS", "EEG"))
self.rbAllForward.setText(_translate("FormGS", "All Forward"))
self.rbAllResidual.setText(_translate("FormGS", "All Residual"))
self.rbPartForward.setText(_translate("FormGS", "Part Forward"))
self.rbPartResidual.setText(_translate("FormGS", "Part Residual"))
def pbEEG_Callback(self):
global s, nC, nSamples, nSamplesPre, nTrials, srate, trialsName
global categoryName, nCategory
import config
from mff import read_mff_header, read_mff_data
import matplotlib.pyplot as plt
import numpy as np
options = QtWidgets.QFileDialog.Options()
mfffilename, _ = QtWidgets.QFileDialog.getOpenFileNames(self.pbEEG, "Select a mff file", "", "mff files (*.mff)", options= options)
filePath = mfffilename[0]
hdr = read_mff_header.read_mff_header(filePath)
nC = hdr['nChans'] ; config.nC = nC
nSamples = hdr['nSamples'] ; config.nSamples = nSamples
nSamplesPre = hdr['nSamplesPre'] ; config.nSamplesPre = nSamplesPre
nTrials = hdr['nTrials'] ; config.nTrials = nTrials
srate = hdr['Fs'] ; config.srate = srate
summaryInfo = hdr['orig'] ; # config.nC = nC
trialsName = summaryInfo['epochLabels'] ; config.trialsName = trialsName
categoryName = list(set(trialsName)) ; config.categoryName = categoryName
nCategory = len(categoryName) ; config.nCategory = nCategory
for i in range(nTrials):
self.cbTrial.addItem(trialsName[i])
data = read_mff_data.read_mff_data(filePath, 'epoch', 1, hdr['nTrials'], hdr)
SegStatus = hdr['orig']['epochSegStatus']
GoodSeg = []; BadSeg = []; #epochLabels = [];
for i in range(len(SegStatus)):
if SegStatus[i] == 'bad' :
BadSeg.append(i)
else :
GoodSeg.append(i)
nTrials = len(GoodSeg)
print('nC:%d' %nC)
print('nSamples:%d' %nSamples)
print('nTrials:%d' %nTrials)
print('nCategory:%d' %nCategory)
print('categoryName:%s' %categoryName)
# print('categoryName:%s' %trialsName)
## average reference
H = np.identity(nC) - np.ones((nC, nC))/nC
s = np.zeros((nC, nSamples, nTrials))
sGFP = np.zeros((nSamples, nTrials))
if nTrials > 1:
for i in range(nTrials):
s[:,:,i] = np.dot(H, data[:,:,GoodSeg[i]])
sGFP[:,i] = np.std(s[:,:,i], axis=0)
# s2 = s[:,:,i] * s[:,:,i]
# gfp = s2.mean(axis=0)
# sGFP = np.sqrt(gfp)
else :
s = np.dot(H, data)
sGFP = np.std(s, axis=0)
# s2 = s * s
# gfp = s2.mean(axis=0)
# sGFP = np.sqrt(gfp)
baseline = (nSamplesPre * 1000 / srate) ; config.baseline = baseline
msSamples = np.arange(0, nSamples,1) * 1000/srate - baseline
config.msSamples = msSamples
# global f1
if nTrials == nCategory :
# f1 = plt.figure
plt.plot(msSamples, sGFP)
plt.title('gfp')
plt.xlabel('ms')
plt.legend(trialsName, loc='best')
plt.show()
print('EEG is ERP.')
#eventsName = trialsName
else :
# f1 = plt.figure
plt.plot(msSamples, sGFP)
plt.title('gfp')
plt.xlabel('ms')
plt.show()
print('EEG is Single trial. There are',nTrials,'trials. ')
#eventsName = categoryName
config.nSamples = nSamples
config.msSamples = msSamples
config.nTrials = nTrials
config.trialsName = trialsName
config.s = s
config.sGFP = sGFP
print("EEG data is loaded.")
# self.pbEEG.configure(background = "red")
return s
def pbHM_Callback(self):
options = QtWidgets.QFileDialog.DontResolveSymlinks | QtWidgets.QFileDialog.ShowDirsOnly
HMdir = QtWidgets.QFileDialog.getExistingDirectory(self.pbHM,
"Select a Head Model Directory.",
self.pbHM.text(), options=options)
import os
from braink import read_lfm
import config
nE = config.nE
nC = nE + 1
if os.path.exists(HMdir+'/fdmForwardMatrixOriented'):
K = read_lfm.forward(HMdir+'/fdmForwardMatrixOriented', config.nE)
print K
print("fdmForwardMatrixOriented is loaded. ")
elif os.path.exists(HMdir+'/Leadfield.lfm'):
K = read_lfm.lfm(HMdir+'/Leadfield.lfm', config.nE)
print("Leadfield.lfm is loaded. ")
print K
else:
print("LFM is not loaded. ")
nV = K.shape[1]
config.K = K
config.nV = nV
config.nC = nC
os.system("open /Applications/EAV/EAV.app")
return
def pbEst_Callback(self):
from SourceRun import Ui_FormSourceRun
self.FormSourceRun = QtWidgets.QWidget()
self.uiEst = Ui_FormSourceRun()
self.uiEst.setupUi(self.FormSourceRun)
self.FormSourceRun.show()
return #sden
def editTH_Callback(self):
global thresholdcutoff ;
thresholdcutoff = self.listThreshold.value()
print('Lowest %d(percent) of dipoles are cut off.' %thresholdcutoff)
return
def editStart_Callback(self):
import config
startMS = self.editStart.text()
startMS = int(startMS)
config.startMS = startMS
return
def editEnd_Callback(self):
import config
import matplotlib.pyplot as plt
import numpy as np
endMS = self.editEnd.text()
endMS = int(endMS)
config.endMS = endMS
print('From %d to %d ms' %(config.startMS, config.endMS))
# f1 = plt.figure
plt.plot(config.msSamples, config.sGFP)
plt.title('sum(phi^2)')
plt.xlabel('ms')
plt.plot([config.startMS, config.startMS], [np.min(config.sGFP), np.max(config.sGFP)], 'k-', lw=2)
plt.plot([config.endMS, config.endMS], [np.min(config.sGFP), np.max(config.sGFP)], 'k-', lw=2)
if config.nTrials == config.nCategory :
plt.legend(config.trialsName, loc='best')
# else:
plt.show()
print('EEG is Single trial. There are %d trials.' %config.nTrials)
return
def pbStat_Callback(self):
from StatRun import Ui_FormStat
self.FormStat = QtWidgets.QWidget()
self.uiStat = Ui_FormStat()
self.uiStat.setupUi(self.FormStat)
self.FormStat.show()
return #sden
def pbVis_Callback(self):
import matplotlib.pyplot as plt
import numpy as np
import config
# import os
# os.system("open /Applications/EAV/EAV.app")
sdenMean = config.sdenMean
sdenSigma = config.sdenSigma
sdenT = config.sdenT
sMean = config.sMean
sSigma = config.sSigma
sT = config.sT
nSigChan = config.nSigChan
nSigVox = config.nSigVox
msSamples = config.msSamples
startMS = config.startMS
ii = np.where( msSamples == startMS )[0]
fig, ax = plt.subplots(4,2,figsize=(20,10))
ax[0,0].plot(msSamples, sMean.T)
ax[0,0].set_xlim([msSamples[0], msSamples[-1]])
ax[0,0].set_ylabel('mean')
ax[0,0].set_title('EEG')
ax[1,0].plot(msSamples, sSigma.T)
ax[1,0].set_xlim([msSamples[0], msSamples[-1]])
ax[1,0].set_ylabel('sdv')
ax[2,0].plot(msSamples, sT.T)
ax[2,0].set_xlim([msSamples[0], msSamples[-1]])
ax[2,0].set_ylabel('Normal')
# ax[2,0].axhline(vu, color='black', lw=2)
# ax[2,0].axhline(vl, color='black', lw=2)
ax[3,0].plot(msSamples, nSigChan )
ax[3,0].axvline(msSamples[ii], color='black', lw=2)
#ax[3,0].set_ylim([-1, max(nSigChan)+1])
ax[3,0].set_xlim([msSamples[0], msSamples[-1]])
ax[3,0].set_ylabel('Num Sig.Channels')
ax[3,0].set_xlabel('ms')
#ax[3,0].legend()
ax[0,1].plot(msSamples, sdenMean.T)
ax[0,1].set_xlim([msSamples[0], msSamples[-1]])
ax[0,1].set_ylabel('mean')
ax[0,1].set_title('Source')
ax[1,1].plot(msSamples, sdenSigma.T)
ax[1,1].set_xlim([msSamples[0], msSamples[-1]])
ax[1,1].set_ylabel('sdv')
ax[2,1].plot(msSamples, sdenT.T)
ax[2,1].set_xlim([msSamples[0], msSamples[-1]])
ax[2,1].set_ylabel('Normal')
# ax[2,1].axhline(sdenvu, color='black', lw=2)
# ax[2,1].axhline(sdenvl, color='black', lw=2)
ax[3,1].plot(msSamples, nSigVox, c='black', label= 'l+r')
ax[3,1].axvline(msSamples[ii], color='black', lw=2)
#ax[3,1].set_ylim([-5, max(nSigVox)+5])
ax[3,1].set_xlim([msSamples[0], msSamples[-1]])
ax[3,1].set_ylabel('Num Sig.Voxels')
ax[3,1].set_xlabel('ms')
#ax[3,1].legend()
plt.show()
sdenTSig = config.sdenTSig
sT = config.sT
# sTSig = config.sTSig
from RabbitMQ import Connection
c = Connection.Connection('localhost')
c.connect()
c.sendOrientedData(abs(sdenTSig[:, ii]) , "Oriented", "3:00pm")
c.sendEEGData(sT[:,ii], "Oriented", "3:00pm")
c.disconnect()
class Ui_FormGS(object):
def setupUi(self, FormGS):
FormGS.setObjectName("FormGS")
FormGS.resize(790, 373)
self.pbEEG = QtWidgets.QPushButton(FormGS)
self.pbEEG.setGeometry(QtCore.QRect(20, 20, 180, 60))
self.pbEEG.setObjectName("pbEEG")
self.pbHM = QtWidgets.QPushButton(FormGS)
self.pbHM.setGeometry(QtCore.QRect(210, 20, 180, 60))
self.pbHM.setObjectName("pbHM")
self.pbEst = QtWidgets.QPushButton(FormGS)
self.pbEst.setGeometry(QtCore.QRect(400, 20, 180, 60))
self.pbEst.setObjectName("pbEst")
self.pbStat = QtWidgets.QPushButton(FormGS)
self.pbStat.setGeometry(QtCore.QRect(590, 20, 180, 60))
self.pbStat.setObjectName("pbStat")
self.pbVis = QtWidgets.QPushButton(FormGS)
self.pbVis.setGeometry(QtCore.QRect(590, 88, 180, 150))
self.pbVis.setObjectName("pbVis")
self.pbQuit = QtWidgets.QPushButton(FormGS)
self.pbQuit.setGeometry(QtCore.QRect(590, 245, 180, 110))
self.pbQuit.setObjectName("pbQuit")
self.pbTopo = QtWidgets.QPushButton(FormGS)
self.pbTopo.setGeometry(QtCore.QRect(400, 245, 180, 110))
self.pbTopo.setObjectName("pbTopo")
self.frame = QtWidgets.QFrame(FormGS)
self.frame.setGeometry(QtCore.QRect(25, 90, 170, 140))
self.frame.setFrameShape(QtWidgets.QFrame.StyledPanel)
self.frame.setFrameShadow(QtWidgets.QFrame.Raised)
self.frame.setObjectName("frame")
self.cbTrial = QtWidgets.QComboBox(self.frame)
self.cbTrial.setGeometry(QtCore.QRect(50, 30, 110, 26))
self.cbTrial.setObjectName("cbTrial")
self.labelTrial = QtWidgets.QLabel(self.frame)
self.labelTrial.setGeometry(QtCore.QRect(10, 35, 40, 16))
self.labelTrial.setObjectName("labelTrial")
self.labelThreshold = QtWidgets.QLabel(self.frame)
self.labelThreshold.setGeometry(QtCore.QRect(10, 80, 80, 16))
self.labelThreshold.setObjectName("labelThreshold")
self.sliderThreshold = QtWidgets.QSlider(self.frame)
self.sliderThreshold.setGeometry(QtCore.QRect(15, 105, 141, 22))
self.sliderThreshold.setMaximum(100)
self.sliderThreshold.setOrientation(QtCore.Qt.Horizontal)
self.sliderThreshold.setObjectName("sliderThreshold")
self.listThreshold = QtWidgets.QSpinBox(self.frame)
self.listThreshold.setGeometry(QtCore.QRect(100, 77, 57, 26))
self.listThreshold.setObjectName("listThreshold")
self.txtEpoch = QtWidgets.QFrame(FormGS)
self.txtEpoch.setGeometry(QtCore.QRect(215, 90, 170, 140))
self.txtEpoch.setFrameShape(QtWidgets.QFrame.StyledPanel)
self.txtEpoch.setFrameShadow(QtWidgets.QFrame.Raised)
self.txtEpoch.setObjectName("txtEpoch")
self.labelStart = QtWidgets.QLabel(self.txtEpoch)
self.labelStart.setGeometry(QtCore.QRect(20, 35, 40, 16))
self.labelStart.setObjectName("labelStart")
self.labelEnd = QtWidgets.QLabel(self.txtEpoch)
self.labelEnd.setGeometry(QtCore.QRect(20, 85, 40, 16))
self.labelEnd.setObjectName("labelEnd")
self.editStart = QtWidgets.QLineEdit(self.txtEpoch)
self.editStart.setGeometry(QtCore.QRect(80, 30, 70, 23))
self.editStart.setObjectName("editStart")
self.editEnd = QtWidgets.QLineEdit(self.txtEpoch)
self.editEnd.setGeometry(QtCore.QRect(80, 80, 70, 23))
self.editEnd.setObjectName("editEnd")
# self.editEnd.setReadOnly(True)
self.txtMovie = QtWidgets.QFrame(FormGS)
self.txtMovie.setGeometry(QtCore.QRect(405, 90, 170, 140))
self.txtMovie.setFrameShape(QtWidgets.QFrame.StyledPanel)
self.txtMovie.setFrameShadow(QtWidgets.QFrame.Raised)
self.txtMovie.setObjectName("txtMovie")
self.rbMovie = QtWidgets.QRadioButton(self.txtMovie)
self.rbMovie.setGeometry(QtCore.QRect(20, 20, 102, 20))
self.rbMovie.setChecked(True)
self.rbMovie.setObjectName("rbMovie")
self.rbAveragEpoch = QtWidgets.QRadioButton(self.txtMovie)
self.rbAveragEpoch.setGeometry(QtCore.QRect(20, 90, 120, 20))
self.rbAveragEpoch.setObjectName("rbAveragEpoch")
self.cbColor = QtWidgets.QCheckBox(self.txtMovie)
self.cbColor.setGeometry(QtCore.QRect(40, 50, 90, 20))
self.cbColor.setObjectName("cbColor")
self.txtTopomap = QtWidgets.QFrame(FormGS)
self.txtTopomap.setGeometry(QtCore.QRect(25, 250, 360, 100))
self.txtTopomap.setFrameShape(QtWidgets.QFrame.StyledPanel)
self.txtTopomap.setFrameShadow(QtWidgets.QFrame.Raised)
self.txtTopomap.setObjectName("txtTopomap")
self.rbEEG = QtWidgets.QRadioButton(self.txtTopomap)
self.rbEEG.setGeometry(QtCore.QRect(10, 40, 50, 20))
self.rbEEG.setChecked(True)
self.rbEEG.setObjectName("rbEEG")
self.rbAllForward = QtWidgets.QRadioButton(self.txtTopomap)
self.rbAllForward.setGeometry(QtCore.QRect(100, 20, 100, 20))
self.rbAllForward.setObjectName("rbAllForward")
self.rbAllResidual = QtWidgets.QRadioButton(self.txtTopomap)
self.rbAllResidual.setGeometry(QtCore.QRect(100, 60, 100, 20))
self.rbAllResidual.setObjectName("rbAllResidual")
self.rbPartForward = QtWidgets.QRadioButton(self.txtTopomap)
self.rbPartForward.setGeometry(QtCore.QRect(225, 20, 102, 20))
self.rbPartForward.setObjectName("rbPartForward")
self.rbPartResidual = QtWidgets.QRadioButton(self.txtTopomap)
self.rbPartResidual.setGeometry(QtCore.QRect(225, 60, 102, 20))
self.rbPartResidual.setObjectName("rbPartResidual")
self.retranslateUi(FormGS)
self.pbEEG.clicked.connect(self.pbEEG_Callback)
self.pbHM.clicked.connect(self.pbHM_Callback)
self.pbEst.clicked.connect(self.pbEst_Callback)
self.pbStat.clicked.connect(self.pbStat_Callback)
self.sliderThreshold.valueChanged['int'].connect(
self.listThreshold.setValue)
self.listThreshold.valueChanged['int'].connect(
self.sliderThreshold.setValue)
self.listThreshold.editingFinished.connect(self.editTH_Callback)
self.editStart.editingFinished.connect(self.editStart_Callback)
self.editEnd.editingFinished.connect(self.editEnd_Callback)
self.pbVis.clicked.connect(self.pbVis_Callback)
self.pbQuit.clicked.connect(FormGS.close)
# import HeadModelOpen
# self.pbQuit.clicked.connect(self.FormHM.close)
# self.pbQuit.clicked.connect(self.FormSourceRun.close)
QtCore.QMetaObject.connectSlotsByName(FormGS)
FormGS.setTabOrder(self.pbEEG, self.pbHM)
FormGS.setTabOrder(self.pbHM, self.pbEst)
FormGS.setTabOrder(self.pbEst, self.pbStat)
FormGS.setTabOrder(self.pbStat, self.cbTrial)
FormGS.setTabOrder(self.cbTrial, self.listThreshold)
FormGS.setTabOrder(self.listThreshold, self.sliderThreshold)
FormGS.setTabOrder(self.sliderThreshold, self.editStart)
FormGS.setTabOrder(self.editStart, self.editEnd)
FormGS.setTabOrder(self.editEnd, self.rbMovie)
FormGS.setTabOrder(self.rbMovie, self.cbColor)
FormGS.setTabOrder(self.cbColor, self.rbAveragEpoch)
FormGS.setTabOrder(self.rbAveragEpoch, self.pbVis)
FormGS.setTabOrder(self.pbVis, self.rbEEG)
FormGS.setTabOrder(self.rbEEG, self.rbAllForward)
FormGS.setTabOrder(self.rbAllForward, self.rbAllResidual)
FormGS.setTabOrder(self.rbAllResidual, self.rbPartForward)
FormGS.setTabOrder(self.rbPartForward, self.rbPartResidual)
FormGS.setTabOrder(self.rbPartResidual, self.pbTopo)
FormGS.setTabOrder(self.pbTopo, self.pbQuit)
def retranslateUi(self, FormGS):
_translate = QtCore.QCoreApplication.translate
FormGS.setWindowTitle(_translate("FormGS", "GeoSource"))
self.pbEEG.setText(_translate("FormGS", "EEG"))
self.pbHM.setText(_translate("FormGS", "Head Model"))
self.pbEst.setText(_translate("FormGS", "Estimate"))
self.pbStat.setText(_translate("FormGS", "Stat"))
self.pbVis.setText(_translate("FormGS", "Visualize"))
self.pbQuit.setText(_translate("FormGS", "Quit"))
self.pbTopo.setText(_translate("FormGS", "Topomap"))
self.labelTrial.setText(_translate("FormGS", "Trial"))
self.labelThreshold.setText(_translate("FormGS", "Threshold(%)"))
# self.listThreshold.setText(_translate("FormGS", "0"))
self.labelStart.setText(_translate("FormGS", "Start"))
self.labelEnd.setText(_translate("FormGS", "End"))
self.editStart.setText(_translate("FormGS", "0"))
self.editEnd.setText(_translate("FormGS", "0"))
self.rbMovie.setText(_translate("FormGS", "Movie"))
self.rbAveragEpoch.setText(_translate("FormGS", "Average Epoch"))
self.cbColor.setText(_translate("FormGS", "Color Lock"))
self.rbEEG.setText(_translate("FormGS", "EEG"))
self.rbAllForward.setText(_translate("FormGS", "All Forward"))
self.rbAllResidual.setText(_translate("FormGS", "All Residual"))
self.rbPartForward.setText(_translate("FormGS", "Part Forward"))
self.rbPartResidual.setText(_translate("FormGS", "Part Residual"))
def pbEEG_Callback(self):
global s, nC, nSamples, nSamplesPre, nTrials, srate, trialsName
global categoryName, nCategory
import config
from mff import read_mff_header, read_mff_data
import matplotlib.pyplot as plt
import numpy as np
options = QtWidgets.QFileDialog.Options()
mfffilename, _ = QtWidgets.QFileDialog.getOpenFileNames(
self.pbEEG,
"Select a mff file",
"",
"mff files (*.mff)",
options=options)
filePath = mfffilename[0]
hdr = read_mff_header.read_mff_header(filePath)
nC = hdr['nChans']
config.nC = nC
nSamples = hdr['nSamples']
config.nSamples = nSamples
nSamplesPre = hdr['nSamplesPre']
config.nSamplesPre = nSamplesPre
nTrials = hdr['nTrials']
config.nTrials = nTrials
srate = hdr['Fs']
config.srate = srate
summaryInfo = hdr['orig']
# config.nC = nC
trialsName = summaryInfo['epochLabels']
config.trialsName = trialsName
categoryName = list(set(trialsName))
config.categoryName = categoryName
nCategory = len(categoryName)
config.nCategory = nCategory
for i in range(nTrials):
self.cbTrial.addItem(trialsName[i])
data = read_mff_data.read_mff_data(filePath, 'epoch', 1,
hdr['nTrials'], hdr)
SegStatus = hdr['orig']['epochSegStatus']
GoodSeg = []
BadSeg = []
#epochLabels = [];
for i in range(len(SegStatus)):
if SegStatus[i] == 'bad':
BadSeg.append(i)
else:
GoodSeg.append(i)
nTrials = len(GoodSeg)
print('nC:%d' % nC)
print('nSamples:%d' % nSamples)
print('nTrials:%d' % nTrials)
print('nCategory:%d' % nCategory)
print('categoryName:%s' % categoryName)
# print('categoryName:%s' %trialsName)
## average reference
H = np.identity(nC) - np.ones((nC, nC)) / nC
s = np.zeros((nC, nSamples, nTrials))
sGFP = np.zeros((nSamples, nTrials))
if nTrials > 1:
for i in range(nTrials):
s[:, :, i] = np.dot(H, data[:, :, GoodSeg[i]])
sGFP[:, i] = np.std(s[:, :, i], axis=0)
# s2 = s[:,:,i] * s[:,:,i]
# gfp = s2.mean(axis=0)
# sGFP = np.sqrt(gfp)
else:
s = np.dot(H, data)
sGFP = np.std(s, axis=0)
# s2 = s * s
# gfp = s2.mean(axis=0)
# sGFP = np.sqrt(gfp)
baseline = (nSamplesPre * 1000 / srate)
config.baseline = baseline
msSamples = np.arange(0, nSamples, 1) * 1000 / srate - baseline
config.msSamples = msSamples
# global f1
if nTrials == nCategory:
# f1 = plt.figure
plt.plot(msSamples, sGFP)
plt.title('gfp')
plt.xlabel('ms')
plt.legend(trialsName, loc='best')
plt.show()
print('EEG is ERP.')
#eventsName = trialsName
else:
# f1 = plt.figure
plt.plot(msSamples, sGFP)
plt.title('gfp')
plt.xlabel('ms')
plt.show()
print('EEG is Single trial. There are', nTrials, 'trials. ')
#eventsName = categoryName
config.nSamples = nSamples
config.msSamples = msSamples
config.nTrials = nTrials
config.trialsName = trialsName
config.s = s
config.sGFP = sGFP
print("EEG data is loaded.")
# self.pbEEG.configure(background = "red")
return s
def pbHM_Callback(self):
options = QtWidgets.QFileDialog.DontResolveSymlinks | QtWidgets.QFileDialog.ShowDirsOnly
HMdir = QtWidgets.QFileDialog.getExistingDirectory(
self.pbHM,
"Select a Head Model Directory.",
self.pbHM.text(),
options=options)
import os
from braink import read_lfm
import config
nE = config.nE
nC = nE + 1
if os.path.exists(HMdir + '/fdmForwardMatrixOriented'):
K = read_lfm.forward(HMdir + '/fdmForwardMatrixOriented',
config.nE)
print K
print("fdmForwardMatrixOriented is loaded. ")
elif os.path.exists(HMdir + '/Leadfield.lfm'):
K = read_lfm.lfm(HMdir + '/Leadfield.lfm', config.nE)
print("Leadfield.lfm is loaded. ")
print K
else:
print("LFM is not loaded. ")
nV = K.shape[1]
config.K = K
config.nV = nV
config.nC = nC
os.system("open /Applications/EAV/EAV.app")
return
def pbEst_Callback(self):
from SourceRun import Ui_FormSourceRun
self.FormSourceRun = QtWidgets.QWidget()
self.uiEst = Ui_FormSourceRun()
self.uiEst.setupUi(self.FormSourceRun)
self.FormSourceRun.show()
return #sden
def editTH_Callback(self):
global thresholdcutoff
thresholdcutoff = self.listThreshold.value()
print('Lowest %d(percent) of dipoles are cut off.' % thresholdcutoff)
return
def editStart_Callback(self):
import config
startMS = self.editStart.text()
startMS = int(startMS)
config.startMS = startMS
return
def editEnd_Callback(self):
import config
import matplotlib.pyplot as plt
import numpy as np
endMS = self.editEnd.text()
endMS = int(endMS)
config.endMS = endMS
print('From %d to %d ms' % (config.startMS, config.endMS))
# f1 = plt.figure
plt.plot(config.msSamples, config.sGFP)
plt.title('sum(phi^2)')
plt.xlabel('ms')
plt.plot(
[config.startMS, config.startMS],
[np.min(config.sGFP), np.max(config.sGFP)],
'k-',
lw=2)
plt.plot(
[config.endMS, config.endMS],
[np.min(config.sGFP), np.max(config.sGFP)],
'k-',
lw=2)
if config.nTrials == config.nCategory:
plt.legend(config.trialsName, loc='best')
# else:
plt.show()
print('EEG is Single trial. There are %d trials.' % config.nTrials)
return
def pbStat_Callback(self):
from StatRun import Ui_FormStat
self.FormStat = QtWidgets.QWidget()
self.uiStat = Ui_FormStat()
self.uiStat.setupUi(self.FormStat)
self.FormStat.show()
return #sden
def pbVis_Callback(self):
import matplotlib.pyplot as plt
import numpy as np
import config
# import os
# os.system("open /Applications/EAV/EAV.app")
sdenMean = config.sdenMean
sdenSigma = config.sdenSigma
sdenT = config.sdenT
sMean = config.sMean
sSigma = config.sSigma
sT = config.sT
nSigChan = config.nSigChan
nSigVox = config.nSigVox
msSamples = config.msSamples
startMS = config.startMS
ii = np.where(msSamples == startMS)[0]
fig, ax = plt.subplots(4, 2, figsize=(20, 10))
ax[0, 0].plot(msSamples, sMean.T)
ax[0, 0].set_xlim([msSamples[0], msSamples[-1]])
ax[0, 0].set_ylabel('mean')
ax[0, 0].set_title('EEG')
ax[1, 0].plot(msSamples, sSigma.T)
ax[1, 0].set_xlim([msSamples[0], msSamples[-1]])
ax[1, 0].set_ylabel('sdv')
ax[2, 0].plot(msSamples, sT.T)
ax[2, 0].set_xlim([msSamples[0], msSamples[-1]])
ax[2, 0].set_ylabel('Normal')
# ax[2,0].axhline(vu, color='black', lw=2)
# ax[2,0].axhline(vl, color='black', lw=2)
ax[3, 0].plot(msSamples, nSigChan)
ax[3, 0].axvline(msSamples[ii], color='black', lw=2)
#ax[3,0].set_ylim([-1, max(nSigChan)+1])
ax[3, 0].set_xlim([msSamples[0], msSamples[-1]])
ax[3, 0].set_ylabel('Num Sig.Channels')
ax[3, 0].set_xlabel('ms')
#ax[3,0].legend()
ax[0, 1].plot(msSamples, sdenMean.T)
ax[0, 1].set_xlim([msSamples[0], msSamples[-1]])
ax[0, 1].set_ylabel('mean')
ax[0, 1].set_title('Source')
ax[1, 1].plot(msSamples, sdenSigma.T)
ax[1, 1].set_xlim([msSamples[0], msSamples[-1]])
ax[1, 1].set_ylabel('sdv')
ax[2, 1].plot(msSamples, sdenT.T)
ax[2, 1].set_xlim([msSamples[0], msSamples[-1]])
ax[2, 1].set_ylabel('Normal')
# ax[2,1].axhline(sdenvu, color='black', lw=2)
# ax[2,1].axhline(sdenvl, color='black', lw=2)
ax[3, 1].plot(msSamples, nSigVox, c='black', label='l+r')
ax[3, 1].axvline(msSamples[ii], color='black', lw=2)
#ax[3,1].set_ylim([-5, max(nSigVox)+5])
ax[3, 1].set_xlim([msSamples[0], msSamples[-1]])
ax[3, 1].set_ylabel('Num Sig.Voxels')
ax[3, 1].set_xlabel('ms')
#ax[3,1].legend()
plt.show()
sdenTSig = config.sdenTSig
sT = config.sT
# sTSig = config.sTSig
from RabbitMQ import Connection
c = Connection.Connection('localhost')
c.connect()
c.sendOrientedData(abs(sdenTSig[:, ii]), "Oriented", "3:00pm")
c.sendEEGData(sT[:, ii], "Oriented", "3:00pm")
c.disconnect()
