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PermuStat.py
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PermuStat.py
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# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'PermuStat.ui'
# Created: Mon Apr 6 15:58:15 2015
# by: PyQt4 UI code generator 4.11.1
#
# WARNING! All changes made in this file will be lost!
import sip
sip.setapi('QString', 2)
import sys
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
def _fromUtf8(s):
return s
try:
_encoding = QtGui.QApplication.UnicodeUTF8
def _translate(context, text, disambig):
return QtGui.QApplication.translate(context, text, disambig, _encoding)
except AttributeError:
def _translate(context, text, disambig):
return QtGui.QApplication.translate(context, text, disambig)
class Ui_FormStat(object):
def setupUi(self, FormStat):
FormStat.setObjectName(_fromUtf8("FormStat"))
FormStat.resize(432, 650)
##---------------------------------------------------------------------
self.tabPermuStat = QtGui.QTabWidget(FormStat)
self.tabPermuStat.setEnabled(True)
self.tabPermuStat.setGeometry(QtCore.QRect(20, 10, 390, 340))
self.tabPermuStat.setMaximumSize(QtCore.QSize(600, 16777215))
self.tabPermuStat.setFocusPolicy(QtCore.Qt.NoFocus)
self.tabPermuStat.setTabPosition(QtGui.QTabWidget.North)
self.tabPermuStat.setObjectName(_fromUtf8("tabPermuStat"))
##---------------------------------------------------------------------
self.tabData = QtGui.QWidget()
self.tabData.setObjectName(_fromUtf8("tabData"))
self.pbMFF = QtGui.QPushButton(self.tabData)
self.pbMFF.setGeometry(QtCore.QRect(20, 10, 341, 32))
self.pbMFF.setObjectName(_fromUtf8("pbMFF"))
self.frSource = QtGui.QFrame(self.tabData)
self.frSource.setGeometry(QtCore.QRect(30, 50, 320, 250))
self.frSource.setFrameShape(QtGui.QFrame.StyledPanel)
self.frSource.setFrameShadow(QtGui.QFrame.Raised)
self.frSource.setObjectName(_fromUtf8("frSource"))
self.pbHeadModel = QtGui.QPushButton(self.frSource)
self.pbHeadModel.setGeometry(QtCore.QRect(10, 10, 300, 32))
self.pbHeadModel.setObjectName(_fromUtf8("pbHeadModel"))
self.frMethod = QtGui.QFrame(self.frSource)
self.frMethod.setGeometry(QtCore.QRect(20, 50, 280, 40))
self.frMethod.setFrameShape(QtGui.QFrame.StyledPanel)
self.frMethod.setFrameShadow(QtGui.QFrame.Raised)
self.frMethod.setObjectName(_fromUtf8("frMethod"))
self.label_Method = QtGui.QLabel(self.frMethod)
self.label_Method.setGeometry(QtCore.QRect(20, 10, 71, 16))
self.label_Method.setObjectName(_fromUtf8("label_Method"))
self.cbMethod = QtGui.QComboBox(self.frMethod)
self.cbMethod.setGeometry(QtCore.QRect(150, 8, 120, 26))
self.cbMethod.setObjectName(_fromUtf8("cbMethod"))
self.cbMethod.addItems(["MN", "sMN"])
# self.cbMethod.addItem(_fromUtf8("MN"))
# self.cbMethod.addItem(_fromUtf8("sMN"))
self.frReg = QtGui.QFrame(self.frSource)
self.frReg.setGeometry(QtCore.QRect(20, 100, 280, 71))
self.frReg.setFrameShape(QtGui.QFrame.StyledPanel)
self.frReg.setFrameShadow(QtGui.QFrame.Raised)
self.frReg.setObjectName(_fromUtf8("frReg"))
self.rbTikhonov = QtGui.QRadioButton(self.frReg)
self.rbTikhonov.setGeometry(QtCore.QRect(20, 10, 91, 20))
self.rbTikhonov.setObjectName(_fromUtf8("rbTikh"))
self.rbTikhonov.setChecked(True)
self.rbLcurve = QtGui.QRadioButton(self.frReg)
self.rbLcurve.setGeometry(QtCore.QRect(20, 40, 81, 20))
self.rbLcurve.setObjectName(_fromUtf8("rbLcurve"))
self.label_alpha_Tikh = QtGui.QLabel(self.frReg)
self.label_alpha_Tikh.setGeometry(QtCore.QRect(110, 10, 81, 16))
self.label_alpha_Tikh.setObjectName(_fromUtf8("label_alpha_Tikh"))
self.leTikhonov = QtGui.QLineEdit(self.frReg)
self.leTikhonov.setGeometry(QtCore.QRect(200, 10, 60, 21))
self.leTikhonov.setObjectName(_fromUtf8("leTikhonov"))
self.pbEstimate = QtGui.QPushButton(self.frSource)
self.pbEstimate.setGeometry(QtCore.QRect(10, 180, 300, 32))
self.pbEstimate.setObjectName(_fromUtf8("pbEstimate"))
self.EstimateBar = QtGui.QProgressBar(self.frSource)
self.EstimateBar.setGeometry(15, 215, 290, 25)
self.EstimateBar.setObjectName(_fromUtf8("EstimateBar"))
self.EstimateBar.setMinimum(0)
self.EstimateBar.setMaximum(100)
self.tabPermuStat.addTab(self.tabData, _fromUtf8(""))
##---------------------------------------------------------------------
self.tabSource = QtGui.QWidget()
self.tabSource.setObjectName(_fromUtf8("tabSource"))
self.rbScalp = QtGui.QRadioButton(self.tabSource)
self.rbScalp.setGeometry(QtCore.QRect(100, 30, 170, 20))
self.rbScalp.setChecked(True)
self.rbScalp.setObjectName(_fromUtf8("rbScalp"))
self.rbSource = QtGui.QRadioButton(self.tabSource)
self.rbSource.setGeometry(QtCore.QRect(100, 70, 170, 20))
self.rbSource.setObjectName(_fromUtf8("rbSource"))
self.tabPermuStat.addTab(self.tabSource, _fromUtf8(""))
##---------------------------------------------------------------------
self.tabLevel = QtGui.QWidget()
self.tabLevel.setObjectName(_fromUtf8("tabLevel"))
self.rbIndividual = QtGui.QRadioButton(self.tabLevel)
self.rbIndividual.setGeometry(QtCore.QRect(80, 30, 170, 20))
self.rbIndividual.setChecked(True)
self.rbIndividual.setObjectName(_fromUtf8("rbIndividual"))
self.rbGroup = QtGui.QRadioButton(self.tabLevel)
self.rbGroup.setGeometry(QtCore.QRect(80, 80, 170, 20))
self.rbGroup.setObjectName(_fromUtf8("rbGroup"))
self.tabPermuStat.addTab(self.tabLevel, _fromUtf8(""))
##---------------------------------------------------------------------
self.tabParametric = QtGui.QWidget()
self.tabParametric.setObjectName(_fromUtf8("tabParametric"))
self.rbPara = QtGui.QRadioButton(self.tabParametric)
self.rbPara.setGeometry(QtCore.QRect(100, 30, 170, 20))
self.rbPara.setChecked(True)
self.rbPara.setObjectName(_fromUtf8("rbPara"))
self.rbNonPara = QtGui.QRadioButton(self.tabParametric)
self.rbNonPara.setGeometry(QtCore.QRect(100, 70, 170, 20))
self.rbNonPara.setObjectName(_fromUtf8("rbNonPara"))
self.tabPermuStat.addTab(self.tabParametric, _fromUtf8(""))
##---------------------------------------------------------------------
self.tabStat = QtGui.QWidget()
self.tabStat.setObjectName(_fromUtf8("tabStat"))
self.label_SigLev = QtGui.QLabel(self.tabStat)
self.label_SigLev.setGeometry(QtCore.QRect(40, 30, 110, 16))
self.label_SigLev.setObjectName(_fromUtf8("label"))
self.label_NumSim = QtGui.QLabel(self.tabStat)
self.label_NumSim.setGeometry(QtCore.QRect(40, 110, 110, 16))
self.label_NumSim.setObjectName(_fromUtf8("label_NumSim"))
self.label_Output = QtGui.QLabel(self.tabStat)
self.label_Output.setGeometry(QtCore.QRect(40, 70, 110, 16))
self.label_Output.setObjectName(_fromUtf8("label_Output"))
self.editSigLevel = QtGui.QLineEdit(self.tabStat)
self.editSigLevel.setGeometry(QtCore.QRect(170, 30, 100, 21))
self.editSigLevel.setObjectName(_fromUtf8("editSigLevel"))
self.editOutput = QtGui.QLineEdit(self.tabStat)
self.editOutput.setGeometry(QtCore.QRect(170, 70, 100, 21))
self.editOutput.setObjectName(_fromUtf8("editOutput"))
self.editNumSim = QtGui.QLineEdit(self.tabStat)
self.editNumSim.setGeometry(QtCore.QRect(170, 110, 100, 21))
self.editNumSim.setObjectName(_fromUtf8("editNumSim"))
self.tabPermuStat.addTab(self.tabStat, _fromUtf8(""))
##---------------------------------------------------------------------
self.tabTest = QtGui.QWidget()
self.tabTest.setObjectName(_fromUtf8("tabTest"))
self.rbOneT = QtGui.QRadioButton(self.tabTest)
self.rbOneT.setGeometry(QtCore.QRect(20, 20, 141, 20))
self.rbOneT.setChecked(True)
self.rbOneT.setCheckable(True)
self.rbOneT.setObjectName(_fromUtf8("rbOneT"))
self.rbTwoT = QtGui.QRadioButton(self.tabTest)
self.rbTwoT.setGeometry(QtCore.QRect(20, 80, 141, 20))
self.rbTwoT.setObjectName(_fromUtf8("rbTwoT"))
self.rbTwoT.setCheckable(True)
self.rbPairT = QtGui.QRadioButton(self.tabTest)
self.rbPairT.setGeometry(QtCore.QRect(20, 170, 141, 20))
self.rbPairT.setObjectName(_fromUtf8("rbPairT"))
self.rbPairT.setCheckable(True)
self.rbAnova = QtGui.QRadioButton(self.tabTest)
self.rbAnova.setGeometry(QtCore.QRect(20, 260, 141, 20))
self.rbAnova.setObjectName(_fromUtf8("rbAnova"))
self.rbAnova.setCheckable(True)
self.label_OneT = QtGui.QLabel(self.tabTest)
self.label_OneT.setGeometry(QtCore.QRect(70, 50, 81, 16))
self.label_OneT.setObjectName(_fromUtf8("label_OneT"))
self.label_TwoT1 = QtGui.QLabel(self.tabTest)
self.label_TwoT1.setGeometry(QtCore.QRect(70, 105, 81, 16))
self.label_TwoT1.setObjectName(_fromUtf8("label_TwoT1"))
self.label_TwoT2 = QtGui.QLabel(self.tabTest)
self.label_TwoT2.setGeometry(QtCore.QRect(70, 135, 81, 16))
self.label_TwoT2.setObjectName(_fromUtf8("label_TwoT2"))
self.label_PairT1 = QtGui.QLabel(self.tabTest)
self.label_PairT1.setGeometry(QtCore.QRect(70, 195, 81, 16))
self.label_PairT1.setObjectName(_fromUtf8("label_PairT1"))
self.label_PairT2 = QtGui.QLabel(self.tabTest)
self.label_PairT2.setGeometry(QtCore.QRect(70, 225, 81, 16))
self.label_PairT2.setObjectName(_fromUtf8("label_PairT2"))
self.cbOneTCat = QtGui.QComboBox(self.tabTest)
self.cbOneTCat.setGeometry(QtCore.QRect(180, 45, 141, 26))
self.cbOneTCat.setObjectName(_fromUtf8("cbOneTCat"))
self.cbTwoTCat1 = QtGui.QComboBox(self.tabTest)
self.cbTwoTCat1.setGeometry(QtCore.QRect(180, 100, 141, 26))
self.cbTwoTCat1.setObjectName(_fromUtf8("cbTwoTCat1"))
self.cbTwoTCat2 = QtGui.QComboBox(self.tabTest)
self.cbTwoTCat2.setGeometry(QtCore.QRect(180, 130, 141, 26))
self.cbTwoTCat2.setObjectName(_fromUtf8("cbTwoTCat2"))
self.cbPairTCat1 = QtGui.QComboBox(self.tabTest)
self.cbPairTCat1.setGeometry(QtCore.QRect(180, 190, 141, 26))
self.cbPairTCat1.setObjectName(_fromUtf8("cbPairTCat1"))
self.cbPairTCat2 = QtGui.QComboBox(self.tabTest)
self.cbPairTCat2.setGeometry(QtCore.QRect(180, 220, 141, 26))
self.cbPairTCat2.setObjectName(_fromUtf8("cbPairTCat2"))
self.tabPermuStat.addTab(self.tabTest, _fromUtf8(""))
##---------------------------------------------------------------------
self.pbRunStat = QtGui.QPushButton(FormStat)
self.pbRunStat.setGeometry(QtCore.QRect(20, 355, 390, 45))
self.pbRunStat.setObjectName(_fromUtf8("pbRunStat"))
##---------------------------------------------------------------------
self.pbSaveStat = QtGui.QPushButton(FormStat)
self.pbSaveStat.setGeometry(QtCore.QRect(20, 400, 390, 45))
self.pbSaveStat.setObjectName(_fromUtf8("pbSaveStat"))
##---------------------------------------------------------------------
self.formGroupBox = QtGui.QGroupBox(FormStat)
self.formGroupBox.setGeometry(QtCore.QRect(25, 450, 385, 145))
self.formGroupBox.setObjectName(_fromUtf8("formGroupBox"))
self.label_Time = QtGui.QLabel(self.formGroupBox)
self.label_Time.setGeometry(QtCore.QRect(80, 15, 100, 16))
self.label_Time.setObjectName(_fromUtf8("label_Time"))
self.editTime = QtGui.QLineEdit(self.formGroupBox)
self.editTime.setGeometry(QtCore.QRect(200, 15, 100, 21))
self.editTime.setObjectName(_fromUtf8("editTime"))
self.label_Channel = QtGui.QLabel(self.formGroupBox)
self.label_Channel.setGeometry(QtCore.QRect(80, 45, 100, 16))
self.label_Channel.setObjectName(_fromUtf8("label_Channel"))
self.editChannel = QtGui.QLineEdit(self.formGroupBox)
self.editChannel.setGeometry(QtCore.QRect(200, 45, 100, 21))
self.editChannel.setObjectName(_fromUtf8("editChannel"))
self.label_Dipole = QtGui.QLabel(self.formGroupBox)
self.label_Dipole.setGeometry(QtCore.QRect(80, 75, 100, 16))
self.label_Dipole.setObjectName(_fromUtf8("label_Dipole"))
self.editDipole = QtGui.QLineEdit(self.formGroupBox)
self.editDipole.setGeometry(QtCore.QRect(200, 75, 100, 21))
self.editDipole.setObjectName(_fromUtf8("editDipole"))
self.pbEAVStat = QtGui.QPushButton(self.formGroupBox)
self.pbEAVStat.setGeometry(QtCore.QRect(40, 110, 300, 32))
self.pbEAVStat.setObjectName(_fromUtf8("pbEAVStat"))
##---------------------------------------------------------------------
self.pbCloseStat = QtGui.QPushButton(FormStat)
self.pbCloseStat.setGeometry(QtCore.QRect(20, 600, 390, 45))
self.pbCloseStat.setObjectName(_fromUtf8("pbCloseStat"))
##---------------------------------------------------------------------
self.pbMFF.clicked.connect(self.pbMFF_Callback)
self.pbHeadModel.clicked.connect(self.pbHeadModel_Callback)
self.cbMethod.activated.connect(self.cbMethod_Callback)
self.pbEstimate.clicked.connect(self.pbEstimate_Callback)
# self.pbEstimate.clicked.connect(self.doAction)
self.cbOneTCat.activated.connect(self.cbOneTCat_Callback)
self.cbTwoTCat1.activated.connect(self.cbTwoTCat1_Callback)
self.cbTwoTCat2.activated.connect(self.cbTwoTCat2_Callback)
self.cbPairTCat1.activated.connect(self.cbPairTCat1_Callback)
self.cbPairTCat2.activated.connect(self.cbPairTCat2_Callback)
self.pbRunStat.clicked.connect(self.pbRunStat_Callback)
self.pbSaveStat.clicked.connect(self.pbSaveStat_Callback)
self.pbEAVStat.clicked.connect(self.pbEAVStat_Callback)
self.pbCloseStat.clicked.connect(self.pbCloseStat_Callback)
self.pbCloseStat.clicked.connect(FormStat.close)
self.retranslateUi(FormStat)
self.tabPermuStat.setCurrentIndex(0)
QtCore.QMetaObject.connectSlotsByName(FormStat)
##-------------------------------------------------------------------------
def retranslateUi(self, FormStat):
FormStat.setWindowTitle(_translate("FormStat", "PermuStat", None))
self.pbMFF.setText(_translate("FormStat", "MFF", None))
self.pbHeadModel.setText(_translate("FormStat", "Head Model", None))
self.label_Method.setText(_translate("FormStat", "Method : ", None))
self.rbTikhonov.setText(_translate("FormStat", "Tikhonov :", None))
self.rbLcurve.setText(_translate("FormStat", "L-curve ", None))
self.label_alpha_Tikh.setText(_translate("FormStat", "alpha = 10^", None))
self.leTikhonov.setText(_translate("FormStat", "-2", None))
self.cbMethod.setItemText(0, _translate("FormStat", "MN", None))
self.cbMethod.setItemText(1, _translate("FormStat", "sMN", None))
self.pbEstimate.setText(_translate("FormStat", "Estimate", None))
self.tabPermuStat.setTabText(self.tabPermuStat.indexOf(self.tabData), _translate("FormStat", "Data", None))
self.rbScalp.setText(_translate("FormStat", "Scalp", None))
self.rbSource.setText(_translate("FormStat", "Source", None))
self.tabPermuStat.setTabText(self.tabPermuStat.indexOf(self.tabSource), _translate("FormStat", "Source", None))
self.rbIndividual.setText(_translate("FormStat", "Individual (First Level)", None))
self.rbGroup.setText(_translate("FormStat", "Group (Second level)", None))
self.tabPermuStat.setTabText(self.tabPermuStat.indexOf(self.tabLevel), _translate("FormStat", "Level", None))
self.rbPara.setText(_translate("FormStat", "Parametric", None))
self.rbNonPara.setText(_translate("FormStat", "NonParametric", None))
self.tabPermuStat.setTabText(self.tabPermuStat.indexOf(self.tabParametric), _translate("FormStat", "Parametric", None))
self.label_SigLev.setText(_translate("FormStat", "Significant Level", None))
self.label_NumSim.setText(_translate("FormStat", "Num. Simulation", None))
self.label_Output.setText(_translate("FormStat", "Output Suffix", None))
self.editSigLevel.setText(_translate("FormStat", "0.05", None))
self.editOutput.setText(_translate("FormStat", "out", None))
self.editNumSim.setText(_translate("FormStat", "100", None))
self.tabPermuStat.setTabText(self.tabPermuStat.indexOf(self.tabStat), _translate("FormStat", "Stat", None))
self.rbOneT.setText(_translate("FormStat", "One Sample T-test", None))
self.rbTwoT.setText(_translate("FormStat", "Two Sample T-test", None))
self.rbPairT.setText(_translate("FormStat", "Paired T-test", None))
self.rbAnova.setText(_translate("FormStat", "ANOVA", None))
self.label_OneT.setText(_translate("FormStat", "Category", None))
self.label_TwoT1.setText(_translate("FormStat", "Category 1", None))
self.label_TwoT2.setText(_translate("FormStat", "Category 2", None))
self.label_PairT1.setText(_translate("FormStat", "Category 1", None))
self.label_PairT2.setText(_translate("FormStat", "Category 2", None))
self.tabPermuStat.setTabText(self.tabPermuStat.indexOf(self.tabTest), _translate("FormStat", "Test", None))
self.pbRunStat.setText(_translate("FormStat", "Run", None))
self.pbSaveStat.setText(_translate("FormStat", "Reciprocity", None))
self.label_Time.setText(_translate("FormStat", "Time (ms)", None))
self.label_Channel.setText(_translate("FormStat", "Channel", None))
self.label_Dipole.setText(_translate("FormStat", "Dipole", None))
self.editTime.setText(_translate("FormStat", "0", None))
self.editChannel.setText(_translate("FormStat", "0", None))
self.editDipole.setText(_translate("FormStat", "0", None))
self.pbEAVStat.setText(_translate("FormStat", "View", None))
self.pbCloseStat.setText(_translate("FormStat", "Close", None))
##-------------------------------------------------------------------------
def pbMFF_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 numpy as np
options = QtGui.QFileDialog.Options()
mfffilenames = QtGui.QFileDialog.getOpenFileNames(self.pbMFF, "Select a mff file", "", "mff files (*.mff)", options= options)
filePath = mfffilenames[0] #[0]
print('%s' %filePath)
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
baseline = (nSamplesPre * 1000 / srate) ; config.baseline = baseline
msSamples = np.arange(0, nSamples,1) * 1000/srate - baseline
config.msSamples = msSamples
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(nCategory):
self.cbOneTCat.addItem(categoryName[i])
self.cbTwoTCat1.addItem(categoryName[i])
self.cbTwoTCat2.addItem(categoryName[i])
self.cbPairTCat1.addItem(categoryName[i])
self.cbPairTCat2.addItem(categoryName[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)
## average reference
H = np.identity(nC) - np.ones((nC, nC))/nC
s = np.zeros(data.shape)
if nTrials > 1 :
for i in range(nTrials):
s[:,:,i] = np.dot(H, data[:,:, GoodSeg[i]])
else :
s = np.dot(H, data)
whichCat = np.zeros((nTrials, nCategory))
for j in range(nCategory):
for i in range(nTrials):
if (trialsName[i] == categoryName[j]):
whichCat[i,j] = 1
whichCat = np.array(whichCat, dtype='i')
config.s = s
config.whichCat = whichCat
config.categoryName = categoryName
print('nC:%d' %nC)
print('nSamples:%d' %nSamples)
print('nTrials:%d' %nTrials)
print('nCategory:%d' %nCategory)
for i in range(nCategory):
print('categoryName:%s' %categoryName[i])
print("EEG data is loaded.")
return s
##-------------------------------------------------------------------------
def pbHeadModel_Callback(self):
options = QtGui.QFileDialog.DontResolveSymlinks | QtGui.QFileDialog.ShowDirsOnly
HMdir = QtGui.QFileDialog.getExistingDirectory(self.pbHeadModel,
"Select a Head Model Directory.",
self.pbHeadModel.text(), options=options)
import os
from braink import read_lfm
import config
import glob
lfm_fname = glob.glob(HMdir+'/*.lfm')
if os.path.exists(HMdir+'/fdmForwardMatrixOriented'):
K = read_lfm.forward(HMdir+'/fdmForwardMatrixOriented', config.nE)
print("fdmForwardMatrixOriented is loaded. ")
elif len(lfm_fname) > 0: # elif os.path.exists(HMdir+'/Leadfield.lfm'):
K = read_lfm.lfm(lfm_fname[0], config.nE)
print("Leadfield.lfm is loaded. ")
else:
print("Either fdmForwardMatrixOriented or *.lfm are not loaded. ")
# nV = K.shape[1]
config.K = K
config.nV = K.shape[1]
return K
##-------------------------------------------------------------------------
def cbMethod_Callback(self, MethodIndex):
import config
if MethodIndex == 0:
config.MethodVal = 0
# print(MethodIndex)
print('MN is selected. ')
elif MethodIndex == 1:
config.MethodVal = 1
# print(MethodIndex)
print('sMN is selected. ')
else:
print("Inverse Method is not selected. ")
return
##-------------------------------------------------------------------------
def pbEstimate_Callback(self):
import config
from swcm import Imatrix, Lcurve
import numpy as np
# import pdb
# pdb.pm()
MethodVal = config.MethodVal
K = config.K
s = config.s
nC, nSamples, nTrials = s.shape
nV = K.shape[1]
if self.rbTikhonov.isChecked():
poweralpha = self.leTikhonov.text()
poweralpha = int(poweralpha)
alpha = pow(10, poweralpha)
print("alpha = %3.2e " %alpha)
else :
logalpha = Lcurve.MN(s[:,0,0], K)
poweralpha = logalpha[0]
alpha = pow(10, poweralpha)
print("from Lcurve alpha=%3.2e" %alpha)
if MethodVal == 0:
Imat = Imatrix.MN(alpha, K)
elif MethodVal == 1:
Imat = Imatrix.sMN(alpha, K)
else:
print("Inverse Method is not selected. ")
sden = np.zeros((nV, nSamples, nTrials))
for i in range(nTrials):
sden[:,:,i] = np.dot(Imat, s[:,:,i])
print("Source is estimated")
config.sden = sden
return sden
# def timerEvent(self, event):
# self.timer = QtCore.QBasicTimer()
# self.step = 0
# if self.step >= 100:
# self.timer.stop()
# self.pbEstimate.setText('Finished')
# return
# self.step = self.step + 1
# self.EstimateBar.setValue(self.step)
# def doAction(self, val):
# self.timer = QtCore.QBasicTimer()
# self.step = 0
# self.EstimateBar.setValue(val)
## perct = "{0}%".format(val)
# if self.timer.isActive():
# self.timer.stop()
## self.EstimateBar.setText('Start')
# else:
# self.timer.start(100, self.EstimateBar)
## self.EstimateBar.setText('Stop')
##-------------------------------------------------------------------------
def cbOneTCat_Callback(self, Index):
import config
print('nCategory= %d'%config.nCategory)
for i in range(config.nCategory):
if Index == i:
config.OneTCatVal = i
print('Category[%d] (%s) is selected.' %(config.OneTCatVal, config.categoryName[i]))
##-------------------------------------------------------------------------
def cbTwoTCat1_Callback(self, Index):
import config
for i in range(config.nCategory):
if Index == i:
config.TwoTCatVal1 = i
print('Category[%d] (%s) is selected.' %(config.TwoTCatVal1, config.categoryName[i]))
##-------------------------------------------------------------------------
def cbTwoTCat2_Callback(self, Index):
import config
for i in range(config.nCategory):
if Index == i:
config.TwoTCatVal2 = i
print('Category[%d] (%s) is selected.' %(config.TwoTCatVal2, config.categoryName[i]))
##-------------------------------------------------------------------------
def cbPairTCat1_Callback(self, Index):
import config
for i in range(config.nCategory):
if Index == i:
config.PairTCatVal1 = i
print('Category[%d] (%s) is selected.' %(config.PairTCatVal1, config.categoryName[i]))
##-------------------------------------------------------------------------
def cbPairTCat2_Callback(self, Index):
import config
for i in range(config.nCategory):
if Index == i:
config.PairTCatVal2 = i
print('Category[%d] (%s) is selected.' %(config.PairTCatVal2, config.categoryName[i]))
##-------------------------------------------------------------------------
def pbRunStat_Callback(self):
import numpy as np
import config
from permustat import permustat_fun, perm_plot
msSamples = config.msSamples
s = config.s
sden = config.sden
categoryName = config.categoryName
whichCat = config.whichCat
nCategory = config.nCategory
#---------------------------------------------------------------------
SigLevel = self.editSigLevel.text()
SigLevel = float(SigLevel)
print("Significant level is %3.2f" %SigLevel)
NumSim = self.editNumSim.text()
NumSim = int(NumSim)
if self.rbPara.isChecked():
config.ParaVal = 0
print("Parametric is selected")
else:
config.ParaVal = 1
print("Non-Parametric is selected and Num Sim is %d" %NumSim)
##---------------------------------------------------------------------
if self.rbOneT.isChecked():
catName = categoryName[config.OneTCatVal]
print("One sample T-test:%s" %catName)
if self.rbScalp.isChecked():
X = s[:,:, (whichCat[:, config.OneTCatVal]>0)]
else:
X = sden[:,:, (whichCat[:, config.OneTCatVal]>0)]
XMean = np.mean(X, axis=2)
XSigma = np.std(X, axis=2)
statOut = permustat_fun.one_sample_t(X, SigLevel)
perm_plot.oneT(XMean, XSigma, statOut['T'], statOut['nSigS'], catName, msSamples)
config.Stat = statOut['T']
elif self.rbTwoT.isChecked():
catName1 = categoryName[config.TwoTCatVal1]
catName2 = categoryName[config.TwoTCatVal2]
print('Two sample T-test: %s vs %s' %(catName1, catName2))
if self.rbScalp.isChecked():
X1 = s[:,:, (whichCat[:, config.TwoTCatVal1]>0)]
X2 = s[:,:, (whichCat[:, config.TwoTCatVal2]>0)]
else:
X1 = sden[:,:, (whichCat[:, config.TwoTCatVal1]>0)]
X2 = sden[:,:, (whichCat[:, config.TwoTCatVal2]>0)]
XMean1 = np.mean(X1, axis=2); XSigma1 = np.std(X1, axis=2);
XMean2 = np.mean(X2, axis=2); XSigma2 = np.std(X2, axis=2);
statOut1 = permustat_fun.one_sample_t(X1, SigLevel/2)
statOut2 = permustat_fun.one_sample_t(X2, SigLevel/2)
if self.rbPara.isChecked():
statOut = permustat_fun.two_sample_t(X1, X2, SigLevel)
perm_plot.twoT(XMean1, XSigma1, statOut1['T'], statOut1['nSigS'], catName1,
XMean2, XSigma2, statOut2['T'], statOut2['nSigS'], catName2, statOut['T'], statOut['nSigS'], msSamples)
else:
statOut = permustat_fun.two_sample_permu(X1, X2, SigLevel/2, NumSim)
logPvalST = np.log(statOut['Pval'])
perm_plot.permT(statOut['T'], logPvalST, msSamples)
config.Stat = statOut['T']
elif self.rbPairT.isChecked():
catName1 = categoryName[config.PairTCatVal1]
catName2 = categoryName[config.PairTCatVal2]
print('Pair T-test: %s vs %s' %(catName1, catName2))
if self.rbScalp.isChecked():
X1 = s[:,:, (whichCat[:, config.PairTCatVal1]>0)]
X2 = s[:,:, (whichCat[:, config.PairTCatVal2]>0)]
else:
X1 = sden[:,:, (whichCat[:, config.PairTCatVal1]>0)]
X2 = sden[:,:, (whichCat[:, config.PairTCatVal2]>0)]
XMean1 = np.mean(X1, axis=2); XSigma1 = np.std(X1, axis=2);
XMean2 = np.mean(X2, axis=2); XSigma2 = np.std(X2, axis=2);
statOut1 = permustat_fun.one_sample_t(X1, SigLevel/2)
statOut2 = permustat_fun.one_sample_t(X2, SigLevel/2)
if self.rbPara.isChecked():
statOut = permustat_fun.pairt(X1, X2, SigLevel)
perm_plot.pairT(XMean1, XSigma1, statOut1['T'], statOut1['nSigS'], catName1,
XMean2, XSigma2, statOut2['T'], statOut2['nSigS'], catName2, statOut['T'], statOut['nSigS'], msSamples)
else:
statOut = permustat_fun.pairt_permu(X1, X2, SigLevel/2, NumSim)
logPvalST = np.log(statOut['Pval'])
perm_plot.permPairT(statOut['T'], logPvalST, msSamples)
config.Stat = statOut['T']
elif self.rbAnova.isChecked():
if self.rbScalp.isChecked():
statOut = permustat_fun.anova_f(s, whichCat, nCategory, SigLevel)
else:
statOut = permustat_fun.anova_f(sden, whichCat, nCategory, SigLevel)
perm_plot.anova(statOut['F'], statOut['Pval'], statOut['Sig'], msSamples)
config.Stat = statOut['F']
config.Pval = statOut['Pval']
config.Sig = statOut['Sig']
config.StatOut = statOut
return statOut
##-------------------------------------------------------------------------
def pbSaveStat_Callback(self):
import os
# os.system("open /Applications/EAV/Mimir.app")
os.system("open /Applications/EAV/Reciprocity.app")
# import config
# Stat = config.Stat
# Sig = config.Sig
# Pval = config.Pval
#
# OutputSuffix = self.editOutput.text()
# print("OutputSuffix is %s" %OutputSuffix)
#
# f=open("Stat_"+OutputSuffix+".bin","wb")
# f.write(Stat)
# f.close()
#
# f=open("PvalST_"+OutputSuffix+".bin","wb")
# f.write(Pval)
# f.close()
#
# f=open("SigST_"+OutputSuffix+".bin","wb")
# f.write(Sig)
# f.close()
##-------------------------------------------------------------------------
def pbEAVStat_Callback(self):
import config
import matplotlib.pyplot as plt
from RabbitMQ import Connection
import numpy as np
from pandas import DataFrame
import pandas as pd
pd.options.display.float_format = '{:,.3f}'.format
statOut = config.StatOut
XT = config.Stat; Sig = config.Sig; # Pval = config.Pval
msSamples = config.msSamples
EAVtime = self.editTime.text(); EAVtime = int(EAVtime)
# print("Time is %d" %EAVtime)
SampleTime = np.where(msSamples == EAVtime)[0]
# print("SampleTime is %d" %SampleTime)
EAVch = self.editChannel.text(); EAVch = int(EAVch)
# print("Channel is %d" %EAVch)
EAVdipole = self.editDipole.text(); EAVdipole = int(EAVdipole)
# print("Dipole is %d" %EAVdipole)
##---------------------------------------------------------------------
if self.rbScalp.isChecked():
config.SourceVal = 0
print("Scalp is selected")
i = EAVch ;
figCh = plt.figure()
ax = figCh.add_subplot(111)
ax.plot(msSamples, XT[EAVch, :])
ax.axvline(EAVtime, color='r')
ax.set_xlim([msSamples[0],msSamples[-1]])
ax.set_title('Electrode %d' %EAVch)
plt.show()
else:
config.SourceVal = 1
print("Source is selected")
i = EAVdipole ;
figCh = plt.figure()
ax = figCh.add_subplot(111)
ax.plot(msSamples, XT[EAVdipole, :])
ax.axvline(EAVtime, color='r')
ax.set_xlim([msSamples[0],msSamples[-1]])
ax.set_title('Dipole %d' %EAVdipole)
plt.show()
j = SampleTime;
if self.rbAnova.isChecked():
tbl_one = [[statOut['df_b'], float(statOut['SS_b'][i,j]), float(statOut['MS_b'][i,j]), float(statOut['F'][i,j]),
float(statOut['Pval'][i,j]), ('***' if statOut['Sig'][i,j] == 1 else '')],
[statOut['df_w'], float(statOut['SS_w'][i,j]), float(statOut['MS_w'][i,j]), '', '', ''],
[statOut['df_b']+statOut['df_w'], float(statOut['SS_t'][i,j]), '', '', '', '']]
anova = DataFrame(tbl_one, index=['Between', 'Within', 'Total'], columns=[ 'DF' ,'SS' ,'MS', 'F' , 'Pval', 'Sig'])
print anova
c = Connection.Connection('localhost')
c.connect()
if self.rbScalp.isChecked():
c.sendEEGData(XT[:,SampleTime], "StatEEG", "")
c.sendEEGData(Sig[:,SampleTime], "SigEEG", "")
else:
c.sendOrientedData(XT[:, SampleTime], "StatSource", "")
c.sendOrientedData(Sig[:, SampleTime], "SigSource", "")
c.disconnect()
return
##-------------------------------------------------------------------------
def pbCloseStat_Callback(self):
import matplotlib.pyplot as plt
plt.close("all")
if __name__ == "__main__":
app = QtGui.QApplication(sys.argv)
FormStat = QtGui.QWidget()
ui = Ui_FormStat()
ui.setupUi(FormStat)
FormStat.show()
sys.exit(app.exec_())