def __init__(self, parent=None, setting=None):
super(frmSelectSession, self).__init__(parent)
# inputs
self.SubRange = strRange(setting.SubRange, Unique=True)
if self.SubRange is None:
print("Subject Range is wrong!")
return
self.SubSize = len(self.SubRange)
self.ConRange = strMultiRange(setting.ConRange, self.SubSize)
if self.ConRange is None:
print("Counter Range is wrong!")
return
self.RunRange = strMultiRange(setting.RunRange, self.SubSize)
if self.RunRange is None:
print("Run Range is wrong!")
return
# outputs
self.SubID = None
self.RunID = None
self.ConID = None
self.PASS = False
layout = QFormLayout()
self.lblSub = QLabel("Subject: ")
self.txtSub = QComboBox()
self.txtSub.addItem("", None)
for subindx, sub in enumerate(self.SubRange):
self.txtSub.addItem(str(sub), subindx)
self.txtSub.currentIndexChanged.connect(self.txtSub_isChenged)
layout.addRow(self.lblSub, self.txtSub)
self.lblRun = QLabel("Run: ")
self.txtRun = QComboBox()
layout.addRow(self.lblRun, self.txtRun)
self.lblCon = QLabel("Counter: ")
self.txtCon = QComboBox()
layout.addRow(self.lblCon, self.txtCon)
self.lblTask = QLabel()
self.lblTask.setText("Task:")
self.txtTask = QLineEdit()
self.txtTask.setText(setting.Task)
self.txtTask.setReadOnly(True)
layout.addRow(self.lblTask, self.txtTask)
self.btnOK = QPushButton("OK")
self.btnOK.clicked.connect(self.btnOK_onclick)
self.btnCan = QPushButton("Cancel")
self.btnCan.clicked.connect(self.btnCan_onclick)
layout.addRow(self.btnCan, self.btnOK)
self.setLayout(layout)
self.setWindowTitle("Session Selector")
self.exec_()
def Check(self,
SettingFileName,
isOne=False,
SubID=None,
RunID=None,
ConID=None):
import numpy as np
import os
from Base.utility import fixstr, setParameters3, strRange, strMultiRange
from Base.Setting import Setting
setting = Setting()
setting.Load(SettingFileName)
if setting.empty:
print("Error in loading the setting file!")
return False
else:
if isOne:
Subjects = [SubID]
Counters = [[ConID]]
Runs = [[RunID]]
else:
Subjects = strRange(setting.SubRange, Unique=True)
if Subjects is None:
print("Cannot load Subject Range!")
return False
SubSize = len(Subjects)
Counters = strMultiRange(setting.ConRange, SubSize)
if Counters is None:
print("Cannot load Counter Range!")
return False
Runs = strMultiRange(setting.RunRange, SubSize)
if Runs is None:
print("Cannot load Run Range!")
return False
for si, s in enumerate(Subjects):
for cnt in Counters[si]:
print("Checking script for Subject %d ..." % (s))
for r in Runs[si]:
ScriptAddr = setParameters3(setting.Script, setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\
fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \
fixstr(cnt, setting.ConLen, setting.ConPer))
if os.path.isfile(ScriptAddr):
print("CHECK: " + ScriptAddr + " - checked!")
else:
print("CHECK: " + ScriptAddr + " - not found!")
return False
return True
def btnConvert_click(self):
msgBox = QMessageBox()
tStart = time.time()
Activation = ui.cbActivation.currentData()
LossNorm = ui.cbLossNorm.currentData()
LossType = ui.cbType.currentData()
try:
Layers = strRange(ui.txtLayers.text(), Unique=False)
if Layers is None:
raise Exception('')
except:
msgBox.setText("Layers is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
Alpha = np.float32(ui.txtAlpha.text())
if Alpha < 0:
raise Exception
except:
msgBox.setText("Alpha is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
Iter = np.int32(ui.txtIter.text())
except:
msgBox.setText("Number of iteration is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
BatchSize = np.int32(ui.txtBatch.text())
except:
msgBox.setText("Number of batch is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
ReportStep = np.int32(ui.txtReportStep.text())
except:
msgBox.setText("Number of Report Step is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
LearningRate = np.float32(ui.txtRate.text())
except:
msgBox.setText("Number of Report Step is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if not ui.cbCov.isChecked() and not ui.cbCorr.isChecked():
msgBox.setText("At least, you must select one metric!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Filter
try:
Filter = ui.txtFilter.text()
if not len(Filter):
Filter = None
else:
Filter = Filter.replace("\'", " ").replace(",", " ").replace(
"[", "").replace("]", "").split()
Filter = np.int32(Filter)
except:
print("Filter is wrong!")
return
# OutFile
OutFile = ui.txtOutFile.text()
if not len(OutFile):
msgBox.setText("Please enter out file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
OutData = dict()
# InFile
InFile = ui.txtInFile.text()
if not len(InFile):
msgBox.setText("Please enter input file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if not os.path.isfile(InFile):
msgBox.setText("Input file not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Loading ...")
InData = io.loadmat(InFile)
# Data
if not len(ui.txtData.currentText()):
msgBox.setText("Please enter Input Data variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Label
if not len(ui.txtLabel.currentText()):
msgBox.setText("Please enter Train Label variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Design
if not len(ui.txtDesign.currentText()):
msgBox.setText("Please enter Input Design variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
Design = InData[ui.txtDesign.currentText()]
except:
msgBox.setText("Design value is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
X = InData[ui.txtData.currentText()]
L = InData[ui.txtLabel.currentText()][0]
except:
print("Cannot load data or label")
return
# Task
if not len(ui.txtTask.currentText()):
msgBox.setText("Please enter Task variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Task Val
if not len(ui.txtTaskVal.currentText()):
msgBox.setText("Please enter Task value!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
TaskIDTitle = ui.txtTaskVal.currentText()
except:
msgBox.setText("Task value is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
TaskTitle = InData[ui.txtTask.currentText()][0]
except:
msgBox.setText("Task variable name is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
TaskTitleUnique = np.unique(TaskTitle)
Task = np.zeros(np.shape(TaskTitle))
for ttinx, tt in enumerate(TaskTitle):
for ttlinx, ttl in enumerate(TaskTitleUnique):
if tt[0] == ttl:
Task[ttinx] = ttlinx + 1
break
for ttlinx, ttl in enumerate(TaskTitleUnique):
if TaskIDTitle == ttl:
TaskID = ttlinx + 1
break
OutData["Task"] = TaskIDTitle
# Subject
if not len(ui.txtSubject.currentText()):
msgBox.setText("Please enter Subject variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Subject Val
if not len(ui.txtSubjectVal.currentText()):
msgBox.setText("Please enter Subject value!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
SubID = np.int32(ui.txtSubjectVal.currentText())
except:
msgBox.setText("Subject value is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
Sub = InData[ui.txtSubject.currentText()][0]
except:
msgBox.setText("Subject variable name is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
OutData["SubjectID"] = SubID
# Run
if not len(ui.txtRun.currentText()):
msgBox.setText("Please enter Run variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Run Val
if not len(ui.txtRunVal.currentText()):
msgBox.setText("Please enter Run value!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
RunID = np.int32(ui.txtRunVal.currentText())
except:
msgBox.setText("Run value is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
Run = InData[ui.txtRun.currentText()][0]
except:
msgBox.setText("Run variable name is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
OutData["RunID"] = RunID
# Counter
if not len(ui.txtCounter.currentText()):
msgBox.setText("Please enter Counter variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Counter Val
if not len(ui.txtCounterVal.currentText()):
msgBox.setText("Please enter Counter value!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
ConID = np.int32(ui.txtCounterVal.currentText())
except:
msgBox.setText("Counter value is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
Con = InData[ui.txtCounter.currentText()][0]
except:
msgBox.setText("Counter variable name is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
OutData["CounterID"] = ConID
if Filter is not None:
for fil in Filter:
# Remove Training Set
labelIndx = np.where(L == fil)[0]
Design = np.delete(Design, labelIndx, axis=0)
X = np.delete(X, labelIndx, axis=0)
L = np.delete(L, labelIndx, axis=0)
Task = np.delete(Task, labelIndx, axis=0)
Sub = np.delete(Sub, labelIndx, axis=0)
Run = np.delete(Run, labelIndx, axis=0)
Con = np.delete(Con, labelIndx, axis=0)
print("Class ID = " + str(fil) + " is removed from data.")
# Select Task
TaskIndex = np.where(Task == TaskID)
Design = Design[TaskIndex, :][0]
X = X[TaskIndex, :][0]
L = L[TaskIndex]
Sub = Sub[TaskIndex]
Run = Run[TaskIndex]
Con = Con[TaskIndex]
# Select Subject
SubIndex = np.where(Sub == SubID)
Design = Design[SubIndex, :][0]
X = X[SubIndex, :][0]
L = L[SubIndex]
Run = Run[SubIndex]
Con = Con[SubIndex]
# Select Counter
ConIndex = np.where(Con == ConID)
Design = Design[ConIndex, :][0]
X = X[ConIndex, :][0]
L = L[ConIndex]
Run = Run[ConIndex]
# Select Run
RunIndex = np.where(Run == RunID)
Design = Design[RunIndex, :][0]
X = X[RunIndex, :][0]
L = L[RunIndex] # This will only use in supervised methods
LUnique = np.unique(L)
LNum = np.shape(LUnique)[0]
OutData["Label"] = LUnique
OutData["ModelAnalysis"] = "Tensorflow.Session.Deep.RSA"
if np.shape(X)[0] == 0:
msgBox.setText("The selected data is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if ui.cbScale.isChecked():
X = preprocessing.scale(X)
print("Data is scaled to N(0,1).")
print("Running Deep RSA ...")
# RSA Method
OutData['Method'] = dict()
OutData['Method']['Layers'] = ui.txtLayers.text()
OutData['Method']['Alpha'] = Alpha
OutData['Method']['Activation'] = Activation
OutData['Method']['LossNorm'] = LossNorm
OutData['Method']['LearningRate'] = LearningRate
OutData['Method']['NumIter'] = Iter
OutData['Method']['BatchSize'] = BatchSize
OutData['Method']['ReportStep'] = ReportStep
OutData['Method']['Verbose'] = ui.cbVerbose.isChecked()
rsa = DeepRSA(layers=Layers, n_iter=Iter, learning_rate=LearningRate,loss_norm=LossNorm,activation=Activation,\
batch_size=BatchSize,report_step=ReportStep,verbose=ui.cbVerbose.isChecked(),\
CPU=ui.cbDevice.currentData(), alpha=Alpha, loss_type=LossType)
Betas, Weights, Biases, loss_vec, MSE, Performance = rsa.fit(
data_vals=X, design_vals=Design)
OutData["LossVec"] = loss_vec
OutData["MSE"] = MSE
OutData["Performance"] = Performance
print("MSE: %f" % (MSE))
if ui.cbBeta.isChecked():
OutData["Betas"] = Betas
OutData["Weights"] = Weights
OutData["Biases"] = Biases
# Calculate Results
if ui.cbCorr.isChecked():
print("Calculating Correlation ...")
Corr = np.corrcoef(Betas)
corClass = SimilarityMatrixBetweenClass(Corr)
OutData["Correlation"] = Corr
OutData["Correlation_min"] = corClass.min()
OutData["Correlation_max"] = corClass.max()
OutData["Correlation_std"] = corClass.std()
OutData["Correlation_mean"] = corClass.mean()
print("Correlation: min: {:3.10f}, max: {:3.10f}, mean: {:3.10f}, std: {:3.10f}".format(corClass.min(), \
corClass.max(), corClass.mean(), corClass.std()))
if ui.cbCov.isChecked():
print("Calculating Covariance ...")
Cov = np.cov(Betas)
covClass = SimilarityMatrixBetweenClass(Cov)
OutData["Covariance"] = Cov
OutData["Covariance_min"] = covClass.min()
OutData["Covariance_max"] = covClass.max()
OutData["Covariance_std"] = covClass.std()
OutData["Covariance_mean"] = covClass.mean()
print("Covariance: min: {:3.10f}, max: {:3.10f}, mean: {:3.10f}, std: {:3.10f}".format(covClass.min(), \
covClass.max(), covClass.mean(), covClass.std()))
OutData["RunTime"] = time.time() - tStart
print("Runtime (s): %f" % (OutData["RunTime"]))
print("Saving results ...")
io.savemat(OutFile, mdict=OutData, do_compression=True)
print("Output is saved.")
if ui.cbDiagram.isChecked():
if ui.cbCorr.isChecked():
fig1 = plt.figure(num=None, figsize=(5, 5), dpi=100)
plt.pcolor(Corr, vmin=-0.1, vmax=1)
plt.xlim([0, LNum])
plt.ylim([0, LNum])
plt.colorbar()
ax = plt.gca()
ax.set_aspect(1)
plt.title(
'DeepRSA: Correlation\nTask: %s\nSub: %d, Counter: %d, Run: %d'
% (TaskIDTitle, SubID, ConID, RunID))
plt.show()
if ui.cbCov.isChecked():
fig2 = plt.figure(num=None, figsize=(5, 5), dpi=100)
plt.pcolor(Cov)
plt.xlim([0, LNum])
plt.ylim([0, LNum])
plt.colorbar()
ax = plt.gca()
ax.set_aspect(1)
plt.title(
'DeepRSA: Covariance\nTask: %s\nSub: %d, Counter: %d, Run: %d'
% (TaskIDTitle, SubID, ConID, RunID))
plt.show()
print("DONE.")
msgBox.setText(
"Gradient Representational Similarity Analysis (RSA) is done.")
msgBox.setIcon(QMessageBox.Information)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
def checkValue(self, ui, checkFiles=True, checkGeneratedFiles=False):
self.empty = True
msgBox = QMessageBox()
FSLDIR = ui.txtFSLDIR.text()
if (os.path.isfile(ui.txtMNI.currentText()) == False):
msgBox = QMessageBox()
msgBox.setText("Cannot find MNI file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if (os.path.isfile(FSLDIR + ui.txtFeat.text()) == False):
msgBox = QMessageBox()
msgBox.setText("Cannot find feat cmd!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if (os.path.isfile(FSLDIR + ui.txtFeat_gui.text()) == False):
msgBox = QMessageBox()
msgBox.setText("Cannot find Feat_gui cmd!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
mainDIR = ui.txtDIR.text()
if not len(mainDIR):
msgBox.setText("There is no main directory")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if not os.path.isdir(mainDIR):
msgBox.setText("Main directory doesn't exist")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Main directory is okay.")
Task = ui.txtTask.currentText()
if not len(Task):
msgBox.setText("There is no task title")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
SubRange = strRange(ui.txtSubRange.text(), Unique=True)
if SubRange is None:
raise Exception
SubSize = len(SubRange)
except:
msgBox.setText("Subject Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Range of subjects is okay!")
try:
SubLen = np.int32(ui.txtSubLen.text())
1 / SubLen
except:
msgBox.setText("Length of subjects must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of subjects is okay!")
try:
ConRange = strMultiRange(ui.txtConRange.text(), SubSize)
if ConRange is None:
raise Exception
if not (len(ConRange) == SubSize):
msgBox.setText("Counter Size must be equal to Subject Size!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
except:
msgBox.setText("Counter Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Counter Range is okay!")
try:
ConLen = np.int32(ui.txtConLen.text())
1 / ConLen
except:
msgBox.setText("Length of counter must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of Counter is okay!")
try:
RunRange = strMultiRange(ui.txtRunRange.text(), SubSize)
if RunRange is None:
raise Exception
if not (len(RunRange) == SubSize):
msgBox.setText("Run Size must be equal to Subject Size!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
except:
msgBox.setText("Run Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Run Range is okay!")
try:
RunLen = np.int32(ui.txtRunLen.value())
1 / RunLen
except:
msgBox.setText("Length of runs must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of runs is valid")
# Check fMRI Images
try:
TR = np.double(ui.txtTR.text())
1 / TR
except:
msgBox.setText("TR must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if TR <= 0:
msgBox.setText("TR must be a positive number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("TR is okay")
try:
FWHM = np.double(ui.txtFWHM.text())
1 / FWHM
except:
msgBox.setText("FWHM must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if FWHM <= 0:
msgBox.setText("FWHM must be a positive number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("FWHM is okay")
try:
TotalVol = np.int32(ui.txtTotalVol.value())
except:
msgBox.setText("Total Volumn must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if TotalVol < 0:
msgBox.setText("Total Volumn must be a positive number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Total Volumn is okay")
try:
DeleteVol = np.int32(ui.txtDeleteVol.value())
except:
msgBox.setText("Delete Volumn must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if DeleteVol < 0:
msgBox.setText("Delete Volumn must be a positive number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Delete Volumn is okay")
try:
HighPass = np.double(ui.txtHighPass.text())
except:
msgBox.setText("High Pass cutoff must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if HighPass <= 0:
msgBox.setText("High Pass cutoff must be a positive number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("High Pass cutoff is okay")
try:
DENL = np.double(ui.txtDENL.text())
except:
msgBox.setText("Noise level must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Noise level is okay")
try:
DETS = np.double(ui.txtDETS.text())
except:
msgBox.setText("Temporal smoothness must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Temporal smoothness is okay")
try:
DEZT = np.double(ui.txtDEZT.text())
except:
msgBox.setText(
"Z threshold in the design efficiency must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Z threshold in the design efficiency is okay")
try:
CTZT = np.double(ui.txtCTZT.text())
except:
msgBox.setText("Z threshold in the clustering must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Z threshold in the clustering is okay")
try:
CTPT = np.double(ui.txtCTPT.text())
except:
msgBox.setText("Clustering P threshold must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Clustering P threshold is okay")
if ui.txtBOLD.text() == "":
msgBox.setText("Structure of the BOLD files is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if ui.txtScript.text() == "":
msgBox.setText("Structure of the script files is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if ui.txtAnat.text() == "":
msgBox.setText("Structure of the Anatomical files is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if ui.txtOnset.text() == "":
msgBox.setText("Structure of the BOLD files is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if ui.txtBET.text() == "":
msgBox.setText("Structure of the BET files is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if ui.txtBETPDF.text() == "":
msgBox.setText("Structure of the BET report (PDF) is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if ui.txtAnalysis.text() == "":
msgBox.setText("Structure of the analysis folder is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if ui.txtEventDIR.text() == "":
msgBox.setText("Structure of the event folders is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if ui.txtCondPre.text() == "":
msgBox.setText("The prefix of condition files is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
ECodes = ui.txtEvents.toPlainText()
if ECodes == "":
msgBox.setText("Event code is empty")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Event codes are okay")
if checkFiles:
print("Validating files ...")
for si, s in enumerate(SubRange):
for c in ConRange[si]:
print("Analyzing Subject %d, Counter %d ..." % (s, c))
# checking anat file
addr = setParameters3(ui.txtAnat.text(),mainDIR, fixstr(s, SubLen, ui.txtSubPer.text()), "",\
ui.txtTask.currentText(),fixstr(c, ConLen, ui.txtConPer.text()))
if os.path.isfile(addr):
print(addr, " - OKAY.")
else:
print(addr, " - file not find!")
return False
if checkGeneratedFiles and ui.cbRegAnat.isChecked():
# BET Files
addr = setParameters3(
ui.txtBET.text(), mainDIR,
fixstr(s, SubLen, ui.txtSubPer.text()), "",
ui.txtTask.currentText(),
fixstr(c, ConLen, ui.txtConPer.text()))
if os.path.isfile(addr):
print(addr, " - OKAY.")
else:
print(addr, " - file not find!")
return False
for r in RunRange[si]:
# BOLD File Check
addr = setParameters3(ui.txtBOLD.text(),mainDIR, fixstr(s, SubLen, ui.txtSubPer.text()), \
fixstr(r,RunLen,ui.txtRunPer.text()), ui.txtTask.currentText(),fixstr(c, ConLen, ui.txtConPer.text()))
if os.path.isfile(addr):
print(addr, " - OKAY.")
else:
print(addr, " - file not find!")
return False
# Event File Check
if ui.cbMode.currentIndex() == 0:
addr = setParameters3(ui.txtOnset.text(), mainDIR, fixstr(s, SubLen, ui.txtSubPer.text()), \
fixstr(r,RunLen,ui.txtRunPer.text()), ui.txtTask.currentText(),fixstr(c, ConLen, ui.txtConPer.text()))
if os.path.isfile(addr):
print(addr, " - OKAY.")
else:
print(addr, " - file not find!")
return False
if checkGeneratedFiles and ui.cbMode.currentIndex(
) == 0:
addr = setParameters3(ui.txtEventDIR.text(),mainDIR, fixstr(s, SubLen, ui.txtSubPer.text()), \
fixstr(r,RunLen,ui.txtRunPer.text()), ui.txtTask.currentText(),fixstr(c, ConLen, ui.txtConPer.text()))
if os.path.isdir(addr):
print(addr, " - OKAY.")
try:
Cond = io.loadmat(addr +
ui.txtCondPre.text() +
".mat")
for fileID in range(
1, Cond["Cond"].shape[0] + 1):
if os.path.isfile(
addr + ui.txtCondPre.text() +
"_" + str(fileID) + ".tab"):
print(addr + ui.txtCondPre.text() +
"_" + str(fileID) +
".tab - OKAY.")
else:
print(addr + ui.txtCondPre.text() +
"_" + str(fileID) +
".tab - file not find!")
return False
except:
print(addr + ui.txtCondPre.text() +
".mat - loading error!")
return False
else:
print(addr + ui.txtCondPre.text() +
".mat - file not find!")
return False
self.Version = getSettingVersion()
self.Mode = ui.cbMode.currentIndex()
self.mainDIR = mainDIR
self.MNISpace = ui.txtMNI.currentText()
self.SubRange = ui.txtSubRange.text()
self.SubLen = SubLen
self.SubPer = ui.txtSubPer.text()
self.ConRange = ui.txtConRange.text()
self.ConLen = ConLen
self.ConPer = ui.txtConPer.text()
self.Task = str(Task)
self.RunRange = ui.txtRunRange.text()
self.RunLen = str(RunLen)
self.RunPer = ui.txtRunPer.text()
self.BOLD = ui.txtBOLD.text()
self.Onset = ui.txtOnset.text()
self.AnatDIR = ui.txtAnat.text()
self.BET = ui.txtBET.text()
self.BETPDF = ui.txtBETPDF.text()
self.Analysis = ui.txtAnalysis.text()
self.Script = ui.txtScript.text()
self.EventFolder = ui.txtEventDIR.text()
self.EventCodes = ui.txtEvents.toPlainText()
self.CondPre = ui.txtCondPre.text()
self.TR = TR
self.FWHM = FWHM
self.DeleteVol = DeleteVol
self.TotalVol = TotalVol
self.HighPass = HighPass
self.DENL = DENL
self.DETS = DETS
self.DEZT = DEZT
self.CTZT = CTZT
self.CTPT = CTPT
TimeSlice = getTimeSliceID(ui.cbSliceTime.currentText())
if TimeSlice is None:
print("Error in Slice Time!")
return False
self.TimeSlice = np.int32(TimeSlice)
self.Motion = ui.cbMotionCorrection.isChecked()
self.Anat = ui.cbRegAnat.isChecked()
self.empty = False
return True
def run(self,SettingFileName, betcmd=None):
import os
from Base.utility import fixstr,setParameters3, strRange, strMultiRange
from Base.Setting import Setting
if betcmd is None:
print("Cannot find bet cmd")
return
if not os.path.isfile(betcmd):
print("Cannot find bet cmd")
return
setting = Setting()
setting.Load(SettingFileName)
if (setting.empty) or (setting.Anat == False) :
if setting.empty:
print("Error in loading the setting file!")
if not setting.Anat:
print("This feature is disable for in setting file. Please turn it on from Advance menu!")
return False
else:
Subjects = strRange(setting.SubRange,Unique=True)
if Subjects is None:
print("Cannot load Subject Range!")
return False
SubSize = len(Subjects)
Counters = strMultiRange(setting.ConRange,SubSize)
if Counters is None:
print("Cannot load Counter Range!")
return False
Runs = strMultiRange(setting.RunRange,SubSize)
if Runs is None:
print("Cannot load Run Range!")
return False
Jobs = list()
for sindx, s in enumerate(Subjects):
for cnt in Counters[sindx]:
print("Analyzing Subject %d, Counter %d ..." % (s, cnt))
InAddr = setParameters3(setting.AnatDIR,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),"", setting.Task,
fixstr(cnt, setting.ConLen, setting.ConPer))
InFile = setParameters3(setting.AnatDIR,"", fixstr(s, setting.SubLen, setting.SubPer),"", setting.Task,
fixstr(cnt, setting.ConLen, setting.ConPer))
OutAddr = setParameters3(setting.BET,setting.mainDIR,fixstr(s, setting.SubLen, setting.SubPer),"", setting.Task,
fixstr(cnt, setting.ConLen, setting.ConPer))
PDFAddr = setParameters3(setting.BETPDF,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),"", setting.Task,
fixstr(cnt, setting.ConLen, setting.ConPer))
if not os.path.isfile(InAddr):
print(InAddr, " - file not find!")
return False
else:
files = [OutAddr, PDFAddr]
thread = BrainExtractorThread(bet=betcmd, InAddr=InAddr, OutAddr=OutAddr, PDFAddr=PDFAddr,\
InFile=InFile, files=files)
Jobs.append(["BrainExtractor", InFile, thread])
print("Job: Anatomical Brain Extractor for Subject %d, Counter %d is created." % (s, cnt))
return True, Jobs
def run(self,SettingFileName):
from Base.utility import fixstr,setParameters3, strRange, strMultiRange
from Base.Setting import Setting
setting = Setting()
setting.Load(SettingFileName)
if setting.empty:
print("Error in loading the setting file!")
return False
else:
Subjects = strRange(setting.SubRange,Unique=True)
if Subjects is None:
print("Cannot load Subject Range!")
return False
SubSize = len(Subjects)
Counters = strMultiRange(setting.ConRange,SubSize)
if Counters is None:
print("Cannot load Counter Range!")
return False
Runs = strMultiRange(setting.RunRange,SubSize)
if Runs is None:
print("Cannot load Run Range!")
return False
for si, s in enumerate(Subjects):
for cnt in Counters[si]:
print("Analyzing Subject %d, Counter %d ..." % (s, cnt))
for r in Runs[si]:
ScriptAddr = setParameters3(setting.Script,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\
fixstr(r, setting.RunLen, setting.RunPer), setting.Task,\
fixstr(cnt, setting.ConLen, setting.ConPer))
ScriptOutputAddr = setParameters3(setting.Analysis,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\
fixstr(r, setting.RunLen, setting.RunPer), setting.Task,\
fixstr(cnt, setting.ConLen, setting.ConPer))
BOLDaddr = setParameters3(setting.BOLD,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\
fixstr(r, setting.RunLen, setting.RunPer), setting.Task,\
fixstr(cnt, setting.ConLen, setting.ConPer))
MRIFile = nb.load(BOLDaddr)
# Generate Script
scriptFile = open(ScriptAddr,"w")
scriptFile.write("\n# FEAT version number\nset fmri(version) 6.00\n\n# Are we in MELODIC?\nset fmri(inmelodic) 0\n\n")
scriptFile.write("# Analysis level\n# 1 : First-level analysis\n# 2 : Higher-level analysis\nset fmri(level) 1\n\n")
scriptFile.write("# Which stages to run\n# 0 : No first-level analysis (registration and/or group stats only)\n")
scriptFile.write("# 7 : Full first-level analysis\n# 1 : Pre-processing\n# 2 : Statistics\nset fmri(analysis) 7\n\n")
scriptFile.write("# Use relative filenames\nset fmri(relative_yn) 0\n\n")
scriptFile.write("# Balloon help\nset fmri(help_yn) 1\n\n")
scriptFile.write("# Run Featwatcher\nset fmri(featwatcher_yn) 0\n\n")
scriptFile.write("# Cleanup first-level standard-space images\nset fmri(sscleanup_yn) 0\n\n")
scriptFile.write("# Output directory\nset fmri(outputdir) \"" + ScriptOutputAddr + "\"\n\n")
# TR
scriptFile.write("# TR(s)\nset fmri(tr) %0.6f \n\n" % setting.TR)
# Total Volumes
if setting.TotalVol == 0:
print("Auto Detect Total Volumes = " + str(get_mri_shape(MRIFile)[3]) + ", File: " + BOLDaddr)
scriptFile.write("# Total volumes\nset fmri(npts) " + str(get_mri_shape(MRIFile)[3]) + "\n\n")
else:
scriptFile.write("# Total volumes\nset fmri(npts) " + str(setting.TotalVol) + "\n\n")
# Delete Volumes
scriptFile.write("# Delete volumes\nset fmri(ndelete) " + str(setting.DeleteVol) + "\n\n")
scriptFile.write("# Perfusion tag/control order\nset fmri(tagfirst) 1\n\n")
scriptFile.write("# Number of first-level analyses\nset fmri(multiple) 1\n\n")
scriptFile.write("# Higher-level input type\n# 1 : Inputs are lower-level FEAT directories\n# 2 : Inputs are cope images from FEAT directories\nset fmri(inputtype) 2\n\n")
scriptFile.write("# Carry out pre-stats processing?\nset fmri(filtering_yn) 1\n\n")
scriptFile.write("# Brain/background threshold, %\nset fmri(brain_thresfh) 10\n\n")
scriptFile.write("# Critical z for design efficiency calculation\nset fmri(critical_z) " + str(setting.DEZT) + "\n\n")
scriptFile.write("# Noise level\nset fmri(noise) " + str(setting.DENL) + "\n\n# Noise AR(1)\nset fmri(noisear) " + str(setting.DETS) + "\n\n")
# Motion Correction: ALWAYS ON
scriptFile.write("# Motion correction\n# 0 : None\n# 1 : MCFLIRT\nset fmri(mc) 1\n\n")
scriptFile.write("# Spin-history (currently obsolete)\nset fmri(sh_yn) 0\n\n")
scriptFile.write("# B0 fieldmap unwarping?\nset fmri(regunwarp_yn) 0\n\n")
scriptFile.write("# EPI dwell time (ms)\nset fmri(dwell) 0.7\n\n")
scriptFile.write("# EPI TE (ms)\nset fmri(te) 35\n\n")
scriptFile.write("# % Signal loss threshold\nset fmri(signallossthresh) 10\n\n")
scriptFile.write("# Unwarp direction\nset fmri(unwarp_dir) y-\n\n")
scriptFile.write("# Slice timing correction\n# 0 : None\n# 1 : Regular up (0, 1, 2, 3, ...)\n# 2 : Regular down\n")
scriptFile.write("# 3 : Use slice order file\n# 4 : Use slice timings file\n# 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )\n")
# Slice Timing
scriptFile.write("set fmri(st) " + str(setting.TimeSlice) + "\n\n")
scriptFile.write("# Slice timings file\nset fmri(st_file) \"\"\n\n")
scriptFile.write("# BET brain extraction\nset fmri(bet_yn) 1\n\n")
# FWHM
scriptFile.write("# Spatial smoothing FWHM (mm)\nset fmri(smooth) " + str(setting.FWHM) + "\n\n")
scriptFile.write("# Intensity normalization\nset fmri(norm_yn) 0\n\n")
scriptFile.write("# Perfusion subtraction\nset fmri(perfsub_yn) 0\n\n")
scriptFile.write("# Highpass temporal filtering\nset fmri(temphp_yn) 1\n\n")
scriptFile.write("# Lowpass temporal filtering\nset fmri(templp_yn) 0\n\n")
scriptFile.write("# MELODIC ICA data exploration\nset fmri(melodic_yn) 0\n\n")
scriptFile.write("# Carry out main stats?\nset fmri(stats_yn) 1\n\n")
scriptFile.write("# Carry out prewhitening?\nset fmri(prewhiten_yn) 1\n\n")
scriptFile.write("# Add motion parameters to model\n# 0 : No\n# 1 : Yes\nset fmri(motionevs) 1\nset fmri(motionevsbeta) \"\"\nset fmri(scriptevsbeta) \"\"\n\n")
scriptFile.write("# Robust outlier detection in FLAME?\nset fmri(robust_yn) 0\n\n")
scriptFile.write("# Higher-level modelling\n# 3 : Fixed effects\n# 0 : Mixed Effects: Simple OLS\n# 2 : Mixed Effects: FLAME 1\n# 1 : Mixed Effects: FLAME 1+2\nset fmri(mixed_yn) 2\n\n")
# Conditions
ConditionFile = setParameters3(setting.EventFolder,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\
fixstr(r, setting.RunLen, setting.RunPer), setting.Task, fixstr(cnt, setting.ConLen, setting.ConPer)) + setting.CondPre + ".mat"
Cond = io.loadmat(ConditionFile)
Conditions = Cond["Cond"]
CondLen = len(Conditions)
scriptFile.write("# Number of EVs\nset fmri(evs_orig) "+str(CondLen)+"\nset fmri(evs_real) "+str(CondLen)+"\nset fmri(evs_vox) 0\n\n")
scriptFile.write("# Number of contrasts\nset fmri(ncon_orig) "+str(CondLen)+"\nset fmri(ncon_real) "+str(CondLen)+"\n\n")
scriptFile.write("# Number of F-tests\nset fmri(nftests_orig) 0\nset fmri(nftests_real) 0\n\n")
scriptFile.write("# Add constant column to design matrix? (obsolete)\nset fmri(constcol) 0\n\n")
scriptFile.write("# Carry out post-stats steps?\nset fmri(poststats_yn) 1\n\n")
scriptFile.write("# Pre-threshold masking?\nset fmri(threshmask) \"\"\n\n")
# Clustering
scriptFile.write("# Thresholding\n# 0 : None\n# 1 : Uncorrected\n# 2 : Voxel\n# 3 : Cluster\nset fmri(thresh) 3\n\n")
scriptFile.write("# P threshold\nset fmri(prob_thresh) " + str(setting.CTPT) + "\n\n")
scriptFile.write("# Z threshold\nset fmri(z_thresh) " + str(setting.CTZT) + "\n\n")
scriptFile.write("# Z min/max for colour rendering\n# 0 : Use actual Z min/max\n# 1 : Use preset Z min/max\nset fmri(zdisplay) 0\n\n")
scriptFile.write("# Z min in colour rendering\nset fmri(zmin) 2\n\n")
scriptFile.write("# Z max in colour rendering\nset fmri(zmax) 8\n\n")
scriptFile.write("# Colour rendering type\n# 0 : Solid blobs\n# 1 : Transparent blobs\nset fmri(rendertype) 1\n\n")
scriptFile.write("# Background image for higher-level stats overlays\n# 1 : Mean highres\n# 2 : First highres\n# 3 : Mean functional\n# 4 : First functional\n# 5 : Standard space template\nset fmri(bgimage) 1\n\n")
scriptFile.write("# Create time series plots\nset fmri(tsplot_yn) 1\n\n")
scriptFile.write("# Registration to initial structural\nset fmri(reginitial_highres_yn) 0\n\n")
scriptFile.write("# Search space for registration to initial structural\n# 0 : No search\n# 90 : Normal search\n# 180 : Full search\nset fmri(reginitial_highres_search) 90\n\n")
scriptFile.write("# Degrees of Freedom for registration to initial structural\nset fmri(reginitial_highres_dof) 3\n\n")
# Anat
if setting.Anat:
scriptFile.write("# Registration to main structural\nset fmri(reghighres_yn) 1\n\n")
scriptFile.write("# Search space for registration to main structural\n# 0 : No search\n# 90 : Normal search\n# 180 : Full search\nset fmri(reghighres_search) 90\n\n")
scriptFile.write("# Degrees of Freedom for registration to main structural\nset fmri(reghighres_dof) 12\n\n")
else:
scriptFile.write("# Registration to main structural\nset fmri(reghighres_yn) 0\n\n")
scriptFile.write("# Search space for registration to main structural\n# 0 : No search\n# 90 : Normal search\n# 180 : Full search\nset fmri(reghighres_search) 90\n\n")
scriptFile.write("# Degrees of Freedom for registration to main structural\nset fmri(reghighres_dof) BBR\n\n")
# Standard Space
scriptFile.write("# Registration to standard image?\nset fmri(regstandard_yn) 1\n\n")
scriptFile.write("# Use alternate reference images?\nset fmri(alternateReference_yn) 0\n\n")
# Get {FSLDIR}
#StandardTemp = os.path.dirname(os.path.realpath(__file__)) + "/MNI152_T1_2mm_brain"
scriptFile.write("# Standard image\nset fmri(regstandard) \"" + setting.MNISpace + "\"\n\n")
scriptFile.write("# Search space for registration to standard space\n# 0 : No search\n# 90 : Normal search\n# 180 : Full search\nset fmri(regstandard_search) 90\n\n")
scriptFile.write("# Degrees of Freedom for registration to standard space\nset fmri(regstandard_dof) 12\n\n")
scriptFile.write("# Do nonlinear registration from structural to standard space?\nset fmri(regstandard_nonlinear_yn) 0\n\n")
scriptFile.write("# Control nonlinear warp field resolution\nset fmri(regstandard_nonlinear_warpres) 10 \n\n")
# High Pass
scriptFile.write("# High pass filter cutoff\nset fmri(paradigm_hp) %d\n\n" % setting.HighPass)
# Total Voxel
TotalVoxel = get_mri_shape(MRIFile)[0] * get_mri_shape(MRIFile)[1] * get_mri_shape(MRIFile)[2] * get_mri_shape(MRIFile)[3]
scriptFile.write("# Total voxels\nset fmri(totalVoxels) " + str(TotalVoxel) + "\n\n\n")
scriptFile.write("# Number of lower-level copes feeding into higher-level analysis\nset fmri(ncopeinputs) 0\n\n")
scriptFile.write("# 4D AVW data or FEAT directory (1)\nset feat_files(1) \"" + BOLDaddr + "\"\n\n")
scriptFile.write("# Add confound EVs text file\nset fmri(confoundevs) 0\n\n")
# Align to structural MRI
if setting.Anat:
AnatAddr = setParameters3(setting.BET,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),"",setting.Task,\
fixstr(cnt, setting.ConLen, setting.ConPer))
scriptFile.write("# Subject's structural image for analysis 1\nset highres_files(1) \"" + AnatAddr + "\"\n\n")
# Condition Files
for cond in range(1,CondLen + 1):
scriptFile.write("# EV " + str(cond) + " title\nset fmri(evtitle"+str(cond)+") \""+Conditions[cond-1][1][0]+"\"\n\n")
scriptFile.write("# Basic waveform shape (EV " + str(cond) + ")\n# 0 : Square\n# 1 : Sinusoid\n# 2 : Custom (1 entry per volume)\n# 3 : Custom (3 column format)\n# 4 : Interaction\n# 10 : Empty (all zeros)\nset fmri(shape" + str(cond) + ") 3\n\n")
scriptFile.write("# Convolution (EV " + str(cond) + ")\n# 0 : None\n# 1 : Gaussian\n# 2 : Gamma\n# 3 : Double-Gamma HRF\n# 4 : Gamma basis functions\n# 5 : Sine basis functions\n# 6 : FIR basis functions\nset fmri(convolve" + str(cond) + ") 2\n\n")
scriptFile.write("# Convolve phase (EV " + str(cond) + ")\nset fmri(convolve_phase" + str(cond) + ") 0\n\n")
scriptFile.write("# Apply temporal filtering (EV " + str(cond) + ")\nset fmri(tempfilt_yn" + str(cond) + ") 1\n\n")
scriptFile.write("# Add temporal derivative (EV " + str(cond) + ")\nset fmri(deriv_yn" + str(cond) + ") 0\n\n")
ConditionFile = setParameters3(setting.EventFolder,setting.mainDIR, fixstr(s, setting.SubLen,setting.SubPer), \
fixstr(r, setting.RunLen, setting.RunPer), setting.Task,\
fixstr(cnt, setting.ConLen, setting.ConPer)) + setting.CondPre + "_" + str(cond) + ".tab"
scriptFile.write("# Custom EV file (EV " + str(cond) + ")\nset fmri(custom" + str(cond) + ") \"" + ConditionFile + "\"\n\n")
scriptFile.write("# Gamma sigma (EV " + str(cond) + ")\nset fmri(gammasigma" + str(cond) + ") 3\n\n")
scriptFile.write("# Gamma delay (EV " + str(cond) + ")\nset fmri(gammadelay" + str(cond) + ") 6\n\n")
for ev in range(0,CondLen + 1):
scriptFile.write("# Orthogonalise EV " + str(cond) + " wrt EV " + str(ev) + "\nset fmri(ortho" + str(cond) + "." + str(ev) + ") 0\n\n")
scriptFile.write("# Contrast & F-tests mode\n# real : control real EVs\n# orig : control original EVs\nset fmri(con_mode_old) orig\nset fmri(con_mode) orig\n\n")
# Contrast & F-tests mode
for cond in range(1,CondLen + 1):
scriptFile.write("# Display images for contrast_real " + str(cond) + "\nset fmri(conpic_real." + str(cond) + ") 1\n\n")
scriptFile.write("# Title for contrast_real " + str(cond) + "\nset fmri(conname_real." + str(cond) + ") \"" + Conditions[cond-1][1][0] + "\"\n\n")
for ev in range(1, CondLen + 1):
if ev == cond:
scriptFile.write("# Real contrast_real vector " + str(cond) + " element " + str(ev) + "\nset fmri(con_real" + str(cond) + "." + str(ev) + ") " + str(CondLen) + "\n\n")
else:
scriptFile.write("# Real contrast_real vector " + str(cond) + " element " + str(ev) + "\nset fmri(con_real" + str(cond) + "." + str(ev) + ") -1\n\n")
for cond in range(1,CondLen + 1):
scriptFile.write("# Display images for contrast_orig " + str(cond) + "\nset fmri(conpic_orig." + str(cond) + ") 1\n\n")
scriptFile.write("# Title for contrast_orig " + str(cond) + "\nset fmri(conname_orig." + str(cond) + ") \"" + Conditions[cond-1][1][0] + "\"\n\n")
for ev in range(1, CondLen + 1):
if ev == cond:
scriptFile.write("# Real contrast_orig vector " + str(cond) + " element " + str(ev) + "\nset fmri(con_orig" + str(cond) + "." + str(ev) + ") " + str(CondLen) + "\n\n")
else:
scriptFile.write("# Real contrast_orig vector " + str(cond) + " element " + str(ev) + "\nset fmri(con_orig" + str(cond) + "." + str(ev) + ") -1\n\n")
scriptFile.write("# Contrast masking - use >0 instead of thresholding?\nset fmri(conmask_zerothresh_yn) 0\n\n")
scriptFile.write("")
for cond in range(1,CondLen + 1):
for ev in range(1,CondLen + 1):
if cond != ev:
scriptFile.write("# Mask real contrast/F-test " + str(cond) + " with real contrast/F-test " + str(ev) + "?\nset fmri(conmask" + str(cond) + "_" + str(ev) + ") 0\n\n")
scriptFile.write("# Do contrast masking at all?\nset fmri(conmask1_1) 0\n\n")
scriptFile.write("##########################################################\n# Now options that don't appear in the GUI\n\n")
scriptFile.write("# Alternative (to BETting) mask image\nset fmri(alternative_mask) \"\"\n\n")
scriptFile.write("# Initial structural space registration initialisation transform\nset fmri(init_initial_highres) \"\"\n\n")
scriptFile.write("# Structural space registration initialisation transform\nset fmri(init_highres) \"\"\n\n")
scriptFile.write("# Standard space registration initialisation transform\nset fmri(init_standard) \"\"\n\n")
scriptFile.write("# For full FEAT analysis: overwrite existing .feat output dir?\nset fmri(overwrite_yn) 0")
scriptFile.close()
print("SCRIPT: " + ScriptAddr + " is generated!")
def btnRun_onclick(self):
from Base.utility import strRange, strMultiRange
global ui
msgBox = QMessageBox()
SubPer = ui.txtSubPer.text()
RunPer = ui.txtRunPer.text()
ConPer = ui.txtConPer.text()
Input = ui.txtInput.text()
Output = ui.txtOutput.text()
Task = ui.txtTask.text()
DIR = ui.txtDIR.text()
try:
SubRange = strRange(ui.txtSubRange.text(), Unique=True)
if SubRange is None:
raise Exception
SubSize = len(SubRange)
except:
msgBox.setText("Subject Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Range of subjects is okay!")
try:
SubLen = np.int32(ui.txtSubLen.text())
1 / SubLen
except:
msgBox.setText("Length of subjects must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of subjects is okay!")
try:
ConRange = strMultiRange(ui.txtConRange.text(), SubSize)
if ConRange is None:
raise Exception
if not (len(ConRange) == SubSize):
msgBox.setText("Counter Size must be equal to Subject Size!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
except:
msgBox.setText("Counter Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Counter Range is okay!")
try:
ConLen = np.int32(ui.txtConLen.text())
1 / ConLen
except:
msgBox.setText("Length of counter must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of Counter is okay!")
try:
RunRange = strMultiRange(ui.txtRunRange.text(), SubSize)
if RunRange is None:
raise Exception
if not (len(RunRange) == SubSize):
msgBox.setText("Run Size must be equal to Subject Size!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
except:
msgBox.setText("Run Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Run Range is okay!")
try:
RunLen = np.int32(ui.txtRunLen.value())
1 / RunLen
except:
msgBox.setText("Length of runs must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of runs is valid")
if Input == "":
msgBox = QMessageBox()
msgBox.setText("There is no input structure")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if Output == "":
msgBox = QMessageBox()
msgBox.setText("There is no output structure")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if Task == "":
msgBox = QMessageBox()
msgBox.setText("There is no Task name")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if DIR == "":
msgBox = QMessageBox()
msgBox.setText("Please select the main directory")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not os.path.isdir(DIR):
msgBox = QMessageBox()
msgBox.setText("Cannot find the main directory")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
for si, s in enumerate(SubRange):
for c in ConRange[si]:
for r in RunRange[si]:
InAdd = setParameters3(Input,DIR, fixstr(s,SubLen,SubPer),\
fixstr(r,RunLen,RunPer),Task,\
fixstr(c,ConLen,ConPer))
OutAdd = setParameters3(Output,DIR,fixstr(s,SubLen,SubPer),\
fixstr(r,RunLen,RunPer),Task,\
fixstr(c,ConLen,ConPer))
try:
if not os.path.isfile(InAdd):
print(InAdd + " - not found!")
else:
print("MOVE: " + InAdd + " - running ...")
os.rename(InAdd, OutAdd)
print("TO: " + OutAdd + " - DONE!")
except Exception as e:
print(e)
def btnConvert_click(self):
msgBox = QMessageBox()
# OutFile
OutFile = ui.txtOutFile.text()
if not len(OutFile):
msgBox.setText("Please enter out file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
ThresholdType = ui.cbThType.currentData()
MinTh = None
MaxTh = None
if (ThresholdType == "min") or (ThresholdType == "ext"):
try:
MinTh = np.double(ui.txtThMin.text())
except:
msgBox.setText("Min Threshold must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Min Threshold is valid")
if (ThresholdType == "max") or (ThresholdType == "ext"):
try:
MaxTh = np.double(ui.txtThMax.text())
except:
msgBox.setText("Max Threshold must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Max Threshold is valid")
# OutFile
AFNI = ui.txtAFNI.text()
if not len(AFNI):
AFNI = None
else:
CopyFile = ui.txtFAFNI.text()
if not len(CopyFile):
msgBox.setText("Please select 3dcopy command!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not os.path.isfile(CopyFile):
msgBox.setText("Please select 3dcopy command!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
RefitFile = ui.txtFSUMA.text()
if not len(RefitFile):
msgBox.setText("Please select 3drefit command!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not os.path.isfile(RefitFile):
msgBox.setText("Please select 3drefit command!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
# InFile
InFile = ui.txtInFile.text()
if not len(InFile):
msgBox.setText("Please enter input file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not os.path.isfile(InFile):
msgBox.setText("Input file not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not len(ui.txtMatrix.currentText()):
msgBox.setText("Matrix name not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not len(ui.txtCoord.currentText()):
msgBox.setText("Coordinate name not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not len(ui.txtTime.text()):
msgBox.setText("Time points not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
AffineFile = ui.txtSSSpace.currentText()
if not len(AffineFile):
msgBox.setText("Please enter affine reference!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not os.path.isfile(AffineFile):
msgBox.setText("Affine reference not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
AffineHDR = nb.load(AffineFile)
Affine = AffineHDR.affine
Time = strRange(ui.txtTime.text())
if Time is None:
msgBox.setText("Time points is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
try:
InData = mainIO_load(InFile)
Mat = InData[ui.txtMatrix.currentText()]
Coord = InData[ui.txtCoord.currentText()]
imgShape = InData["imgShape"][0]
except:
print("Cannot load data!")
msgBox.setText("Cannot load data!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
ImgData = None
# Filter Mat
for t in Time:
vox = Mat[t, :]
if ui.cbScale.isChecked():
vox = preprocessing.scale(vox)
print("Time Point: " + str(t) + " is normalized.")
if MinTh is not None:
vox[np.where(vox < MinTh)] = 0
print("Time Point: " + str(t) +
", Lower band thresholding is done!")
if MaxTh is not None:
vox[np.where(vox > MaxTh)] = 0
print("Time Point: " + str(t) +
", Upper band thresholding is done!")
img = np.zeros([imgShape[0], imgShape[1], imgShape[2], 1])
for coIndx, _ in enumerate(Coord[0]):
img[Coord[0][coIndx], Coord[1][coIndx], Coord[2][coIndx],
0] = vox[coIndx]
ImgData = img if ImgData is None else np.concatenate(
(ImgData, img), axis=3)
print("Time point: " + str(t) + " is done.")
print("Saving image ...")
NIF = nb.Nifti1Image(ImgData, Affine)
nb.save(NIF, OutFile)
if AFNI is not None:
cmd = CopyFile + " " + OutFile + " " + AFNI
print("Running: " + cmd)
os.system(cmd)
cmd = RefitFile + " -view tlrc -space MNI " + AFNI + " " + AFNI + "+tlrc."
print("Running: " + cmd)
os.system(cmd)
print("DONE!")
msgBox.setText("Image file is generated.")
msgBox.setIcon(QMessageBox.Information)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
def Run(self,
SettingFileName,
isOne=False,
Remove=True,
feat=None,
SubID=None,
RunID=None,
ConID=None):
import numpy as np
import os, subprocess
from Base.utility import fixstr, setParameters3, strRange, strMultiRange
from Base.Setting import Setting
if (feat == None) or (os.path.isfile(feat) == False):
print("Cannot find feat cmd!")
return False, None
Jobs = list()
setting = Setting()
setting.Load(SettingFileName)
if setting.empty:
print("Error in loading the setting file!")
return False, None
else:
if isOne:
Subjects = [SubID]
Counters = [[ConID]]
Runs = [[RunID]]
else:
Subjects = strRange(setting.SubRange, Unique=True)
if Subjects is None:
print("Cannot load Subject Range!")
return False, None
SubSize = len(Subjects)
Counters = strMultiRange(setting.ConRange, SubSize)
if Counters is None:
print("Cannot load Counter Range!")
return False, None
Runs = strMultiRange(setting.RunRange, SubSize)
if Runs is None:
print("Cannot load Run Range!")
return False, None
for si, s in enumerate(Subjects):
for cnt in Counters[si]:
print("Run script for Subject %d ..." % (s))
for r in Runs[si]:
ScriptAddr = setParameters3(setting.Script,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer), \
fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \
fixstr(cnt, setting.ConLen, setting.ConPer))
ScriptTitle = setParameters3(setting.Script, "", fixstr(s, setting.SubLen, setting.SubPer), \
fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \
fixstr(cnt, setting.ConLen, setting.ConPer))
ScriptOutputAddr = setParameters3(setting.Analysis, setting.mainDIR,
fixstr(s, setting.SubLen, setting.SubPer), \
fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \
fixstr(cnt, setting.ConLen, setting.ConPer)) + ".feat"
files = [ScriptOutputAddr + "/filtered_func_data.nii.gz", ScriptOutputAddr + \
"/mask.nii.gz", ScriptOutputAddr + "/cluster_mask_zstat1.nii.gz"]
cmd = ScriptAddr
report = ScriptOutputAddr + "/report_log.html"
thread = PreprocessThread(feat=feat, cmd=cmd, report=report, files=files, \
remove=Remove, removefile=ScriptOutputAddr)
Jobs.append(["Preprocess", ScriptTitle, thread])
print("Job for " + ScriptAddr + " - is created!")
return True, Jobs
def btnLoadEvent_click(self):
global ui, dialog
msgBox = QMessageBox()
mainDIR = ui.txtSSDIR.text()
Task = ui.txtSSTask.text()
# Check Directory
if not len(mainDIR):
msgBox.setText("There is no main directory")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if not os.path.isdir(mainDIR):
msgBox.setText("Main directory doesn't exist")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Main directory is okay.")
if not len(Task):
msgBox.setText("There is no task title")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
SubRange = strRange(ui.txtSSSubRange.text(),Unique=True)
if SubRange is None:
raise Exception
SubSize = len(SubRange)
except:
msgBox.setText("Subject Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Range of subjects is okay!")
try:
SubLen = np.int32(ui.txtSSSubLen.text())
1 / SubLen
except:
msgBox.setText("Length of subjects must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of subjects is okay!")
try:
ConRange = strMultiRange(ui.txtSSConRange.text(),SubSize)
if ConRange is None:
raise Exception
if not (len(ConRange) == SubSize):
msgBox.setText("Counter Size must be equal to Subject Size!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
except:
msgBox.setText("Counter Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Counter Range is okay!")
try:
ConLen = np.int32(ui.txtSSConLen.text())
1 / ConLen
except:
msgBox.setText("Length of counter must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of Counter is okay!")
try:
RunRange = strMultiRange(ui.txtSSRunRange.text(),SubSize)
if RunRange is None:
raise Exception
if not (len(RunRange) == SubSize):
msgBox.setText("Run Size must be equal to Subject Size!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
except:
msgBox.setText("Run Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Run Range is okay!")
try:
RunLen = np.int32(ui.txtSSRunLen.value())
1 / RunLen
except:
msgBox.setText("Length of runs must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of runs is valid")
if ui.txtEventDIR.text() == "":
msgBox.setText("Structure of the event folders is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if ui.txtCondPre.text() == "":
msgBox.setText("The prefix of condition files is empty!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
setting = Setting()
setting.mainDIR = mainDIR
setting.Task = Task
setting.SubRange= ui.txtSSSubRange.text()
setting.SubLen = np.int32(SubLen)
setting.SubPer = ui.txtSSSubPer.text()
setting.ConRange= ui.txtSSConRange.text()
setting.ConLen = np.int32(ConLen)
setting.ConPer = ui.txtSSConPer.text()
setting.RunRange= ui.txtSSRunRange.text()
setting.RunLen = np.int32(RunLen)
setting.RunPer = ui.txtSSRunPer.text()
sSess = frmSelectSession(None, setting=setting)
if not sSess.PASS:
return
EventFolder = setParameters3(ui.txtEventDIR.text(), mainDIR, fixstr(int(sSess.SubID), setting.SubLen, setting.SubPer), \
fixstr(int(sSess.RunID), int(setting.RunLen), setting.RunPer), setting.Task, \
fixstr(sSess.ConID, int(setting.ConLen), setting.ConPer))
CondFile = EventFolder + ui.txtCondPre.text() + ".mat"
if not os.path.isfile(CondFile):
print("Cannot find condition mat file!")
return
try:
conditions = io.loadmat(CondFile)
except:
print("Cannot load condition mat file!")
return
NumCond = len(conditions["Cond"])
ui.txtSSCondFrom.setValue(1)
ui.txtSSCondTo.setValue(NumCond)
ui.txtSSCondLen.setValue(len(str(NumCond)))
ui.txtSSCondPer.setText("")
def btnRUN_click(self):
global ui
msgBox = QMessageBox()
mainDIR = ui.txtSSDIR.text()
Task = ui.txtSSTask.text()
# Check Directory
if not len(mainDIR):
msgBox.setText("There is no main directory")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if not os.path.isdir(mainDIR):
msgBox.setText("Main directory doesn't exist")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Main directory is okay.")
if not len(Task):
msgBox.setText("There is no task title")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
SubRange = strRange(ui.txtSSSubRange.text(),Unique=True)
if SubRange is None:
raise Exception
SubSize = len(SubRange)
except:
msgBox.setText("Subject Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Range of subjects is okay!")
try:
SubLen = np.int32(ui.txtSSSubLen.text())
1 / SubLen
except:
msgBox.setText("Length of subjects must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of subjects is okay!")
try:
ConRange = strMultiRange(ui.txtSSConRange.text(),SubSize)
if ConRange is None:
raise Exception
if not (len(ConRange) == SubSize):
msgBox.setText("Counter Size must be equal to Subject Size!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
except:
msgBox.setText("Counter Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Counter Range is okay!")
try:
ConLen = np.int32(ui.txtSSConLen.text())
1 / ConLen
except:
msgBox.setText("Length of counter must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of Counter is okay!")
try:
RunRange = strMultiRange(ui.txtSSRunRange.text(),SubSize)
if RunRange is None:
raise Exception
if not (len(RunRange) == SubSize):
msgBox.setText("Run Size must be equal to Subject Size!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
except:
msgBox.setText("Run Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Run Range is okay!")
try:
RunLen = np.int32(ui.txtSSRunLen.value())
1 / RunLen
except:
msgBox.setText("Length of runs must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of runs is valid")
try:
CondFrom = np.int32(ui.txtSSCondFrom.value())
1 / CondFrom
except:
msgBox.setText("Condition From must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
CondTo = np.int32(ui.txtSSCondTo.value())
1 / CondTo
except:
msgBox.setText("Condition To must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if CondTo < CondFrom:
msgBox.setText("Condition To is smaller then Subject From!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Counter is valid")
try:
CondLen = np.int32(ui.txtSSCondLen.text())
1 / CondLen
except:
msgBox.setText("Length of condition must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of condition is valid")
Space = ui.txtSSSpace.currentText()
if not len(Space):
msgBox.setText("Please enter a affine file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if not Space == DefaultSpace():
if not os.path.isfile(Space):
msgBox = QMessageBox()
msgBox.setText("Affine file not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
print("Affine file is okay.")
In = ui.txtSSInFile.currentText()
if not len(In):
msgBox.setText("Please enter input file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
Out = ui.txtOutROI.text()
if not len(Out):
msgBox.setText("Please enter output file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
ThresholdType = ui.cbThType.currentData()
if (ThresholdType == "min") or (ThresholdType == "ext"):
try:
MinTh = np.double(ui.txtThMin.text())
except:
msgBox.setText("Min Threshold must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Min Threshold is valid")
if (ThresholdType == "max") or (ThresholdType == "ext"):
try:
MaxTh = np.double(ui.txtThMax.text())
except:
msgBox.setText("Max Threshold must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Max Threshold is valid")
print("Checking files ...")
for si, s in enumerate(SubRange):
for cnt in ConRange[si]:
print("Analyzing Subject %d, Counter %d ..." % (s,cnt))
# SubDIR = setting.mainDIR + "/" + "sub-" + fixstr(s, SubLen, setting.SubPer)
for r in RunRange[si]:
for cnd in range(CondFrom, CondTo + 1):
InFile = setParameters3(In, mainDIR, fixstr(s, SubLen, ui.txtSSSubPer.text()),\
fixstr(r, RunLen, ui.txtSSRunPer.text()), ui.txtSSTask.text(),\
fixstr(cnt, ConLen, ui.txtSSConPer.text()), fixstr(cnd, CondLen, ui.txtSSCondPer.text()))
if os.path.isfile(InFile):
print(InFile + " - is OKAY.")
else:
print(InFile + " - not found!")
return
if ui.cbMetric.currentData() == "inter":
print("Calculating ROI ...")
ROIData = None
for si, s in enumerate(SubRange):
for cnt in ConRange[si]:
print("Analyzing Subject %d, Counter %d ..." % (s,cnt))
for r in RunRange[si]:
for cnd in range(CondFrom, CondTo + 1):
InFile = setParameters3(In, mainDIR, fixstr(s, SubLen, ui.txtSSSubPer.text()), \
fixstr(r, RunLen, ui.txtSSRunPer.text()), ui.txtSSTask.text(), \
fixstr(cnt, ConLen, ui.txtSSConPer.text()),
fixstr(cnd, CondLen, ui.txtSSCondPer.text()))
MaskHDR = nb.load(InFile)
MaskData = MaskHDR.get_data()
if ThresholdType == "no":
MaskData[np.where(MaskData != 0)] = 1
elif ThresholdType == "min":
MaskData[np.where(MaskData < MinTh)] = 0
MaskData[np.where(MaskData != 0)] = 1
elif ThresholdType == "max":
MaskData[np.where(MaskData > MaxTh)] = 0
MaskData[np.where(MaskData != 0)] = 1
elif ThresholdType == "ext":
MaskData[np.where(MaskData > MaxTh)] = 0
MaskData[np.where(MaskData < MinTh)] = 0
MaskData[np.where(MaskData != 0)] = 1
if ROIData is None:
if Space == DefaultSpace():
affineHDR = nb.load(InFile)
else:
affineHDR = nb.load(Space)
ROIData = MaskData.copy()
else:
if not np.shape(ROIData) == np.shape(MaskData):
print("All mask must include the same size data (tensor)")
return
else:
ROIData = ROIData + MaskData
ROIData[np.where(ROIData != 0)] = 1
print(InFile + " - is calculated!")
NumVoxels = np.shape(ROIData)
NumVoxels = NumVoxels[0] * NumVoxels[1] * NumVoxels[2]
print("Number of all voxels: %d " % NumVoxels)
NumROIVoxel = len(ROIData[np.where(ROIData != 0)])
print("Number of selected voxles in ROI: %d" % NumROIVoxel)
ROIHDR = nb.Nifti1Image(ROIData, affineHDR.affine)
nb.save(ROIHDR,Out)
print("ROI is generated!")
msgBox.setText("ROI is generated!\nNumber of all voxels: " + str(NumVoxels) + \
"\nNumber of selected voxles in ROI: " + str(NumROIVoxel))
msgBox.setIcon(QMessageBox.Information)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
def btnRun_onclick(self):
from Base.utility import strRange, strMultiRange
global ui
msgBox = QMessageBox()
SubPer = ui.txtSubPer.text()
RunPer = ui.txtRunPer.text()
ConPer = ui.txtConPer.text()
Input = ui.txtInput.text()
Output = ui.txtOutput.text()
Task = ui.txtTask.text()
DIR = ui.txtDIR.text()
Script = ui.txtScript.text()
try:
SubRange = strRange(ui.txtSubRange.text(), Unique=True)
if SubRange is None:
raise Exception
SubSize = len(SubRange)
except:
msgBox.setText("Subject Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Range of subjects is okay!")
try:
SubLen = np.int32(ui.txtSubLen.text())
1 / SubLen
except:
msgBox.setText("Length of subjects must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of subjects is okay!")
try:
ConRange = strMultiRange(ui.txtConRange.text(), SubSize)
if ConRange is None:
raise Exception
if not (len(ConRange) == SubSize):
msgBox.setText("Counter Size must be equal to Subject Size!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
except:
msgBox.setText("Counter Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Counter Range is okay!")
try:
ConLen = np.int32(ui.txtConLen.text())
1 / ConLen
except:
msgBox.setText("Length of counter must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of Counter is okay!")
try:
RunRange = strMultiRange(ui.txtRunRange.text(), SubSize)
if RunRange is None:
raise Exception
if not (len(RunRange) == SubSize):
msgBox.setText("Run Size must be equal to Subject Size!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
except:
msgBox.setText("Run Range is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Run Range is okay!")
try:
RunLen = np.int32(ui.txtRunLen.value())
1 / RunLen
except:
msgBox.setText("Length of runs must be an integer number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Length of runs is valid")
if Input == "":
msgBox = QMessageBox()
msgBox.setText("There is no input structure")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if Task == "":
msgBox = QMessageBox()
msgBox.setText("There is no Task name")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if DIR == "":
msgBox = QMessageBox()
msgBox.setText("Please select the main directory")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if Script == "":
msgBox = QMessageBox()
msgBox.setText("Script structure is not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not os.path.isdir(DIR):
msgBox = QMessageBox()
msgBox.setText("Cannot find the main directory")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
RepCount = 0
for si, s in enumerate(SubRange):
for c in ConRange[si]:
for r in RunRange[si]:
SFile = setParameters3(Script, DIR, fixstr(s,SubLen,SubPer),\
fixstr(r,RunLen,RunPer),Task,\
fixstr(c,ConLen,ConPer))
if ui.cbInDynamic.isChecked():
InValue = setParameters3(Input,DIR, fixstr(s,SubLen,SubPer),\
fixstr(r,RunLen,RunPer),Task,\
fixstr(c,ConLen,ConPer))
else:
InValue = Input
if ui.cbOutDynamic.isChecked():
OutValue = setParameters3(Output,DIR, fixstr(s,SubLen,SubPer),\
fixstr(r,RunLen,RunPer),Task,\
fixstr(c,ConLen,ConPer))
else:
OutValue = Output
CountCurrRep = RepCount
print("SCRIPT: " + SFile)
print("Replacing " + InValue + " to " + OutValue + "...")
try:
if not os.path.isfile(SFile):
print(SFile + " - not found!")
else:
scriptFile = open(SFile, "r")
scriptContent = scriptFile.read()
scriptFile.close()
while scriptContent.find(InValue) != -1:
scriptContent = scriptContent.replace(
InValue, OutValue, 1)
RepCount = RepCount + 1
except Exception as e:
print(e)
CountCurrRep = RepCount - CountCurrRep
if not ui.cbDEMO.isChecked():
scriptFile = open(SFile, "w")
scriptFile.write(scriptContent)
scriptFile.close()
print(str(CountCurrRep) + " is replaced!")
else:
print("DEMO: " + str(CountCurrRep) + " is found!")
if ui.cbDEMO.isChecked():
msgBox.setText(str(RepCount) + " items are found!")
else:
msgBox.setText(str(RepCount) + " items are replaced!")
msgBox.setIcon(QMessageBox.Information)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
pass
def btnConvert_click(self):
msgBox = QMessageBox()
tStart = time.time()
Activation = ui.cbActivation.currentData()
LossNorm = ui.cbLossNorm.currentData()
try:
Layers = strRange(ui.txtLayers.text(), Unique=False)
if Layers is None:
raise Exception('')
except:
msgBox.setText("Layers is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
KIter = np.int32(ui.txtKIter.text())
except:
msgBox.setText("Number of iteration is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
RIter = np.int32(ui.txtRIter.text())
except:
msgBox.setText("Number of iteration is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
BatchSize = np.int32(ui.txtBatch.text())
except:
msgBox.setText("Number of batch is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
ReportStep = np.int32(ui.txtReportStep.text())
except:
msgBox.setText("Number of Report Step is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
LearningRate = np.float32(ui.txtRate.text())
except:
msgBox.setText("Number of Report Step is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if not ui.cbCov.isChecked() and not ui.cbCorr.isChecked():
msgBox.setText("At least, you must select one metric!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Filter
try:
Filter = ui.txtFilter.text()
if not len(Filter):
Filter = None
else:
Filter = Filter.replace("\'", " ").replace(",", " ").replace(
"[", "").replace("]", "").split()
Filter = np.int32(Filter)
except:
print("Filter is wrong!")
return
# OutFile
OutFile = ui.txtOutFile.text()
if not len(OutFile):
msgBox.setText("Please enter out file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
OutData = dict()
# InFile
InFile = ui.txtInFile.text()
if not len(InFile):
msgBox.setText("Please enter input file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if not os.path.isfile(InFile):
msgBox.setText("Input file not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Loading ...")
InData = io.loadmat(InFile)
# Data
if not len(ui.txtData.currentText()):
msgBox.setText("Please enter Input Data variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Label
if not len(ui.txtLabel.currentText()):
msgBox.setText("Please enter Train Label variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Design
if not len(ui.txtDesign.currentText()):
msgBox.setText("Please enter Input Design variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
Design = InData[ui.txtDesign.currentText()]
except:
msgBox.setText("Design value is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
X = InData[ui.txtData.currentText()]
L = InData[ui.txtLabel.currentText()][0]
if ui.cbScale.isChecked() and not ui.rbScale.isChecked():
X = preprocessing.scale(X)
print("Whole of data is scaled X~N(0,1).")
except:
print("Cannot load data or label")
return
# Task
if not len(ui.txtTask.currentText()):
msgBox.setText("Please enter Task variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
TaskTitle = InData[ui.txtTask.currentText()][0]
except:
msgBox.setText("Task variable name is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
TaskTitleUnique = np.unique(TaskTitle)
Task = np.zeros(np.shape(TaskTitle))
for ttinx, tt in enumerate(TaskTitle):
for ttlinx, ttl in enumerate(TaskTitleUnique):
if tt[0] == ttl:
Task[ttinx] = ttlinx + 1
break
# Subject
if not len(ui.txtSubject.currentText()):
msgBox.setText("Please enter Subject variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
Sub = InData[ui.txtSubject.currentText()][0]
except:
msgBox.setText("Subject variable name is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Run
if not len(ui.txtRun.currentText()):
msgBox.setText("Please enter Run variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
Run = InData[ui.txtRun.currentText()][0]
except:
msgBox.setText("Run variable name is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Counter
if not len(ui.txtCounter.currentText()):
msgBox.setText("Please enter Counter variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
try:
Con = InData[ui.txtCounter.currentText()][0]
except:
msgBox.setText("Counter variable name is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if Filter is not None:
for fil in Filter:
# Remove Training Set
labelIndx = np.where(L == fil)[0]
Design = np.delete(Design, labelIndx, axis=0)
X = np.delete(X, labelIndx, axis=0)
L = np.delete(L, labelIndx, axis=0)
Task = np.delete(Task, labelIndx, axis=0)
Sub = np.delete(Sub, labelIndx, axis=0)
Run = np.delete(Run, labelIndx, axis=0)
Con = np.delete(Con, labelIndx, axis=0)
print("Class ID = " + str(fil) + " is removed from data.")
try:
Unit = np.int32(ui.txtUnit.text())
except:
msgBox.setText("Unit for the test set must be a number!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if Unit < 1:
msgBox.setText("Unit for the test set must be greater than zero!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Calculating Levels ...")
GroupFold = None
FoldStr = ""
if ui.cbFSubject.isChecked():
if not ui.rbFRun.isChecked():
GroupFold = [Sub]
FoldStr = "Subject"
else:
GroupFold = np.concatenate(([Sub], [Run]))
FoldStr = "Subject+Run"
if ui.cbFTask.isChecked():
GroupFold = np.concatenate(
(GroupFold, [Task])) if GroupFold is not None else [Task]
FoldStr = FoldStr + "+Task"
if ui.cbFCounter.isChecked():
GroupFold = np.concatenate(
(GroupFold, [Con])) if GroupFold is not None else [Con]
FoldStr = FoldStr + "+Counter"
if FoldStr == "":
FoldStr = "Whole-Data"
GUFold = [1]
ListFold = [1]
UniqFold = [1]
GroupFold = [1]
UnitFold = np.ones((1, np.shape(X)[0]))
else:
GroupFold = np.transpose(GroupFold)
UniqFold = np.array(list(set(tuple(i)
for i in GroupFold.tolist())))
FoldIDs = np.arange(len(UniqFold)) + 1
if len(UniqFold) <= Unit:
msgBox.setText(
"Unit must be smaller than all possible levels! Number of all levels is: "
+ str(len(UniqFold)))
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if np.mod(len(UniqFold), Unit):
msgBox.setText(
"Unit must be divorceable to all possible levels! Number of all levels is: "
+ str(len(UniqFold)))
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
ListFold = list()
for gfold in GroupFold:
for ufoldindx, ufold in enumerate(UniqFold):
if (ufold == gfold).all():
currentID = FoldIDs[ufoldindx]
break
ListFold.append(currentID)
ListFold = np.int32(ListFold)
if Unit == 1:
UnitFold = np.int32(ListFold)
else:
UnitFold = np.int32((ListFold - 0.1) / Unit) + 1
GUFold = np.unique(UnitFold)
FoldInfo = dict()
FoldInfo["Unit"] = Unit
FoldInfo["Group"] = GroupFold
FoldInfo["Order"] = FoldStr
FoldInfo["List"] = ListFold
FoldInfo["Unique"] = UniqFold
FoldInfo["Folds"] = UnitFold
OutData["FoldInfo"] = FoldInfo
OutData["ModelAnalysis"] = "Tensorflow.Group.Single-Deep-Kernel.RSA"
print("Number of all levels is: " + str(len(UniqFold)))
# RSA Method
OutData['Method'] = dict()
OutData['Method']['Layers'] = ui.txtLayers.text()
OutData['Method']['Activation'] = Activation
OutData['Method']['LossNorm'] = LossNorm
OutData['Method']['LearningRate'] = LearningRate
OutData['Method']['KernelIter'] = KIter
OutData['Method']['RSAIter'] = RIter
OutData['Method']['BatchSize'] = BatchSize
OutData['Method']['ReportStep'] = ReportStep
OutData['Method']['Verbose'] = ui.cbVerbose.isChecked()
TData = list()
TReg = list()
print("Reshaping Data ...")
for foldID, fold in enumerate(GUFold):
print("Reshaping level " + str(foldID + 1), " of ",
str(len(UniqFold)), " ...")
Index = np.where(UnitFold == fold)
# Whole-Data
if FoldStr == "Whole-Data" and np.shape(Index)[0]:
Index = [Index[1]]
XLi = X[Index]
RegLi = Design[Index]
if ui.cbScale.isChecked() and ui.rbScale.isChecked():
XLi = preprocessing.scale(XLi)
print("Whole of data is scaled X%d~N(0,1)." % (foldID + 1))
TData.append(XLi)
TReg.append(RegLi)
print("Running Deep Group RSA ...")
rsa = DeepGroupRSA(layers=Layers, kernel_iter = KIter, rsa_iter = RIter, learning_rate=LearningRate,
loss_norm=LossNorm, activation=Activation, \
batch_size=BatchSize, report_step=ReportStep, verbose=ui.cbVerbose.isChecked(), \
NCat=np.shape(Design)[1], NVoxel=np.shape(X)[1], CPU=ui.cbDevice.currentData())
Betas, Eps, Weights, Bias, MSE, loss_mat = rsa.fit(data_vals=TData,
design_vals=TReg)
OutData["Weight"] = Weights
OutData["Bias"] = Bias
OutData["Perfromance"] = MSE
OutData["Perfromance_Average"] = rsa.AMSE
OutData["Perfromance_std"] = np.std(rsa.AMSE)
OutData["LossMat"] = loss_mat
print("Average Performance: %f" % (OutData["Perfromance"]))
print("Calculating cov & corr ... ")
AvgCov = None
AvgCorr = None
for beta_id, beta in enumerate(Betas):
OutData["BetaL" + str(beta_id)] = beta
if ui.cbCov.isChecked():
co = np.cov(beta)
OutData["Cov" + str(beta_id)] = co
AvgCov = co if AvgCov is None else AvgCov + co
if ui.cbCorr.isChecked():
cr = np.corrcoef(beta)
OutData["Corr" + str(beta_id)] = cr
AvgCorr = cr if AvgCorr is None else AvgCorr + cr
for eps_id, ep in enumerate(Eps):
OutData["EpsL" + str(eps_id)] = ep
if ui.cbCov.isChecked():
AvgCov = AvgCov / len(TData)
covClass = SimilarityMatrixBetweenClass(AvgCov)
OutData["Covariance"] = AvgCov
OutData["Covariance_min"] = covClass.min()
OutData["Covariance_max"] = covClass.max()
OutData["Covariance_mean"] = covClass.mean()
OutData["Covariance_std"] = covClass.std()
if ui.cbCorr.isChecked():
AvgCorr = AvgCorr / len(TData)
corClass = SimilarityMatrixBetweenClass(AvgCorr)
OutData["Correlation"] = AvgCorr
OutData["Correlation_min"] = corClass.min()
OutData["Correlation_max"] = corClass.max()
OutData["Correlation_mean"] = corClass.mean()
OutData["Correlation_std"] = corClass.std()
OutData["RunTime"] = time.time() - tStart
print("Runtime (s): %f" % (OutData["RunTime"]))
print("Saving results ...")
io.savemat(OutFile, mdict=OutData, do_compression=True)
print("Output is saved.")
if ui.cbDiagram.isChecked():
if ui.cbCorr.isChecked():
fig1 = plt.figure(num=None, figsize=(5, 5), dpi=100)
plt.pcolor(AvgCorr, vmin=-0.1, vmax=1)
plt.xlim([0, np.shape(AvgCorr)[0]])
plt.ylim([0, np.shape(AvgCorr)[0]])
plt.colorbar()
ax = plt.gca()
ax.set_aspect(1)
plt.title('Deep Group RSA: Correlation\nLevel: ' + FoldStr)
plt.show()
if ui.cbCov.isChecked():
fig2 = plt.figure(num=None, figsize=(5, 5), dpi=100)
plt.pcolor(AvgCov)
plt.xlim([0, np.shape(AvgCov)[0]])
plt.ylim([0, np.shape(AvgCov)[0]])
plt.colorbar()
ax = plt.gca()
ax.set_aspect(1)
plt.title('Deep Group RSA: Covariance\nLevel: ' + FoldStr)
plt.show()
print("DONE.")
msgBox.setText(
"Group Level Single-Deep-Kernel Representational Similarity Analysis is done."
)
msgBox.setIcon(QMessageBox.Information)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
