def btnSSSettingReload_click(self):
global ui
filename = ui.txtSSSetting.currentText()
if os.path.isfile(filename):
if len(filename):
setting = Setting()
setting.Load(filename)
if np.double(setting.Version) < np.double(getSettingVersion()):
print("WARNING: You are using different version of Easy fMRI!!!")
msgBox = QMessageBox()
msgBox.setText("This version of setting is not supported!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not setting.empty:
ui.txtSSSetting.setCurrentText(filename)
ui.txtSSDIR.setText(setting.mainDIR)
ui.txtSSTask.setText(setting.Task)
ui.txtSSSubLen.setValue(setting.SubLen)
ui.txtSSSubPer.setText(setting.SubPer)
ui.txtSSConLen.setValue(setting.ConLen)
ui.txtSSConPer.setText(setting.ConPer)
ui.txtSSRunPer.setText(setting.RunPer)
ui.txtSSRunLen.setValue(setting.RunLen)
ui.txtSSSubRange.setText(setting.SubRange)
ui.txtSSConRange.setText(setting.ConRange)
ui.txtSSRunRange.setText(setting.RunRange)
ui.txtEventDIR.setText(setting.EventFolder)
ui.txtCondPre.setText(setting.CondPre)
else:
print("Setting file not found!")
def btnSSSetting_click(self):
global ui
if os.path.isfile(ui.txtSSSetting.currentText()):
currDir = os.path.dirname(ui.txtSSSetting.currentText())
else:
currDir = ""
filename = LoadFile("Open setting file ...",
['easy fMRI setting (*.ez)'], 'ez', currDir)
if len(filename):
if not os.path.isfile(filename):
msgBox = QMessageBox()
msgBox.setText("Setting file not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
setting = Setting()
setting.Load(filename)
if np.double(setting.Version) < np.double(getSettingVersion()):
print(
"WARNING: You are using different version of Easy fMRI!!!")
msgBox = QMessageBox()
msgBox.setText("This version of setting is not supported!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not setting.empty:
ui.txtSSSetting.setCurrentText(filename)
ui.txtSSDIR.setText(setting.mainDIR)
ui.txtSSTask.setText(setting.Task)
ui.txtSSSubRange.setText(setting.SubRange)
ui.txtSSSubLen.setValue(setting.SubLen)
ui.txtSSSubPer.setText(setting.SubPer)
ui.txtSSConRange.setText(setting.ConRange)
ui.txtSSConLen.setValue(setting.ConLen)
ui.txtSSConPer.setText(setting.ConPer)
ui.txtSSRunRange.setText(setting.RunRange)
ui.txtSSRunPer.setText(setting.RunPer)
ui.txtSSRunLen.setValue(setting.RunLen)
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 checkGUI(self, ui, SettingFileName, checkGeneratedFiles=False):
# init Empty
self.Version = getSettingVersion()
self.Mode = None
self.mainDIR = None
self.MNISpace = None
self.Task = None
self.SubRange = None
self.SubLen = None
self.SubPer = None
self.ConRange = None
self.ConLen = None
self.ConPer = None
self.RunRange = None
self.RunLen = None
self.RunPer = None
self.Onset = None
self.BOLD = None
self.AnatDIR = None
self.EventFolder = None
self.CondPre = None
self.BET = None
self.BETPDF = None
self.Analysis = None
self.Script = None
self.TR = None
self.FWHM = None
self.TotalVol = 0
self.DeleteVol = 0
self.Motion = True
self.Anat = True
self.HighPass = None
self.DENL = None
self.DETS = None
self.DEZT = None
self.CTZT = None
self.CTPT = None
self.TimeSlice = None
self.EventCodes = None
self.empty = True
self.checkValue(ui, checkGeneratedFiles=checkGeneratedFiles)
if self.empty:
print("Error in GUI parameters")
return None
else:
if not len(SettingFileName):
print("Cannot find setting file")
return None
else:
try:
config = cp.ConfigParser()
config.read(SettingFileName)
if self.mainDIR != config['DEFAULT']['maindir']:
return True
if self.Mode != np.int32(config['DEFAULT']['mode']):
return True
if self.MNISpace != config['DEFAULT']['mni_space']:
return True
elif self.Task != config['DEFAULT']['task']:
return True
elif self.SubRange != config['DEFAULT']['sub_range']:
return True
elif np.double(self.SubLen) != np.double(
config['DEFAULT']['sub_len']):
return True
elif self.SubPer != config['DEFAULT']['sub_perfix']:
return True
elif self.ConRange != config['DEFAULT']['con_range']:
return True
elif np.double(self.ConLen) != np.double(
config['DEFAULT']['con_len']):
return True
elif self.ConPer != config['DEFAULT']['con_perfix']:
return True
elif self.RunRange != config['DEFAULT']['run_range']:
return True
elif np.double(self.RunLen) != np.double(
config['DEFAULT']['run_len']):
return True
elif self.RunPer != config['DEFAULT']['run_perfix']:
return True
elif self.BOLD != config['DEFAULT']['bold']:
return True
elif self.Onset != config['DEFAULT']['onset']:
return True
elif self.AnatDIR != config['DEFAULT']['anat_dir']:
return True
elif self.BET != config['DEFAULT']['bet']:
return True
elif self.BETPDF != config['DEFAULT']['bet_pdf']:
return True
elif self.Analysis != config['DEFAULT']['analysis']:
return True
elif self.Script != config['DEFAULT']['script']:
return True
elif self.EventFolder != config['DEFAULT']['event_dir']:
return True
elif self.CondPre != config['DEFAULT']['cond_per']:
return True
elif self.EventCodes != decoding(
config['CODE']['event_code']):
return True
elif np.double(self.TR) != np.double(
config['DEFAULT']['TR']):
return True
elif np.double(self.FWHM) != np.double(
config['DEFAULT']['FWHM']):
return True
elif np.double(self.DeleteVol) != np.double(
config['DEFAULT']['deletevol']):
return True
elif np.double(self.TotalVol) != np.double(
config['DEFAULT']['totalvol']):
return True
elif self.Motion != Str2Bool(config['DEFAULT']['motion']):
return True
elif self.Anat != Str2Bool(config['DEFAULT']['anat']):
return True
elif self.HighPass != np.double(
config['DEFAULT']['highpass']):
return True
elif self.DENL != np.double(config['DEFAULT']['denl']):
return True
elif self.DETS != np.double(config['DEFAULT']['dets']):
return True
elif self.DEZT != np.double(config['DEFAULT']['dezt']):
return True
elif self.CTZT != np.double(config['DEFAULT']['ctzt']):
return True
elif self.CTPT != np.double(config['DEFAULT']['ctpt']):
return True
elif self.TimeSlice != np.int32(
config['DEFAULT']['timeslice']):
return True
return False
except:
print("Error in loading!")
return None