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 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()
DataFiles = ui.txtDataFiles.toPlainText()
if not len(DataFiles):
print("WARNING: Please load data files!")
msgBox.setText("Please load data files!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
OutDataFormat = ui.txtDIOutDAT.text()
if not len(OutDataFormat):
msgBox.setText("Please enter output data format!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
try:
SubLen = np.int32(ui.txtDISubLen.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:
ConLen = np.int32(ui.txtDIConLen.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:
RunLen = np.int32(ui.txtDIRunLen.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 not ui.cbFSubject.isChecked():
if not ui.cbFTask.isChecked():
if not ui.cbFCounter.isChecked():
msgBox.setText("You must at least select one Fold Level!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# Label
if not len(ui.txtLabel.currentText()):
msgBox.setText("Please enter Label variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
if not len(ui.txtData.currentText()):
msgBox.setText("Please enter Data variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
TrainVal = ui.txtTrain.text()
if not len(TrainVal):
msgBox.setText("Please enter train perfix!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
TestVal = ui.txtTest.text()
if not len(TestVal):
msgBox.setText("Please enter test perfix!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# 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
try:
InData = io.loadmat(InFile, appendmat=False)
except:
print("Cannot load data file!")
msgBox.setText("Cannot load data file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
try:
DataFiles = InData["Integration"][ui.txtData.currentText()][0][0]
except:
print("Cannot load data files!")
msgBox.setText("Cannot load data files!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
# 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:
Subject = InData[ui.txtSubject.currentText()]
except:
print("Cannot load Subject ID")
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:
Task = InData[ui.txtTask.currentText()]
TaskIndex = Task.copy()
TaskList = list()
for tasindx, tas in enumerate(np.unique(Task)):
TaskIndex[Task == tas] = tasindx + 1
TaskList.append([tasindx + 1, tas])
except:
print("Cannot load Task ID")
return
# 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()]
except:
print("Cannot load Run ID")
return
# 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:
Counter = InData[ui.txtCounter.currentText()]
except:
print("Cannot load Counter ID")
return
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("Checking data files ...")
DataStream = np.transpose(
np.concatenate((TaskIndex, Subject, Counter, Run)))
DataStrUniq = list(
np.transpose(
np.array(list(set(tuple(i) for i in DataStream.tolist())))))
DataTasks = list()
for taskid in DataStrUniq[0]:
for taskls in TaskList:
if taskls[0] == taskid:
DataTasks.append(taskls[1])
DataStrUniq = np.transpose(DataStrUniq)
DataTasks = np.transpose(DataTasks)
for datindx, dat in enumerate(DataStrUniq):
SubID = dat[1]
CouID = dat[2]
RunID = dat[3]
TaskID = DataTasks[0][datindx]
dfile = setParameters3(OutDataFormat,"",fixstr(SubID,SubLen,ui.txtDISubPer.text()),\
fixstr(RunID,RunLen,ui.txtDIRunPer.text()),TaskID,\
fixstr(CouID,ConLen,ui.txtDIConPer.text()))
if dfile in DataFiles:
print(dfile + " is okay.")
else:
print(dfile + " is not found!")
msgBox.setText(dfile + " is not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
print("Calculating Folds ...")
GroupFold = np.transpose(DataStrUniq.copy())
FoldStr = ""
if not ui.cbFSubject.isChecked():
GroupFold[1] = -1
GroupFold[3] = -1
else:
if not ui.rbFRun.isChecked():
GroupFold[3] = -1
FoldStr = "Subject"
else:
FoldStr = "Subject+Run"
if not ui.cbFTask.isChecked():
GroupFold[0] = -1
else:
FoldStr = FoldStr + "+Task"
if not ui.cbFCounter.isChecked():
GroupFold[2] = -1
else:
FoldStr = FoldStr + "+Counter"
GroupFold = np.transpose(GroupFold)
UniqFold = np.array(list(set(tuple(i) for i in GroupFold.tolist())))
if len(UniqFold) <= Unit:
msgBox.setText(
"Unit for the test set must be smaller than all possible folds! Number of all folds 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 for the test set must be divorceable to all possible folds! Number of all folds is: "
+ str(len(UniqFold)))
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
FoldIDs = np.arange(len(UniqFold)) + 1
if not Unit == 1:
FoldIDs = np.int32((FoldIDs - 0.1) / Unit) + 1
DataStructure = list(InData["Integration"]["DataStructure"][0][0])
try:
FoldCounter = np.int32(InData["FoldCounter"][0][0]) + 1
except:
FoldCounter = 1
FoldInfo = dict()
FoldInfo["Unit"] = Unit
FoldInfo["Group"] = GroupFold
FoldInfo["Order"] = FoldStr
FoldInfo["Unique"] = UniqFold
FoldInfo["FoldID"] = FoldIDs
FoldInfo["TrainVal"] = TrainVal
FoldInfo["TestVal"] = TestVal
GUFold = np.unique(FoldIDs)
print("Number of all folds is: " + str(len(UniqFold)))
for foldID, fold in enumerate(GUFold):
print("Generating Fold " + str(foldID + 1), " of ",
str(len(np.unique(FoldIDs))), " ...")
Train_Info = UniqFold[FoldIDs != fold]
Test_Info = UniqFold[FoldIDs == fold]
currentTrainList = list()
currentTestList = list()
if not ui.cbFSubject.isChecked():
if ui.cbFTask.isChecked() and not ui.cbFCounter.isChecked():
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[0] == datastr[0]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[0] == datastr[0]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
elif not ui.cbFTask.isChecked() and ui.cbFCounter.isChecked():
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[2] == datastr[2]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[2] == datastr[2]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
else:
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[0] == datastr[0] and trinf[2] == datastr[
2]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[0] == datastr[0] and teinf[2] == datastr[
2]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
elif not ui.rbFRun.isChecked():
if not ui.cbFTask.isChecked() and not ui.cbFCounter.isChecked(
):
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[1] == datastr[1]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[1] == datastr[1]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
elif ui.cbFTask.isChecked() and not ui.cbFCounter.isChecked():
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[0] == datastr[0] and trinf[1] == datastr[
1]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[0] == datastr[0] and teinf[1] == datastr[
1]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
elif not ui.cbFTask.isChecked() and ui.cbFCounter.isChecked():
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[1] == datastr[1] and trinf[2] == datastr[
2]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[1] == datastr[1] and teinf[2] == datastr[
2]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
else:
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[0] == datastr[0] and trinf[1] == datastr[
1] and trinf[2] == datastr[2]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[0] == datastr[0] and teinf[1] == datastr[
1] and teinf[2] == datastr[2]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
else:
if not ui.cbFTask.isChecked() and not ui.cbFCounter.isChecked(
):
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[1] == datastr[1] and trinf[3] == datastr[
3]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[1] == datastr[1] and teinf[3] == datastr[
3]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
elif ui.cbFTask.isChecked() and not ui.cbFCounter.isChecked():
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[0] == datastr[0] and trinf[1] == datastr[
1] and trinf[3] == datastr[3]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[0] == datastr[0] and teinf[1] == datastr[
1] and teinf[3] == datastr[3]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
elif not ui.cbFTask.isChecked() and ui.cbFCounter.isChecked():
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[1] == datastr[1] and trinf[2] == datastr[
2] and trinf[3] == datastr[3]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[1] == datastr[1] and teinf[2] == datastr[
2] and teinf[3] == datastr[3]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
else:
for trinf in Train_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if trinf[0] == datastr[0] and trinf[1] == datastr[
1] and trinf[2] == datastr[2] and trinf[
3] == datastr[3]:
currentTrainList.append(
[datastr, DataTasks[0][datastrindx]])
for teinf in Test_Info:
for datastrindx, datastr in enumerate(DataStrUniq):
if teinf[0] == datastr[0] and teinf[1] == datastr[
1] and teinf[2] == datastr[2] and trinf[
3] == datastr[3]:
currentTestList.append(
[datastr, DataTasks[0][datastrindx]])
if not len(DataStrUniq
) == len(currentTestList) + len(currentTrainList):
print("WARNING: There are some confilcts between test set and train set!", len(DataStrUniq), \
" is not ", len(currentTestList), " + ", len(currentTrainList))
currTrainFiles = list()
currTestFiles = list()
for currTrain in currentTrainList:
dfile = setParameters3(OutDataFormat, "", fixstr(currTrain[0][1], SubLen, ui.txtDISubPer.text()), \
fixstr(currTrain[0][3], RunLen, ui.txtDIRunPer.text()), currTrain[1], \
fixstr(currTrain[0][2], ConLen, ui.txtDIConPer.text()))
currTrainFiles.append(dfile)
for currTest in currentTestList:
dfile = setParameters3(OutDataFormat, "", fixstr(currTest[0][1], SubLen, ui.txtDISubPer.text()), \
fixstr(currTest[0][3], RunLen, ui.txtDIRunPer.text()), currTest[1], \
fixstr(currTest[0][2], ConLen, ui.txtDIConPer.text()))
currTestFiles.append(dfile)
currTrainVal = TrainVal.replace("$FOLD$", str(fold))
currTestVal = TestVal.replace("$FOLD$", str(fold))
DataStructure.append(currTrainVal)
DataStructure.append(currTestVal)
FoldInfo[currTrainVal + "_files"] = np.array(currTrainFiles,
dtype=object)
FoldInfo[currTestVal + "_files"] = np.array(currTestFiles,
dtype=object)
FoldInfo["DataStructure"] = np.array(DataStructure, dtype=object)
InData["FoldInfo" + str(FoldCounter)] = FoldInfo
#InData["DataFold"] = np.array(DataStructure,dtype=object)
InData["FoldCounter"] = FoldCounter
print("Saving ...")
io.savemat(InFile, InData, appendmat=False, do_compression=True)
print("DONE.")
print("Cross validation is done.")
msgBox.setText("Cross validation is done.")
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 run(self, SettingFileName):
import numpy as np
import scipy.io as io
import os
from Base.utility import fixstr, setParameters3
from Base.Setting import Setting, strRange, strMultiRange
setting = Setting()
setting.Load(SettingFileName)
if setting.empty:
print("Error in loading the setting file!")
return False
else:
self.ConditionTitles = []
Events = []
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
# COLECT ALL EVENTS AND CALCULATE THE LIST OF CONDITION
for si, s in enumerate(Subjects):
for cnt in Counters[si]:
print("Analyzing Subject %d, Counter %d ..." % (s, cnt))
for r in Runs[si]:
# Event File Check
EventAddr = setParameters3(setting.Onset,setting.mainDIR,fixstr(s, setting.SubLen, setting.SubPer)\
,fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \
fixstr(cnt, setting.ConLen, setting.ConPer))
EventFolder = 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))
#EventFolder = SubDIR + "/func/" + "sub-" + fixstr(s, SubLen, setting.SubPer) + "_task-" + setting.Task + "_run-" + \
#fixstr(r, RunLen, setting.RunPer) + "_events/"
MatAddr = EventFolder + setting.CondPre + ".mat"
if not os.path.isfile(EventAddr):
print(EventAddr, " - file not find!")
return False
else:
file = open(EventAddr, "r")
lines = file.readlines()
file.close()
dir = {}
dir.clear()
for k in range(0, len(lines)):
Event = lines[k].rsplit()
try:
allvars = dict(locals(), **globals())
exec(setting.EventCodes, allvars, allvars)
except Exception as e:
print(
"Event codes generated following error:\n"
)
print(e)
return False
try:
RowStartID = allvars['RowStartID']
except:
print(
"Cannot find RowStartID variable in event code"
)
return False
try:
Condition = allvars['Condition']
except:
print(
"Cannot find Condition variable in event code"
)
return False
try:
Onset = allvars['Onset']
except:
print(
"Cannot find Onset variable in event code"
)
return False
try:
Duration = allvars['Duration']
except:
print(
"Cannot find Duration variable in event code"
)
return False
try:
Skip = int(allvars["Skip"])
except:
print(
"Cannot find Skip variable in event code"
)
return False
if RowStartID <= k and Skip == 0:
# Create Condition Directory
try:
value = dir[Condition]
value.append(
[float(Onset),
float(Duration)])
dir[Condition] = value
except KeyError:
value = list()
value.append(
[float(Onset),
float(Duration)])
dir[Condition] = value
for condinx, cond in enumerate(dir):
self.add_condTitle(
title=cond,
ConditionTitles=self.ConditionTitles)
Events.append([MatAddr, EventFolder, dir])
print(
"Subject %d, Counter %d, Run %d is verified." %
(s, cnt, r))
# Create Standard Condition Titles list
conditions = []
for cond in self.ConditionTitles:
conditions.append([
setting.CondPre + "_" +
str(self.get_condID(cond[0], self.ConditionTitles)),
cond[0]
])
conditions = np.array(conditions, dtype=object)
# Normalized the condition titile for all events
StandardEvents = []
for event in Events:
StandardEvent = dict()
StandardEvent["Cond"] = conditions
for cond in event[2]:
StandardEvent[setting.CondPre + "_" + str(
self.get_condID(
cond, self.ConditionTitles))] = event[2][cond]
# Add list of titles
StandardEvents.append([event[0], event[1], StandardEvent])
print("Events were normalized! Generating event files ...")
# Save Files
for event in StandardEvents:
try:
os.mkdir(event[1])
except:
pass
io.savemat(event[0], event[2])
for tabs in event[2]:
if tabs == "Cond":
conFile = open(event[1] + tabs + ".txt", "w")
for con in event[2][tabs]:
conFile.write(
str(con[0]) + "\t" + str(con[1]) + "\n")
conFile.close()
else:
tabFile = open(event[1] + tabs + ".tab", "w")
for onset in event[2][tabs]:
tabFile.write(
str(onset[0]) + "\t" + str(onset[1]) + "\t1\n")
tabFile.close()
print("EVENT: " + event[1] + " is generated!")
# Check Tab File
for cond in conditions:
for si, s in enumerate(Subjects):
for cnt in Counters[si]:
print(
"Checking Tab Files: Subject %d, Counter %d ..." %
(s, cnt))
for r in Runs[si]:
EventFolder = 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))
fname = EventFolder + cond[0] + '.tab'
if os.path.isfile(fname):
print(fname + " - is okay.")
else:
tabfile = open(fname, "w")
tabfile.write("0\t0\t0\n")
tabfile.close()
print(fname + " - is EMPTY!")
# Report
print("List of generated conditions:")
print("Condition ID\tCondition Title")
for cond in conditions:
print("\t" + cond[0] + "\t\t\t" + cond[1])
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 btnReport_click(self):
msgBox = QMessageBox()
# 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
if not len(ui.txtData.currentText()):
msgBox.setText("Please enter Data variable name!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
# 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
# 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
# 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
# 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
print("Loading data ...")
InData = io.loadmat(InFile)
try:
X = InData[ui.txtData.currentText()]
except:
print("Cannot load data")
return
try:
Subject = InData[ui.txtSubject.currentText()]
except:
print("Cannot load Subject ID")
return
try:
Run = InData[ui.txtRun.currentText()]
except:
print("Cannot load Run ID")
return
try:
Counter = InData[ui.txtCounter.currentText()]
except:
print("Cannot load Counter ID")
return
try:
Task = InData[ui.txtTask.currentText()]
TaskIndex = Task.copy()
for tasindx, tas in enumerate(np.unique(Task)):
TaskIndex[Task == tas] = tasindx + 1
except:
print("Cannot load Subject ID")
return
Unit = 1
print("Calculating Alignment Level ...")
GroupFold = None
FoldStr = ""
if ui.cbFSubject.isChecked():
if not ui.rbFRun.isChecked():
GroupFold = Subject
FoldStr = "Subject"
else:
GroupFold = np.concatenate((Subject,Run))
FoldStr = "Subject+Run"
if ui.cbFTask.isChecked():
GroupFold = np.concatenate((GroupFold,TaskIndex)) if GroupFold is not None else TaskIndex
FoldStr = FoldStr + "+Task"
if ui.cbFCounter.isChecked():
GroupFold = np.concatenate((GroupFold,Counter)) if GroupFold is not None else Counter
FoldStr = FoldStr + "+Counter"
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 for the test set must be smaller than all possible folds! Number of all folds 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 for the test set must be divorceable to all possible folds! Number of all folds 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
FoldInfo = dict()
FoldInfo["Unit"] = Unit
FoldInfo["Group"] = GroupFold
FoldInfo["Order"] = FoldStr
FoldInfo["List"] = ListFold
FoldInfo["Unique"] = UniqFold
FoldInfo["Folds"] = UnitFold
GUFold = np.unique(UnitFold)
ui.txtReport.clear()
print("Number of data in this level is " + str(len(UniqFold)))
ui.txtReport.append("Number of data in this level is " + str(len(UniqFold)))
FoldSizeStr = str(len(UniqFold))
FirstShape = None
for foldID, fold in enumerate(GUFold):
Shape = np.shape(X[np.where(UnitFold == fold)])
str2 = ""
if FirstShape is None:
FirstShape = Shape
elif Shape != FirstShape:
str2 = " - Problem"
print("Shape of " + fixstr(foldID + 1,len(FoldSizeStr)) + "-th data of " + FoldSizeStr + " is " + str(Shape) + str2)
ui.txtReport.append("Shape of " + fixstr(foldID + 1,len(FoldSizeStr)) + "-th data of " + FoldSizeStr + " is " + str(Shape) + str2)
ui.tabWidget.setCurrentIndex(2)
