def __init__(self, parent=None, setting=None): super(frmSelectSession, self).__init__(parent) # inputs self.SubRange = strRange(setting.SubRange, Unique=True) if self.SubRange is None: print("Subject Range is wrong!") return self.SubSize = len(self.SubRange) self.ConRange = strMultiRange(setting.ConRange, self.SubSize) if self.ConRange is None: print("Counter Range is wrong!") return self.RunRange = strMultiRange(setting.RunRange, self.SubSize) if self.RunRange is None: print("Run Range is wrong!") return # outputs self.SubID = None self.RunID = None self.ConID = None self.PASS = False layout = QFormLayout() self.lblSub = QLabel("Subject: ") self.txtSub = QComboBox() self.txtSub.addItem("", None) for subindx, sub in enumerate(self.SubRange): self.txtSub.addItem(str(sub), subindx) self.txtSub.currentIndexChanged.connect(self.txtSub_isChenged) layout.addRow(self.lblSub, self.txtSub) self.lblRun = QLabel("Run: ") self.txtRun = QComboBox() layout.addRow(self.lblRun, self.txtRun) self.lblCon = QLabel("Counter: ") self.txtCon = QComboBox() layout.addRow(self.lblCon, self.txtCon) self.lblTask = QLabel() self.lblTask.setText("Task:") self.txtTask = QLineEdit() self.txtTask.setText(setting.Task) self.txtTask.setReadOnly(True) layout.addRow(self.lblTask, self.txtTask) self.btnOK = QPushButton("OK") self.btnOK.clicked.connect(self.btnOK_onclick) self.btnCan = QPushButton("Cancel") self.btnCan.clicked.connect(self.btnCan_onclick) layout.addRow(self.btnCan, self.btnOK) self.setLayout(layout) self.setWindowTitle("Session Selector") self.exec_()
def Check(self, SettingFileName, isOne=False, SubID=None, RunID=None, ConID=None): import numpy as np import os from Base.utility import fixstr, setParameters3, strRange, strMultiRange from Base.Setting import Setting setting = Setting() setting.Load(SettingFileName) if setting.empty: print("Error in loading the setting file!") return False else: if isOne: Subjects = [SubID] Counters = [[ConID]] Runs = [[RunID]] else: Subjects = strRange(setting.SubRange, Unique=True) if Subjects is None: print("Cannot load Subject Range!") return False SubSize = len(Subjects) Counters = strMultiRange(setting.ConRange, SubSize) if Counters is None: print("Cannot load Counter Range!") return False Runs = strMultiRange(setting.RunRange, SubSize) if Runs is None: print("Cannot load Run Range!") return False for si, s in enumerate(Subjects): for cnt in Counters[si]: print("Checking script for Subject %d ..." % (s)) for r in Runs[si]: ScriptAddr = setParameters3(setting.Script, setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer),\ fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \ fixstr(cnt, setting.ConLen, setting.ConPer)) if os.path.isfile(ScriptAddr): print("CHECK: " + ScriptAddr + " - checked!") else: print("CHECK: " + ScriptAddr + " - not found!") return False return True
def 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 Run(self, SettingFileName, isOne=False, Remove=True, feat=None, SubID=None, RunID=None, ConID=None): import numpy as np import os, subprocess from Base.utility import fixstr, setParameters3, strRange, strMultiRange from Base.Setting import Setting if (feat == None) or (os.path.isfile(feat) == False): print("Cannot find feat cmd!") return False, None Jobs = list() setting = Setting() setting.Load(SettingFileName) if setting.empty: print("Error in loading the setting file!") return False, None else: if isOne: Subjects = [SubID] Counters = [[ConID]] Runs = [[RunID]] else: Subjects = strRange(setting.SubRange, Unique=True) if Subjects is None: print("Cannot load Subject Range!") return False, None SubSize = len(Subjects) Counters = strMultiRange(setting.ConRange, SubSize) if Counters is None: print("Cannot load Counter Range!") return False, None Runs = strMultiRange(setting.RunRange, SubSize) if Runs is None: print("Cannot load Run Range!") return False, None for si, s in enumerate(Subjects): for cnt in Counters[si]: print("Run script for Subject %d ..." % (s)) for r in Runs[si]: ScriptAddr = setParameters3(setting.Script,setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer), \ fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \ fixstr(cnt, setting.ConLen, setting.ConPer)) ScriptTitle = setParameters3(setting.Script, "", fixstr(s, setting.SubLen, setting.SubPer), \ fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \ fixstr(cnt, setting.ConLen, setting.ConPer)) ScriptOutputAddr = setParameters3(setting.Analysis, setting.mainDIR, fixstr(s, setting.SubLen, setting.SubPer), \ fixstr(r, setting.RunLen, setting.RunPer), setting.Task, \ fixstr(cnt, setting.ConLen, setting.ConPer)) + ".feat" files = [ScriptOutputAddr + "/filtered_func_data.nii.gz", ScriptOutputAddr + \ "/mask.nii.gz", ScriptOutputAddr + "/cluster_mask_zstat1.nii.gz"] cmd = ScriptAddr report = ScriptOutputAddr + "/report_log.html" thread = PreprocessThread(feat=feat, cmd=cmd, report=report, files=files, \ remove=Remove, removefile=ScriptOutputAddr) Jobs.append(["Preprocess", ScriptTitle, thread]) print("Job for " + ScriptAddr + " - is created!") return True, Jobs
def btnLoadEvent_click(self): global ui, dialog msgBox = QMessageBox() mainDIR = ui.txtSSDIR.text() Task = ui.txtSSTask.text() # Check Directory if not len(mainDIR): msgBox.setText("There is no main directory") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False if not os.path.isdir(mainDIR): msgBox.setText("Main directory doesn't exist") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Main directory is okay.") if not len(Task): msgBox.setText("There is no task title") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False try: SubRange = strRange(ui.txtSSSubRange.text(),Unique=True) if SubRange is None: raise Exception SubSize = len(SubRange) except: msgBox.setText("Subject Range is wrong!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Range of subjects is okay!") try: SubLen = np.int32(ui.txtSSSubLen.text()) 1 / SubLen except: msgBox.setText("Length of subjects must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Length of subjects is okay!") try: ConRange = strMultiRange(ui.txtSSConRange.text(),SubSize) if ConRange is None: raise Exception if not (len(ConRange) == SubSize): msgBox.setText("Counter Size must be equal to Subject Size!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False except: msgBox.setText("Counter Range is wrong!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Counter Range is okay!") try: ConLen = np.int32(ui.txtSSConLen.text()) 1 / ConLen except: msgBox.setText("Length of counter must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Length of Counter is okay!") try: RunRange = strMultiRange(ui.txtSSRunRange.text(),SubSize) if RunRange is None: raise Exception if not (len(RunRange) == SubSize): msgBox.setText("Run Size must be equal to Subject Size!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False except: msgBox.setText("Run Range is wrong!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Run Range is okay!") try: RunLen = np.int32(ui.txtSSRunLen.value()) 1 / RunLen except: msgBox.setText("Length of runs must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Length of runs is valid") if ui.txtEventDIR.text() == "": msgBox.setText("Structure of the event folders is empty!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False if ui.txtCondPre.text() == "": msgBox.setText("The prefix of condition files is empty!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False setting = Setting() setting.mainDIR = mainDIR setting.Task = Task setting.SubRange= ui.txtSSSubRange.text() setting.SubLen = np.int32(SubLen) setting.SubPer = ui.txtSSSubPer.text() setting.ConRange= ui.txtSSConRange.text() setting.ConLen = np.int32(ConLen) setting.ConPer = ui.txtSSConPer.text() setting.RunRange= ui.txtSSRunRange.text() setting.RunLen = np.int32(RunLen) setting.RunPer = ui.txtSSRunPer.text() sSess = frmSelectSession(None, setting=setting) if not sSess.PASS: return EventFolder = setParameters3(ui.txtEventDIR.text(), mainDIR, fixstr(int(sSess.SubID), setting.SubLen, setting.SubPer), \ fixstr(int(sSess.RunID), int(setting.RunLen), setting.RunPer), setting.Task, \ fixstr(sSess.ConID, int(setting.ConLen), setting.ConPer)) CondFile = EventFolder + ui.txtCondPre.text() + ".mat" if not os.path.isfile(CondFile): print("Cannot find condition mat file!") return try: conditions = io.loadmat(CondFile) except: print("Cannot load condition mat file!") return NumCond = len(conditions["Cond"]) ui.txtSSCondFrom.setValue(1) ui.txtSSCondTo.setValue(NumCond) ui.txtSSCondLen.setValue(len(str(NumCond))) ui.txtSSCondPer.setText("")
def btnRUN_click(self): global ui msgBox = QMessageBox() mainDIR = ui.txtSSDIR.text() Task = ui.txtSSTask.text() # Check Directory if not len(mainDIR): msgBox.setText("There is no main directory") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False if not os.path.isdir(mainDIR): msgBox.setText("Main directory doesn't exist") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Main directory is okay.") if not len(Task): msgBox.setText("There is no task title") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False try: SubRange = strRange(ui.txtSSSubRange.text(),Unique=True) if SubRange is None: raise Exception SubSize = len(SubRange) except: msgBox.setText("Subject Range is wrong!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Range of subjects is okay!") try: SubLen = np.int32(ui.txtSSSubLen.text()) 1 / SubLen except: msgBox.setText("Length of subjects must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Length of subjects is okay!") try: ConRange = strMultiRange(ui.txtSSConRange.text(),SubSize) if ConRange is None: raise Exception if not (len(ConRange) == SubSize): msgBox.setText("Counter Size must be equal to Subject Size!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False except: msgBox.setText("Counter Range is wrong!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Counter Range is okay!") try: ConLen = np.int32(ui.txtSSConLen.text()) 1 / ConLen except: msgBox.setText("Length of counter must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Length of Counter is okay!") try: RunRange = strMultiRange(ui.txtSSRunRange.text(),SubSize) if RunRange is None: raise Exception if not (len(RunRange) == SubSize): msgBox.setText("Run Size must be equal to Subject Size!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False except: msgBox.setText("Run Range is wrong!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Run Range is okay!") try: RunLen = np.int32(ui.txtSSRunLen.value()) 1 / RunLen except: msgBox.setText("Length of runs must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Length of runs is valid") try: CondFrom = np.int32(ui.txtSSCondFrom.value()) 1 / CondFrom except: msgBox.setText("Condition From must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False try: CondTo = np.int32(ui.txtSSCondTo.value()) 1 / CondTo except: msgBox.setText("Condition To must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False if CondTo < CondFrom: msgBox.setText("Condition To is smaller then Subject From!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Counter is valid") try: CondLen = np.int32(ui.txtSSCondLen.text()) 1 / CondLen except: msgBox.setText("Length of condition must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Length of condition is valid") Space = ui.txtSSSpace.currentText() if not len(Space): msgBox.setText("Please enter a affine file!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False if not Space == DefaultSpace(): if not os.path.isfile(Space): msgBox = QMessageBox() msgBox.setText("Affine file not found!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return print("Affine file is okay.") In = ui.txtSSInFile.currentText() if not len(In): msgBox.setText("Please enter input file!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False Out = ui.txtOutROI.text() if not len(Out): msgBox.setText("Please enter output file!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False ThresholdType = ui.cbThType.currentData() if (ThresholdType == "min") or (ThresholdType == "ext"): try: MinTh = np.double(ui.txtThMin.text()) except: msgBox.setText("Min Threshold must be a number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Min Threshold is valid") if (ThresholdType == "max") or (ThresholdType == "ext"): try: MaxTh = np.double(ui.txtThMax.text()) except: msgBox.setText("Max Threshold must be a number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Max Threshold is valid") print("Checking files ...") for si, s in enumerate(SubRange): for cnt in ConRange[si]: print("Analyzing Subject %d, Counter %d ..." % (s,cnt)) # SubDIR = setting.mainDIR + "/" + "sub-" + fixstr(s, SubLen, setting.SubPer) for r in RunRange[si]: for cnd in range(CondFrom, CondTo + 1): InFile = setParameters3(In, mainDIR, fixstr(s, SubLen, ui.txtSSSubPer.text()),\ fixstr(r, RunLen, ui.txtSSRunPer.text()), ui.txtSSTask.text(),\ fixstr(cnt, ConLen, ui.txtSSConPer.text()), fixstr(cnd, CondLen, ui.txtSSCondPer.text())) if os.path.isfile(InFile): print(InFile + " - is OKAY.") else: print(InFile + " - not found!") return if ui.cbMetric.currentData() == "inter": print("Calculating ROI ...") ROIData = None for si, s in enumerate(SubRange): for cnt in ConRange[si]: print("Analyzing Subject %d, Counter %d ..." % (s,cnt)) for r in RunRange[si]: for cnd in range(CondFrom, CondTo + 1): InFile = setParameters3(In, mainDIR, fixstr(s, SubLen, ui.txtSSSubPer.text()), \ fixstr(r, RunLen, ui.txtSSRunPer.text()), ui.txtSSTask.text(), \ fixstr(cnt, ConLen, ui.txtSSConPer.text()), fixstr(cnd, CondLen, ui.txtSSCondPer.text())) MaskHDR = nb.load(InFile) MaskData = MaskHDR.get_data() if ThresholdType == "no": MaskData[np.where(MaskData != 0)] = 1 elif ThresholdType == "min": MaskData[np.where(MaskData < MinTh)] = 0 MaskData[np.where(MaskData != 0)] = 1 elif ThresholdType == "max": MaskData[np.where(MaskData > MaxTh)] = 0 MaskData[np.where(MaskData != 0)] = 1 elif ThresholdType == "ext": MaskData[np.where(MaskData > MaxTh)] = 0 MaskData[np.where(MaskData < MinTh)] = 0 MaskData[np.where(MaskData != 0)] = 1 if ROIData is None: if Space == DefaultSpace(): affineHDR = nb.load(InFile) else: affineHDR = nb.load(Space) ROIData = MaskData.copy() else: if not np.shape(ROIData) == np.shape(MaskData): print("All mask must include the same size data (tensor)") return else: ROIData = ROIData + MaskData ROIData[np.where(ROIData != 0)] = 1 print(InFile + " - is calculated!") NumVoxels = np.shape(ROIData) NumVoxels = NumVoxels[0] * NumVoxels[1] * NumVoxels[2] print("Number of all voxels: %d " % NumVoxels) NumROIVoxel = len(ROIData[np.where(ROIData != 0)]) print("Number of selected voxles in ROI: %d" % NumROIVoxel) ROIHDR = nb.Nifti1Image(ROIData, affineHDR.affine) nb.save(ROIHDR,Out) print("ROI is generated!") msgBox.setText("ROI is generated!\nNumber of all voxels: " + str(NumVoxels) + \ "\nNumber of selected voxles in ROI: " + str(NumROIVoxel)) msgBox.setIcon(QMessageBox.Information) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_()
def btnRun_onclick(self): from Base.utility import strRange, strMultiRange global ui msgBox = QMessageBox() SubPer = ui.txtSubPer.text() RunPer = ui.txtRunPer.text() ConPer = ui.txtConPer.text() Input = ui.txtInput.text() Output = ui.txtOutput.text() Task = ui.txtTask.text() DIR = ui.txtDIR.text() Script = ui.txtScript.text() try: SubRange = strRange(ui.txtSubRange.text(), Unique=True) if SubRange is None: raise Exception SubSize = len(SubRange) except: msgBox.setText("Subject Range is wrong!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Range of subjects is okay!") try: SubLen = np.int32(ui.txtSubLen.text()) 1 / SubLen except: msgBox.setText("Length of subjects must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Length of subjects is okay!") try: ConRange = strMultiRange(ui.txtConRange.text(), SubSize) if ConRange is None: raise Exception if not (len(ConRange) == SubSize): msgBox.setText("Counter Size must be equal to Subject Size!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False except: msgBox.setText("Counter Range is wrong!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Counter Range is okay!") try: ConLen = np.int32(ui.txtConLen.text()) 1 / ConLen except: msgBox.setText("Length of counter must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Length of Counter is okay!") try: RunRange = strMultiRange(ui.txtRunRange.text(), SubSize) if RunRange is None: raise Exception if not (len(RunRange) == SubSize): msgBox.setText("Run Size must be equal to Subject Size!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False except: msgBox.setText("Run Range is wrong!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Run Range is okay!") try: RunLen = np.int32(ui.txtRunLen.value()) 1 / RunLen except: msgBox.setText("Length of runs must be an integer number") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return False print("Length of runs is valid") if Input == "": msgBox = QMessageBox() msgBox.setText("There is no input structure") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return if Task == "": msgBox = QMessageBox() msgBox.setText("There is no Task name") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return if DIR == "": msgBox = QMessageBox() msgBox.setText("Please select the main directory") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return if Script == "": msgBox = QMessageBox() msgBox.setText("Script structure is not found!") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return if not os.path.isdir(DIR): msgBox = QMessageBox() msgBox.setText("Cannot find the main directory") msgBox.setIcon(QMessageBox.Critical) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() return RepCount = 0 for si, s in enumerate(SubRange): for c in ConRange[si]: for r in RunRange[si]: SFile = setParameters3(Script, DIR, fixstr(s,SubLen,SubPer),\ fixstr(r,RunLen,RunPer),Task,\ fixstr(c,ConLen,ConPer)) if ui.cbInDynamic.isChecked(): InValue = setParameters3(Input,DIR, fixstr(s,SubLen,SubPer),\ fixstr(r,RunLen,RunPer),Task,\ fixstr(c,ConLen,ConPer)) else: InValue = Input if ui.cbOutDynamic.isChecked(): OutValue = setParameters3(Output,DIR, fixstr(s,SubLen,SubPer),\ fixstr(r,RunLen,RunPer),Task,\ fixstr(c,ConLen,ConPer)) else: OutValue = Output CountCurrRep = RepCount print("SCRIPT: " + SFile) print("Replacing " + InValue + " to " + OutValue + "...") try: if not os.path.isfile(SFile): print(SFile + " - not found!") else: scriptFile = open(SFile, "r") scriptContent = scriptFile.read() scriptFile.close() while scriptContent.find(InValue) != -1: scriptContent = scriptContent.replace( InValue, OutValue, 1) RepCount = RepCount + 1 except Exception as e: print(e) CountCurrRep = RepCount - CountCurrRep if not ui.cbDEMO.isChecked(): scriptFile = open(SFile, "w") scriptFile.write(scriptContent) scriptFile.close() print(str(CountCurrRep) + " is replaced!") else: print("DEMO: " + str(CountCurrRep) + " is found!") if ui.cbDEMO.isChecked(): msgBox.setText(str(RepCount) + " items are found!") else: msgBox.setText(str(RepCount) + " items are replaced!") msgBox.setIcon(QMessageBox.Information) msgBox.setStandardButtons(QMessageBox.Ok) msgBox.exec_() pass