def save_cfg_dicomdir(self):
"""Function intended to save the DICOM directory once button is pressed"""
self.cfg['folders']['dicom'] = self.working_dir
Configuration.save_config(self.cfg['folders']["rootdir"], self.cfg)
Output.msg_box(
text="Folder changed in the configuration file to {}".format(
self.working_dir),
title='Changed folder')
def closeEvent(self, event):
"""saves the settings found here as a yaml file which may be loaded the next time as the configuration used"""
self.cfg["preprocess"]["dcm2nii"][
"OutputFileStruct"] = self.lineEditFilename.text()
self.cfg["preprocess"]["dcm2nii"][
"IncludeFiles"] = self.lineEditIncludeFiles.text()
Configuration.save_config(self.cfg["folders"]["rootdir"], self.cfg)
event.accept()
def closeEvent(self, event):
"""saves the settings found here as a yaml file which may be loaded the next time as the configuration used"""
self.cfg["lead_detection"]["PaCER"][
"metal_threshold"] = self.lineEditMetalThreshold.text()
self.cfg["lead_detection"]["PaCER"][
"snr_threshold"] = self.lineEditSNRThreshold.text()
self.cfg["lead_detection"]["PaCER"]["lambda"] = int(
self.lineEditLambda.text())
Configuration.save_config(ROOTDIR, self.cfg)
event.accept()
def redefineDefault(self):
"""redefines which template is set as default on the right list and in the cfg-file"""
if not self.selected_subj_Gen:
Output.msg_box(text="No template selected. Please indicate new default one.", title="No data selected")
return
elif len(self.selected_subj_Gen) > 1:
Output.msg_box(text="Please select only one image as default.", title="Too many templates selected")
return
else:
default_template = [FileOperations.return_full_filename(self.wdirTemplate, x) for x in self.selected_subj_Gen]
self.cfg['folders']['default_template'] = default_template[0]
Configuration.save_config(ROOTDIR, self.cfg)
self.run_reload_files()
def change_workingdir(self):
"""A new window appears in which the working directory can be set; besides, data is stored in the preferences
file so that they will be loaded automatically next time"""
self.working_dir = QFileDialog.getExistingDirectory(
self,
directory=self.working_dir,
caption='Change working directory')
self.label_workingdir.setText('Working DIR: {}'.format(
self.working_dir))
self.mInput.clear()
items = FileOperations.list_folders(self.working_dir, prefix='')
self.addAvailableItems(items)
if self.option_gui == 'dcm2niix':
self.cfg['folders']['dicom'] = self.working_dir
Configuration.save_config(self.cfg['folders']["rootdir"], self.cfg)
def closeEvent(self, event):
"""saves the settings found here as a yaml file which may be loaded the next time as the configuration used"""
self.cfg["preprocess"]["ANTsN4"]["prefix"] = self.lineEditPrefix.text()
self.cfg["preprocess"]["ANTsN4"]["shrink-factor"] = int(self.lineEditShrink.text())
self.cfg["preprocess"]["ANTsN4"]["bspline-fitting"] = int(self.lineEditBSplineDist.text())
self.cfg["preprocess"]["ANTsN4"]["convergence"][0] = int(self.lineEditConv1.text())
self.cfg["preprocess"]["ANTsN4"]["convergence"][1] = int(self.lineEditConv2.text())
self.cfg["preprocess"]["ANTsN4"]["convergence"][2] = int(self.lineEditConv3.text())
self.cfg["preprocess"]["ANTsN4"]["convergence"][3] = int(self.lineEditConv4.text())
self.cfg["preprocess"]["ANTsN4"]["threshold"] = float(self.lineEditTolerance.text())
self.cfg["preprocess"]["ANTsN4"]["dti_prefix"] = self.lineEditDiffPrefix.text()
self.cfg["preprocess"]["registration"]["prefix"] = self.lineEditPrefixRegistration.text()
self.cfg["preprocess"]["registration"]["resample_spacing"] = self.lineResampleSpacing.text()
self.cfg["preprocess"]["normalisation"]["sequences"] = self.lineEditNormalisationSequences.text()
Configuration.save_config(ROOTDIR, self.cfg)
event.accept()
def __init__(self, parent=None):
super(TabContent, self).__init__()
self.selected_subj_Gen = ''
self.selected_subj_ANT = ''
self.cfg = Configuration.load_config(ROOTDIR)
if os.path.isdir(self.cfg['folders']['nifti']):
self.niftidir = self.cfg['folders']['nifti']
else:
self.niftidir = os.getcwd()
self.cfg['folders']['rootdir'] = ROOTDIR
Configuration.save_config(ROOTDIR, self.cfg)
# General layout for the tab view and initialisation of tabs
self.layout = QVBoxLayout(self)
self.tabs = QTabWidget()
self.tabs.resize(150, 100)
self.layout.addWidget(self.tabs)
# Customize tabs
# ============================== Tab 1 - General ==============================
self.tab1 = GuiTabGeneral()
self.tabs.addTab(self.tab1, "General")
# ============================== Tab 2 - Work on templates ==============================
self.tab2 = GuiTabTemplate()
self.tabs.addTab(self.tab2, "Template")
# ============================== Tab 3 - ANTs routines ==============================
self.tab3 = GuiTabPreprocessANTs()
self.tabs.addTab(self.tab3, "Preprocess Imaging (ANTsPy)")
# ============================== Tab 3 - Lead detection ==============================
self.tab4 = GuiTabDetectLeads()
self.tabs.addTab(self.tab4, "Detect leads (Pacer)")
# Add tabs to widget
self.layout.addWidget(self.tabs)
self.setLayout(self.layout)
def __init__(self, parent=None):
super(QWidget, self).__init__(parent)
# Load configuration files and general settings
self.cfg = Configuration.load_config(ROOTDIR)
if os.path.isdir(self.cfg['folders']['dicom']):
self.dicomdir = self.cfg['folders']['dicom']
else:
self.dicomdir = FileOperations.set_wdir_in_config(self.cfg, foldername='dicom', init=True)
self.cfg['folders']['dicom'] = self.dicomdir
self.cfg['folders']['rootdir'] = ROOTDIR
Configuration.save_config(ROOTDIR, self.cfg)
# Create general layout
self.tot_layout = QVBoxLayout(self)
self.mid_layout = QHBoxLayout(self)
# ============================ Create upper of GUI, i.e. working directory ============================
self.folderboxDcm2nii = QGroupBox("Directory (DICOM-files)")
self.HBoxUpperDcm2nii = QVBoxLayout(self.folderboxDcm2nii)
self.label_dicomdir = QLabel('dicom DIR: {}'.format(self.dicomdir))
self.HBoxUpperDcm2nii.addWidget(self.label_dicomdir)
self.btn_dicomdir = QPushButton('Change working \ndirectory')
self.btn_dicomdir.setFixedSize(150, 40)
self.btn_dicomdir.clicked.connect(self.change_dicomdir)
self.btn_savedir = QPushButton('Save directory \nto config file')
self.btn_savedir.setFixedSize(150, 40)
self.btn_savedir.setToolTip(Output.split_lines(setToolTips.saveDirButton()))
self.btn_savedir.clicked.connect(self.save_cfg)
hlay_upper = QHBoxLayout()
hlay_upper.addWidget(self.btn_dicomdir)
hlay_upper.addWidget(self.btn_savedir)
hlay_upper.addStretch(1)
self.HBoxUpperDcm2nii.addLayout(hlay_upper)
# ==================== Create Content for Lists, i.e. input/output ====================
self.listboxInputDcm2nii = QGroupBox('Available subjects in working directory')
self.listboxInput = QVBoxLayout(self.listboxInputDcm2nii)
self.mInput = QListWidget()
self.listboxInput.addWidget(self.mInput)
self.mButtonToAvailable = QPushButton("<<")
self.mBtnMoveToAvailable = QPushButton(">")
self.mBtnMoveToSelected = QPushButton("<")
self.mButtonToSelected = QPushButton(">>")
self.mBtnUp = QPushButton("Up")
self.mBtnDown = QPushButton("Down")
self.listboxOutputDcm2nii = QGroupBox('Subjects to process')
self.listboxOutput = QVBoxLayout(self.listboxOutputDcm2nii)
self.mOutput = QListWidget()
self.listboxOutput.addWidget(self.mOutput)
# First column on the left side
vlay = QVBoxLayout()
vlay.addStretch()
vlay.addWidget(self.mBtnMoveToAvailable)
vlay.addWidget(self.mBtnMoveToSelected)
vlay.addStretch()
vlay.addWidget(self.mButtonToAvailable)
vlay.addWidget(self.mButtonToSelected)
vlay.addStretch()
# Second column on the right side
vlay2 = QVBoxLayout()
vlay2.addStretch()
vlay2.addWidget(self.mBtnUp)
vlay2.addWidget(self.mBtnDown)
vlay2.addStretch()
# ==================== Lower part of GUI, i.e. Preferences/Start estimation ====================
self.btn_preferences = QPushButton("Preferences")
self.btn_preferences.clicked.connect(self.settings_show)
self.btn_run_dcm2niix = QPushButton("Run dcm2niix")
self.btn_run_dcm2niix.setToolTip(setToolTips.run_dcm2niix())
self.btn_run_dcm2niix.clicked.connect(self.start_converting)
hlay_bottom = QHBoxLayout()
hlay_bottom.addStretch(1)
hlay_bottom.addWidget(self.btn_preferences)
hlay_bottom.addWidget(self.btn_run_dcm2niix)
hlay_bottom.addStretch()
# ==================== Set all contents to general Layout =======================
self.mid_layout.addWidget(self.listboxInputDcm2nii)
self.mid_layout.addLayout(vlay)
self.mid_layout.addWidget(self.listboxOutputDcm2nii)
self.mid_layout.addLayout(vlay2)
self.tot_layout.addWidget(self.folderboxDcm2nii)
self.tot_layout.addLayout(self.mid_layout)
self.tot_layout.addLayout(hlay_bottom)
try:
self.mInput.clear()
items = FileOperations.list_folders(inputdir=self.cfg['folders']['dicom'], prefix='', files2lookfor='')
items = self.check_for_complete_input(list(items))
self.add_available_subj(items)
except FileExistsError:
print('{} without any valid files/folders, continuing ...'.format(self.dicomdir))
self.update_buttons_status()
self.connections()
def save_cfg(self):
"""Function intended to save the DICOM directory once button is pressed"""
self.cfg['folders']['dicom'] = self.dicomdir
Configuration.save_config(self.cfg['folders']['rootdir'], self.cfg)
Output.msg_box(text="Folder changed in configuration to {}".format(self.dicomdir), title="Changed folder")
def __init__(self, parent=None):
super(GuiTabDetectLeads, self).__init__(parent)
self.selected_subj_ANT = ''
# General settings/variables/helper files needed at some point
self.cfg = Configuration.load_config(ROOTDIR)
if os.path.isdir(self.cfg['folders']['nifti']):
self.niftidir = self.cfg['folders']['nifti']
else:
self.niftidir = FileOperations.set_wdir_in_config(
self.cfg, foldername='nifti', init=True)
self.cfg['folders']['nifti'] = self.niftidir
self.cfg['folders']['rootdir'] = ROOTDIR
Configuration.save_config(ROOTDIR, self.cfg)
self.lay = QHBoxLayout(self)
self.tab = QWidget()
# Customize tab
# ============================== Tab 3 - Lead detection routines ==============================
self.tab.layout = QHBoxLayout()
self.tab.setLayout(self.tab.layout)
# ------------------------- Upper left part (Folder) ------------------------- #
self.FolderboxTab = QGroupBox("Directory")
self.HBoxUpperLeftTab = QVBoxLayout(self.FolderboxTab)
self.lblWdirTab = QLabel('wDIR: {}'.format(self.niftidir))
self.HBoxUpperLeftTab.addWidget(self.lblWdirTab)
self.btnChangeWdir = QPushButton('Change working directory')
self.btnChangeWdir.clicked.connect(self.change_wdir)
self.btnReloadFilesTab = QPushButton('Reload files')
self.btnReloadFilesTab.clicked.connect(self.run_reload_files)
self.HBoxUpperLeftTab.addWidget(self.btnChangeWdir)
self.HBoxUpperLeftTab.addWidget(self.btnReloadFilesTab)
# ------------------------- Middle left part (Settings) ------------------------- #
self.SettingsTabLeadDetect = QGroupBox("Preferences")
self.HBoxMiddleLeftTabExt = QVBoxLayout(self.SettingsTabLeadDetect)
self.btn_LeadDetectSettings = QPushButton('Settings \nLead detection')
self.btn_LeadDetectSettings.clicked.connect(
self.run_PreferencesLeadDetection)
self.btn_LeadDetectSettings.setToolTip(setToolTips.ANTsSettings())
self.HBoxMiddleLeftTabExt.addWidget(self.btn_LeadDetectSettings)
# ------------------------- Middle left part (Processing) ------------------------- #
self.ActionsTabANTs = QGroupBox("Lead detection routines")
self.HBoxMiddleLeftTab = QVBoxLayout(self.ActionsTabANTs)
self.btn_LeadDetectPacer = QPushButton('PaCER algorithm')
self.btn_LeadDetectPacer.clicked.connect(self.run_LeadDetectionPaCER)
self.btn_RefineDetectedLeads = QPushButton('Refine detected leads')
self.btn_RefineDetectedLeads.clicked.connect(self.run_ManualCorrection)
self.HBoxMiddleLeftTab.addWidget(self.btn_LeadDetectPacer)
self.HBoxMiddleLeftTab.addWidget(self.btn_RefineDetectedLeads)
# ------------------------- Lower left part (Processing) ------------------------- #
self.QualityTabLeadDetect = QGroupBox(
"Quality checks for Lead detection")
self.HBoxLowerLeftTab = QVBoxLayout(self.QualityTabLeadDetect)
self.btn_QC_LeadDetect = QPushButton(
'Check lead detection \nin viewer')
self.btn_QC_LeadDetect.setToolTip(setToolTips.compareNIFTIfiles())
self.btn_QC_LeadDetect.clicked.connect(self.VisualiseLeadDetection)
self.HBoxLowerLeftTab.addWidget(self.btn_QC_LeadDetect)
# -------------------- Right part (Subject list) ----------------------- #
self.listbox = QGroupBox('Available subjects')
self.HBoxUpperRightTab = QVBoxLayout(self.listbox)
self.availableNiftiTab = QListWidget()
self.availableNiftiTab.setSelectionMode(
QAbstractItemView.ExtendedSelection)
itemsTab = FileOperations.list_folders(
self.niftidir, prefix=self.cfg['folders']['prefix'])
self.add_available_items(self.availableNiftiTab, itemsTab, msg='no')
self.availableNiftiTab.itemSelectionChanged.connect(
self.change_list_item)
self.HBoxUpperRightTab.addWidget(self.availableNiftiTab)
# Combine all Boxes for Tab 2 Layout
self.LeftboxTabANTs = QGroupBox()
self.HBoxTabLeadDetectLeft = QVBoxLayout(self.LeftboxTabANTs)
self.HBoxTabLeadDetectLeft.addWidget(self.FolderboxTab)
self.HBoxTabLeadDetectLeft.addStretch(1)
self.HBoxTabLeadDetectLeft.addWidget(self.SettingsTabLeadDetect)
self.HBoxTabLeadDetectLeft.addWidget(self.ActionsTabANTs)
self.HBoxTabLeadDetectLeft.addWidget(self.QualityTabLeadDetect)
self.tab.layout.addWidget(self.LeftboxTabANTs)
self.tab.layout.addWidget(self.listbox)
self.lay.addWidget(self.tab)
def __init__(self, parent=None):
super(GuiTabTemplate, self).__init__(parent)
self.selected_subj_Gen = ''
self.wdirTemplate = os.path.join(ROOTDIR, 'ext', 'templates')
# General settings/variables/helper files needed needed at some point
self.cfg = Configuration.load_config(ROOTDIR)
if os.path.isdir(self.cfg['folders']['nifti']):
self.niftidir = self.cfg['folders']['nifti']
else:
self.niftidir = FileOperations.set_wdir_in_config(self.cfg, foldername='nifti', init=True)
self.cfg['folders']['rootdir'] = ROOTDIR
Configuration.save_config(ROOTDIR, self.cfg)
self.lay = QHBoxLayout(self)
self.tab = QWidget()
# Customize tab
# ============================== Tab 1 - General ==============================
self.tab.layout = QHBoxLayout()
self.tab.setLayout(self.tab.layout)
# ------------------------- Upper left part (Folder) ------------------------- #
self.FolderboxTab = QGroupBox("Directory (Templates)")
self.HBoxUpperLeftTab = QVBoxLayout(self.FolderboxTab)
self.dirTemplates = QLabel('wDIR: {}'.format(self.wdirTemplate))
self.HBoxUpperLeftTab.addWidget(self.dirTemplates)
self.btnChangeWdir = QPushButton('Change working directory')
self.btnChangeWdir.setDisabled(True)
self.btnReloadFilesTab = QPushButton('Reload files')
self.btnReloadFilesTab.clicked.connect(self.run_reload_files)
self.HBoxUpperLeftTab.addWidget(self.btnChangeWdir)
self.HBoxUpperLeftTab.addWidget(self.btnReloadFilesTab)
# ------------------------- Lower left part (Processing) ------------------------- #
self.ActionsTab = QGroupBox("Functions")
self.HBoxLowerLeftTab = QVBoxLayout(self.ActionsTab)
self.btn_new_default = QPushButton('Set new \ndefault')
# self.btn_subj_details.setToolTip(setToolTips.subjectDetails()) TODO: new ToolTip needed
self.btn_new_default.clicked.connect(self.redefineDefault)
self.btn_viewer = QPushButton('View selected \nTemplate in viewer')
# self.btn_viewer.setToolTip(setToolTips.displayFolderContent()) TODO: new ToolTip needed
self.btn_viewer.clicked.connect(self.view_template)
self.create_SST = QPushButton('Create Study-specific\ntemplate')
# self.btn_renaming.setToolTip(setToolTips.renameFolders()) TODO: new ToolTip needed
self.create_SST.clicked.connect(self.create_StudySpecificTemplate)
self.HBoxLowerLeftTab.addWidget(self.btn_viewer)
self.HBoxLowerLeftTab.addWidget(self.btn_new_default)
self.HBoxLowerLeftTab.addWidget(self.create_SST)
# -------------------- Right part (Subject list) ----------------------- #
self.listbox = QGroupBox('Available subjects')
self.HBoxUpperRightTab = QVBoxLayout(self.listbox)
self.availableTemplates = QListWidget()
self.availableTemplates.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.availableTemplates.itemSelectionChanged.connect(self.change_list_item)
itemsTab = set(FileOperations.list_files_in_folder(self.wdirTemplate))
self.add_available_templates(self.availableTemplates, itemsTab)
self.HBoxUpperRightTab.addWidget(self.availableTemplates)
# Combine all Boxes for General Tab Layout
self.LeftboxTab = QGroupBox()
self.HBoxTabLeft = QVBoxLayout(self.LeftboxTab)
self.HBoxTabLeft.addWidget(self.FolderboxTab)
self.HBoxTabLeft.addStretch()
self.HBoxTabLeft.addWidget(self.ActionsTab)
self.tab.layout.addWidget(self.LeftboxTab)
self.tab.layout.addWidget(self.listbox)
self.lay.addWidget(self.tab)
def comboChangedDetectionMethod(self):
self.cfg["lead_detection"]["PaCER"][
"detection_method"] = self.lineDetectionMethod.currentText()
Configuration.save_config(ROOTDIR, self.cfg)
def __init__(self, parent=None):
super(GuiTabPreprocessANTs, self).__init__(parent)
self.selected_subj_ANT = ''
self.cfg = Configuration.load_config(ROOTDIR)
if os.path.isdir(self.cfg['folders']['nifti']):
self.niftidir = self.cfg['folders']['nifti']
else:
self.niftidir = FileOperations.set_wdir_in_config(self.cfg, foldername='nifti', init=True)
self.cfg['folders']['nifti'] = self.niftidir
self.cfg['folders']['rootdir'] = ROOTDIR
Configuration.save_config(ROOTDIR, self.cfg)
# Customize tab
self.lay = QHBoxLayout(self)
self.tab = QWidget()
self.tab.layout = QHBoxLayout()
self.tab.setLayout(self.tab.layout)
# ------------------------- Upper left part (Folder) ------------------------- #
self.FolderboxTab = QGroupBox('Directory (NIFTI-files)')
self.HBoxUpperLeftTab = QVBoxLayout(self.FolderboxTab)
self.lblWdirTab = QLabel('wDIR: {}'.format(self.niftidir))
self.HBoxUpperLeftTab.addWidget(self.lblWdirTab)
self.btnChangeWdir = QPushButton('Change working directory')
self.btnChangeWdir.setToolTip(setToolTips.ChangeWdirNIFTI())
self.btnChangeWdir.clicked.connect(self.change_wdir)
self.btnReloadFilesTab = QPushButton('Reload files')
self.btnReloadFilesTab.clicked.connect(self.run_reload_files)
self.HBoxUpperLeftTab.addWidget(self.btnChangeWdir)
self.HBoxUpperLeftTab.addWidget(self.btnReloadFilesTab)
# ------------------------- Middle left part (Preferences) ------------------------- #
self.SettingsTabANTs = QGroupBox('Preferences')
self.HBoxMiddleLeftTabExt = QVBoxLayout(self.SettingsTabANTs)
self.btn_ANTsettings = QPushButton('ANT Settings')
self.btn_ANTsettings.clicked.connect(self.run_ANTsPreferences)
self.btn_ANTsettings.setToolTip(setToolTips.ANTsSettings())
self.HBoxMiddleLeftTabExt.addWidget(self.btn_ANTsettings)
# ------------------------- Middle left part (ANTs routines) ------------------------- #
self.ActionsTabANTs = QGroupBox('ANTs routines')
self.HBoxMiddleLeftTab = QVBoxLayout(self.ActionsTabANTs)
self.btn_N4BiasCorr = QPushButton('N4BiasCorrect')
self.btn_N4BiasCorr.setToolTip(setToolTips.N4BiasCorrection())
self.btn_N4BiasCorr.clicked.connect(self.run_n4Bias_corr)
self.btn_MRIreg = QPushButton('MR-Registration')
self.btn_MRIreg.setToolTip(setToolTips.RegisterMRI2template())
self.btn_MRIreg.clicked.connect(self.run_RegisterMRI2template)
self.btn_CTreg = QPushButton('CT-Registration')
self.btn_CTreg.setToolTip(setToolTips.RegisterCT2MRI())
self.btn_CTreg.clicked.connect(self.run_RegisterCT2MRI)
self.HBoxMiddleLeftTab.addWidget(self.btn_N4BiasCorr)
self.HBoxMiddleLeftTab.addWidget(self.btn_MRIreg)
self.HBoxMiddleLeftTab.addWidget(self.btn_CTreg)
# ------------------------- Lower left part (Processing) ------------------------- #
self.QualityTabANTs = QGroupBox('Quality checks for ANTs preprocessing')
self.HBoxLowerLeftTab = QVBoxLayout(self.QualityTabANTs)
self.btn_QC_ANTsPreproc = QPushButton('View available \nNIFTI-files in viewer')
self.btn_QC_ANTsPreproc.setToolTip(setToolTips.compareNIFTIfiles())
self.btn_QC_ANTsPreproc.clicked.connect(self.display_nifti_files)
self.HBoxLowerLeftTab.addWidget(self.btn_QC_ANTsPreproc)
# -------------------- Right part (Subject list) ----------------------- #
self.listbox = QGroupBox('Available subjects')
self.HBoxUpperRightTab = QVBoxLayout(self.listbox)
self.availableNiftiTab = QListWidget()
self.availableNiftiTab.setSelectionMode(QAbstractItemView.ExtendedSelection)
itemsTab = FileOperations.list_folders(self.niftidir, prefix=self.cfg['folders']['prefix'])
self.add_available_items(self.availableNiftiTab, itemsTab, msg='no')
self.availableNiftiTab.itemSelectionChanged.connect(self.change_list_item)
self.HBoxUpperRightTab.addWidget(self.availableNiftiTab)
# Combine all Boxes for Tab 2 Layout
self.LeftboxTabANTs = QGroupBox()
self.HBoxTabANTsLeft = QVBoxLayout(self.LeftboxTabANTs)
self.HBoxTabANTsLeft.addWidget(self.FolderboxTab)
self.HBoxTabANTsLeft.addStretch(1)
self.HBoxTabANTsLeft.addWidget(self.SettingsTabANTs)
self.HBoxTabANTsLeft.addWidget(self.ActionsTabANTs)
self.HBoxTabANTsLeft.addWidget(self.QualityTabANTs)
self.tab.layout.addWidget(self.LeftboxTabANTs)
self.tab.layout.addWidget(self.listbox)
self.lay.addWidget(self.tab)
def comboChangedNormalisation(self):
self.cfg["preprocess"]["normalisation"]["template_image"] = self.lineTemplatesAvailable.currentText()
Configuration.save_config(ROOTDIR, self.cfg)
def comboChangedRegDefault(self):
self.cfg["preprocess"]["registration"]["registration_method"] = self.lineRegistrationMethod.currentText()
Configuration.save_config(ROOTDIR, self.cfg)
def __init__(self, parent=None):
super(GuiTabGeneral, self).__init__(parent)
self.selected_subj_Gen = ''
# General settings/variables/helper files needed needed at some point
self.cfg = Configuration.load_config(ROOTDIR)
if os.path.isdir(self.cfg['folders']['nifti']):
self.niftidir = self.cfg['folders']['nifti']
else:
self.niftidir = FileOperations.set_wdir_in_config(
self.cfg, foldername='nifti', init=True)
# self.cfg['folders']['rootdir'] = ROOTDIR ## changed 2021/02/23
Configuration.save_config(ROOTDIR, self.cfg)
self.lay = QHBoxLayout(self)
self.tab = QWidget()
# Customize tab
# ============================== Tab 1 - General ==============================
self.tab.layout = QHBoxLayout()
self.tab.setLayout(self.tab.layout)
# ------------------------- Upper left part (Folder) ------------------------- #
self.FolderboxTab = QGroupBox("Directory (NIFTI-files)")
self.HBoxUpperLeftTab = QVBoxLayout(self.FolderboxTab)
self.lblWdirTab = QLabel('wDIR: {}'.format(self.niftidir))
self.HBoxUpperLeftTab.addWidget(self.lblWdirTab)
self.btnChangeWdir = QPushButton('Change working directory')
self.btnChangeWdir.setToolTip(setToolTips.ChangeWdirDICOM())
self.btnChangeWdir.clicked.connect(self.change_wdir)
self.btnReloadFilesTab = QPushButton('Reload files')
self.btnReloadFilesTab.clicked.connect(self.run_reload_files)
self.HBoxUpperLeftTab.addWidget(self.btnChangeWdir)
self.HBoxUpperLeftTab.addWidget(self.btnReloadFilesTab)
# ------------------------- Lower left part (Processing) ------------------------- #
self.ActionsTab = QGroupBox("Functions")
self.HBoxLowerLeftTab = QVBoxLayout(self.ActionsTab)
self.btn_subj_details = QPushButton('Subject details')
self.btn_subj_details.setToolTip(setToolTips.subjectDetails())
self.btn_subj_details.clicked.connect(self.openDetails)
self.btn_dcm2nii = QPushButton('Dcm2niix')
self.btn_dcm2nii.setToolTip(setToolTips.runDCM2NII())
self.btn_dcm2nii.clicked.connect(self.run_DCM2NII)
self.btn_viewer = QPushButton('View available \nNIFTI-files in viewer')
self.btn_viewer.setToolTip(setToolTips.displayFolderContent())
self.btn_viewer.clicked.connect(self.show_nifti_files)
self.btn_renaming = QPushButton('Rename\nfolders')
self.btn_renaming.setToolTip(setToolTips.renameFolders())
self.btn_renaming.clicked.connect(self.run_rename_folders)
self.HBoxLowerLeftTab.addWidget(self.btn_subj_details)
self.HBoxLowerLeftTab.addWidget(self.btn_dcm2nii)
self.HBoxLowerLeftTab.addWidget(self.btn_viewer)
self.HBoxLowerLeftTab.addWidget(self.btn_renaming)
# -------------------- Right part (Subject list) ----------------------- #
self.listbox = QGroupBox('Available subjects')
self.HBoxUpperRightTab = QVBoxLayout(self.listbox)
self.availableNiftiTab = QListWidget()
self.availableNiftiTab.setSelectionMode(
QAbstractItemView.ExtendedSelection)
self.availableNiftiTab.itemSelectionChanged.connect(
self.change_list_item)
itemsTab = FileOperations.list_folders(
self.niftidir, prefix=self.cfg['folders']['prefix'])
self.add_available_items(self.availableNiftiTab, itemsTab)
self.HBoxUpperRightTab.addWidget(self.availableNiftiTab)
# Combine all Boxes for General Tab Layout
self.LeftboxTab = QGroupBox()
self.HBoxTabLeft = QVBoxLayout(self.LeftboxTab)
self.HBoxTabLeft.addWidget(self.FolderboxTab)
self.HBoxTabLeft.addStretch()
self.HBoxTabLeft.addWidget(self.ActionsTab)
self.tab.layout.addWidget(self.LeftboxTab)
self.tab.layout.addWidget(self.listbox)
self.lay.addWidget(self.tab)
