def change_wdir(self):
"""A new window appears in which the working directory for NIFTI-files can be set; if set, this is stored
in the configuration file, so that upon the next start there is the same folder selected automatically"""
self.niftidir = QFileDialog.getExistingDirectory(
self, 'Please select the directory of nii-files')
if not self.niftidir == "":
self.lblWdirTab.setText('wDIR: {}'.format(self.niftidir))
self.cfg["folders"]["nifti"] = self.niftidir
with open(os.path.join(ROOTDIR, 'config_imagingTB.yaml'),
'wb') as settings_mod:
yaml.safe_dump(self.cfg,
settings_mod,
default_flow_style=False,
explicit_start=True,
allow_unicode=True,
encoding='utf-8')
self.availableNiftiTab.clear()
itemsChanged = HF.list_folders(self.cfg["folders"]["nifti"],
self.cfg["folders"]["prefix"])
self.add_available_items(self.availableNiftiTab, itemsChanged)
else:
self.niftidir = self.cfg["folders"]["nifti"]
def run_reload_files(self):
"""Reloads files, e.g. after renaming them"""
self.cfg = HF.LittleHelpers.load_config(self.cfg["folders"]["rootdir"])
self.availableNiftiTab.clear()
itemsChanged = HF.list_folders(self.cfg["folders"]["nifti"],
prefix=self.cfg["folders"]["prefix"])
self.add_available_items(self.availableNiftiTab, itemsChanged)
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 = HF.list_folders(self.working_dir, prefix='')
self.addAvailableItems(items)
if self.option_gui == "dcm2niix":
self.cfg["folders"]["dicom"] = self.working_dir
HF.LittleHelpers.save_config(self.cfg["folders"]["rootdir"],
self.cfg)
def __init__(self, working_directory, _option_gui, parent=None):
super(QWidget, self).__init__(parent)
self.cfg = HF.LittleHelpers.load_config(ROOTDIR)
self.option_gui = _option_gui
# ============================ Different options available ============================
if self.option_gui == 'dcm2niix':
if os.path.isdir(self.cfg["folders"]["dicom"]):
self.working_dir = self.cfg["folders"]["dicom"]
else:
self.working_dir = os.getcwd()
options = {
'folderbox_title': "Directory (DICOM-files)",
'str_labelDir': 'DICOM DIR: {}'.format(self.working_dir),
'runBTN_label': 'Run processing'
}
elif self.option_gui == "displayNiftiFiles":
if not working_directory:
HF.msg_box(
text='Please provide a valid folder. Terminating this GUI.',
title='No folder provided')
self.close()
return
else:
self.working_dir = working_directory
options = {
'folderbox_title': "Directory (nifti-files)",
'str_labelDir': 'subjects\' DIR: {}'.format(self.working_dir),
'runBTN_label': 'View files'
}
else:
HF.msg_box(
text=
'Please provide a valid option such as "dcm2niix" or "displayNiftiFiles". '
'Terminating the GUI',
title='Wrong input as option')
self.close()
return
# Create general layout
self.tot_layout = QVBoxLayout(self)
self.mid_layout = QHBoxLayout(self)
# ============================ Create upper of GUI, i.e. working directory ============================
self.label_folderbox = QGroupBox(options["folderbox_title"])
self.HBoxUpperTwoListGUI = QVBoxLayout(self.label_folderbox)
self.label_workingdir = QLabel(options["str_labelDir"])
self.HBoxUpperTwoListGUI.addWidget(self.label_workingdir)
self.btn_workingdir = QPushButton('Change working \ndirectory')
self.btn_workingdir.setFixedSize(150, 40)
self.btn_workingdir.setDisabled(True)
if self.option_gui == "dcm2niix":
self.btn_workingdir.setEnabled(True)
self.btn_workingdir.clicked.connect(self.change_workingdir)
self.btn_savedir = QPushButton('Save directory \nto config file')
self.btn_savedir.setFixedSize(150, 40)
self.btn_savedir.setDisabled(True)
if self.option_gui == "dcm2niix":
self.btn_savedir.setEnabled(True)
self.btn_savedir.setToolTip(
HF.LittleHelpers.split_lines(setToolTips.saveDirButton()))
self.btn_savedir.clicked.connect(self.save_cfg_dicomdir)
hlay_upper = QHBoxLayout()
hlay_upper.addWidget(self.btn_workingdir)
hlay_upper.addWidget(self.btn_savedir)
hlay_upper.addStretch(1)
self.HBoxUpperTwoListGUI.addLayout(hlay_upper)
# ==================== Create Content for Lists, i.e. input/output ====================
self.listboxInputGUITwoList = QGroupBox(
'Available items in working directory')
self.listboxInput = QVBoxLayout(self.listboxInputGUITwoList)
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.listboxOutputGUITwoLIst = QGroupBox('Items to process')
self.listboxOutput = QVBoxLayout(self.listboxOutputGUITwoLIst)
self.mOutput = QListWidget()
self.listboxOutput.addWidget(self.mOutput)
# First column (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 (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.setDisabled(True)
self.btn_preferences.clicked.connect(self.settings_show)
if self.option_gui == "dcm2niix":
self.btn_preferences.setEnabled(True)
self.btn_run_command = QPushButton(options["runBTN_label"])
if self.option_gui == "dcm2niix":
self.btn_run_command.setToolTip(setToolTips.run_dcm2niix())
else:
self.btn_run_command.setToolTip(
setToolTips.run_CheckRegistration())
self.btn_run_command.clicked.connect(self.start_process)
hlay_bottom = QHBoxLayout()
hlay_bottom.addStretch(1)
hlay_bottom.addWidget(self.btn_preferences)
hlay_bottom.addWidget(self.btn_run_command)
hlay_bottom.addStretch()
# ==================== Set all contents to general Layout =======================
self.mid_layout.addWidget(self.listboxInputGUITwoList)
self.mid_layout.addLayout(vlay)
self.mid_layout.addWidget(self.listboxOutputGUITwoLIst)
self.mid_layout.addLayout(vlay2)
self.tot_layout.addWidget(self.label_folderbox)
self.tot_layout.addLayout(self.mid_layout)
self.tot_layout.addLayout(hlay_bottom)
try:
self.mInput.clear()
if self.option_gui == 'dcm2niix':
items = HF.list_folders(self.working_dir, prefix='')
else:
items = HF.list_files_in_folder(inputdir=self.working_dir,
contains='',
suffix='nii')
self.addAvailableItems(items)
except FileExistsError:
print('{} without any valid files/folders, continuing ...'.format(
self.working_dir))
self.update_buttons_status()
self.connections()
def __init__(self, parent=None, ROOTDIR=''):
super(GuiTabGeneral, self).__init__(parent)
self.selected_subj_Gen = ''
# General settings/variables/helper files needed needed at some point
if not ROOTDIR:
ROOTDIR = os.path.abspath(
os.path.join(os.path.dirname(__file__), os.pardir))
self.cfg = HF.LittleHelpers.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
HF.LittleHelpers.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 = HF.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)
def __init__(self, parent=None, ROOTDIR=''):
super(GuiTabDetectLeads, self).__init__(parent)
self.selected_subj_ANT = ''
# General settings/variables/helper files needed needed at some point
if not ROOTDIR:
from dependencies import ROOTDIR
self.cfg = HF.LittleHelpers.load_config(
ROOTDIR) # load configuration file/options from file
if os.path.isdir(self.cfg["folders"]["nifti"]):
self.niftidir = self.cfg["folders"]["nifti"]
else:
self.niftidir = os.getcwd()
self.cfg["folders"]["rootdir"] = ROOTDIR
HF.LittleHelpers.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 (Bugra-Files)")
self.HBoxUpperLeftTab = QVBoxLayout(self.FolderboxTab)
self.lblWdirTab = QLabel('wDIR: {}'.format(self.niftidir))
self.HBoxUpperLeftTab.addWidget(self.lblWdirTab)
#TODO: is it possible to summarize the working directoy ? If the path is too long the list of available subjects gets too small
self.btnChangeWdir = QPushButton('Change working directory')
self.btnChangeWdir.clicked.connect(self.change_wdir)
#if changing folder is canceled, the whole script shuts down (macOS Catalina)
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)
# self.HBoxLowerLeftTab.addWidget(self.btn_RegQC)
#TODO: whatsoever (?); accurate
#TODO: view available (...); in tooltips correction instaed of correcion
#TODO: additionally.view available in General -> tooltips: subject instead of just subj
# -------------------- Right part (Subject list) ----------------------- #
self.listbox = QGroupBox('Available subjects')
self.HBoxUpperRightTab = QVBoxLayout(self.listbox)
self.availableNiftiTab = QListWidget()
self.availableNiftiTab.setSelectionMode(
QAbstractItemView.ExtendedSelection)
itemsTab = HF.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(GuiTabPreprocessANTs, self).__init__(parent)
self.selected_subj_ANT = ''
self.cfg = HF.LittleHelpers.load_config(ROOTDIR)
if os.path.isdir(self.cfg["folders"]["nifti"]):
self.niftidir = self.cfg["folders"]["nifti"]
else:
self.niftidir = os.getcwd()
HF.LittleHelpers.save_config(ROOTDIR, self.cfg)
self.lay = QHBoxLayout(self)
self.tab = QWidget()
# Customize tab
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.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.compare_n4Bias_results)
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 = HF.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)