def openDetails(self):
"""opens details file which has additional information on subjects """
import subprocess
fileName = os.path.join(self.cfg["folders"]["nifti"],
'subjdetails.csv')
if os.path.isfile(fileName):
subprocess.Popen(["xdg-open", ''.join(fileName)])
else:
HF.msg_box(text='Subject details are not available!',
title='Detail file not found')
def run_ManualCorrection(self):
"""wrapper which starts the plotting routine for the detected lead which enables manual corrections"""
if len(self.selected_subj_ANT) != 1:
HF.msg_box(text="Please select one and only one subject",
title="Subjects selected")
return
else:
msg = "Are you sure you want to process the following subject:\n\n" \
"{}".format(''.join(' -> {}\n'.format(c) for c in self.selected_subj_ANT))
ret = QMessageBox.question(self, 'MessageBox', msg,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.Yes)
if ret == QMessageBox.Yes:
plotElecModel.PlotRoutines(subject=self.selected_subj_ANT[0],
inputfolder=os.path.join(
self.niftidir,
self.selected_subj_ANT[0]))
def run_LeadDetectionPaCER(self):
"""wrapper to start lead detection with PaCER routines translated to python; original data can be found at:
https://github.com/adhusch/PaCER/"""
if len(self.selected_subj_ANT) > 1:
HF.msg_box(
text=
"Please select only one subject, as multiprocessing for lead detection is not intended",
title="Too many subjects selected")
return
else:
msg = "Are you sure you want to process the following subject:\n\n" \
"{}".format(''.join(' -> {}\n'.format(c) for c in self.selected_subj_ANT))
ret = QMessageBox.question(self, 'MessageBox', msg,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.Yes)
if ret == QMessageBox.Yes:
LeadDetectionRoutines.PaCER_script(
subjects=self.selected_subj_ANT)
def run_RegisterMRI2template(self):
"""Wrapper to run the coregistration routines for the MRI (moving image) to MRI templates (fixed image)
specified in the config file using ANTs routines"""
if not self.selected_subj_ANT:
HF.msg_box(
text=
"No folder selected. To proceed, please indicate what folder to process. "
"(For this option, numerous folders are possible for batch processing)",
title="No subject selected")
else:
msg = "Are you sure you want to coregister the preoperative imaging in the following folders:\n\n" \
"{}".format(''.join(' -> {}\n'.format(c) for c in self.selected_subj_ANT))
ret = QMessageBox.question(self, 'MessageBox', msg,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.Yes)
if ret == QMessageBox.Yes:
ANTspyRoutines.RegistrationANTs().CoregisterMRI2template(
subjects=self.selected_subj_ANT)
def run_n4Bias_corr(self):
"""wrapper to start the preprocessing, that is the GUI in which the different options for ANTs routines
are displayed"""
if not self.selected_subj_ANT:
HF.msg_box(
text=
"No folder selected. To proceed, please indicate what folder to process. "
"(For this option, numerous folders are possible for batch processing)",
title="No subject selected")
else:
msg = "Are you sure you want to process all NIFTI-files in the following folders:\n\n" \
"{}".format(''.join(' -> {}\n'.format(c) for c in self.selected_subj_ANT))
ret = QMessageBox.question(self, 'MessageBox', msg,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.Yes)
if ret == QMessageBox.Yes:
ANTspyRoutines.RegistrationANTs().N4BiasCorrection(
subjects=self.selected_subj_ANT)
def run_RegisterCT2MRI(self):
"""Wrapper to run the coregistration routines for the CT (moving image) to the T1-sequence of the MRI
(fixed image) using ANTs routines"""
if not self.selected_subj_ANT:
HF.msg_box(
text=
"No folder selected. To proceed, please indicate what folder to process. "
"(For this option, numerous folders are possible for batch processing)",
title="No subject selected")
else:
msg = "Are you sure you want to coregister the postoperative CT imaging in the following folders:\n\n" \
"{}".format(''.join(' -> {}\n'.format(c) for c in self.selected_subj_ANT))
ret = QMessageBox.question(self, 'MessageBox', msg,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.Yes)
if ret == QMessageBox.Yes:
ANTspyRoutines.RegistrationANTs().CoregisterCT2MRI(
subjects=self.selected_subj_ANT,
input_folder=self.cfg["folders"]["nifti"])
def VisualiseLeadDetection(self):
"""wrapper to start comparisons between pre- and post-processed images after N4BiasCorrection"""
if not self.selected_subj_ANT:
HF.msg_box(
text=
"No folder selected. To proceed, please select at least one.",
title="No subject selected")
return
elif len(self.selected_subj_ANT) > 1:
HF.msg_box(text="Please select only one subj.",
title="Too many subjects selected")
return
else:
image_folder = os.path.join(
self.cfg["folders"]["nifti"],
self.selected_subj_ANT[0]) # Is the index necessary
self.SelectFiles = TwoListGUI(working_directory=image_folder,
option_gui="displayNiftiFiles")
self.SelectFiles.show()
def show_nifti_files(self):
"""this function opens a list dialog and enables selecting NIFTI files for e.g. check the content (identical
function as in GUITabPreprocessANTs.py."""
if not self.selected_subj_Gen:
HF.msg_box(
text=
"No folder selected. To proceed, please indicate what folder to process.",
title="No subject selected")
return
elif len(self.selected_subj_Gen) > 1:
HF.msg_box(
text=
"Please select only one folder to avoid loading too many images",
title="Too many subjects selected")
return
else:
image_folder = os.path.join(self.cfg["folders"]["nifti"],
self.selected_subj_Gen[0])
self.SelectFiles = TwoListGUI(working_directory=image_folder,
option_gui="displayNiftiFiles")
self.SelectFiles.show()
def compare_n4Bias_results(self):
"""this function enables to select NIFTI files and e.g. compare the results obtained at this step."""
if not self.selected_subj_ANT:
HF.msg_box(
text=
"No folder selected. To proceed, please indicate what folder to process.",
title="No subject selected")
return
elif len(self.selected_subj_ANT) > 1:
HF.LittleHelpers.msg_box(
text=
"Please select only one folder to avoid loading too many images",
title="Too many subjects selected")
return
else:
image_folder = os.path.join(
self.cfg["folders"]["nifti"],
self.selected_subj_ANT[0]) # Is the index necessary
self.SelectFiles = TwoListGUI(working_directory=image_folder,
option_gui="displayNiftiFiles")
self.SelectFiles.show()
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()