def change_dicomdir(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.dicomdir = FileOperations.set_wdir_in_config(self.cfg, foldername='dicom')
self.label_dicomdir.setText('dicomDIR: {}'.format(self.dicomdir))
self.cfg['folders']['dicom'] = self.dicomdir
self.mInput.clear()
items = FileOperations.list_folders(inputdir=self.cfg['folders']['dicom'], prefix='', files2lookfor='')
self.add_available_subj(items)
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 = FileOperations.set_wdir_in_config(self.cfg, foldername='nifti')
self.lblWdirTab.setText('wDIR: {}'.format(self.niftidir))
self.cfg['folders']['nifti'] = self.niftidir
self.availableNiftiTab.clear()
itemsChanged = FileOperations.list_folders(self.niftidir, self.cfg['folders']['prefix'])
self.add_available_items(self.availableNiftiTab, itemsChanged)
def run_reload_files(self):
"""Reloads files, e.g. after renaming them"""
self.cfg = Configuration.load_config(ROOTDIR)
self.availableNiftiTab.clear()
itemsChanged = FileOperations.list_folders(self.cfg['folders']['nifti'], prefix=self.cfg['folders']['prefix'])
self.add_available_items(self.availableNiftiTab, itemsChanged)
def run_reload_files(self):
"""Reloads files, e.g. after renaming them"""
self.cfg = Configuration.load_config(self.cfg['folders']['rootdir'])
self.availableTemplates.clear()
itemsTab = set(FileOperations.list_files_in_folder(self.wdirTemplate))
self.add_available_templates(self.availableTemplates, itemsTab)
def N4BiasCorrection_multiprocessing(self, file2rename, subj, input_folder, status):
"""Does the Bias correction taking advantage of the multicores, so that multiple subjects can be processed in
parallel; For that a list of tuples including the entire filename and the subject to be processed are entered"""
status.put(tuple([mp.current_process().name, subj, os.path.split(file2rename)[1]]))
filename_save = os.path.join(input_folder, self.cfg['preprocess']['ANTsN4']['prefix'] +
os.path.split(file2rename)[1])
# Start with N4 Bias correction for sequences specified before
original_image = ants.image_read(os.path.join(input_folder, file2rename))
rescaler_nonneg = ants.contrib.RescaleIntensity(10, 100) # to avoid values <0 causing problems w/ log data
if self.cfg['preprocess']['ANTsN4']['denoise'] == 'yes': # takes forever and therefore not used by default
original_image = ants.denoise_image(image=original_image, noise_model='Rician')
min_orig, max_orig = original_image.min(), original_image.max()
if not os.path.split(file2rename)[1].startswith(self.cfg['preprocess']['ANTsN4']['dti_prefix']):
original_image_nonneg = rescaler_nonneg.transform(original_image)
else:
original_image_nonneg = original_image
bcorr_image = n4biascorr(original_image_nonneg, mask=None,
shrink_factor=self.cfg['preprocess']['ANTsN4']['shrink-factor'],
convergence={'iters': self.cfg['preprocess']['ANTsN4']['convergence'],
'tol': self.cfg['preprocess']['ANTsN4']['threshold']},
spline_param=self.cfg['preprocess']['ANTsN4']['bspline-fitting'],
verbose=bool(self.verbose), weight_mask=None)
if not os.path.split(file2rename)[1].startswith(self.cfg['preprocess']['ANTsN4']['dti_prefix']):
rescaler = ants.contrib.RescaleIntensity(min_orig, max_orig)
bcorr_image = rescaler.transform(bcorr_image)
# difference between both images is saved for debugging purposes
diff_image = original_image - bcorr_image
FileOperations.create_folder(os.path.join(input_folder, "debug")) # only creates folder if not present
ants.image_write(diff_image, filename=os.path.join(input_folder, "debug", "diff_biasCorr_" +
os.path.split(file2rename)[1]))
spacing = self.cfg['preprocess']['registration']['resample_spacing']
bcorr_image = Imaging.resampleANTs(mm_spacing=spacing, ANTsImageObject=bcorr_image,
file_id=filename_save, method=int(self.cfg['preprocess']
['registration']
['resample_method']))
ants.image_write(bcorr_image, filename=filename_save)
def view_template(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:
Output.msg_box(text="No image selected. Please indicate image(s) to load.", title="No templates selected")
return
else:
template_list = [FileOperations.return_full_filename(self.wdirTemplate, x) for x in self.selected_subj_Gen]
Imaging.load_imageviewer('itk-snap', template_list) # to-date, only itk-snap available. could be changed
def CoregisterCT2MRI(self,
subjects,
input_folder,
fixed_image='reg_run[0-9]_bc_t1'):
"""Co-registration of postoperative CT to preoperative MRI for further analyses in same space; before registration
presence of registered MRI data is ensured to avoid redundancy"""
print('\nStarting co-registration for {} subject(s)'.format(
len(subjects)))
allfiles = FileOperations.get_filelist_as_tuple(inputdir=input_folder,
subjects=subjects)
self.check_for_normalisation(subjects)
regex_complete = ['CT_', '{}_'.format(fixed_image.upper())]
included_sequences = [
x for x in list(
filter(re.compile(r"^(?!~).*").match, regex_complete))
]
file_ID_CT, file_ID_MRI = ([] for _ in range(2))
[
file_ID_CT.append(x) for x in allfiles
if 'run' not in x[0] and re.search(
r'\w+{}.'.format(included_sequences[0]), x[0], re.IGNORECASE)
and x[0].endswith('.nii')
]
[
file_ID_MRI.append(x) for x in
allfiles # for simplicity written in a second line as regexp is slightly different
if re.search(r'\w+(?!_).({}).'.format(included_sequences[1]), x[0],
re.IGNORECASE) and x[0].endswith('.nii')
]
if not file_ID_MRI:
Output.msg_box(text="Bias-corrected MRI not found!",
title="Preprocessed MRI unavailable")
return
fileIDs = list(FileOperations.inner_join(file_ID_CT, file_ID_MRI))
self.wrapper_multiprocessing(fileIDs, subjects, 'CT')
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 CoregisterMRI2template(self, subjects):
"""Co-Registration of preoperative MRI to specific template"""
print('\nStarting Co-Registration for {} subject(s)'.format(
len(subjects)))
all_files = FileOperations.get_filelist_as_tuple(
inputdir=self.cfg['folders']['nifti'], subjects=subjects)
sequences = self.cfg['preprocess']['normalisation']['sequences'].split(
sep=',') # sequences of interest
template = glob.glob(
os.path.join(
ROOTDIR, 'ext', 'templates',
self.cfg['preprocess']['normalisation']['template_image'] +
'/*'))
fileIDs = []
for idx, seqs in enumerate(sequences):
file_template = [
x for x in template
if re.search(r'\w+.({}).'.format(seqs), x, re.IGNORECASE)
] # corresponding template
if not file_template:
Output.msg_box(
text=
"No template found. Please ensure templates are installed at './ext/templates'",
title="Template missing!"
) # TODO install templates by default!
return
regex_complete = '{}{}'.format(
self.cfg['preprocess']['ANTsN4']['prefix'], seqs)
files_subj = [
x for x in all_files
if x[0].endswith('.nii') and 'run' not in x[0]
and re.search(r'\w+(?!_).({}).'.format(regex_complete), x[0],
re.IGNORECASE)
]
fileIDs.extend(
tuple([(file_template[0], file_id, subj)
for file_id, subj in files_subj]))
if not fileIDs:
Output.msg_box(
text="No bias-corrected MRI found. Please double-check",
title="Preprocessed MRI missing")
return
self.wrapper_multiprocessing(fileIDs, subjects, 'MRI')
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 ANTsCoregisterMultiprocessing(self,
file_fixed,
file_moving,
subj,
input_folder,
flag,
step,
status,
run=1):
"""Performs Co-Registration taking advantage of multicores, i.e. multiple subjects processed in parallel"""
status.put(tuple([file_fixed, file_moving, subj]))
prev_reg = glob.glob(
os.path.join(input_folder + "/" +
self.cfg['preprocess'][flag]['prefix'] + 'run*' +
os.path.basename(file_moving)))
if not prev_reg:
print('\tNo previous registration found, starting with first run')
filename_save = os.path.join(
input_folder, self.cfg['preprocess'][flag]['prefix'] + 'run' +
str(run) + '_' + os.path.basename(file_moving))
elif re.search(r'\w+{}.'.format('CT_'), file_moving,
re.IGNORECASE) and file_moving.endswith('.nii'):
print('\tNo second run for CT-MRI registrations possible.')
return
else:
allruns = [
re.search(r'\w+(run)([\d.]+)', x).group(2) for x in prev_reg
]
lastrun = int(sorted(allruns)[-1])
file_moving = os.path.join(
input_folder,
self.cfg["preprocess"]["registration"]["prefix"] + 'run' +
str(lastrun) + '_' +
os.path.basename(file_moving)) # update for second run
run = lastrun + 1
n4prefix = self.cfg['preprocess']['ANTsN4']['prefix']
basename = '{}{}'.format(n4prefix, file_moving.split(n4prefix)[1])
filename_save = os.path.join(
input_folder, self.cfg['preprocess'][flag]['prefix'] + 'run' +
str(run) + '_' + basename)
print(filename_save)
log_filename = os.path.join(
ROOTDIR, 'logs',
"log_Registration_using_ANTs_{}_run_{}_".format(subj, str(run)) +
time.strftime("%Y%m%d-%H%M%S") + '.txt')
imaging = dict()
for idx, file_id in enumerate([file_fixed, file_moving]):
sequence = ants.image_read(
file_id) # load data and resample images if necessary
imaging[idx] = Imaging.resampleANTs(
mm_spacing=self.cfg['preprocess']['registration']
['resample_spacing'],
ANTsImageObject=sequence,
file_id=file_id,
method=int(
self.cfg['preprocess']['registration']['resample_method']))
if run == 1:
metric = self.cfg['preprocess']['registration']['metric'][0]
else:
self.cfg['preprocess']['registration'][
'default_registration'] = 'yes' # TODO: must be changed if non-default works
metric = self.cfg['preprocess']['registration']['metric'][0]
if self.cfg['preprocess']['registration'][
'default_registration'] == 'yes':
registered_images = self.default_registration(imaging,
file_fixed,
file_moving,
log_filename,
metric=metric,
step=step)
else:
registered_images = self.custom_registration(
imaging, file_fixed, file_moving, input_folder + '/',
log_filename, run)
key2rename = {
'fwdtransforms':
['{}_0GenericAffineRegistration.mat'.format(step), 1],
'invtransforms': ['{}_1InvWarpMatrix.mat'.format(step), 0]
}
for key, value in key2rename.items():
Transform = ants.read_transform(registered_images[key][value[1]])
ants.write_transform(Transform,
os.path.join(input_folder, value[0]))
ants.image_write(registered_images['warpedmovout'],
filename=filename_save)
FileOperations.create_folder(os.path.join(input_folder, "debug"))
if run > 1: # Previous registrations are moved to debug-folder
prev_reg = ''.join(prev_reg) if type(
prev_reg) == list else prev_reg
filename_dest = re.sub(
r'({}run[0-9]_)+({})'.format(
self.cfg['preprocess']['registration']['prefix'],
self.cfg['preprocess']['ANTsN4']['prefix']),
'{}RUNPREV{}_{}'.format(
self.cfg['preprocess']['registration']['prefix'], lastrun,
self.cfg['preprocess']['ANTsN4']['prefix']),
os.path.basename(prev_reg))
shutil.move(prev_reg,
os.path.join(input_folder, 'debug', filename_dest))
create_mask = True
if create_mask and 't1' in file_moving and not os.path.isfile(
os.path.join(input_folder, 'brainmask_T1.nii')):
Imaging.create_brainmask(
input_folder,
subj=subj,
registered_images=registered_images['warpedmovout'])
def PaCER_script(subjects, inputfolder=''):
"""wrapper script for all steps included in the PaCER algorithm"""
print("\nLead detection of {} subject(s)".format(len(subjects)))
inputfolder = cfg['folders']['nifti'] if not inputfolder else inputfolder # select default input folder
LW = LeadWorks() # load the class including necessary functions
# Look for data files containing CT imaging including the brainMask and load this into workspace
available_files = FileOperations.get_filelist_as_tuple(inputdir=inputfolder, subjects=subjects)
regex2lookfor = 'reg_' + 'run[0-9]', 'brainmask_'
file_id_CTimaging = [file_tuple for file_tuple in available_files
if re.search(r'\w.({}).'.format(regex2lookfor[0]), file_tuple[0], re.IGNORECASE)
and file_tuple[0].endswith('.nii') and 'CT' in file_tuple[0]]
file_id_brainMask = [file_tuple for file_tuple in available_files
if re.search(r'\w.({}).'.format(regex2lookfor[1]), file_tuple[0], re.IGNORECASE)
and file_tuple[0].endswith('.nii')]
if any(t > 2 for t in [len(k) for k in file_id_CTimaging]):
print("More than one files for imaging or brainmask available. Please double-check!")
return
if not file_id_brainMask:
warnings.warn(message="\tNo brain mask was found, trying to obtain a mask using ANTSpyNET routines")
regex2lookforT1 = cfg['preprocess']['normalisation']['prefix'] + 'run'
file_id_T1 = [file_tuple for file_tuple in available_files
if re.search(r'\w.({}).'.format(regex2lookforT1), file_tuple[0], re.IGNORECASE)
and 't1' in file_tuple[0] and file_tuple[0].endswith('.nii')]
if not file_id_T1:
Output.msg_box(text='No T1-sequence imaging available. BrainMask extraction impossible.',
title='T1 sequences missing")')
return
else:
T1imaging = ants.image_read(file_id_T1[0][0])
file_id_brainMask = Imaging.create_brainmask(input_folder=inputfolder, subj=''.join(subjects),
registered_images=T1imaging)
file_id_brainMask = [file_id_brainMask] if type(file_id_brainMask) == tuple else file_id_brainMask
fileID = list(FileOperations.inner_join(file_id_brainMask, file_id_CTimaging)) # joins all to single list
metal_threshold = int(cfg['lead_detection']['PaCER']['metal_threshold'])
elecModels, intensityProfiles, skelSkalms = LW.electrodeEstimation(fileID[0], threshold=metal_threshold)
elecModels, skelSkalms, intensityProfiles, _ = \
LeadProperties.estimate_hemisphere(elecModels, intensityProfiles, skelSkalms) # returns hemisphere from coords.
filename_save = os.path.join(os.path.join(inputfolder, subjects[0]), 'elecModels_' + subjects[0] + '.pkl')
with open(filename_save, "wb") as f:
pickle.dump(elecModels, f)
pickle.dump(intensityProfiles, f)
pickle.dump(skelSkalms, f)
sides = ['left', 'right']
rotation_default, rotation_mod = [{k: [] for k in sides} for _ in range(2)]
for s in sides:
rotation_default[s] = function_wrapper(subj=subjects[0], side=s)
rotation_mod[s] = Configuration.rotation_dict_mod() # creates an empty array to save modified data later
filename_save = os.path.join(os.path.join(inputfolder, subjects[0]), 'rotation_' + subjects[0] + '.pkl')
with open(filename_save, "wb") as f:
pickle.dump(rotation_default, f)
pickle.dump(rotation_mod, f)
print("Finished with lead detection!")
# TODO: it does not return to the empty command line.
return
def N4BiasCorrection(self, subjects):
"""N4BiasCorrection according to N.J. Tustison, ..., and J.C. Gee.
"N4ITK: Improved N3 Bias Correction" IEEE Transactions on Medical Imaging, 29(6):1310-1320, June 2010."""
print('\nDebiasing imaging of {} subject(s)'.format(len(subjects)))
allfiles = FileOperations.get_filelist_as_tuple(inputdir=self.cfg['folders']['nifti'], subjects=subjects)
strings2exclude = ['CT', self.cfg['preprocess']['ANTsN4']['prefix'], 'reg_run', 'Mask', 'Warp', 'Registration']
allfiles = [x for x in allfiles if x[0].endswith('.nii') and not
any(re.search(r'\w+(?!_).({})|^({})\w+.'.format(z, z), os.path.basename(x[0]), re.IGNORECASE)
for z in strings2exclude)]
file_id_DTI = [x for x in allfiles if (x[0].endswith('.nii') and self.cfg['preprocess']['ANTsN4']['dti_prefix']
in x[0]) and not
any(re.search(r'\w+(?!_).({})|^({})\w+.'.format(z, z), os.path.basename(x[0]), re.IGNORECASE)
for z in strings2exclude)]
file_id_noDTI = [x for x in allfiles if (x[0].endswith('.nii') and not
self.cfg['preprocess']['ANTsN4']['dti_prefix'] in x[0]) and not
any(re.search(r'\w+(?!_).({})|^({})\w+.'.format(z, z), os.path.basename(x[0]), re.IGNORECASE)
for z in strings2exclude)]
seq = 'struct' # For debugging purposes
if not seq:
fileIDs = allfiles
elif seq == 'struct':
fileIDs = list(set(allfiles) - set(file_id_DTI))
elif seq == 'dwi':
fileIDs = list(set(allfiles) - set(file_id_noDTI))
start_multi = time.time()
status = mp.Queue()
processes = [mp.Process(target=self.N4BiasCorrection_multiprocessing,
args=(name_file, no_subj, os.path.join(self.cfg['folders']['nifti'], no_subj), status))
for name_file, no_subj in fileIDs]
for p in processes:
p.start()
while any([p.is_alive() for p in processes]):
while not status.empty():
process, no_subj, filename = status.get()
print("Process: {}; Debiasing {}, filename: {}".format(process, no_subj, filename))
time.sleep(0.1)
for p in processes:
p.join()
# Functions creating/updating pipeline log, which document individually all steps along with settings
for subjID in subjects:
allfiles_subj = [os.path.split(files_subj)[1] for files_subj, subj_no in fileIDs if subj_no == subjID]
log_text = "{} files successfully processed (@{}): {}, \n\n Mean Duration per subject: {:.2f} secs" \
.format(len(set(allfiles_subj)), time.strftime("%Y%m%d-%H%M%S"),
'\n\t{}'.format('\n\t'.join(os.path.split(x)[1] for x in sorted(set(allfiles_subj)))),
(time.time() - start_multi) / len(subjects))
Output.logging_routine(text=Output.split_lines(log_text), cfg=self.cfg,
subject=str(subjID), module='N4BiasCorrection',
opt=self.cfg['preprocess']['ANTsN4'], project="")
print('\nIn total, a list of {} subject(s) was processed \nOverall, bias correction took '
'{:.1f} secs.'.format(len(subjects), time.time() - start_multi))
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 __init__(self, working_directory, _option_gui, parent=None):
super(QWidget, self).__init__(parent)
self.cfg = Configuration.load_config(ROOTDIR)
self.option_gui = _option_gui
# ============================ Different options available ============================
if self.option_gui == 'dcm2niix':
working_dir = self.cfg['folders']['dicom']
self.working_dir = working_dir if os.path.isdir(
working_dir) else 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:
Output.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:
Output.msg_box(
text=
"Please provide a valid option such as 'dcm2niix' or 'displayNiftiFiles'. "
"Terminating the GUI",
title="Wrong input as option")
self.close()
return
# ============================ Start creating layout ============================
# 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(
Output.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 = FileOperations.list_folders(self.working_dir,
prefix='')
else:
items = FileOperations.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):
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 dcm2niix_multiprocessing(self, name_subj, no_subj, dcm2niix_bin,
last_idx, total_subj, status):
"""function intended to provide multiprocessing approach to speed up extraction of DICOM data to nifti files"""
modalities = ['CT', 'MRI']
if self.logfile:
log_filename = os.path.join(
ROOTDIR, 'logs', 'log_DCM2NII_' + str(no_subj + last_idx) +
time.strftime("%Y%m%d-%H%M%S"))
else:
log_filename = os.devnull
subj_outdir = os.path.join(
self.outdir,
self.cfg['folders']['prefix'] + str(no_subj + last_idx))
FileOperations.create_folder(subj_outdir)
start_time_subject = time.time()
keptfiles, deletedfiles = ([] for _ in range(2))
for mod in modalities:
status.put((name_subj, mod, no_subj, total_subj))
input_folder_name = os.path.join(self.inputdir, name_subj + mod)
# input_folder_files = [f.path for f in os.scandir(input_folder_name)
# if (f.is_dir() and ('100' in f.path or 'DICOM' in f.path or '001' in f.path))]
input_folder_files = []
[
input_folder_files.append(item)
for item in os.listdir(input_folder_name)
if (os.path.isdir(os.path.join(input_folder_name, item)) and (
'100' in item or 'DICOM' in item or '001' in item))
]
orig_stdout = sys.stdout
sys.stdout = open(log_filename, 'w')
for folder in input_folder_files:
subprocess.call(
[
dcm2niix_bin,
'-a',
'y', # anonimisation of DICOM data
'-b',
self.cfg['preprocess']['dcm2nii']['BIDSsidecar'][0],
'-z',
self.cfg['preprocess']['dcm2nii']['OutputCompression']
[0],
'-f',
self.cfg['preprocess']['dcm2nii']['OutputFileStruct'],
'-o',
subj_outdir,
'-w',
str(self.cfg['preprocess']['dcm2nii']
['NameConflicts']),
'-v',
str(self.cfg['preprocess']['dcm2nii']['Verbosity']),
'-x',
str(self.cfg['preprocess']['dcm2nii']['ReorientCrop']),
folder
],
stdout=sys.stdout,
stderr=subprocess.STDOUT)
sys.stdout.close()
sys.stdout = orig_stdout
files_kept, files_deleted = self.select_sequences(subj_outdir)
keptfiles.extend(files_kept)
deletedfiles.extend(files_deleted)
# Functions creating/updating pipeline log, which document individually all steps along with settings
log_text = "{} files successfully converted: {}, \n\nand {} deleted: {}.\nDuration: {:.2f} secs" \
.format(len(set(keptfiles)),
'\n\t{}'.format('\n\t'.join(os.path.split(x)[1] for x in sorted(set(keptfiles)))),
len(set(deletedfiles)),
'\n\t{}'.format('\n\t'.join(os.path.split(x)[1] for x in sorted(set(deletedfiles)))),
time.time() - start_time_subject)
Output.logging_routine(text=Output.split_lines(log_text),
cfg=self.cfg,
subject=self.cfg['folders']['prefix'] +
str(no_subj),
module='dcm2nii',
opt=self.cfg['preprocess']['dcm2nii'],
project="")
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(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 __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)