class MainWnd(QMainWindow):
def __init__(self):
super().__init__()
self.exporter = Exporter()
self.initUI()
self.controlTower = None
def setControlTower(self, ct):
self.controlTower = ct
def initUI(self):
self.menuBar = QMenuBar(self)
self.menuBar.setNativeMenuBar(False)
file_menu = self.menuBar.addMenu('File')
file_menu.addAction('New', self.save)
file_menu.addAction('Open', self.save)
file_menu.addAction('Close', self.save)
file_menu.addAction('Save', self.save)
file_menu.addAction('Save as', self.save)
file_menu.addAction('Quit', self.quit)
repo_menu = self.menuBar.addMenu('Repository')
repo_menu.addAction('private')
repo_menu.addAction('global')
config_menu = self.menuBar.addMenu('Tools')
config_menu.addAction('Preferences')
config_menu.addAction('Export', self.export)
box_menu = config_menu.addMenu('Box')
box_menu.addAction('New combo box', self.createCompositeBox)
box_menu.addAction('New Code box', self.createCodeBox)
window_menu = self.menuBar.addMenu('Window')
window_menu.addAction('Description')
help_menu = self.menuBar.addMenu('Help')
help_menu.addAction('online document', self.quit)
self.setMenuBar(self.menuBar)
self.setWindowTitle('Athena')
self.statusBar().show()
def createCodeBox(self):
self.controlTower.createNewBox('CODE')
def createCompositeBox(self):
self.controlTower.createNewBox('COMPOSITION')
def save(self):
pass
def export(self):
exporter = Exporter()
exporter.processExport(self.controlTower.getOpenedBox())
def quit(self):
sys.exit(0)
class MainWindow(QMainWindow):
def __init__(self, application, *args, **kwargs):
super(MainWindow, self).__init__(*args, **kwargs)
self.printer_thread = WorkerThread()
self.printer_thread.message.connect(self.standardOutputWritten)
self.printer_thread.start()
self.app = application
self.app.setStyle("Fusion")
self.__set_interface()
self.__set_layouts()
self.__set_stylesheet()
self.__set_connections()
self.__set_params()
def closeEvent(self, event):
self.printer_thread.stop()
def __set_interface(self):
self.button_width = 0.35
self.button_height = 0.05
self.setWindowTitle("GSI-RADS")
self.__getScreenDimensions()
self.setGeometry(self.left, self.top, self.width, self.height)
self.setMaximumWidth(self.width)
#self.setMaximumHeight(self.height)
self.setMinimumWidth(self.width)
self.setMinimumHeight(self.height)
self.move(self.width / 2, self.height / 2)
self.menu_bar = QMenuBar(self)
self.menu_bar.setNativeMenuBar(
False
) # https://stackoverflow.com/questions/25261760/menubar-not-showing-for-simple-qmainwindow-code-qt-creator-mac-os
self.file_menu = self.menu_bar.addMenu('File')
self.import_dicom_action = QAction(
QIcon(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'images/database-icon.png')), 'Import DICOM',
self)
self.import_dicom_action.setShortcut('Ctrl+D')
self.file_menu.addAction(self.import_dicom_action)
self.quit_action = QAction('Quit', self)
self.quit_action.setShortcut("Ctrl+Q")
self.file_menu.addAction(self.quit_action)
self.settings_menu = self.menu_bar.addMenu('Settings')
self.settings_seg_menu = self.settings_menu.addMenu("Segmentation...")
self.settings_seg_preproc_menu = self.settings_seg_menu.addMenu(
"Preprocessing...")
self.settings_seg_preproc_menu_p1_action = QAction(
"Brain-masking off (P1)", checkable=True)
self.settings_seg_preproc_menu_p2_action = QAction(
"Brain-masking on (P2)", checkable=True)
self.settings_seg_preproc_menu_p2_action.setChecked(True)
self.settings_seg_preproc_menu.addAction(
self.settings_seg_preproc_menu_p1_action)
self.settings_seg_preproc_menu.addAction(
self.settings_seg_preproc_menu_p2_action)
self.help_menu = self.menu_bar.addMenu('Help')
self.readme_action = QAction(
QIcon(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'images/readme-icon.jpeg')), 'Tutorial', self)
self.readme_action.setShortcut("Ctrl+R")
self.help_menu.addAction(self.readme_action)
self.about_action = QAction(
QIcon(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'images/about-icon.png')), 'About', self)
self.about_action.setShortcut("Ctrl+A")
self.help_menu.addAction(self.about_action)
self.help_action = QAction(
QIcon.fromTheme("help-faq"), "Help", self
) # Default icons can be found here: https://specifications.freedesktop.org/icon-naming-spec/icon-naming-spec-latest.html#guidelines
self.help_action.setShortcut("Ctrl+J")
self.help_menu.addAction(self.help_action)
self.input_image_lineedit = QLineEdit()
self.input_image_lineedit.setFixedWidth(self.width *
(0.93 - self.button_width / 2))
self.input_image_lineedit.setFixedHeight(self.height *
self.button_height)
self.input_image_lineedit.setReadOnly(True)
self.input_image_pushbutton = QPushButton('Input MRI')
self.input_image_pushbutton.setFixedWidth(self.height *
self.button_width)
self.input_image_pushbutton.setFixedHeight(self.height *
self.button_height)
self.input_segmentation_lineedit = QLineEdit()
self.input_segmentation_lineedit.setReadOnly(True)
self.input_segmentation_lineedit.setFixedWidth(
self.width * (0.93 - self.button_width / 2))
self.input_segmentation_lineedit.setFixedHeight(self.height *
self.button_height)
self.input_segmentation_pushbutton = QPushButton('Input segmentation')
self.input_segmentation_pushbutton.setFixedWidth(self.height *
self.button_width)
self.input_segmentation_pushbutton.setFixedHeight(self.height *
self.button_height)
self.output_folder_lineedit = QLineEdit()
self.output_folder_lineedit.setReadOnly(True)
self.output_folder_lineedit.setFixedWidth(
self.width * (0.93 - self.button_width / 2))
self.output_folder_lineedit.setFixedHeight(self.height *
self.button_height)
self.output_folder_pushbutton = QPushButton('Output destination')
self.output_folder_pushbutton.setFixedWidth(self.height *
self.button_width)
self.output_folder_pushbutton.setFixedHeight(self.height *
self.button_height)
self.run_button = QPushButton('Run diagnosis')
self.run_button.setFixedWidth(self.height * self.button_width)
self.run_button.setFixedHeight(self.height * self.button_height)
self.main_display_tabwidget = QTabWidget()
self.tutorial_textedit = QPlainTextEdit()
self.tutorial_textedit.setReadOnly(True)
self.tutorial_textedit.setFixedWidth(self.width * 0.97)
self.tutorial_textedit.setPlainText(
"HOW TO USE THE SOFTWARE: \n"
" 1) Click 'Input MRI...' to select from your file explorer the MRI scan to process (unique file).\n"
" 1*) Alternatively, Click File > Import DICOM... if you wish to process an MRI scan as a DICOM sequence.\n"
" 2) Click 'Output destination' to choose a directory where to save the results \n"
" 3) (OPTIONAL) Click 'Input segmentation' to choose a tumor segmentation mask file, if nothing is provided the internal model with generate the segmentation automatically \n"
" 4) Click 'Run diagnosis' to perform the analysis. The human-readable version will be displayed in the interface.\n"
" \n"
"NOTE: \n"
"The output folder is populated automatically with the following: \n"
" * The diagnosis results in human-readable text (report.txt) and Excel-ready format (report.csv).\n"
" * The automatic segmentation masks of the brain and the tumor in the original patient space (input_brain_mask.nii.gz and input_tumor_mask.nii.gz).\n"
" * The input volume and tumor segmentation mask in MNI space in the sub-directory named \'registration\'.\n"
)
self.main_display_tabwidget.addTab(self.tutorial_textedit, 'Tutorial')
self.prompt_lineedit = QPlainTextEdit()
self.prompt_lineedit.setReadOnly(True)
self.prompt_lineedit.setFixedWidth(self.width * 0.97)
self.main_display_tabwidget.addTab(self.prompt_lineedit, 'Logging')
self.results_textedit = QPlainTextEdit()
self.results_textedit.setReadOnly(True)
self.results_textedit.setFixedWidth(self.width * 0.97)
self.main_display_tabwidget.addTab(self.results_textedit, 'Results')
self.sintef_logo_label = QLabel()
self.sintef_logo_label.setPixmap(
QPixmap(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'images/sintef-logo.png')))
self.sintef_logo_label.setFixedWidth(0.95 * (self.width / 3))
self.sintef_logo_label.setFixedHeight(
1 * (self.height * self.button_height))
self.sintef_logo_label.setScaledContents(True)
self.stolavs_logo_label = QLabel()
self.stolavs_logo_label.setPixmap(
QPixmap(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'images/stolavs-logo.png')))
self.stolavs_logo_label.setFixedWidth(0.95 * (self.width / 3))
self.stolavs_logo_label.setFixedHeight(
1 * (self.height * self.button_height))
self.stolavs_logo_label.setScaledContents(True)
self.amsterdam_logo_label = QLabel()
self.amsterdam_logo_label.setPixmap(
QPixmap(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'images/amsterdam-logo.png')))
self.amsterdam_logo_label.setFixedWidth(0.95 * (self.width / 3))
self.amsterdam_logo_label.setFixedHeight(
1 * (self.height * self.button_height))
self.amsterdam_logo_label.setScaledContents(True)
def __set_layouts(self):
self.input_volume_hbox = QHBoxLayout()
self.input_volume_hbox.addStretch(1)
self.input_volume_hbox.addWidget(self.input_image_lineedit)
self.input_volume_hbox.addWidget(self.input_image_pushbutton)
self.input_volume_hbox.addStretch(1)
self.input_seg_hbox = QHBoxLayout()
self.input_seg_hbox.addStretch(1)
self.input_seg_hbox.addWidget(self.input_segmentation_lineedit)
self.input_seg_hbox.addWidget(self.input_segmentation_pushbutton)
self.input_seg_hbox.addStretch(1)
self.output_dir_hbox = QHBoxLayout()
self.output_dir_hbox.addStretch(1)
self.output_dir_hbox.addWidget(self.output_folder_lineedit)
self.output_dir_hbox.addWidget(self.output_folder_pushbutton)
self.output_dir_hbox.addStretch(1)
self.run_action_hbox = QHBoxLayout()
self.run_action_hbox.addStretch(1)
self.run_action_hbox.addWidget(self.run_button)
self.run_action_hbox.addStretch(1)
self.dump_area_hbox = QHBoxLayout()
self.dump_area_hbox.addStretch(1)
self.dump_area_hbox.addWidget(self.main_display_tabwidget)
self.dump_area_hbox.addStretch(1)
self.logos_hbox = QHBoxLayout()
self.logos_hbox.addStretch(1)
self.logos_hbox.addWidget(self.sintef_logo_label)
self.logos_hbox.addWidget(self.stolavs_logo_label)
self.logos_hbox.addWidget(self.amsterdam_logo_label)
self.logos_hbox.addStretch(1)
self.main_vbox = QVBoxLayout()
self.main_vbox.addWidget(self.menu_bar)
#self.main_vbox.addStretch(1)
self.main_vbox.addLayout(self.input_volume_hbox)
self.main_vbox.addLayout(self.output_dir_hbox)
self.main_vbox.addLayout(self.input_seg_hbox)
self.main_vbox.addLayout(self.run_action_hbox)
#self.main_vbox.addStretch(1)
self.main_vbox.addLayout(self.dump_area_hbox)
self.main_vbox.addLayout(self.logos_hbox)
#self.main_vbox.addStretch(1)
self.central_label = QLabel()
self.central_label.setLayout(self.main_vbox)
self.setCentralWidget(self.central_label)
def __set_stylesheet(self):
self.central_label.setStyleSheet(
'QLabel{background-color: qlineargradient(spread:pad, x1:0.5, y1:1, x2:0.5, y2:0, stop:0 rgba(207, 209, 207, 255), stop:1 rgba(230, 229, 230, 255));}'
)
self.menu_bar.setStyleSheet(get_stylesheet('QMenuBar'))
self.input_image_lineedit.setStyleSheet(get_stylesheet('QLineEdit'))
self.input_image_pushbutton.setStyleSheet(
get_stylesheet('QPushButton'))
self.input_segmentation_lineedit.setStyleSheet(
get_stylesheet('QLineEdit'))
self.input_segmentation_pushbutton.setStyleSheet(
get_stylesheet('QPushButton'))
self.output_folder_lineedit.setStyleSheet(get_stylesheet('QLineEdit'))
self.output_folder_pushbutton.setStyleSheet(
get_stylesheet('QPushButton'))
self.results_textedit.setStyleSheet(get_stylesheet('QTextEdit'))
self.prompt_lineedit.setStyleSheet(get_stylesheet('QTextEdit'))
self.run_button.setStyleSheet(get_stylesheet('QPushButton'))
def __set_connections(self):
self.run_button.clicked.connect(self.diagnose_main_wrapper)
self.input_image_pushbutton.clicked.connect(
self.run_select_input_image)
self.input_segmentation_pushbutton.clicked.connect(
self.run_select_input_segmentation)
self.output_folder_pushbutton.clicked.connect(
self.run_select_output_folder)
self.readme_action.triggered.connect(self.readme_action_triggered)
self.about_action.triggered.connect(self.about_action_triggered)
self.quit_action.triggered.connect(self.quit_action_triggered)
self.import_dicom_action.triggered.connect(
self.import_dicom_action_triggered)
self.help_action.triggered.connect(self.help_action_triggered)
self.settings_seg_preproc_menu_p1_action.triggered.connect(
self.settings_seg_preproc_menu_p1_action_triggered)
self.settings_seg_preproc_menu_p2_action.triggered.connect(
self.settings_seg_preproc_menu_p2_action_triggered)
def __set_params(self):
self.input_image_filepath = ''
self.input_annotation_filepath = ''
self.output_folderpath = ''
def __getScreenDimensions(self):
screen = self.app.primaryScreen()
size = screen.size()
self.left = size.width() / 2
self.top = size.height() / 2
self.width = 0.4 * size.width()
self.height = 0.4 * size.height()
def readme_action_triggered(self):
popup = QMessageBox()
popup.setWindowTitle('Tutorial')
popup.setText(
"HOW TO USE THE SOFTWARE: \n"
" 1) Click 'Input MRI...' to select from your file explorer the MRI scan to process (unique file).\n"
" 1*) Alternatively, Click File > Import DICOM... if you wish to process an MRI scan as a DICOM sequence.\n"
" 2) Click 'Output destination' to choose a directory where to save the results \n"
" 3) (OPTIONAL) Click 'Input segmentation' to choose a tumor segmentation mask file, if nothing is provided the internal model with generate the segmentation automatically \n"
" 4) Click 'Run diagnosis' to perform the analysis. The human-readable version will be displayed in the interface.\n"
" \n"
"NOTE: \n"
"The output folder is populated automatically with the following: \n"
" * The diagnosis results in human-readable text (report.txt) and Excel-ready format (report.csv).\n"
" * The automatic segmentation masks of the brain and the tumor in the original patient space (input_brain_mask.nii.gz and input_tumor_mask.nii.gz).\n"
" * The input volume and tumor segmentation mask in MNI space in the sub-directory named \'registration\'.\n"
)
popup.exec_()
def about_action_triggered(self):
popup = QMessageBox()
popup.setWindowTitle('About')
popup.setText(
'Software developed as part of a collaboration between: \n'
' * Departement of Health Research, SINTEF\n'
' * St. Olavs hospital, Trondheim University Hospital\n'
' * Amsterdam University Medical Center\n\n'
'Contact: David Bouget, Andre Pedersen\n\n'
'For questions about the software, please visit:\n'
'https://github.com/SINTEFMedtek/GSI-RADS\n'
'For questions about the methodological aspect, please refer to the original publication:\n'
'https://www.mdpi.com/2072-6694/13/12/2854/review_report')
popup.exec_()
def quit_action_triggered(self):
self.printer_thread.stop()
sys.exit()
def diagnose_main_wrapper(self):
self.run_diagnosis_thread = threading.Thread(target=self.run_diagnosis)
self.run_diagnosis_thread.daemon = True # using daemon thread the thread is killed gracefully if program is abruptly closed
self.run_diagnosis_thread.start()
def run_diagnosis(self):
if not os.path.exists(self.input_image_filepath) or not os.path.exists(
self.output_folderpath):
self.standardOutputWritten(
'Process could not be started - The 1st and 2nd above-fields must be filled in.\n'
)
return
self.run_button.setEnabled(False)
self.prompt_lineedit.clear()
self.main_display_tabwidget.setCurrentIndex(1)
QApplication.processEvents(
) # to immidiently update GUI after button is clicked
self.seg_preprocessing_scheme = 'P1' if self.settings_seg_preproc_menu_p1_action.isChecked(
) else 'P2'
try:
start_time = time.time()
print('Initialize - Begin (Step 0/6)')
from diagnosis.main import diagnose_main
print('Initialize - End (Step 0/6)')
print('Step runtime: {} seconds.'.format(
np.round(time.time() - start_time, 3)) + "\n")
diagnose_main(
input_volume_filename=self.input_image_filepath,
input_segmentation_filename=self.input_annotation_filepath,
output_folder=self.output_folderpath,
preprocessing_scheme=self.seg_preprocessing_scheme)
except Exception as e:
print('{}'.format(traceback.format_exc()))
self.run_button.setEnabled(True)
self.standardOutputWritten(
'Process could not be completed - Issue arose.\n')
QApplication.processEvents()
return
self.run_button.setEnabled(True)
results_filepath = os.path.join(
ResourcesConfiguration.getInstance().output_folder, 'report.txt')
self.results_textedit.setPlainText(open(results_filepath, 'r').read())
self.main_display_tabwidget.setCurrentIndex(2)
def run_select_input_image(self):
input_image_filedialog = QFileDialog()
self.input_image_filepath = input_image_filedialog.getOpenFileName(
self, 'Select input T1 MRI', '~',
"Image files (*.nii *.nii.gz *.nrrd *.mha *.mhd)")[0]
self.input_image_lineedit.setText(self.input_image_filepath)
def run_select_input_segmentation(self):
filedialog = QFileDialog()
self.input_annotation_filepath = filedialog.getOpenFileName(
self, 'Select input segmentation file', '~',
"Image files (*.nii *.nii.gz)")[0]
self.input_segmentation_lineedit.setText(
self.input_annotation_filepath)
def import_dicom_action_triggered(self):
filedialog = QFileDialog()
filedialog.setFileMode(QFileDialog.DirectoryOnly)
self.input_image_filepath = filedialog.getExistingDirectory(
self, 'Select DICOM folder', '~')
self.input_image_lineedit.setText(self.input_image_filepath)
def run_select_output_folder(self):
filedialog = QFileDialog()
filedialog.setFileMode(QFileDialog.DirectoryOnly)
self.output_folderpath = filedialog.getExistingDirectory(
self, 'Select output folder', '~')
self.output_folder_lineedit.setText(self.output_folderpath)
def standardOutputWritten(self, text):
self.prompt_lineedit.moveCursor(QTextCursor.End)
self.prompt_lineedit.insertPlainText(text)
QApplication.processEvents()
def help_action_triggered(self):
# opens browser with specified url, directs user to Issues section of GitHub repo
QDesktopServices.openUrl(
QUrl("https://github.com/SINTEFMedtek/GSI-RADS/issues"))
def settings_seg_preproc_menu_p1_action_triggered(self, status):
if status:
self.settings_seg_preproc_menu_p2_action.setChecked(False)
else:
self.settings_seg_preproc_menu_p2_action.setChecked(True)
def settings_seg_preproc_menu_p2_action_triggered(self, status):
if status:
self.settings_seg_preproc_menu_p1_action.setChecked(False)
else:
self.settings_seg_preproc_menu_p1_action.setChecked(True)
class Ui_MainWindow(object):
def setupUi(self, MainWindow):
MainWindow.resize(1280, 720)
self.central_widget = QWidget(MainWindow)
self.splitter = QSplitter(self.central_widget)
self.splitter.setChildrenCollapsible(False)
self.splitter.setOpaqueResize(True)
self.main_grid_layout = QGridLayout(self.central_widget)
self.main_grid_layout.addWidget(self.splitter)
self.main_grid_layout.setSizeConstraint(QLayout.SetDefaultConstraint)
self.tab_widget = QTabWidget(self.central_widget)
self.tab_widget.setMinimumSize(QSize(500, 0))
self._set_up_component_tree_view()
self.splitter.addWidget(self.tab_widget)
self._set_up_3d_view()
MainWindow.setCentralWidget(self.central_widget)
self._set_up_menus(MainWindow)
self.tab_widget.setCurrentIndex(0)
QMetaObject.connectSlotsByName(MainWindow)
self.splitter.setStretchFactor(0, 0)
self.splitter.setStretchFactor(1, 1)
def _set_up_3d_view(self):
self.sceneWidget.setMinimumSize(QSize(600, 0))
self.splitter.addWidget(self.sceneWidget)
def _set_up_component_tree_view(self):
self.sceneWidget = InstrumentView(self.splitter)
self.component_tree_view_tab = ComponentTreeViewTab(
scene_widget=self.sceneWidget, parent=self
)
self.tab_widget.addTab(self.component_tree_view_tab, "")
def _set_up_menus(self, MainWindow: QObject):
self.menu_bar = QMenuBar()
self.menu_bar.setGeometry(QRect(0, 0, 1280, 720))
self.file_menu = QMenu(self.menu_bar)
MainWindow.setMenuBar(self.menu_bar)
self.status_bar = QStatusBar(MainWindow)
MainWindow.setStatusBar(self.status_bar)
self.open_json_file_action = QAction(MainWindow)
self.open_json_file_action.setShortcut(QKeySequence("Ctrl+O"))
self.export_to_filewriter_JSON_action = QAction(MainWindow)
self.export_to_filewriter_JSON_action.setShortcut(QKeySequence("Ctrl+S"))
self.file_menu.addAction(self.open_json_file_action)
self.file_menu.addAction(self.export_to_filewriter_JSON_action)
self.view_menu = QMenu(self.menu_bar)
self.show_action_labels = QAction(MainWindow)
self.show_action_labels.setCheckable(True)
self.show_action_labels.setChecked(True)
self.simple_tree_view = QAction(MainWindow)
self.simple_tree_view.setCheckable(True)
self.about_window = QAction(MainWindow)
self.view_menu.addAction(self.about_window)
self.view_menu.addAction(self.show_action_labels)
self.view_menu.addAction(self.simple_tree_view)
self.menu_bar.addAction(self.file_menu.menuAction())
self.menu_bar.addAction(self.view_menu.menuAction())
self._set_up_titles(MainWindow)
def _set_up_titles(self, MainWindow):
MainWindow.setWindowTitle("NeXus Constructor")
self.tab_widget.setTabText(
self.tab_widget.indexOf(self.component_tree_view_tab), "Nexus Structure"
)
self.file_menu.setTitle("File")
self.open_json_file_action.setText("Open File writer JSON file")
self.export_to_filewriter_JSON_action.setText("Export to File writer JSON")
self.view_menu.setTitle("View")
self.show_action_labels.setText("Show Button Labels")
self.simple_tree_view.setText("Use Simple Tree Model View")
self.about_window.setText("About")
self.menu_bar.setNativeMenuBar(False)
