def __init__(self, analysis_type, study_directory=None, import_study=False):
super(MainWindow, self).__init__()
if ApplicationStudy is None:
self._init_class()
self.ui = loadUi(self.uifile, self)
toolbar_action_group = QtGui.QActionGroup(self)
toolbar_action_group.addAction(self.ui.action_axial_view)
toolbar_action_group.addAction(self.ui.action_coronal_view)
self._init_action_handlers()
self._analysis_type = analysis_type
self.study = ApplicationStudy(self._analysis_type)
self.runner = self._create_runner(self.study)
self.study_model = LazyStudyModel(self.study, self.runner)
self.analysis_model = LazyAnalysisModel()
self.viewport_model = IntraAnalysisViewportModel(self.analysis_model)
self.viewport_widget = IntraAnalysisViewportWidget(self.viewport_model, self)
self.setCentralWidget(self.viewport_widget)
self.study_view = SubjectsWidget(self.study_model)
self.ui.study_widget_dock.setWidget(self.study_view)
self.setCorner(QtCore.Qt.TopRightCorner, QtCore.Qt.RightDockWidgetArea)
self.setCorner(QtCore.Qt.BottomRightCorner, QtCore.Qt.RightDockWidgetArea)
self.setCorner(QtCore.Qt.TopLeftCorner, QtCore.Qt.LeftDockWidgetArea)
self.setCorner(QtCore.Qt.BottomLeftCorner, QtCore.Qt.LeftDockWidgetArea)
self.runner_view = RunnerView(self.study_model)
self.ui.runner_widget_dock.setWidget(self.runner_view)
self.setWindowTitle(self._window_title())
self.dialogs = {}
self.study_model.current_subject_changed.connect(self.on_current_subject_changed)
self.on_current_subject_changed()
if study_directory is not None:
if import_study:
self._create_inplace_study(study_directory)
else:
self._try_open_study_from_directory(study_directory)
class MainWindow(QtGui.QMainWindow):
uifile = os.path.join(ui_directory, "main_window.ui")
def _init_class(self):
global ApplicationStudy
if settings.tests.mock:
from morphologist.core.tests.mocks.study import MockStudy
ApplicationStudy = MockStudy
else:
ApplicationStudy = Study
def __init__(self, analysis_type, study_directory=None, import_study=False):
super(MainWindow, self).__init__()
if ApplicationStudy is None:
self._init_class()
self.ui = loadUi(self.uifile, self)
toolbar_action_group = QtGui.QActionGroup(self)
toolbar_action_group.addAction(self.ui.action_axial_view)
toolbar_action_group.addAction(self.ui.action_coronal_view)
self._init_action_handlers()
self._analysis_type = analysis_type
self.study = ApplicationStudy(self._analysis_type)
self.runner = self._create_runner(self.study)
self.study_model = LazyStudyModel(self.study, self.runner)
self.analysis_model = LazyAnalysisModel()
self.viewport_model = IntraAnalysisViewportModel(self.analysis_model)
self.viewport_widget = IntraAnalysisViewportWidget(self.viewport_model, self)
self.setCentralWidget(self.viewport_widget)
self.study_view = SubjectsWidget(self.study_model)
self.ui.study_widget_dock.setWidget(self.study_view)
self.setCorner(QtCore.Qt.TopRightCorner, QtCore.Qt.RightDockWidgetArea)
self.setCorner(QtCore.Qt.BottomRightCorner, QtCore.Qt.RightDockWidgetArea)
self.setCorner(QtCore.Qt.TopLeftCorner, QtCore.Qt.LeftDockWidgetArea)
self.setCorner(QtCore.Qt.BottomLeftCorner, QtCore.Qt.LeftDockWidgetArea)
self.runner_view = RunnerView(self.study_model)
self.ui.runner_widget_dock.setWidget(self.runner_view)
self.setWindowTitle(self._window_title())
self.dialogs = {}
self.study_model.current_subject_changed.connect(self.on_current_subject_changed)
self.on_current_subject_changed()
if study_directory is not None:
if import_study:
self._create_inplace_study(study_directory)
else:
self._try_open_study_from_directory(study_directory)
def _init_action_handlers(self):
self._new_study_action_handler = None
self._import_study_action_handler = None
self._edit_study_action_handler = None
def _try_open_study_from_directory(self, study_directory):
try:
study = ApplicationStudy.from_study_directory(study_directory)
except StudySerializationError as e:
title = "Cannot load study"
msg = "'%s':\n%s" % (study_directory, e)
QtGui.QMessageBox.critical(self, title, msg)
else:
self.set_study(study)
def _create_inplace_study(self, study_directory):
QtGui.QApplication.instance().setOverrideCursor(QtCore.Qt.WaitCursor)
pb = _create_import_progress_dialog()
QtGui.QApplication.instance().processEvents()
study = ApplicationStudy.from_organized_directory(
self._analysis_type, study_directory, progress_callback=pb.update_value
)
self.set_study(study)
study.save_to_backup_file()
pb.deleteLater()
del pb
QtGui.QApplication.instance().restoreOverrideCursor()
def _create_runner(self, study):
return SomaWorkflowRunner(study)
# this slot is automagically connected
@QtCore.Slot()
def on_action_new_study_triggered(self):
msg = "Stop current running analysis and create a new study ?"
if self._runner_still_running_after_stopping_asked_to_user(msg):
return
self._new_study_action_handler = NewStudyActionHandler(self._analysis_type, self)
self._new_study_action_handler.study_updated.connect(self.on_study_action_handler_study_updated)
self._new_study_action_handler.start()
# this slot is automagically connected
@QtCore.Slot()
def on_action_import_study_triggered(self):
msg = "Stop current running analysis and import a study ?"
if self._runner_still_running_after_stopping_asked_to_user(msg):
return
self._import_study_action_handler = ImportStudyActionHandler(self._analysis_type, self)
self._import_study_action_handler.study_updated.connect(self.on_study_action_handler_study_updated)
self._import_study_action_handler.start()
# this slot is automagically connected
@QtCore.Slot()
def on_action_edit_study_triggered(self):
msg = "Stop current running analysis and edit the current study ?"
if self._runner_still_running_after_stopping_asked_to_user(msg):
return
self._edit_study_action_handler = EditStudyActionHandler(self.study, self)
self._edit_study_action_handler.study_updated.connect(self.on_study_action_handler_study_updated)
self._edit_study_action_handler.start()
@QtCore.Slot(Study)
def on_study_action_handler_study_updated(self, study):
self.set_study(study)
self._try_save_to_backup_file()
self.runner.set_study(study)
# this slot is automagically connected
@QtCore.Slot()
def on_action_open_study_triggered(self):
msg = "Stop current running analysis and open a study ?"
if self._runner_still_running_after_stopping_asked_to_user(msg):
return
study_directory = QtGui.QFileDialog.getExistingDirectory(
parent=self.ui,
caption="Open a study directory",
directory="",
options=QtGui.QFileDialog.DontUseNativeDialog,
)
if study_directory:
self._try_open_study_from_directory(study_directory)
def _runner_still_running_after_stopping_asked_to_user(self, msg="Stop current running analysis ?"):
if self.runner.is_running():
title = "Analyses are currently running"
answer = QtGui.QMessageBox.question(self, title, msg, QtGui.QMessageBox.Yes, QtGui.QMessageBox.Cancel)
if answer == QtGui.QMessageBox.Yes:
self.runner.stop()
return False
else:
return True
return False
def _try_save_to_backup_file(self):
try:
self.study.save_to_backup_file()
except StudySerializationError as e:
QtGui.QMessageBox.critical(self, "Cannot save the study", "%s" % (e))
# this slot is automagically connected
@QtCore.Slot()
def on_action_export_morphometry_triggered(self):
self.save_morphometry(ALL_SUBJECTS)
# this slot is automagically connected
@QtCore.Slot()
def on_action_export_selection_morphometry_triggered(self):
subject_ids = self.study_model.get_selected_subject_ids()
self.save_morphometry(subject_ids)
def save_morphometry(self, subject_ids):
msg = "Stop current running analysis and save " + "availables morphometry data ?"
if self._runner_still_running_after_stopping_asked_to_user(msg):
return
filter = "CSV (*.csv)"
morphometry_filepath = QtGui.QFileDialog.getSaveFileName(
self.ui,
caption="Choose morphometry output file",
directory="",
options=QtGui.QFileDialog.DontUseNativeDialog,
filter=filter,
)
if morphometry_filepath == "":
return
if subject_ids is ALL_SUBJECTS:
subject_ids = six.iterkeys(self.study.subjects)
command = ["python", "-m", "brainvisa.axon.runprocess", "concatenatefiles"]
morpho_files = []
subjects = []
for subject_id in subject_ids:
analysis = self.study.analyses[subject_id]
analysis.propagate_parameters()
csv_filepath = getattr(analysis.pipeline.process, IntraAnalysisParameterNames.MORPHOMETRY_CSV)
print("morpho file:", csv_filepath)
# ignore none-existing files
if os.path.isfile(csv_filepath):
print("exists.")
morpho_files.append(csv_filepath)
subject_name = analysis.subject.name
subjects.append(subject_name)
print("morpho_files:", morpho_files)
command += ['"' + repr(morpho_files) + '"', '"' + repr(subjects) + '"', morphometry_filepath]
print("command:", " ".join(command))
os.system(" ".join(command))
@QtCore.Slot()
def on_current_subject_changed(self):
subject_id = self.study_model.get_current_subject_id()
if subject_id:
analysis = self.study.analyses[subject_id]
self.analysis_model.set_analysis(analysis)
def set_study(self, study):
self.study = study
self.runner = self._create_runner(self.study)
self.study_model.set_study_and_runner(self.study, self.runner)
if not self.study.has_subjects():
self.analysis_model.remove_analysis()
self.setWindowTitle(self._window_title())
def _window_title(self):
title = "Morphologist - %s" % self.study.study_name
if settings.tests.mock:
title += "--- MOCK MODE ---"
return title
def closeEvent(self, event):
msg = "Stop current running analysis and quit ?"
if self._runner_still_running_after_stopping_asked_to_user(msg):
event.ignore()
else:
if hasattr(self, "browser"):
del self.browser
event.accept()
# this slot is automagically connected
@QtCore.Slot()
def on_action_runner_settings_triggered(self):
dialog = RunnerSettingsDialog(settings, self.study, self)
dialog.show()
# this slot is automagically connected
@QtCore.Slot(bool)
def on_action_axial_view_toggled(self, checked):
if checked:
self.viewport_widget.set_object3d_views_view_type(ViewType.AXIAL)
# this slot is automagically connected
@QtCore.Slot(bool)
def on_action_coronal_view_toggled(self, checked):
if checked:
self.viewport_widget.set_object3d_views_view_type(ViewType.CORONAL)
@QtCore.Slot()
def on_action_documentation_triggered(self):
if not hasattr(self, "browser"):
self.browser = QtWebKit.QWebView()
self.browser.setWindowTitle("Morphologist UI documentation")
self.browser.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.browser.destroyed.connect(self._remove_browser)
version = "%d.%d" % (info.version_major, info.version_minor)
help_index = os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(__file__))))
help_index = os.path.join(help_index, "share", "doc", "morphologist-ui-%s" % version, "index.html")
print("help_index:", help_index)
self.browser.setUrl(QtCore.QUrl.fromLocalFile(help_index))
self.browser.show()
self.browser.raise_()
def _remove_browser(self):
del self.browser
@QtCore.Slot()
def on_action_brainvisa_configuration_triggered(self):
from soma.wip.application.api import Application
from soma.qtgui.api import ApplicationQtGUI
from brainvisa.configuration import neuroConfig
configuration = Application().configuration
appGUI = ApplicationQtGUI()
dialog = appGUI.createEditionDialog(configuration, parent=None, live=False, modal=True)
from soma.qt4gui.configuration_qt4gui import ConfigurationWidget
from soma.qt_gui.qt_backend import QtGui
# remove the database panel and icon
stackw = dialog.findChild(QtGui.QStackedWidget)
dbwidget = stackw.widget(1)
stackw.removeWidget(dbwidget)
listw = dialog.findChild(QtGui.QSplitter).findChild(QtGui.QListWidget)
listw.takeItem(1)
result = dialog.exec_()
if result:
dialog.setObject(configuration)
appGUI.closeEditionDialog(dialog)
# if appGUI.edit(configuration, live=False, modal=True):
if result:
# from brainvisa.configuration import axon_capsul_config_link
# axon_capsul_config_link.axon_to_capsul_config_sync(self.study)
configuration.save(neuroConfig.userOptionFile)
try:
self.study.save_to_backup_file()
except StudySerializationError as e:
pass # study is not saved, don't notify