def main():
""" Entry point for standalone testing/debugging. """
from pyanno.ui.model_data_view import ModelDataView
model = ModelBtLoopDesign.create_initial_state(5)
model_data_view = ModelDataView()
model_data_view.set_model(model)
# open model_data_view
model_data_view.configure_traits(view='traits_view')
return model, model_data_view
def main():
""" Entry point for standalone testing/debugging. """
from pyanno.ui.model_data_view import ModelDataView
model = ModelBtLoopDesign.create_initial_state(5)
model_data_view = ModelDataView()
model_data_view.set_model(model)
# open model_data_view
model_data_view.configure_traits(view='traits_view')
return model, model_data_view
class PyannoApplication(HasTraits):
database = Instance(PyannoDatabase)
main_window = Instance(ModelDataView)
database_window = Instance(DatabaseView)
database_ui = Instance(UI)
logging_level = Int(logging.INFO)
pyanno_pathname = Str
db_window_open = Property(Bool)
def _get_db_window_open(self):
return (self.database_ui is not None
and self.database_ui.control is not None)
def open(self):
self._start_logging()
self._open_pyanno_database()
self._open_main_window()
def close(self):
self.database.close()
logger.info('Closing pyAnno -- Goodbye!')
def _start_logging(self):
logging.basicConfig(level=self.logging_level)
logger.info('Starting pyAnno')
def _create_pyanno_directory(self):
"""Create a pyanno directort in the user's home if it is missing."""
home_dir = os.getenv('HOME') or os.getenv('HOMEPATH')
logger.debug('Found home directory at ' + str(home_dir))
self.pyanno_pathname = os.path.join(home_dir, PYANNO_PATH_NAME)
try:
logger.debug('Creating pyAnno directory at ' + self.pyanno_pathname)
os.makedirs(self.pyanno_pathname)
except OSError as e:
logger.debug('pyAnno directory already existing')
if e.errno != errno.EEXIST:
raise
def _open_pyanno_database(self):
# database filename
self._create_pyanno_directory()
db_filename = os.path.join(self.pyanno_pathname,
DATABASE_FILENAME)
self.database = PyannoDatabase(db_filename)
def _open_main_window(self):
self.main_window = ModelDataView(application=self)
model = ModelBt.create_initial_state(5, 8)
self.main_window.set_model(model=model)
self.main_window.configure_traits()
def open_database_window(self):
if self.db_window_open:
# windows exists, raise
self.database_ui.control.Raise()
else:
# window was closed or not existent
logger.debug('Open database window')
database_window = DatabaseView(database=self.database,
application=self)
database_ui = database_window.edit_traits(kind='live')
self.database_window = database_window
self.database_ui = database_ui
def close_database_window(self):
# wx specific
self.database_ui.control.Close()
def update_window_from_database_record(self, record):
"""Update main window from pyanno database record.
"""
self.main_window.set_from_database_record(record)
def add_current_state_to_database(self):
mdv = self.main_window
# file name may contain unicode characters
data_id = mdv.annotations_view.annotations_container.name
if data_id is '':
data_id = 'anonymous_annotations'
elif type(data_id) is unicode:
u_data_id = unicodedata.normalize('NFKD', data_id)
data_id = u_data_id.encode('ascii','ignore')
try:
self.database.store_result(
data_id,
mdv.annotations_view.annotations_container,
mdv.model,
mdv.log_likelihood
)
except PyannoValueError as e:
logger.info(e)
errmsg = e.args[0]
error('Error: ' + errmsg)
if self.db_window_open:
self.database_window.db_updated = True
def _create_debug_database(self):
"""Create and populate a test database in a temporary file.
"""
from tempfile import mktemp
from pyanno.modelA import ModelA
from pyanno.modelB import ModelB
from pyanno.annotations import AnnotationsContainer
# database filename
tmp_filename = mktemp(prefix='tmp_pyanno_db_')
db = PyannoDatabase(tmp_filename)
def _create_new_entry(model, annotations, id):
value = model.log_likelihood(annotations)
ac = AnnotationsContainer.from_array(annotations, name=id)
db.store_result(id, ac, model, value)
# populate database
model = ModelA.create_initial_state(5)
annotations = model.generate_annotations(100)
_create_new_entry(model, annotations, 'test_id')
modelb = ModelB.create_initial_state(5, 8)
_create_new_entry(modelb, annotations, 'test_id')
annotations = model.generate_annotations(100)
_create_new_entry(modelb, annotations, 'test_id2')
self.database = db
class PyannoApplication(HasTraits):
database = Instance(PyannoDatabase)
main_window = Instance(ModelDataView)
database_window = Instance(DatabaseView)
database_ui = Instance(UI)
logging_level = Int(logging.INFO)
pyanno_pathname = Str
db_window_open = Property(Bool)
def _get_db_window_open(self):
return (self.database_ui is not None
and self.database_ui.control is not None)
def open(self):
self._start_logging()
self._open_pyanno_database()
self._open_main_window()
def close(self):
self.database.close()
logger.info('Closing pyAnno -- Goodbye!')
def _start_logging(self):
logging.basicConfig(level=self.logging_level)
logger.info('Starting pyAnno')
def _create_pyanno_directory(self):
"""Create a pyanno directort in the user's home if it is missing."""
home_dir = os.getenv('HOME') or os.getenv('HOMEPATH')
logger.debug('Found home directory at ' + str(home_dir))
self.pyanno_pathname = os.path.join(home_dir, PYANNO_PATH_NAME)
try:
logger.debug('Creating pyAnno directory at ' +
self.pyanno_pathname)
os.makedirs(self.pyanno_pathname)
except OSError as e:
logger.debug('pyAnno directory already existing')
if e.errno != errno.EEXIST:
raise
def _open_pyanno_database(self):
# database filename
self._create_pyanno_directory()
db_filename = os.path.join(self.pyanno_pathname, DATABASE_FILENAME)
self.database = PyannoDatabase(db_filename)
def _open_main_window(self):
self.main_window = ModelDataView(application=self)
model = ModelBt.create_initial_state(5, 8)
self.main_window.set_model(model=model)
self.main_window.configure_traits()
def open_database_window(self):
if self.db_window_open:
# windows exists, raise
self.database_ui.control.Raise()
else:
# window was closed or not existent
logger.debug('Open database window')
database_window = DatabaseView(database=self.database,
application=self)
database_ui = database_window.edit_traits(kind='live')
self.database_window = database_window
self.database_ui = database_ui
def close_database_window(self):
# wx specific
self.database_ui.control.Close()
def update_window_from_database_record(self, record):
"""Update main window from pyanno database record.
"""
self.main_window.set_from_database_record(record)
def add_current_state_to_database(self):
mdv = self.main_window
# file name may contain unicode characters
data_id = mdv.annotations_view.annotations_container.name
if data_id is '':
data_id = 'anonymous_annotations'
elif type(data_id) is unicode:
u_data_id = unicodedata.normalize('NFKD', data_id)
data_id = u_data_id.encode('ascii', 'ignore')
try:
self.database.store_result(
data_id, mdv.annotations_view.annotations_container, mdv.model,
mdv.log_likelihood)
except PyannoValueError as e:
logger.info(e)
errmsg = e.args[0]
error('Error: ' + errmsg)
if self.db_window_open:
self.database_window.db_updated = True
def _create_debug_database(self):
"""Create and populate a test database in a temporary file.
"""
from tempfile import mktemp
from pyanno.modelA import ModelA
from pyanno.modelB import ModelB
from pyanno.annotations import AnnotationsContainer
# database filename
tmp_filename = mktemp(prefix='tmp_pyanno_db_')
db = PyannoDatabase(tmp_filename)
def _create_new_entry(model, annotations, id):
value = model.log_likelihood(annotations)
ac = AnnotationsContainer.from_array(annotations, name=id)
db.store_result(id, ac, model, value)
# populate database
model = ModelA.create_initial_state(5)
annotations = model.generate_annotations(100)
_create_new_entry(model, annotations, 'test_id')
modelb = ModelB.create_initial_state(5, 8)
_create_new_entry(modelb, annotations, 'test_id')
annotations = model.generate_annotations(100)
_create_new_entry(modelb, annotations, 'test_id2')
self.database = db