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
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
def main():
""" Entry point for standalone testing/debugging. """
from tempfile import mktemp
from contextlib import closing
# database filename
tmp_filename = mktemp(prefix='tmp_pyanno_db_')
with closing(PyannoDatabase(tmp_filename)) as db:
# populate database
model = ModelA.create_initial_state(5)
annotations = model.generate_annotations(100)
_create_new_entry(model, annotations, 'test_id', db)
modelb = ModelB.create_initial_state(5, 8)
_create_new_entry(modelb, annotations, 'test_id', db)
annotations = model.generate_annotations(100)
_create_new_entry(modelb, annotations, 'test_id2', db)
# create view
database_view = DatabaseView(database=db)
database_view.edit_traits(view='traits_view')
return model, database_view
def main():
""" Entry point for standalone testing/debugging. """
from tempfile import mktemp
from contextlib import closing
# database filename
tmp_filename = mktemp(prefix='tmp_pyanno_db_')
with closing(PyannoDatabase(tmp_filename)) as db:
# populate database
model = ModelA.create_initial_state(5)
annotations = model.generate_annotations(100)
_create_new_entry(model, annotations, 'test_id', db)
modelb = ModelB.create_initial_state(5, 8)
_create_new_entry(modelb, annotations, 'test_id', db)
annotations = model.generate_annotations(100)
_create_new_entry(modelb, annotations, 'test_id2', db)
# create view
database_view = DatabaseView(database=db)
database_view.edit_traits(view='traits_view')
return model, database_view
def _create_model_from_dialog(cls, dialog):
# create prior alpha from user choice
# prior strength multiplies the dirichlet parameters alpha
alpha = (np.array(ALPHA_DEFAULT) - 1.) * dialog.prior_strength + 1.
alpha = create_band_matrix(dialog.nclasses, alpha)
model = ModelB.create_initial_state(dialog.nclasses,
dialog.nannotators,
alpha=alpha)
return model
def main():
""" Entry point for standalone testing/debugging. """
from pyanno.models import ModelB
model = ModelB.create_initial_state(4, 5)
anno = model.generate_annotations(100)
samples = model.sample_posterior_over_accuracy(anno, 10)
model_view = ModelBView(model=model)
model_view.plot_theta_samples(samples)
model_view.configure_traits(view='traits_view')
return model, model_view
