def test_from_array(self):
        x = np.array([
            [1, 2, -1, 3],
            [-1, -1, np.nan, 1],
            [1, 3, 3, 2]
        ])

        expected = np.array([
            [0, 1, MV, 2],
            [MV, MV, MV, 0],
            [0, 2, 2, 1]
        ])

        anno = AnnotationsContainer.from_array(x)
        np.testing.assert_equal(anno.annotations, expected)

        self.assertEqual(anno.nclasses, 3)
        self.assertEqual(anno.labels, [1, 2, 3])
        self.assertEqual(anno.missing_values, [np.nan, -1])

        # now using a list-of-lists
        x = x.tolist()
        anno = AnnotationsContainer.from_array(x)
        np.testing.assert_equal(anno.annotations, expected)

        self.assertEqual(anno.nclasses, 3)
        self.assertEqual(anno.labels, [1, 2, 3])
        self.assertEqual(anno.missing_values, [np.nan, -1])

        # inconsistent number of elements
        x[1] = [1, 2]
        self.assertRaises(PyannoValueError,
                          AnnotationsContainer.from_array,
                          x)
Example #2
0
 def _new_annotations_fired(self):
     """Create an empty annotations set."""
     annotations = CreateNewAnnotationsDialog.create_annotations_dialog()
     if annotations is not None:
         name = self.application.database.get_available_id()
         anno_cont = AnnotationsContainer.from_array(annotations, name=name)
         self.set_annotations(anno_cont)
def estimate_quality_instance_level(annotations, pmids):
    m, workers = get_M_overall(annotations, pmids)
    instance_model = ModelB.create_initial_state(2, len(workers))
    anno = AnnotationsContainer.from_array(m, missing_values=[2])
    instance_model.map(anno.annotations) 
    proxy_skill = (instance_model.theta[:,0,0] + instance_model.theta[:,1,1]) / 2.0
    return dict(zip(workers, proxy_skill))
Example #4
0
    def setUp(self):
        self.tmp_filename = mktemp(prefix='tmp_pyanno_db_')

        # fixtures
        self.model1 = ModelA.create_initial_state(4)
        self.annotations1 = self.model1.generate_annotations(100)
        self.value1 = self.model1.log_likelihood(self.annotations1)
        self.anno_container1 = AnnotationsContainer.from_array(
            self.annotations1)
        self.data_id1 = 'bogus.txt'

        self.model2 = ModelB.create_initial_state(4, 8)
        self.annotations2 = self.model2.generate_annotations(100)
        self.value2 = self.model2.log_likelihood(self.annotations2)
        self.anno_container2 = AnnotationsContainer.from_array(
            self.annotations2)
        self.data_id2 = 'bogus2.txt'
Example #5
0
    def setUp(self):
        self.tmp_filename = mktemp(prefix='tmp_pyanno_db_')

        # fixtures
        self.model1 = ModelA.create_initial_state(4)
        self.annotations1 = self.model1.generate_annotations(100)
        self.value1 = self.model1.log_likelihood(self.annotations1)
        self.anno_container1 = AnnotationsContainer.from_array(
            self.annotations1)
        self.data_id1 = 'bogus.txt'

        self.model2 = ModelB.create_initial_state(4, 8)
        self.annotations2 = self.model2.generate_annotations(100)
        self.value2 = self.model2.log_likelihood(self.annotations2)
        self.anno_container2 = AnnotationsContainer.from_array(
            self.annotations2)
        self.data_id2 = 'bogus2.txt'
Example #6
0
 def _new_annotations_fired(self):
     """Create an empty annotations set."""
     annotations = CreateNewAnnotationsDialog.create_annotations_dialog()
     if annotations is not None:
         name = self.application.database.get_available_id()
         anno_cont = AnnotationsContainer.from_array(annotations,
                                                     name=name)
         self.set_annotations(anno_cont)
 def _edit_data_fired(self):
     data_view = DataView(data=self.annotations_container.raw_annotations)
     data_view.edit_traits(kind='livemodal', parent=self.info.ui.control)
     self.annotations_container = AnnotationsContainer.from_array(
         data_view.data, name=self.annotations_container.name)
     if self.application is not None:
         self.application.main_window.set_annotations(
             self.annotations_container)
 def _edit_data_fired(self):
     data_view = DataView(data=self.annotations_container.raw_annotations)
     data_view.edit_traits(kind='livemodal', parent=self.info.ui.control)
     self.annotations_container = AnnotationsContainer.from_array(
         data_view.data,
         name = self.annotations_container.name
     )
     if self.application is not None:
         self.application.main_window.set_annotations(
             self.annotations_container)
def main():
    """ Entry point for standalone testing/debugging. """

    from pyanno.modelBt_loopdesign import ModelBtLoopDesign
    model = ModelBtLoopDesign.create_initial_state(5)
    annotations = model.generate_annotations(2)

    anno = AnnotationsContainer.from_array(annotations, name='blah')
    model_view = AnnotationsView(annotations_container=anno, model=HasTraits())
    model_view.configure_traits()
    return model, annotations, model_view
Example #10
0
def main():
    """ Entry point for standalone testing/debugging. """

    from pyanno.modelBt_loopdesign import ModelBtLoopDesign
    model = ModelBtLoopDesign.create_initial_state(5)
    annotations = model.generate_annotations(2)

    anno = AnnotationsContainer.from_array(annotations, name='blah')
    model_view = AnnotationsView(annotations_container=anno, model=HasTraits())
    model_view.configure_traits()
    return model, annotations, model_view
    def test_from_file_with_commas(self):
        s = """
        1,2,3,
        -1, -1, 1,
        1, 2, 3
        """

        buffer = StringIO(s)
        anno = AnnotationsContainer._from_file_object(buffer)

        expected = np.array([[0, 1, 2], [MV, MV, 0], [0, 1, 2]])
        np.testing.assert_equal(anno.annotations, expected)
    def test_from_array(self):
        x = np.array([[1, 2, -1, 3], [-1, -1, np.nan, 1], [1, 3, 3, 2]])

        expected = np.array([[0, 1, MV, 2], [MV, MV, MV, 0], [0, 2, 2, 1]])

        anno = AnnotationsContainer.from_array(x)
        np.testing.assert_equal(anno.annotations, expected)

        self.assertEqual(anno.nclasses, 3)
        self.assertEqual(anno.labels, [1, 2, 3])
        self.assertEqual(anno.missing_values, [np.nan, -1])

        # now using a list-of-lists
        x = x.tolist()
        anno = AnnotationsContainer.from_array(x)
        np.testing.assert_equal(anno.annotations, expected)

        self.assertEqual(anno.nclasses, 3)
        self.assertEqual(anno.labels, [1, 2, 3])
        self.assertEqual(anno.missing_values, [np.nan, -1])

        # inconsistent number of elements
        x[1] = [1, 2]
        self.assertRaises(PyannoValueError, AnnotationsContainer.from_array, x)
Example #13
0
    def test_from_file_with_commas(self):
        s = """
        1,2,3,
        -1, -1, 1,
        1, 2, 3
        """

        buffer = StringIO(s)
        anno = AnnotationsContainer._from_file_object(buffer)

        expected = np.array([
            [0, 1, 2],
            [MV, MV, 0],
            [0, 1, 2]
        ])
        np.testing.assert_equal(anno.annotations, expected)
def estimate_quality_for_q(annotations, qnum, pmids=None):
    m, workers = get_M_q(annotations, qnum, pmids=pmids)
    q_model = ModelB.create_initial_state(2, len(workers))
    anno = AnnotationsContainer.from_array(m, missing_values=[2])
    q_model.map(anno.annotations)
    '''
    pi[k] is the probability of label k
    theta[j,k,k'] is the probability that 
        annotator j reports label k' for an 
        item whose real label is k, i.e. 
        P( annotator j chooses k' | real label = k)
    '''
    # this is a simple mean of sensitivity and specificity
    # @TODO revisit?
    proxy_skill = (q_model.theta[:, 0, 0] + q_model.theta[:, 1, 1]) / 2.0
    return dict(zip(workers, proxy_skill))
    def test_from_file_numerical_labels(self):
        s = """
         1 -1  2
         2  1  3
        -1 -1  3
        """

        buffer = StringIO(s)
        anno = AnnotationsContainer._from_file_object(buffer)

        expected = np.array([[0, MV, 1], [1, 0, 2], [MV, MV, 2]])
        np.testing.assert_equal(anno.annotations, expected)

        self.assertEqual(anno.nclasses, 3)
        self.assertEqual(anno.labels, ['1', '2', '3'])
        self.assertEqual(anno.missing_values, ['-1'])
    def test_from_file_string_labels(self):
        s = """
        D B A A B
        C A * C A
        B B D D *
        """

        buffer = StringIO(s)
        anno = AnnotationsContainer._from_file_object(buffer)

        self.assertEqual(anno.nclasses, 4)
        self.assertEqual(anno.nannotators, 5)
        # labels should be sorted
        self.assertEqual(anno.labels, ['A', 'B', 'C', 'D'])
        self.assertEqual(anno.missing_values, ['*'])

        expected = np.array(
            [[3, 1, 0, 0, 1], [2, 0, MV, 2, 0], [1, 1, 3, 3, MV]], dtype=int)
        np.testing.assert_equal(anno.annotations, expected)
Example #17
0
    def test_from_file_numerical_labels(self):
        s = """
         1 -1  2
         2  1  3
        -1 -1  3
        """

        buffer = StringIO(s)
        anno = AnnotationsContainer._from_file_object(buffer)

        expected = np.array([
            [0, MV, 1],
            [1, 0, 2],
            [MV, MV, 2]
        ])
        np.testing.assert_equal(anno.annotations, expected)

        self.assertEqual(anno.nclasses, 3)
        self.assertEqual(anno.labels, ['1', '2', '3'])
        self.assertEqual(anno.missing_values, ['-1'])
Example #18
0
    def test_from_file_string_labels(self):
        s = """
        D B A A B
        C A * C A
        B B D D *
        """

        buffer = StringIO(s)
        anno = AnnotationsContainer._from_file_object(buffer)

        self.assertEqual(anno.nclasses, 4)
        self.assertEqual(anno.nannotators, 5)
        # labels should be sorted
        self.assertEqual(anno.labels, ['A', 'B', 'C', 'D'])
        self.assertEqual(anno.missing_values, ['*'])

        expected = np.array([
            [3, 1, 0, 0, 1],
            [2, 0, MV, 2, 0],
            [1, 1, 3, 3, MV]
        ], dtype=int)
        np.testing.assert_equal(anno.annotations, expected)
 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)
 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)
Example #21
0
 def _annotations_view_default(self):
     anno = AnnotationsContainer.from_array([[0]], name='<undefined>')
     return AnnotationsView(annotations_container=anno,
                            nclasses=self.model.nclasses,
                            application=self.application,
                            model=HasTraits())
Example #22
0
 def _update_annotations_file(self):
     logger.info('Load file {}'.format(self.annotations_file))
     anno = AnnotationsContainer.from_file(self.annotations_file)
     self.set_annotations(anno)
Example #23
0
 def _update_annotations_file(self):
     logger.info('Load file {}'.format(self.annotations_file))
     anno = AnnotationsContainer.from_file(self.annotations_file)
     self.set_annotations(anno)
Example #24
0
 def _annotations_view_default(self):
     anno = AnnotationsContainer.from_array([[0]], name='<undefined>')
     return AnnotationsView(annotations_container = anno,
                            nclasses = self.model.nclasses,
                            application = self.application,
                            model=HasTraits())