def test_read_tree_with_markers(self):
xml_file = _resource_path("tree_with_markers.xml")
neurolucida_data = read_xml(xml_file)
self.assertEqual(0, neurolucida_data.contours_count())
self.assertEqual(2, neurolucida_data.markers_count())
self.assertEqual(1, neurolucida_data.trees_count())
tree = neurolucida_data.get_tree(0)
marker = neurolucida_data.get_marker(1)
self.assertTrue('colour' in tree)
self.assertTrue('rgb' in tree)
self.assertTrue('type' in tree)
self.assertTrue('leaf' in tree)
self.assertTrue('data' in tree)
self.assertEqual([1.0, 0.0, 1.0], tree['rgb'])
self.assertTrue('colour' in marker)
self.assertTrue('rgb' in marker)
self.assertTrue('name' in marker)
self.assertTrue('type' in marker)
self.assertTrue('varicosity' in marker)
self.assertTrue('data' in marker)
self.assertEqual('Dot', marker['type'])
def test_read_scale(self):
xml_file = _resource_path("scale_example.xml")
neurolucida_data = read_xml(xml_file)
self.assertEqual(1, neurolucida_data.contours_count())
contour = neurolucida_data.get_contour(0)
raw_data = contour['data']
pt1 = raw_data[0]
self.assertAlmostEqual(5276.676, pt1.coordinates()[0])
def test_read_multi_images(self):
xml_file = _resource_path("scale_example_2.xml")
neurolucida_data = read_xml(xml_file)
self.assertEqual(1, neurolucida_data.contours_count())
contour = neurolucida_data.get_contour(0)
raw_data = contour['data']
pt1 = raw_data[0]
self.assertAlmostEqual(14603.48225272, pt1.coordinates()[0])
def test_write_ex_basic_group(self):
ex_file = _resource_path("basic_groups.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
xml_file = _resource_path("tree_with_anatomical_terms.xml")
data = read_xml(xml_file)
write_ex(ex_file, data, {'external_annotation': True})
self.assertTrue(_is_line_in_file(ex_file, " Group name: Thorasic Sympathetic Trunk"))
def test_write_ex_basic(self):
ex_file = _resource_path("basic_vessel.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
xml_file = _resource_path("tracing_vessels_and_markers.xml")
data = read_xml(xml_file)
write_ex(ex_file, data)
self.assertTrue(os.path.exists(ex_file))
def test_write_ex_with_annotation(self):
ex_file = _resource_path("tree_with_annotation.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
xml_file = _resource_path("tree_with_anatomical_terms.xml")
data = read_xml(xml_file)
write_ex(ex_file, data)
self.assertTrue(os.path.exists(ex_file))
def test_write_tree_with_markers(self):
xml_file = _resource_path("tree_with_markers.xml")
neurolucida_data = read_xml(xml_file)
ex_file = _resource_path("tree_with_markers.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
write_ex(ex_file, neurolucida_data)
self.assertTrue(os.path.exists(ex_file))
self.assertTrue(_is_line_in_file(ex_file, " Group name: marker"))
def test_read_tree_with_anatomical_terms(self):
xml_file = _resource_path("tree_with_anatomical_terms.xml")
neurolucida_data = read_xml(xml_file)
self.assertEqual(2, neurolucida_data.trees_count())
tree = neurolucida_data.get_tree(0)
self.assertTrue('colour' in tree)
self.assertTrue('rgb' in tree)
self.assertTrue('type' in tree)
self.assertTrue('leaf' in tree)
self.assertTrue('data' in tree)
self.assertTrue('anatomical term' in tree)
self.assertEqual([0.0, 1.0, 1.0], tree['rgb'])
def test_read_not_xml(self):
not_xml_file = _resource_path("random_file.txt")
contents = read_xml(not_xml_file)
self.assertIsNone(contents)
def test_read_multi_tree_xml(self):
xml_file = os.path.join(here, "resources", "multi_tree.xml")
contents = read_xml(xml_file)
self.assertEqual(3, len(contents))
def test_not_existing_xml_file(self):
xml_file = _resource_path("missing.xml")
contents = read_xml(xml_file)
self.assertIsNone(contents)
def test_read_vessel_xml(self):
xml_file = _resource_path("tracing_vessels_and_markers.xml")
contents = read_xml(xml_file)
self.assertEqual(7, len(contents))
def test_read_basic_contour_xml(self):
xml_file = _resource_path("basic_heart_contours.xml")
contents = read_xml(xml_file)
self.assertEqual(1, len(contents))
def test_read_vessel_xml(self):
xml_file = os.path.join(here, "resources",
"tracing_vessels_and_markers.xml")
contents = read_xml(xml_file)
self.assertEqual(7, len(contents))
def test_read_basic_contour_xml(self):
xml_file = os.path.join(here, "resources", "basic_heart_contours.xml")
contents = read_xml(xml_file)
self.assertEqual(1, len(contents))
def test_read_not_xml(self):
not_xml_file = os.path.join(here, "resources", "random_file.txt")
contents = read_xml(not_xml_file)
self.assertIsNone(contents)
def test_read_multi_tree_xml(self):
xml_file = _resource_path("multi_tree.xml")
contents = read_xml(xml_file)
self.assertEqual(3, len(contents))
def test_not_existing_xml_file(self):
xml_file = os.path.join(here, "resources", "missing.xml")
contents = read_xml(xml_file)
self.assertIsNone(contents)