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_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_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_write_ex_branch(self):
ex_file = _resource_path("multi_tree.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
tree = {'rgb': [0, 0, 0],
'data': [MBFPoint(3, 3, 4, 2), [MBFPoint(2, 1, 5, 7)], [MBFPoint(2, 4, 8, 5.7)]]}
data = MBFData()
data.add_tree(tree)
write_ex(ex_file, data)
self.assertTrue(os.path.exists(ex_file))
def test_write_ex_basic(self):
ex_file = _resource_path("basic_tree.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
tree = {'rgb': [0, 0, 0],
'data': [MBFPoint(3, 3, 4, 2), MBFPoint(2, 1, 5, 7), MBFPoint(3, 1, 4.2, 7.1)]}
data = MBFData()
data.add_tree(tree)
write_ex(ex_file, data)
self.assertTrue(os.path.exists(ex_file))
def test_write_ex_basic(self):
ex_file = _resource_path("basic_contour.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
data = MBFData()
contour = {'colour': '#00ff00', 'rgb': [0, 1, 0], 'closed': True, 'name': 'Heart',
'data': [MBFPoint(3, 3, 4, 1), MBFPoint(2, 1, 5, 1),
MBFPoint(3, 1, 4.2, 1)]}
data.add_contour(contour)
write_ex(ex_file, data)
self.assertTrue(os.path.exists(ex_file))
