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_multi_tree_and_annotation(self):
ex_file = _resource_path("multi_tree_with_annotations.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
xml_file = _resource_path("multi_tree_with_annotations.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 = MBFTree('#000000', '', '', {'points': [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 = MBFTree('#000000', '', '', {'points': [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_puncta(self):
ex_file = _resource_path("puncta.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
xml_file = _resource_path("puncta.xml")
contents = read_xml(xml_file)
write_ex(ex_file, contents)
self.assertTrue(os.path.exists(ex_file))
with open(ex_file) as f:
lines = f.readlines()
self.assertEqual(3370, len(lines))
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)],
'properties': []}
data.add_contour(contour)
write_ex(ex_file, data)
self.assertTrue(os.path.exists(ex_file))
def test_read_puncta_with_set_property(self):
ex_file = _resource_path("puncta_with_set_prop.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
xml_file = _resource_path("puncta_with_set_prop.xml")
contents = read_xml(xml_file)
write_ex(ex_file, contents)
self.assertTrue(os.path.exists(ex_file))
self.assertTrue(_is_line_in_file(ex_file, " Group name: inner submucosal nerve plexus"))
with open(ex_file) as f:
lines = f.readlines()
self.assertEqual(1055, len(lines))
def test_contour_multiple_properties(self):
ex_file = _resource_path("contour_with_multiple_set_properties.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
xml_file = _resource_path("contour_with_multiple_set_properties.xml")
contents = read_xml(xml_file)
self.assertEqual(1, len(contents))
write_ex(ex_file, contents)
self.assertTrue(os.path.exists(ex_file))
self.assertTrue(_is_line_in_file(ex_file, " Group name: inner submucosal nerve plexus"))
self.assertTrue(_is_line_in_file(ex_file, " Group name: Nerve fiber connecting inner submucosal nerve plexus and outer submucosal nerve plexus"))
def main():
options = {}
args = parse_args()
if os.path.exists(args.input_xml):
if args.output_ex is None:
output_ex = args.input_xml + '.ex'
else:
output_ex = args.output_ex
options["external_annotation"] = args.external_annotation
contents = read_xml(args.input_xml)
if contents is None:
sys.exit(-2)
else:
write_ex(output_ex, contents, options)
else:
sys.exit(-1)
def test_tree_with_trace_association(self):
ex_file = _resource_path("tree_with_trace_association.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
xml_file = _resource_path("tree_with_trace_association.xml")
neurolucida_data = read_xml(xml_file)
self.assertEqual(0, neurolucida_data.contours_count())
self.assertEqual(0, neurolucida_data.markers_count())
self.assertEqual(1, neurolucida_data.trees_count())
write_ex(ex_file, neurolucida_data)
self.assertTrue(os.path.exists(ex_file))
self.assertTrue(_is_line_in_file(ex_file, " Group name: http://purl.org/sig/ont/fma/fma15005"))
with open(ex_file) as f:
lines = f.readlines()
self.assertEqual(180, len(lines))
def test_tree_with_set_property(self):
ex_file = _resource_path("tree_with_set_property.ex")
if os.path.exists(ex_file):
os.remove(ex_file)
xml_file = _resource_path("tree_with_set_property.xml")
neurolucida_data = read_xml(xml_file)
self.assertEqual(0, neurolucida_data.contours_count())
self.assertEqual(0, neurolucida_data.markers_count())
self.assertEqual(1, neurolucida_data.trees_count())
write_ex(ex_file, neurolucida_data)
self.assertTrue(os.path.exists(ex_file))
self.assertTrue(_is_line_in_file(ex_file, " Group name: Bob"))
self.assertTrue(_is_line_in_file(ex_file, " Group name: Dave"))
with open(ex_file) as f:
lines = f.readlines()
self.assertEqual(552, len(lines))