def test_maximum_common_subgraph_for_data_pair(self):
"""Load two segmented data frames and track them"""
mesh_sequence = mesh.read_sequence_from_data(
path.join(dirname(__file__), 'data', 'first_few_frames'))
first_mesh = mesh_sequence[0]
second_mesh = mesh_sequence[1]
print 'I am testing...'
subgraph_finder = tracking.LocalisedSubgraphFinder(
first_mesh, second_mesh)
print 'Can I find a subgraph?'
subgraph_finder.find_maximum_common_subgraph()
print len(subgraph_finder.largest_mappings)
post_processor = tracking.PostProcessor(
first_mesh, second_mesh, subgraph_finder.largest_mappings)
post_processor.index_global_ids_from_largest_mappings()
# tracked_ids = tracking.find_maximum_common_subgraph( first_mesh, second_mesh )
first_mesh.plot(path.join(dirname(__file__), 'output',
'first_mesh_tracked.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(first_mesh.elements))
second_mesh.plot(path.join(dirname(__file__), 'output',
'second_mesh_tracked.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(first_mesh.elements))
first_mesh.save(
path.join(dirname(__file__), 'output', 'first_mesh_tracked.mesh'))
second_mesh.save(
path.join(dirname(__file__), 'output', 'second_mesh_tracked.mesh'))
post_processor.tidy_current_mapping()
first_mesh.plot(
path.join(dirname(__file__), 'output',
'first_mesh_tracked_cleaned.pdf'),
color_by_global_id=True,
total_number_of_global_ids=first_mesh.get_num_elements())
second_mesh.plot(
path.join(dirname(__file__), 'output',
'second_mesh_tracked_cleaned.pdf'),
color_by_global_id=True,
total_number_of_global_ids=first_mesh.get_num_elements())
first_mesh.save(
path.join(dirname(__file__), 'output',
'first_mesh_tracked_cleaned.mesh'))
second_mesh.save(
path.join(dirname(__file__), 'output',
'second_mesh_tracked_cleaned.mesh'))
def test_post_processing_for_second_data_pair(self):
"""Load two segmented data frames and track them"""
first_mesh = mesh.load(
path.join(dirname(__file__), 'output',
'second_mesh_tracked_with_third_mesh_cleaned.mesh'))
second_mesh = mesh.load(
path.join(dirname(__file__), 'output',
'third_mesh_tracked_cleaned.mesh'))
largest_mapping = {}
for element in first_mesh.elements:
if element.global_id != None:
second_frame_id = second_mesh.get_element_with_global_id(
element.global_id).id_in_frame
largest_mapping[element.id_in_frame] = second_frame_id
largest_mappings = [largest_mapping]
post_processor = tracking.PostProcessor(first_mesh, second_mesh,
largest_mappings)
post_processor.index_global_ids_from_largest_mappings()
post_processor.post_process_with_data()
first_mesh.plot(
path.join(dirname(__file__), 'output',
'second_mesh_tracked_with_third_mesh_processed.pdf'),
color_by_global_id=True,
total_number_of_global_ids=first_mesh.get_num_elements())
second_mesh.plot(
path.join(dirname(__file__), 'output',
'third_mesh_tracked_processed.pdf'),
color_by_global_id=True,
total_number_of_global_ids=first_mesh.get_num_elements())
first_mesh.save(
path.join(
dirname(__file__), 'output',
'second_mesh_tracked_with_third_mesh_tracked_processed.mesh'))
second_mesh.save(
path.join(dirname(__file__), 'output',
'third_mesh_tracked_processed.mesh'))
def make_division_II_plot(figuresize):
"""We load a mesh where two maximum common subgraphs will be identified, and track the division event"""
mesh_one = mesh.load('standard_ambiguous_division_one.mesh')
mesh_two = copy.deepcopy(mesh_one)
mesh_one.assign_frame_ids_in_order()
mesh_two.assign_frame_ids_randomly()
# build ground truth for testing the mapping
ground_truth = {}
for element_index, element in enumerate(mesh_one.elements):
ground_truth[
element.id_in_frame] = mesh_two.elements[element_index].id_in_frame
# pick the element closest to the centre
most_central_element = mesh_two.find_most_central_element()
mesh_two.divide_element_with_frame_id_in_direction(
most_central_element.id_in_frame, [1.0, 1.0])
subgraph_finder = tracking.ReducedBacktrackingSubgraphFinder(
mesh_one, mesh_two)
subgraph_finder.find_maximum_common_subgraph()
post_processor = tracking.PostProcessor(
mesh_one, mesh_two, [subgraph_finder.largest_mappings[1]])
post_processor.index_global_ids_from_largest_mappings()
tracked_ids = post_processor.mapped_ids
tracked_ids_all = tracked_ids
plotname = 'division_II'
make_difference_plot(mesh_one, mesh_two, tracked_ids, tracked_ids_all,
plotname, figuresize)
def test_post_processing_for_first_data_pair(self):
"""Load two segmented data frames and track them"""
first_mesh = mesh.load(
path.join(dirname(__file__), 'output',
'first_mesh_tracked_cleaned.mesh'))
second_mesh = mesh.load(
path.join(dirname(__file__), 'output',
'second_mesh_tracked_cleaned.mesh'))
largest_mapping = {}
for element in first_mesh.elements:
if element.global_id != None:
second_frame_id = second_mesh.get_element_with_global_id(
element.global_id).id_in_frame
largest_mapping[element.id_in_frame] = second_frame_id
largest_mappings = [largest_mapping]
post_processor = tracking.PostProcessor(first_mesh, second_mesh,
largest_mappings)
post_processor.index_global_ids_from_largest_mappings()
post_processor.post_process_with_data()
first_mesh.plot(
path.join(dirname(__file__), 'output',
'first_mesh_tracked_processed.pdf'),
color_by_global_id=True,
total_number_of_global_ids=first_mesh.get_num_elements())
second_mesh.plot(
path.join(dirname(__file__), 'output',
'second_mesh_tracked_processed.pdf'),
color_by_global_id=True,
total_number_of_global_ids=first_mesh.get_num_elements())
first_mesh.save(
path.join(dirname(__file__), 'output',
'first_mesh_tracked_processed.mesh'))
second_mesh.save(
path.join(dirname(__file__), 'output',
'second_mesh_tracked_processed.mesh'))
global_ids = []
for element in second_mesh.elements:
if element.global_id != None:
if element.global_id in global_ids:
print 'found double global id'
else:
global_ids.append(element.global_id)
global_ids_one = []
for element in first_mesh.elements:
if element.global_id != None:
if element.global_id in global_ids_one:
print 'found double global id'
else:
global_ids_one.append(element.global_id)
self.assertEqual(len(global_ids_one), len(global_ids))