def test_track_multiple_t1_swaps_special_example_7(self):
sys.setrecursionlimit(40000)
first_mesh = mesh.load(path.join(dirname(__file__), 'data', 'multiple_t1_example_7_before.mesh'))
second_mesh = mesh.load(path.join(dirname(__file__), 'data', 'multiple_t1_example_7_after.mesh'))
# build ground truth for testing the mapping
ground_truth = {}
for element_index, element in enumerate(first_mesh.elements):
ground_truth[element.id_in_frame] = second_mesh.elements[element_index].id_in_frame
first_mesh.plot(path.join(dirname(__file__),'output','multiple_t1_example_7_before.pdf'))
second_mesh.plot(path.join(dirname(__file__),'output','multiple_t1_example_7_after.pdf'))
tracking.track(first_mesh, second_mesh)
# tracking.find_maximum_common_subgraph(first_mesh, second_mesh)
first_mesh.plot(path.join(dirname(__file__),'output','multiple_t1_example_7_before.pdf'),
color_by_global_id = True, total_number_of_global_ids = first_mesh.get_num_elements())
second_mesh.plot(path.join(dirname(__file__),'output','multiple_t1_example_7_after.pdf'),
color_by_global_id = True, total_number_of_global_ids = first_mesh.get_num_elements())
print 'evaluate tracking'
tracking_success, number_tracked_cells = tracking.evaluate_tracking(first_mesh,
second_mesh,
ground_truth)
def test_track_division_standard_case(self):
"""We load a mesh where only one maximum common subgraph should be identified, and track the division event"""
mesh_one = mesh.load(
path.join(dirname(__file__), 'data',
'standard_simple_division_one.mesh'))
mesh_two = mesh.load(
path.join(dirname(__file__), 'data',
'standard_simple_division_two.mesh'))
# First pick a cell in the centre
mesh_centre = mesh_two.calculate_centre()
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(most_central_element.id_in_frame)
tracked_ids = tracking.track(mesh_one, mesh_two)
mesh_one.plot(path.join(dirname(__file__), 'output',
'tracked_standard_mesh_before_division.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(tracked_ids))
mesh_two.plot(path.join(dirname(__file__), 'output',
'tracked_standard_mesh_after_division.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(tracked_ids))
# make sure that the entire mesh was tracked (except for the dead cell)
self.assertEqual(len(tracked_ids), mesh_one.get_num_elements() - 2)
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEquals(ground_truth[element_one.id_in_frame],
element_two.id_in_frame)
plt.close('all')
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 make_division_resolved_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])
tracked_ids = tracking.find_maximum_common_subgraph( mesh_one, mesh_two )
for element in mesh_one.elements:
element.global_id = None
for element in mesh_two.elements:
element.global_id = None
tracked_ids_all = tracking.track(mesh_one, mesh_two)
plotname = 'division_all'
make_difference_plot(mesh_one, mesh_two, tracked_ids, tracked_ids_all, plotname, figuresize)
def make_division_resolved_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])
tracked_ids = tracking.find_maximum_common_subgraph(mesh_one, mesh_two)
for element in mesh_one.elements:
element.global_id = None
for element in mesh_two.elements:
element.global_id = None
tracked_ids_all = tracking.track(mesh_one, mesh_two)
plotname = 'division_all'
make_difference_plot(mesh_one, mesh_two, tracked_ids, tracked_ids_all,
plotname, figuresize)
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 test_translation_special_case(self):
"""load first random mesh, move it, and track it.
"""
sys.setrecursionlimit(40000)
large_mesh = mesh.load(path.join(dirname(__file__),'data','special_translation_mesh_one.mesh'))
large_mesh.assign_frame_ids_in_order()
mesh_one = large_mesh.copy_region_of_interest((3,10),(-1,9))
mesh_two = large_mesh.copy_region_of_interest((5,12),(-1,9))
# Build ground truth
ground_truth_indices = {}
for element_index, element in enumerate(mesh_one.elements):
if element.id_in_frame in mesh_two.frame_id_dictionary:
ground_truth_indices[element_index] = mesh_two.frame_id_dictionary[element.id_in_frame]
mesh_one.assign_frame_ids_in_order()
mesh_two.assign_frame_ids_randomly()
ground_truth = {}
for element_index, element in enumerate(mesh_one.elements):
if element_index in ground_truth_indices:
ground_truth[element.id_in_frame] = mesh_two.elements[ground_truth_indices[element_index]].id_in_frame
print 'call tracker'
tracked_ids = tracking.track(mesh_one, mesh_two)
# tracked_ids = tracking.find_maximum_common_subgraph(mesh_one, mesh_two)
print 'tracker returned'
mesh_one.plot(path.join(dirname(__file__),'output', 'special_translation_mesh_one.pdf'), color_by_global_id = True,
total_number_of_global_ids = len(tracked_ids) )
mesh_two.plot(path.join(dirname(__file__),'output', 'special_translation_mesh_two.pdf'), color_by_global_id = True,
total_number_of_global_ids = len(tracked_ids) )
network_one = mesh_one.generate_network()
network_two = mesh_two.generate_network()
self.assertEqual( len(tracked_ids), len(ground_truth) )
# for frame_id in ground_truth:
# if mesh_one.get_element_with_frame_id(frame_id).global_id == None:
# print 'element with this frame id did not get tracked:'
# print frame_id
for global_id in tracked_ids:
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEqual(element_one.get_num_nodes(), element_two.get_num_nodes())
self.assertAlmostEqual(element_one.calculate_area(), element_two.calculate_area())
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEquals( ground_truth[element_one.id_in_frame], element_two.id_in_frame )
def test_save_and_load(self):
"""make a mesh, save, and load it"""
mesh_to_save = mesh.creation.generate_random_tesselation(3,3)
mesh_to_save.save(path.join(dirname(__file__),'output','test_mesh.mesh'))
loaded_mesh = mesh.load(path.join(dirname(__file__),'output','test_mesh.mesh'))
assert( loaded_mesh == mesh_to_save )
self.assertAlmostEqual( loaded_mesh.calculate_total_area(), mesh_to_save.calculate_total_area() )
def test_save_and_load(self):
"""make a mesh, save, and load it"""
mesh_to_save = mesh.creation.generate_random_tesselation(3, 3)
mesh_to_save.save(
path.join(dirname(__file__), 'output', 'test_mesh.mesh'))
loaded_mesh = mesh.load(
path.join(dirname(__file__), 'output', 'test_mesh.mesh'))
assert (loaded_mesh == mesh_to_save)
self.assertAlmostEqual(loaded_mesh.calculate_total_area(),
mesh_to_save.calculate_total_area())
def test_track_special_permutation_mesh(self):
"""generate a small random mesh and track it.
"""
mesh_one = mesh.load(path.join(dirname(__file__),'data','special_permutation_mesh.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
mesh_one.plot(path.join(dirname(__file__),'output','special_permutation_mesh_one.pdf'))
mesh_two.plot(path.join(dirname(__file__),'output','special_permutation_mesh_two_before_tracking.pdf'))
tracked_ids = tracking.track(mesh_one, mesh_two)
mesh_one.plot(path.join(dirname(__file__),'output','special_permutation_mesh_before.pdf'), color_by_global_id = True,
total_number_of_global_ids = mesh_one.get_num_elements())
mesh_two.plot(path.join(dirname(__file__),'output','special_permutation_mesh_after.pdf'), color_by_global_id = True,
total_number_of_global_ids = mesh_one.get_num_elements())
dangling_elements_one = mesh_one.get_dangling_element_ids(ground_truth.keys())
self.assertGreaterEqual(len(tracked_ids),
max(mesh_one.get_num_elements() - 3,
mesh_one.get_num_elements() - len(dangling_elements_one)))
network_one = mesh_one.generate_network()
network_two = mesh_two.generate_network()
for global_id in tracked_ids:
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEqual(element_one.get_num_nodes(), element_two.get_num_nodes())
self.assertEqual(network_one.degree(element_one.id_in_frame), network_two.degree(element_two.id_in_frame))
self.assertAlmostEqual(element_one.calculate_area(), element_two.calculate_area())
np.testing.assert_almost_equal(element_one.calculate_centroid(), element_two.calculate_centroid())
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_translation_special_case_three(self):
"""load third random mesh, move it, and track it.
"""
sys.setrecursionlimit(40000)
large_mesh = mesh.load(path.join(dirname(__file__),'data','special_translation_mesh_three.mesh'))
large_mesh.assign_frame_ids_in_order()
mesh_one = large_mesh.copy_region_of_interest((3,10),(-1,9))
mesh_two = large_mesh.copy_region_of_interest((5,12),(-1,9))
# Build ground truth
ground_truth_indices = {}
for element_index, element in enumerate(mesh_one.elements):
if element.id_in_frame in mesh_two.frame_id_dictionary:
ground_truth_indices[element_index] = mesh_two.frame_id_dictionary[element.id_in_frame]
mesh_one.assign_frame_ids_in_order()
mesh_two.assign_frame_ids_in_reverse_order()
ground_truth = {}
for element_index, element in enumerate(mesh_one.elements):
if element_index in ground_truth_indices:
ground_truth[element.id_in_frame] = mesh_two.elements[ground_truth_indices[element_index]].id_in_frame
# tracked_ids = tracking.find_maximum_common_subgraph(mesh_one, mesh_two)
tracked_ids = tracking.track(mesh_one, mesh_two)
# subgraph_finder = tracking.ReducedBacktrackingSubgraphFinder(mesh_one, mesh_two)
# subgraph_finder.find_maximum_common_subgraph()
# largest_mappings = subgraph_finder.largest_mappings
#
# for mapping_index, large_mapping in enumerate(largest_mappings):
#
# tracked_ids = []
#
# for element_one in mesh_one.elements:
# element_one.global_id = None
#
# for element_two in mesh_two.elements:
# element_two.global_id = None
#
# for global_id, frame_one_id in enumerate(large_mapping):
# mesh_one.get_element_with_frame_id(frame_one_id).global_id = global_id
# mesh_two.get_element_with_frame_id(large_mapping[frame_one_id]).global_id = global_id
# tracked_ids.append(global_id)
#
# mesh_one.index_global_ids()
# mesh_two.index_global_ids()
#
# mesh_one.plot('debug_mesh_special_before_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# mesh_two.plot('debug_mesh_special_after_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
#
mesh_one.plot(path.join(dirname(__file__),'output', 'special_translation_mesh_three_before.pdf'), color_by_global_id = True,
total_number_of_global_ids = len(tracked_ids) )
mesh_two.plot(path.join(dirname(__file__),'output', 'special_translation_mesh_three_after.pdf'), color_by_global_id = True,
total_number_of_global_ids = len(tracked_ids) )
network_one = mesh_one.generate_network()
network_two = mesh_two.generate_network()
self.assertEqual( len(tracked_ids), len(ground_truth) )
for global_id in tracked_ids:
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEqual(element_one.get_num_nodes(), element_two.get_num_nodes())
self.assertAlmostEqual(element_one.calculate_area(), element_two.calculate_area())
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEquals( ground_truth[element_one.id_in_frame], element_two.id_in_frame )
def test_track_special_division_eight(self):
"""read a special mesh, perform a division event, and track it.
"""
sys.setrecursionlimit(40000)
mesh_one = mesh.load(
path.join(dirname(__file__), 'data',
'division_special_mesh_nine.mesh'))
mesh_two = copy.deepcopy(mesh_one)
mesh_one.assign_frame_ids_in_order()
mesh_two.assign_frame_ids_in_reverse_order()
# 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()
file_to_read = open(
path.join(dirname(__file__), 'data',
'division_special_direction_nine.pickle'), 'r')
division_direction = pickle.load(file_to_read)
file_to_read.close()
mesh_two.divide_element_with_frame_id_in_direction(
most_central_element.id_in_frame, division_direction)
mesh_one.plot(
path.join(dirname(__file__), 'output',
'tracked_special_mesh_eight_before_division.pdf'))
mesh_two.plot(
path.join(dirname(__file__), 'output',
'tracked_special_mesh_eight_after_division.pdf'))
tracked_ids = tracking.track(mesh_one, mesh_two)
# tracked_ids = tracking.find_maximum_common_subgraph( mesh_one, mesh_two )
# subgraph_finder = tracking.ReducedBacktrackingSubgraphFinder(mesh_one, mesh_two)
# subgraph_finder.find_maximum_common_subgraph()
# largest_mappings = subgraph_finder.largest_mappings
#
# for mapping_index, large_mapping in enumerate(largest_mappings):
#
# tracked_ids = []
#
# for element_one in mesh_one.elements:
# element_one.global_id = None
#
# for element_two in mesh_two.elements:
# element_two.global_id = None
#
# for global_id, frame_one_id in enumerate(large_mapping):
# mesh_one.get_element_with_frame_id(frame_one_id).global_id = global_id
# mesh_two.get_element_with_frame_id(large_mapping[frame_one_id]).global_id = global_id
# tracked_ids.append(global_id)
#
# mesh_one.index_global_ids()
# mesh_two.index_global_ids()
#
# mesh_one.plot('debug_mesh_special_before_division_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# mesh_two.plot('debug_mesh_special_after_division_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
#
mesh_one.plot(path.join(
dirname(__file__), 'output',
'tracked_special_mesh_eight_before_division.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(tracked_ids))
mesh_two.plot(path.join(
dirname(__file__), 'output',
'tracked_special_mesh_eight_after_division.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(tracked_ids))
# make sure that the entire mesh was tracked (except for the dead cell)
self.assertEqual(len(tracked_ids), mesh_one.get_num_elements() - 1)
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEqual(ground_truth[element_one.id_in_frame],
element_two.id_in_frame)
#
plt.close('all')
from OpenGL.GLU import *
import cv
import mesh
import wx
import cybvh
import random
import quantities as pq
import sounds
if not 'window' in globals():
window = PointWindow(size=(640, 480))
ROULETTE = 0.2
meshname = 'ellipse'
mesh.load(meshname)
mycybvh = cybvh.CyBVH(mesh.mybvh.verts[:, :3].copy(),
np.array(mesh.mybvh.tris)[:, :3].copy(),
mesh.mybvh.nodes)
def reset_sink():
global sink, sinkrad, source
sinkrad = 0.8
source = np.array([0, 0, 0], 'f')
sink = np.array([0, 0, 0], 'f')
if not 'sink' in globals():
reset_sink()
window.Refresh()
def test_track_special_t1_swap_4(self):
"""generate a random mesh, copy it, perform a t1 swap on it, and track it.
"""
sys.setrecursionlimit(40000)
mesh_one = mesh.load(path.join(dirname(__file__), 'data', 'special_t1_mesh_four.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
# Perform T1 swap on mesh two
# First pick a node in the centre
mesh_centre = mesh_two.calculate_centre()
# pick the node closest to the centre
min_distance = 3*mesh_two.calculate_height()
for node in mesh_two.nodes:
distance = np.linalg.norm(node.position - mesh_centre)
if distance < min_distance:
min_distance = distance
most_central_node = node
# pick a node that shares an edge with this central node
for local_index, element_node in enumerate(most_central_node.adjacent_elements[0].nodes):
if element_node.id == most_central_node.id:
num_nodes_this_element = most_central_node.adjacent_elements[0].get_num_nodes()
one_edge_node = most_central_node.adjacent_elements[0].nodes[(local_index+1)%num_nodes_this_element]
break
mesh_two.perform_t1_swap( most_central_node.id, one_edge_node.id )
tracked_ids = tracking.track( mesh_one, mesh_two )
# subgraph_finder = tracking.LocalisedSubgraphFinder(mesh_one, mesh_two)
# subgraph_finder.find_maximum_common_subgraph()
# post_processor = tracking.PostProcessor(mesh_one, mesh_two, subgraph_finder.largest_mappings)
# post_processor.tidy_current_mapping()
# post_processor.index_global_ids_from_largest_mappings()
# network_one = mesh_one.generate_network_of_unidentified_elements()
# print network_one.nodes()
# post_processor.altered_fill_in_by_adjacency(network_one)
# post_processor.index_global_ids()
# subgraph_finder = tracking.LocalisedSubgraphFinder(mesh_one, mesh_two)
# subgraph_finder.find_maximum_common_subgraph()
# largest_mappings = subgraph_finder.largest_mappings
#
# for mapping_index, large_mapping in enumerate(largest_mappings):
#
# tracked_ids = []
#
# for element_one in mesh_one.elements:
# element_one.global_id = None
#
# for element_two in mesh_two.elements:
# element_two.global_id = None
#
# for global_id, frame_one_id in enumerate(large_mapping):
# mesh_one.get_element_with_frame_id(frame_one_id).global_id = global_id
# mesh_two.get_element_with_frame_id(large_mapping[frame_one_id]).global_id = global_id
# tracked_ids.append(global_id)
#
# mesh_one.index_global_ids()
# mesh_two.index_global_ids()
#
# mesh_one.plot('mesh_special_before_division_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# mesh_two.plot('mesh_special_after_division_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
#
mesh_one.plot(path.join(dirname(__file__),'output','tracked_mesh_before_special_t1_swap_four.pdf'), color_by_global_id = True,
total_number_of_global_ids = mesh_one.get_num_elements() )
mesh_two.plot(path.join(dirname(__file__),'output','tracked_mesh_after_special_t1_swap_four.pdf'), color_by_global_id = True,
total_number_of_global_ids = mesh_one.get_num_elements() )
# # make sure that the entire mesh was tracked
# self.assertEqual( len(tracked_ids), mesh_one.get_num_elements() )
# mesh_one.plot(path.join(dirname(__file__),'output','tracked_mesh_before_special_t1_swap_three.pdf'))
# mesh_two.plot(path.join(dirname(__file__),'output','tracked_mesh_after_special_t1_swap_three.pdf'))
#
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEquals( ground_truth[element_one.id_in_frame], element_two.id_in_frame )
plt.close('all')
import core
import mesh
import sys,time
e=core.Environment(sys.argv)
import discr
import exporter
m=mesh.Mesh_3()
m = mesh.load(m,"feelpp3d.geo",0.1)
Xh=discr.Pch_3D_P1(mesh=m)
P0h = discr.Pdh_3D_P0(mesh=m)
u=Xh.elementFromExpr("{sin(2*pi*x)*cos(pi*y)*cos(pi*z)}:x:y:z")
e = exporter.exporter(mesh=m)
e.addScalar("un", 1.)
e.addP1c("u",u);
e.addP0d("pid",discr.pid( P0h ));
e.save()
def test_track_special_case(self):
"""track a cell death event and identify the cells that are involved in rearrangement"""
sys.setrecursionlimit(40000)
mesh_one = mesh.load(path.join(dirname(__file__),'data','special_death_mesh_one.mesh'))
mesh_two = mesh.load(path.join(dirname(__file__),'data','special_death_mesh_two.mesh'))
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.kill_element_with_frame_id(most_central_element.id_in_frame)
mesh_one.plot(path.join(dirname(__file__),'output','not_tracked_mesh_before_death.pdf' ))
mesh_two.plot(path.join(dirname(__file__),'output','not_tracked_mesh_after_death.pdf' ))
tracked_ids = tracking.track( mesh_one, mesh_two )
#
# mesh_one.plot('special_tracked_mesh_before_death.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# mesh_two.plot('special_tracked_mesh_after_death.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# tracked_ids = tracking.find_maximum_common_subgraph( mesh_one, mesh_two )
# subgraph_finder = tracking.LocalisedSubgraphFinder(mesh_one, mesh_two)
# subgraph_finder.find_maximum_common_subgraph()
# tracked_ids = tracking.find_maximum_common_subgraph(mesh_one, mesh_two)
mesh_one.plot(path.join(dirname(__file__),'output','special_tracked_mesh_before_death.pdf'), color_by_global_id = True,
total_number_of_global_ids = len( tracked_ids ) )
mesh_two.plot(path.join(dirname(__file__),'output','special_tracked_mesh_after_death.pdf'), color_by_global_id = True,
total_number_of_global_ids = len( tracked_ids ) )
# largest_mappings = subgraph_finder.largest_mappings
#
# for mapping_index, large_mapping in enumerate(largest_mappings):
#
# tracked_ids = []
#
# for element_one in mesh_one.elements:
# element_one.global_id = None
#
# for element_two in mesh_two.elements:
# element_two.global_id = None
#
# for global_id, frame_one_id in enumerate(large_mapping):
# mesh_one.get_element_with_frame_id(frame_one_id).global_id = global_id
# mesh_two.get_element_with_frame_id(large_mapping[frame_one_id]).global_id = global_id
# tracked_ids.append(global_id)
#
# mesh_one.index_global_ids()
# mesh_two.index_global_ids()
#
# mesh_one.plot('mesh_special_before_death_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# mesh_two.plot('mesh_special_after_death_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
#
# make sure that the entire mesh was tracked (except for the dead cell)
self.assertEqual( len(tracked_ids), mesh_two.get_num_elements() - 2 )
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEquals( ground_truth[element_one.id_in_frame], element_two.id_in_frame )
plt.close('all')
import core
import mesh
import sys, time
e = core.Environment(sys.argv)
import discr
import exporter
m2d = mesh.Mesh_2()
m2d = mesh.load(m2d, "triangle.geo", 0.1)
Xh = discr.Pch_2D_P1(mesh=m2d)
P0h = discr.Pdh_2D_P0(mesh=m2d)
u = Xh.elementFromExpr("{sin(2*pi*x)*cos(pi*y)}:x:y")
e = exporter.exporter(mesh=m2d)
e.addScalar("un", 1.)
e.addP1c("u", u)
e.addP0d("pid", discr.pid(P0h))
e.save()
'test_on_data', 'data', 'first_few_frames',
'Segment_0_002.tif')
# first_mcs = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','first_mesh_tracked.mesh'))
# second_mcs = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','second_mesh_tracked.mesh'))
#
#
# first_mcs_cleaned = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','first_mesh_tracked_cleaned.mesh'))
# second_mcs_cleaned = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','second_mesh_tracked_cleaned.mesh'))
#
#
# first_mcs_tracked = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','first_mesh_tracked_processed.mesh'))
# second_mcs_tracked = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','second_mesh_tracked_processed.mesh'))
first_mcs = mesh.load(
path.join(dirname(__file__), '..', '..', '..', 'test', 'test_on_data',
'output', 'second_mesh_tracked_with_third_mesh.mesh'))
second_mcs = mesh.load(
path.join(dirname(__file__), '..', '..', '..', 'test', 'test_on_data',
'output', 'third_mesh_tracked.mesh'))
sys.setrecursionlimit(40000)
first_mcs_copy = copy.deepcopy(first_mcs)
weakly_connected_global_ids = find_weakly_connected_cells(first_mcs_copy)
first_mcs_cleaned = mesh.load(
path.join(dirname(__file__), '..', '..', '..', 'test', 'test_on_data',
'output', 'second_mesh_tracked_with_third_mesh_cleaned.mesh'))
second_mcs_cleaned = mesh.load(
path.join(dirname(__file__), '..', '..', '..', 'test', 'test_on_data',
import cybvh
import bvh
import numpy as np
import mesh
import time
N_RAYS = 1000
origins = np.random.rand(N_RAYS,3).astype('f')
directions = np.random.rand(N_RAYS,3).astype('f')-0.5
directions /= np.sqrt(np.sum(directions*directions,1))\
.reshape(-1,1).astype('f')
mesh.load('blueghost')
global mycybvh
mycybvh = cybvh.CyBVH(mesh.mybvh.verts[:,:3].copy(),
np.array(mesh.mybvh.tris)[:,:3].copy(),
mesh.mybvh.nodes)
def test_intersect_triangle():
N_TRIS = 100
v0,v1,v2 = np.random.rand(3, N_TRIS, 3).astype('f')
bvht = [bvh.intersect_triangle(origins[i], directions[i],
v0[j], v1[j], v2[j])
for i in range(N_RAYS) for j in range(N_TRIS)]
cybvht = [cybvh.intersect_triangle(origins[i], directions[i],
v0[j], v1[j], v2[j])
for i in range(N_RAYS) for j in range(N_TRIS)]
bvht = np.array(bvht)
import cv
import mesh
import wx
import cybvh
import random
import quantities as pq
import sounds
if not 'window' in globals():
window = PointWindow(size=(640,480))
ROULETTE=0.2
meshname = 'ellipse'
mesh.load(meshname)
mycybvh = cybvh.CyBVH(mesh.mybvh.verts[:,:3].copy(),
np.array(mesh.mybvh.tris)[:,:3].copy(),
mesh.mybvh.nodes)
def reset_sink():
global sink, sinkrad, source
sinkrad = 0.8
source = np.array([0,0,0],'f')
sink = np.array([0,0,0],'f')
if not 'sink' in globals():
reset_sink()
window.Refresh()
def test_track_special_case_seven(self):
"""generate a random mesh, copy it, perform a death event, and find maximum common subgraph
not sure whether this one even works!
"""
sys.setrecursionlimit(40000)
mesh_one = mesh.load(
path.join(dirname(__file__), 'data',
'special_death_mesh_seven.mesh'))
mesh_two = mesh.load(
path.join(dirname(__file__), 'data',
'special_death_mesh_seven.mesh'))
mesh_one.assign_frame_ids_in_order()
mesh_two.assign_frame_ids_in_reverse_order()
# 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.kill_element_with_frame_id(most_central_element.id_in_frame)
tracked_ids = tracking.track(mesh_one, mesh_two)
# subgraph_finder = tracking.ReducedBacktrackingSubgraphFinder(mesh_one, mesh_two)
# subgraph_finder.find_maximum_common_subgraph()
#
# largest_mappings = subgraph_finder.largest_mappings
#
# for mapping_index, large_mapping in enumerate(largest_mappings):
#
# tracked_ids = []
#
# for element_one in mesh_one.elements:
# element_one.global_id = None
#
# for element_two in mesh_two.elements:
# element_two.global_id = None
#
# for global_id, frame_one_id in enumerate(large_mapping):
# mesh_one.get_element_with_frame_id(frame_one_id).global_id = global_id
# mesh_two.get_element_with_frame_id(large_mapping[frame_one_id]).global_id = global_id
# tracked_ids.append(global_id)
#
# mesh_one.index_global_ids()
# mesh_two.index_global_ids()
#
# mesh_one.plot('mesh_special_before_death_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# mesh_two.plot('mesh_special_after_death_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
mesh_one.plot(path.join(dirname(__file__), 'output',
'special_tracked_mesh_7_before_death.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(tracked_ids))
mesh_two.plot(path.join(dirname(__file__), 'output',
'special_tracked_mesh_7_after_death.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(tracked_ids))
dangling_elements_one = mesh_one.get_dangling_element_ids(
ground_truth.keys())
self.assertGreaterEqual(
len(tracked_ids),
max(mesh_one.get_num_elements() - 4,
mesh_one.get_num_elements() - len(dangling_elements_one) - 1))
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEquals(ground_truth[element_one.id_in_frame],
element_two.id_in_frame)
plt.close('all')
import cybvh
import bvh
import numpy as np
import mesh
import time
N_RAYS = 1000
origins = np.random.rand(N_RAYS, 3).astype('f')
directions = np.random.rand(N_RAYS, 3).astype('f') - 0.5
directions /= np.sqrt(np.sum(directions*directions,1))\
.reshape(-1,1).astype('f')
mesh.load('blueghost')
global mycybvh
mycybvh = cybvh.CyBVH(mesh.mybvh.verts[:, :3].copy(),
np.array(mesh.mybvh.tris)[:, :3].copy(),
mesh.mybvh.nodes)
def test_intersect_triangle():
N_TRIS = 100
v0, v1, v2 = np.random.rand(3, N_TRIS, 3).astype('f')
bvht = [
bvh.intersect_triangle(origins[i], directions[i], v0[j], v1[j], v2[j])
for i in range(N_RAYS) for j in range(N_TRIS)
]
cybvht = [
cybvh.intersect_triangle(origins[i], directions[i], v0[j], v1[j],
v2[j]) for i in range(N_RAYS)
def test_translation_special_case_eleven(self):
"""generate a random mesh, move it, and track it.
"""
sys.setrecursionlimit(40000)
large_mesh = mesh.load(path.join(dirname(__file__),'data','special_translation_mesh_thirteen.mesh'))
large_mesh.assign_frame_ids_in_order()
mesh_one = large_mesh.copy_region_of_interest((3,10),(-1,9))
mesh_two = large_mesh.copy_region_of_interest((5,12),(-1,9))
# Build ground truth
ground_truth_indices = {}
for element_index, element in enumerate(mesh_one.elements):
if element.id_in_frame in mesh_two.frame_id_dictionary:
ground_truth_indices[element_index] = mesh_two.frame_id_dictionary[element.id_in_frame]
mesh_one.assign_frame_ids_in_order()
mesh_two.assign_frame_ids_randomly()
ground_truth = {}
for element_index, element in enumerate(mesh_one.elements):
if element_index in ground_truth_indices:
ground_truth[element.id_in_frame] = mesh_two.elements[ground_truth_indices[element_index]].id_in_frame
print 'call tracker'
# tracked_ids = tracking.find_maximum_common_subgraph(mesh_one, mesh_two)
tracked_ids = tracking.track(mesh_one, mesh_two)
print 'tracker returned'
mesh_one.plot(path.join(dirname(__file__),'output','special_translation_mesh_thirteen_before.pdf'),
color_by_global_id = True, total_number_of_global_ids = len(tracked_ids))
mesh_two.plot(path.join(dirname(__file__),'output','special_translation_mesh_thirteen_after.pdf'),
color_by_global_id = True, total_number_of_global_ids = len(tracked_ids))
network_one = mesh_one.generate_network()
network_two = mesh_two.generate_network()
# Find any dangling elements that may not be identifiable through adjacency
dangling_elements_counter = 0
dangling_elements = []
for element_one_id in ground_truth:
element_one = mesh_one.get_element_with_frame_id(element_one_id)
element_two = mesh_two.get_element_with_frame_id(ground_truth[element_one_id])
ids_adjacent_to_element_one = element_one.get_ids_of_adjacent_elements()
ids_adjacent_to_element_two = element_two.get_ids_of_adjacent_elements()
mappable_elements_adjacent_to_elements_one = set(ids_adjacent_to_element_one).intersection(ground_truth.keys())
mappable_elements_adjacent_to_elements_two = set(ids_adjacent_to_element_two).intersection(ground_truth.values())
if (len(mappable_elements_adjacent_to_elements_one) == 1 or
len(mappable_elements_adjacent_to_elements_two) == 1):
dangling_elements_counter += 1
dangling_elements.append(element_one_id)
elif (len(mappable_elements_adjacent_to_elements_one) == 2):
neighbouring_polygon_number_is_the_same = False
for element in mappable_elements_adjacent_to_elements_one:
element_polygon_number = mesh_one.get_element_with_frame_id(element).get_num_nodes()
if element_polygon_number == element_one.get_num_nodes():
dangling_elements.append(element_one_id)
dangling_elements_counter += 1
break
elif (len(mappable_elements_adjacent_to_elements_two) == 2):
neighbouring_polygon_number_is_the_same = False
for element in mappable_elements_adjacent_to_elements_two:
element_polygon_number = mesh_two.get_element_with_frame_id(element).get_num_nodes()
if element_polygon_number == element_two.get_num_nodes():
dangling_elements.append(element_one_id)
dangling_elements_counter += 1
break
for global_id in tracked_ids:
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEqual(element_one.get_num_nodes(), element_two.get_num_nodes())
self.assertAlmostEqual(element_one.calculate_area(), element_two.calculate_area())
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEquals( ground_truth[element_one.id_in_frame], element_two.id_in_frame )
self.assertGreaterEqual( len(tracked_ids), max( len(ground_truth) - dangling_elements_counter, len(ground_truth) - 3 ) )
def test_track_special_case_seven(self):
"""generate a random mesh, copy it, perform a death event, and find maximum common subgraph
not sure whether this one even works!
"""
sys.setrecursionlimit(40000)
mesh_one = mesh.load(path.join(dirname(__file__),'data','special_death_mesh_seven.mesh'))
mesh_two = mesh.load(path.join(dirname(__file__),'data','special_death_mesh_seven.mesh'))
mesh_one.assign_frame_ids_in_order()
mesh_two.assign_frame_ids_in_reverse_order()
# 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.kill_element_with_frame_id(most_central_element.id_in_frame)
tracked_ids = tracking.track( mesh_one, mesh_two )
# subgraph_finder = tracking.ReducedBacktrackingSubgraphFinder(mesh_one, mesh_two)
# subgraph_finder.find_maximum_common_subgraph()
#
# largest_mappings = subgraph_finder.largest_mappings
#
# for mapping_index, large_mapping in enumerate(largest_mappings):
#
# tracked_ids = []
#
# for element_one in mesh_one.elements:
# element_one.global_id = None
#
# for element_two in mesh_two.elements:
# element_two.global_id = None
#
# for global_id, frame_one_id in enumerate(large_mapping):
# mesh_one.get_element_with_frame_id(frame_one_id).global_id = global_id
# mesh_two.get_element_with_frame_id(large_mapping[frame_one_id]).global_id = global_id
# tracked_ids.append(global_id)
#
# mesh_one.index_global_ids()
# mesh_two.index_global_ids()
#
# mesh_one.plot('mesh_special_before_death_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# mesh_two.plot('mesh_special_after_death_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
mesh_one.plot(path.join(dirname(__file__),'output','special_tracked_mesh_7_before_death.pdf'), color_by_global_id = True,
total_number_of_global_ids = len( tracked_ids ) )
mesh_two.plot(path.join(dirname(__file__),'output','special_tracked_mesh_7_after_death.pdf'), color_by_global_id = True,
total_number_of_global_ids = len( tracked_ids ) )
dangling_elements_one = mesh_one.get_dangling_element_ids(ground_truth.keys())
self.assertGreaterEqual(len(tracked_ids),
max(mesh_one.get_num_elements() - 4,
mesh_one.get_num_elements() - len(dangling_elements_one) -1))
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEquals( ground_truth[element_one.id_in_frame], element_two.id_in_frame )
plt.close('all')
def make_three_sided_division_plot():
"""We load a mesh where only one maximum common subgraph should be identified, and track the division event"""
mesh_one = mesh.load(
path.join(dirname(__file__), '..', '..', '..', 'test', 'test_tracking',
'data', 'division_special_mesh_six.mesh'))
mesh_two = mesh.load(
path.join(dirname(__file__), '..', '..', '..', 'test', 'test_tracking',
'data', 'division_special_mesh_six.mesh'))
# First pick a cell in the centre
mesh_centre = mesh_two.calculate_centre()
mesh_one.assign_frame_ids_in_order()
mesh_two.assign_frame_ids_in_order()
most_central_element = mesh_two.find_most_central_element()
most_central_element_id = most_central_element.id_in_frame
file_to_read = open(
path.join(dirname(__file__), '..', '..', '..', 'test', 'test_tracking',
'data', 'division_special_direction_six.pickle'), 'r')
division_direction = pickle.load(file_to_read)
file_to_read.close()
mesh_two.divide_element_with_frame_id_in_direction(
most_central_element.id_in_frame, division_direction)
daughter_cell_id_one = mesh_one.get_maximal_frame_id() + 1
daughter_cell_id_two = mesh_one.get_maximal_frame_id() + 2
cells_adjacent_to_daughter_cell_one = mesh_two.get_element_with_frame_id(
daughter_cell_id_one).get_ids_of_adjacent_elements()
cells_adjacent_to_daughter_cell_two = mesh_two.get_element_with_frame_id(
daughter_cell_id_two).get_ids_of_adjacent_elements()
bordering_cells = set.intersection(
set(cells_adjacent_to_daughter_cell_one),
set(cells_adjacent_to_daughter_cell_two))
first_mesh_polygon_list = []
for element in mesh_one.elements:
this_polygon = mpl.patches.Polygon(
[node.position for node in element.nodes], fill=True)
if element.id_in_frame in bordering_cells:
this_polygon.set_facecolor('slategrey')
elif element.id_in_frame == most_central_element_id:
this_polygon.set_facecolor('lightskyblue')
else:
this_polygon.set_facecolor([1.0, 1.0, 1.0])
first_mesh_polygon_list.append(this_polygon)
first_mesh_polygon_collection = mpl.collections.PatchCollection(
first_mesh_polygon_list, match_original=True)
first_mesh_figure = plt.figure()
first_mesh_figure.gca().add_collection(first_mesh_polygon_collection)
first_mesh_figure.gca().set_aspect('equal')
first_mesh_figure.gca().autoscale_view()
plt.axis('off')
first_mesh_figure.savefig('three_sided_division_first.pdf',
bbox_inches='tight')
plt.close(first_mesh_figure)
second_mesh_polygon_list = []
for element in mesh_two.elements:
this_polygon = mpl.patches.Polygon(
[node.position for node in element.nodes], fill=True)
if element.id_in_frame in bordering_cells:
this_polygon.set_facecolor('slategrey')
elif (element.id_in_frame == daughter_cell_id_one
or element.id_in_frame == daughter_cell_id_two):
this_polygon.set_facecolor('lightskyblue')
else:
this_polygon.set_facecolor('white')
second_mesh_polygon_list.append(this_polygon)
second_mesh_polygon_collection = mpl.collections.PatchCollection(
second_mesh_polygon_list, match_original=True)
second_mesh_figure = plt.figure()
second_mesh_figure.gca().add_collection(second_mesh_polygon_collection)
second_mesh_figure.gca().set_aspect('equal')
second_mesh_figure.gca().autoscale_view()
plt.axis('off')
second_mesh_figure.savefig('three_sided_division_second.pdf',
bbox_inches='tight')
plt.close(second_mesh_figure)
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))
def test_track_special_case(self):
"""track a cell death event and identify the cells that are involved in rearrangement"""
sys.setrecursionlimit(40000)
mesh_one = mesh.load(
path.join(dirname(__file__), 'data',
'special_death_mesh_one.mesh'))
mesh_two = mesh.load(
path.join(dirname(__file__), 'data',
'special_death_mesh_two.mesh'))
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.kill_element_with_frame_id(most_central_element.id_in_frame)
mesh_one.plot(
path.join(dirname(__file__), 'output',
'not_tracked_mesh_before_death.pdf'))
mesh_two.plot(
path.join(dirname(__file__), 'output',
'not_tracked_mesh_after_death.pdf'))
tracked_ids = tracking.track(mesh_one, mesh_two)
#
# mesh_one.plot('special_tracked_mesh_before_death.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# mesh_two.plot('special_tracked_mesh_after_death.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# tracked_ids = tracking.find_maximum_common_subgraph( mesh_one, mesh_two )
# subgraph_finder = tracking.LocalisedSubgraphFinder(mesh_one, mesh_two)
# subgraph_finder.find_maximum_common_subgraph()
# tracked_ids = tracking.find_maximum_common_subgraph(mesh_one, mesh_two)
mesh_one.plot(path.join(dirname(__file__), 'output',
'special_tracked_mesh_before_death.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(tracked_ids))
mesh_two.plot(path.join(dirname(__file__), 'output',
'special_tracked_mesh_after_death.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(tracked_ids))
# largest_mappings = subgraph_finder.largest_mappings
#
# for mapping_index, large_mapping in enumerate(largest_mappings):
#
# tracked_ids = []
#
# for element_one in mesh_one.elements:
# element_one.global_id = None
#
# for element_two in mesh_two.elements:
# element_two.global_id = None
#
# for global_id, frame_one_id in enumerate(large_mapping):
# mesh_one.get_element_with_frame_id(frame_one_id).global_id = global_id
# mesh_two.get_element_with_frame_id(large_mapping[frame_one_id]).global_id = global_id
# tracked_ids.append(global_id)
#
# mesh_one.index_global_ids()
# mesh_two.index_global_ids()
#
# mesh_one.plot('mesh_special_before_death_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# mesh_two.plot('mesh_special_after_death_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
#
# make sure that the entire mesh was tracked (except for the dead cell)
self.assertEqual(len(tracked_ids), mesh_two.get_num_elements() - 2)
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEquals(ground_truth[element_one.id_in_frame],
element_two.id_in_frame)
plt.close('all')
second_filename = path.join(dirname(__file__),'..','..','..','test','test_on_data','data','first_few_frames', 'Segment_0_001.tif') third_filename = path.join(dirname(__file__),'..','..','..','test','test_on_data','data','first_few_frames', 'Segment_0_002.tif') # first_mcs = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','first_mesh_tracked.mesh')) # second_mcs = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','second_mesh_tracked.mesh')) # # # first_mcs_cleaned = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','first_mesh_tracked_cleaned.mesh')) # second_mcs_cleaned = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','second_mesh_tracked_cleaned.mesh')) # # # first_mcs_tracked = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','first_mesh_tracked_processed.mesh')) # second_mcs_tracked = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','second_mesh_tracked_processed.mesh')) first_mcs = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','second_mesh_tracked_with_third_mesh.mesh')) second_mcs = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','third_mesh_tracked.mesh')) sys.setrecursionlimit(40000) first_mcs_copy = copy.deepcopy(first_mcs) weakly_connected_global_ids = find_weakly_connected_cells(first_mcs_copy) first_mcs_cleaned = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','second_mesh_tracked_with_third_mesh_cleaned.mesh')) second_mcs_cleaned = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','third_mesh_tracked_cleaned.mesh')) first_mcs_tracked = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','second_mesh_tracked_with_third_mesh_tracked_processed.mesh')) second_mcs_tracked = mesh.load(path.join(dirname(__file__),'..','..','..','test','test_on_data','output','third_mesh_tracked_processed.mesh'))
def make_four_sided_division_plot():
"""We load a mesh where only one maximum common subgraph should be identified, and track the division event"""
mesh_one = mesh.load(path.join(dirname(__file__),'..','..','..',
'test','test_tracking','data',
'standard_ambiguous_division_one.mesh'))
mesh_two = mesh.load(path.join(dirname(__file__),'..','..','..',
'test','test_tracking','data',
'standard_ambiguous_division_two.mesh'))
# First pick a cell in the centre
mesh_centre = mesh_two.calculate_centre()
mesh_one.assign_frame_ids_in_order()
mesh_two.assign_frame_ids_in_order()
most_central_element = mesh_two.find_most_central_element()
most_central_element_id = most_central_element.id_in_frame
mesh_two.divide_element_with_frame_id_in_direction(most_central_element.id_in_frame,
[1.0,1.0])
daughter_cell_id_one = mesh_one.get_maximal_frame_id() + 1
daughter_cell_id_two = mesh_one.get_maximal_frame_id() + 2
cells_adjacent_to_daughter_cell_one = mesh_two.get_element_with_frame_id(daughter_cell_id_one).get_ids_of_adjacent_elements()
cells_adjacent_to_daughter_cell_two = mesh_two.get_element_with_frame_id(daughter_cell_id_two).get_ids_of_adjacent_elements()
bordering_cells = set.intersection(set(cells_adjacent_to_daughter_cell_one),
set(cells_adjacent_to_daughter_cell_two))
first_mesh_polygon_list = []
for element in mesh_one.elements:
this_polygon = mpl.patches.Polygon([node.position for node in element.nodes],
fill = True)
if element.id_in_frame in bordering_cells:
this_polygon.set_facecolor('slategrey')
elif element.id_in_frame == most_central_element_id:
this_polygon.set_facecolor('lightskyblue')
else:
this_polygon.set_facecolor([1.0, 1.0, 1.0])
first_mesh_polygon_list.append(this_polygon)
first_mesh_polygon_collection = mpl.collections.PatchCollection(first_mesh_polygon_list, match_original = True)
first_mesh_figure = plt.figure()
first_mesh_figure.gca().add_collection(first_mesh_polygon_collection)
first_mesh_figure.gca().set_aspect('equal')
first_mesh_figure.gca().autoscale_view()
plt.axis('off')
first_mesh_figure.savefig('four_sided_division_first.pdf', bbox_inches = 'tight')
plt.close(first_mesh_figure)
second_mesh_polygon_list = []
for element in mesh_two.elements:
this_polygon = mpl.patches.Polygon([node.position for node in element.nodes],
fill = True)
if element.id_in_frame in bordering_cells:
this_polygon.set_facecolor('slategrey')
elif ( element.id_in_frame == daughter_cell_id_one or
element.id_in_frame == daughter_cell_id_two):
this_polygon.set_facecolor('lightskyblue')
else:
this_polygon.set_facecolor('white')
second_mesh_polygon_list.append(this_polygon)
second_mesh_polygon_collection = mpl.collections.PatchCollection(second_mesh_polygon_list, match_original = True)
second_mesh_figure = plt.figure()
second_mesh_figure.gca().add_collection(second_mesh_polygon_collection)
second_mesh_figure.gca().set_aspect('equal')
second_mesh_figure.gca().autoscale_view()
plt.axis('off')
second_mesh_figure.savefig('four_sided_division_second.pdf', bbox_inches = 'tight')
plt.close(second_mesh_figure)
def test_track_division_standard_ambiguous_case(self):
"""We load a mesh where two maximum common subgraphs will be identified, and track the division event"""
mesh_one = mesh.load(
path.join(dirname(__file__), 'data',
'standard_ambiguous_division_one.mesh'))
mesh_two = mesh.load(
path.join(dirname(__file__), 'data',
'standard_ambiguous_division_two.mesh'))
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])
tracked_ids = tracking.track(mesh_one, mesh_two)
# tracked_ids = tracking.find_maximum_common_subgraph( mesh_one, mesh_two )
# subgraph_finder = tracking.ReducedBacktrackingSubgraphFinder(mesh_one, mesh_two)
# subgraph_finder.find_maximum_common_subgraph()
# largest_mappings = subgraph_finder.largest_mappings
#
# for mapping_index, large_mapping in enumerate(largest_mappings):
#
# tracked_ids = []
#
# for element_one in mesh_one.elements:
# element_one.global_id = None
#
# for element_two in mesh_two.elements:
# element_two.global_id = None
#
# for global_id, frame_one_id in enumerate(large_mapping):
# mesh_one.get_element_with_frame_id(frame_one_id).global_id = global_id
# mesh_two.get_element_with_frame_id(large_mapping[frame_one_id]).global_id = global_id
# tracked_ids.append(global_id)
#
# mesh_one.index_global_ids()
# mesh_two.index_global_ids()
#
# mesh_one.plot('mesh_special_before_division_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
# mesh_two.plot('mesh_special_after_division_' + str(mapping_index) + '.pdf', color_by_global_id = True,
# total_number_of_global_ids = len( tracked_ids ) )
mesh_one.plot(path.join(dirname(__file__), 'output',
'tracked_ambiguous_mesh_before_division.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(tracked_ids))
mesh_two.plot(path.join(dirname(__file__), 'output',
'tracked_ambiguous_mesh_after_division.pdf'),
color_by_global_id=True,
total_number_of_global_ids=len(tracked_ids))
# make sure that the entire mesh was tracked (except for the dead cell)
self.assertEqual(len(tracked_ids), mesh_one.get_num_elements() - 2)
for global_id in tracked_ids:
# and that the mapping coincides with the ground truth for all tracked ids
element_one = mesh_one.get_element_with_global_id(global_id)
element_two = mesh_two.get_element_with_global_id(global_id)
self.assertEquals(ground_truth[element_one.id_in_frame],
element_two.id_in_frame)
plt.close('all')
