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_success(t1_percentage, output = False):
"""Perform tracking test on a mesh where t1_number of t1 swaps are randomly performed
Parameters
----------
t1_number : int
How many T1 swaps should be performed
output : bool
whether the meshes should be written to a file. Defaults to False.
Returns
-------
success_boolean : bool
True if tracking successful
average_number_tracked_cells : float
average number of cells that were tracked correctly
"""
print 'making meshes'
first_mesh = mesh.creation.generate_random_tesselation(20,20)
second_mesh = copy.deepcopy(first_mesh)
first_mesh.assign_frame_ids_in_order()
second_mesh.assign_frame_ids_randomly()
# build ground truth for testing the mapping
print 'making ground truth'
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
total_number_edges = len(first_mesh.collect_elements_of_inner_edges())
edges_to_swap = int( 0.01 * t1_percentage * total_number_edges)
print 'applying t1 swaps'
apply_t1_swaps_to_mesh( second_mesh, edges_to_swap )
if output:
first_mesh.save(path.join(dirname(__file__),'output','multiple_t1_before.mesh'))
second_mesh.save(path.join(dirname(__file__),'output','multiple_t1_after.mesh'))
try:
tracking.track(first_mesh, second_mesh)
except:
return 0, 0, 0
if output:
first_mesh.plot(path.join(dirname(__file__),'output','multiple_t1_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_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, number_incorrectly_tracked_cells = tracking.evaluate_tracking(first_mesh,
second_mesh,
ground_truth)
percentage_correctly_tracked_cells = float(number_tracked_cells)/first_mesh.get_num_elements()
percentage_incorrectly_tracked_cells = float(number_incorrectly_tracked_cells)/first_mesh.get_num_elements()
return int(tracking_success), percentage_correctly_tracked_cells, percentage_incorrectly_tracked_cells
def test_success(t1_percentage, output=False):
"""Perform tracking test on a mesh where t1_number of t1 swaps are randomly performed
Parameters
----------
t1_number : int
How many T1 swaps should be performed
output : bool
whether the meshes should be written to a file. Defaults to False.
Returns
-------
success_boolean : bool
True if tracking successful
average_number_tracked_cells : float
average number of cells that were tracked correctly
"""
print 'making meshes'
first_mesh = mesh.creation.generate_random_tesselation(20, 20)
second_mesh = copy.deepcopy(first_mesh)
first_mesh.assign_frame_ids_in_order()
second_mesh.assign_frame_ids_randomly()
# build ground truth for testing the mapping
print 'making ground truth'
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
total_number_edges = len(first_mesh.collect_elements_of_inner_edges())
edges_to_swap = int(0.01 * t1_percentage * total_number_edges)
print 'applying t1 swaps'
apply_t1_swaps_to_mesh(second_mesh, edges_to_swap)
counter = 0
for cell in ground_truth:
this_cell = first_mesh.get_element_with_frame_id(cell)
image_cell = second_mesh.get_element_with_frame_id(ground_truth[cell])
if np.linalg.norm(this_cell.calculate_centroid() -
image_cell.calculate_centroid()) > 0.0001:
counter += 1
print 'tissue with t1 percentage'
print t1_percentage
print 'has this rearranged_cell percentage'
print float(counter) / first_mesh.get_num_elements()
# if output:
# first_mesh.save(path.join(dirname(__file__),'output','multiple_t1_before.mesh'))
# second_mesh.save(path.join(dirname(__file__),'output','multiple_t1_after.mesh'))
#
# try:
# tracking.track(first_mesh, second_mesh)
# except:
# return 0, 0, 0
if output:
first_mesh.plot(
path.join(dirname(__file__), 'output', 'multiple_t1_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_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, number_incorrectly_tracked_cells = tracking.evaluate_tracking(
first_mesh, second_mesh, ground_truth)
percentage_correctly_tracked_cells = float(
number_tracked_cells) / first_mesh.get_num_elements()
percentage_incorrectly_tracked_cells = float(
number_incorrectly_tracked_cells) / first_mesh.get_num_elements()
return int(
tracking_success
), percentage_correctly_tracked_cells, percentage_incorrectly_tracked_cells