def test_track_function_on_second_data(self):
"""Test tracking function on second data pair"""
mesh_sequence = mesh.read_sequence_from_data(
path.join(dirname(__file__), 'data', 'first_few_frames'))
first_mesh = mesh_sequence[1]
second_mesh = mesh_sequence[2]
start_time = time.clock()
tracked_ids = tracking.track(first_mesh, second_mesh)
end_time = time.clock()
print 'total time for second data pair is:'
print end_time - start_time
first_mesh.plot(
path.join(dirname(__file__), 'output',
'second_mesh_tracked_with_third_total.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_total.pdf'),
color_by_global_id=True,
total_number_of_global_ids=first_mesh.get_num_elements())
def test_track_function_on_first_data(self):
"""See whether we can fully track the mesh using the track function of the tracking module"""
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]
start_time = time.clock()
tracked_ids = tracking.track(first_mesh, second_mesh)
end_time = time.clock()
print 'total time for first data pair is:'
print end_time - start_time
first_mesh.plot(
path.join(dirname(__file__), 'output',
'first_mesh_tracked_total.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_total.pdf'),
color_by_global_id=True,
total_number_of_global_ids=first_mesh.get_num_elements())
def test_track_and_write_sequence(self):
mesh_sequence = mesh.read_sequence_from_data(
path.join(dirname(__file__), 'data', 'first_few_frames'))
tracking.track_and_write_sequence(
path.join(dirname(__file__), 'data', 'first_few_frames'),
path.join(dirname(__file__), 'output', 'first_few_frames'))
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_read_sequence(self):
"""Test whether we can read the seedwater output"""
mesh_sequence = mesh.read_sequence_from_data(path.join(dirname(__file__),'data','first_few_frames'))
self.assertEqual(len(mesh_sequence), 3)
for frame_number, this_mesh in enumerate( mesh_sequence ):
print 'reading frame number ' + str(frame_number)
this_network = this_mesh.generate_network()
this_mesh.plot(path.join(dirname(__file__),'output','first_frames_' + str(frame_number) + '.pdf'))
this_network = this_mesh.generate_network()
self.assertGreater( this_mesh.get_num_elements(), 10)
for this_element in this_mesh.elements:
self.assertGreater(this_element.get_num_nodes(), 2)
self.assertGreater(this_element.id_in_frame, 1)
self.assert_(this_network.node[this_element.id_in_frame]['position'] != None )
if not this_element.check_if_on_boundary():
self.assertEqual( this_element.get_num_nodes(), this_network.degree(this_element.id_in_frame))
def xest_network_and_overlay(self):
"overlay ilastik segmentation with real data for visual inspection"
mesh_sequence = mesh.read_sequence_from_data(path.join(dirname(__file__), 'output','converted'))
real_sequence = glob.glob(path.join(dirname(__file__), 'data', 'image_data', '*.tif'))
real_sequence.sort(key=_natural_keys)
output_dir = path.join(dirname(__file__),'output','overlays')
if not path.isdir(output_dir):
os.mkdir(output_dir)
for mesh_counter, mesh_instance in enumerate( mesh_sequence ):
print mesh_counter
name_of_real_image = real_sequence[mesh_counter]
mesh_instance.plot_with_data( path.join(output_dir, str(mesh_counter) + '.pdf' ),
name_of_real_image )
this_network = mesh_instance.generate_network()
def xest_network_and_overlay(self):
"overlay ilastik segmentation with real data for visual inspection"
mesh_sequence = mesh.read_sequence_from_data(
path.join(dirname(__file__), 'output', 'converted'))
real_sequence = glob.glob(
path.join(dirname(__file__), 'data', 'image_data', '*.tif'))
real_sequence.sort(key=_natural_keys)
output_dir = path.join(dirname(__file__), 'output', 'overlays')
if not path.isdir(output_dir):
os.mkdir(output_dir)
for mesh_counter, mesh_instance in enumerate(mesh_sequence):
print mesh_counter
name_of_real_image = real_sequence[mesh_counter]
mesh_instance.plot_with_data(
path.join(output_dir,
str(mesh_counter) + '.pdf'), name_of_real_image)
this_network = mesh_instance.generate_network()