def template_clustering(file,
radius,
order,
show_dyn=False,
show_conn=False,
show_clusters=True,
ena_conn_weight=False,
ccore_flag=False):
sample = read_sample(file)
network = syncnet(sample,
radius,
enable_conn_weight=ena_conn_weight,
ccore=ccore_flag)
(ticks, (dyn_time, dyn_phase)) = timedcall(network.process, order,
solve_type.FAST, show_dyn)
print("Sample: ", file, "\t\tExecution time: ", ticks, "\n")
if (show_dyn == True):
draw_dynamics(dyn_time,
dyn_phase,
x_title="Time",
y_title="Phase",
y_lim=[0, 2 * 3.14])
if (show_conn == True):
network.show_network()
if (show_clusters == True):
clusters = network.get_clusters(0.1)
draw_clusters(sample, clusters)
def template_graph_coloring(positive_weight, negative_weight, filename, reduction = None, title = None):
if (title is None): title = filename;
print("\nGraph Coloring: ", title);
graph = read_graph(filename);
network = syncgcolor(graph.data, positive_weight, negative_weight, reduction);
(t, dyn) = network.process(order = 0.999, solution = solve_type.FAST, collect_dynamic = True);
draw_dynamics(t, dyn, x_title = "Time", y_title = "Phase", y_lim = [0, 2 * 3.14]);
clusters = network.get_clusters();
for index in range(0, len(clusters)):
print("Color #", index, ": ", clusters[index]);
coloring_map = network.get_map_coloring();
print("Number colors: ", max(coloring_map));
draw_graph(graph, coloring_map);
# Check validity of colors
for index_node in range(len(graph.data)):
color_neighbors = [ coloring_map[index] for index in range(len(graph.data[index_node])) if graph.data[index_node][index] != 0 and index_node != index];
#print(index_node, map_coloring[index_node], color_neighbors, assigned_colors, map_coloring, "\n\n");
if (coloring_map[index_node] in color_neighbors):
print("Warining: Incorrect coloring");
return;
def template_segmentation_image(image_file, parameters, steps, time, ccore_flag = True):
image = read_image(image_file);
stimulus = rgb2gray(image);
for pixel_index in range(len(stimulus)):
if (stimulus[pixel_index] < 235): stimulus[pixel_index] = 1;
else: stimulus[pixel_index] = 0;
if (parameters is None):
parameters = legion_parameters();
net = legion_network(len(stimulus), parameters, conn_type.GRID_FOUR, ccore = ccore_flag);
output_dynamic = net.simulate(steps, time, stimulus);
ensembles = output_dynamic.allocate_sync_ensembles();
draw_image_mask_segments(image_file, ensembles);
# draw_dynamics(output_dynamic.time, output_dynamic.output, x_title = "Time", y_title = "x(t)", separate = ensembles);
# just for checking correctness of results - let's use classical algorithm
dbscan_instance = dbscan(image, 3, 4, True);
dbscan_instance.process();
trustable_clusters = dbscan_instance.get_clusters();
draw_dynamics(output_dynamic.time, output_dynamic.output, x_title = "Time", y_title = "x(t)", separate = trustable_clusters);
def template_dynamic_sync(num_osc,
k=1,
q=1,
sim_arg=None,
conn=conn_type.ALL_TO_ALL,
type_solution=solve_type.FAST,
collect_dyn=True,
ccore_flag=False):
network = sync_network(num_osc, k, type_conn=conn, ccore=ccore_flag)
network.cluster = q
if (sim_arg is not None):
(t, dyn_phase) = network.simulate(sim_arg[0],
sim_arg[1],
solution=type_solution,
collect_dynamic=collect_dyn)
else:
(t, dyn_phase) = network.simulate_dynamic(collect_dynamic=collect_dyn,
solution=type_solution)
draw_dynamics(t,
dyn_phase,
x_title="Time",
y_title="Phase",
y_lim=[0, 2 * 3.14])
return network
def show_output_dynamic(pcnn_output_dynamic, separate_representation = False):
"""!
@brief Shows output dynamic (output of each oscillator) during simulation.
"""
draw_dynamics(pcnn_output_dynamic.time, pcnn_output_dynamic.output, x_title = "t", y_title = "y(t)", separate = separate_representation);
def show_output_dynamic(sync_output_dynamic):
"""!
@brief Shows output dynamic (output of each oscillator) during simulation.
@param[in] pcnn_output_dynamic (sync_dynamic): Output dynamic of the Sync network.
"""
draw_dynamics(sync_output_dynamic.time, sync_output_dynamic.output, x_title = "t", y_title = "phase", y_lim = [0, 2 * 3.14]);
def template_dynamic_legion(num_osc, steps, time, conn_type = conn_type.NONE, stimulus = None, params = None, separate_repr = True):
net = legion_network(num_osc, stimulus, type_conn = conn_type, parameters = params);
(t, x, z) = net.simulate(steps, time, solution = solve_type.RK4);
draw_dynamics(t, x, x_title = "Time", y_title = "x(t)", separate = separate_repr);
draw_dynamics(t, z, x_title = "Time", y_title = "z(t)");
ensembles = net.allocate_sync_ensembles(0.1);
print(ensembles);
def show_output_dynamic(pcnn_output_dynamic, separate_representation = False):
"""!
@brief Shows output dynamic (output of each oscillator) during simulation.
@param[in] pcnn_output_dynamic (pcnn_dynamic): Output dynamic of the pulse-coupled neural network.
@param[in] separate_representation (list): Consists of lists of oscillators where each such list consists of oscillator indexes that will be shown on separated stage.
"""
draw_dynamics(pcnn_output_dynamic.time, pcnn_output_dynamic.output, x_title = "t", y_title = "y(t)", separate = separate_representation);
def template_dynamic_pcnn(num_osc, steps, stimulus = None, params = None, conn_type = conn_type.NONE, separate_representation = True, ccore_flag = True):
net = pcnn_network(num_osc, params, conn_type, ccore = ccore_flag);
dynamic = net.simulate(steps, stimulus);
ensembles = dynamic.allocate_sync_ensembles();
print("Number of objects:", len(ensembles), "\nEnsembles:", ensembles);
draw_dynamics(dynamic.time, dynamic.output, x_title = "t", y_title = "y(t)", separate = separate_representation);
return ensembles;
def template_dynamic(num_osc, own_weight = -3, neigh_weight = -1, initial_states = None, initial_outputs = None, steps = 1000, time = 10):
network = hysteresis_network(num_osc, own_weight, neigh_weight);
if (initial_states is not None):
network.states = initial_states;
if (initial_outputs is not None):
network.outputs = initial_outputs;
(t, x) = network.simulate(steps, time);
draw_dynamics(t, x, x_title = "Time", y_title = "x(t)");
def template_dynamic_sync(num_osc, k = 1, q = 1, sim_arg = None, conn = conn_type.ALL_TO_ALL, type_solution = solve_type.FAST, collect_dyn = True, ccore_flag = False):
network = sync_network(num_osc, k, type_conn = conn, ccore = ccore_flag);
network.cluster = q;
if (sim_arg is not None):
(t, dyn_phase) = network.simulate(sim_arg[0], sim_arg[1], solution = type_solution, collect_dynamic = collect_dyn);
else:
(t, dyn_phase) = network.simulate_dynamic(collect_dynamic = collect_dyn, solution = type_solution);
draw_dynamics(t, dyn_phase, x_title = "Time", y_title = "Phase", y_lim = [0, 2 * 3.14]);
return network;
def template_clustering(file, number_clusters, arg_order = 0.999, arg_collect_dynamic = True, ccore_flag = False):
sample = read_sample(file);
network = hsyncnet(sample, number_clusters, ccore = ccore_flag);
(time, dynamic) = network.process(arg_order, collect_dynamic = arg_collect_dynamic);
clusters = network.get_clusters();
if (arg_collect_dynamic == True):
draw_dynamics(time, dynamic, x_title = "Time", y_title = "Phase", y_lim = [0, 2 * 3.14]);
draw_clusters(sample, clusters);
def template_dynamic_legion(num_osc, steps, time, conn_type, stimulus, params = None, separate_repr = True, ccore_flag = True):
net = legion_network(num_osc, params, conn_type, ccore = ccore_flag);
print("Created");
dynamic = net.simulate(steps, time, stimulus, solution = solve_type.RK4);
print("Simulated");
draw_dynamics(dynamic.time, dynamic.output, x_title = "Time", y_title = "x(t)", separate = separate_repr);
draw_dynamics(dynamic.time, dynamic.inhibitor, x_title = "Time", y_title = "z(t)");
ensembles = dynamic.allocate_sync_ensembles(0.1);
print(ensembles);
def template_segmentation_image(source, map_som_size = [5, 5], average_neighbors = 5, sync_order = 0.998, show_dyn = False, show_som_map = False):
data = read_image(source);
network = syncsom(data, map_som_size[0], map_som_size[1]);
(ticks, (dyn_time, dyn_phase)) = timedcall(network.process, average_neighbors, show_dyn, sync_order);
print("Sample: ", source, "\t\tExecution time: ", ticks, "\t\tWinners: ", network.som_layer.get_winner_number(), "\n");
if (show_dyn is True):
draw_dynamics(dyn_time, dyn_phase);
clusters = network.get_clusters();
draw_image_mask_segments(source, clusters);
def show_output_dynamic(pcnn_output_dynamic,
separate_representation=False):
"""!
@brief Shows output dynamic (output of each oscillator) during simulation.
"""
draw_dynamics(pcnn_output_dynamic.time,
pcnn_output_dynamic.output,
x_title="t",
y_title="y(t)",
separate=separate_representation)
def template_dynamic_hhn(num_osc,
steps,
time,
stimulus=None,
params=None,
separate_representation=False):
net = hhn_network(num_osc, stimulus, params)
(t, dyn) = net.simulate(steps, time)
draw_dynamics(t,
dyn,
x_title="Time",
y_title="V",
separate=separate_representation)
def template_graph_coloring(filename, alpha, eps, steps, time, title = None, tolerance = 0.1):
if (title is None): title = filename;
graph = read_graph(filename);
network = hysteresisgcolor(graph.data, alpha, eps);
(t, dyn) = network.simulate(steps, time);
draw_dynamics(t, dyn, x_title = "Time", y_title = "State");
clusters = network.get_clusters(tolerance);
for index in range(0, len(clusters)):
print("Color #", index, ": ", clusters[index]);
coloring_map = network.get_map_coloring(tolerance);
draw_graph(graph, coloring_map);
def template_clustering(file, radius, order, show_dyn = False, show_conn = False, show_clusters = True, ena_conn_weight = False, ccore_flag = False):
sample = read_sample(file);
network = syncnet(sample, radius, enable_conn_weight = ena_conn_weight, ccore = ccore_flag);
(ticks, (dyn_time, dyn_phase)) = timedcall(network.process, order, solve_type.FAST, show_dyn);
print("Sample: ", file, "\t\tExecution time: ", ticks, "\n");
if (show_dyn == True):
draw_dynamics(dyn_time, dyn_phase, x_title = "Time", y_title = "Phase", y_lim = [0, 2 * 3.14]);
if (show_conn == True):
network.show_network();
if (show_clusters == True):
clusters = network.get_clusters(0.1);
draw_clusters(sample, clusters);
def template_dynamic(num_osc,
own_weight=-3,
neigh_weight=-1,
initial_states=None,
initial_outputs=None,
steps=1000,
time=10):
network = hysteresis_network(num_osc, own_weight, neigh_weight)
if (initial_states is not None):
network.states = initial_states
if (initial_outputs is not None):
network.outputs = initial_outputs
(t, x) = network.simulate(steps, time)
draw_dynamics(t, x, x_title="Time", y_title="x(t)")
def template_dynamic_pcnn(num_osc,
steps,
stimulus=None,
params=None,
conn_type=conn_type.NONE,
separate_representation=True,
ccore_flag=True):
net = pcnn_network(num_osc, params, conn_type, ccore=ccore_flag)
dynamic = net.simulate(steps, stimulus)
ensembles = dynamic.allocate_sync_ensembles()
print("Number of objects:", len(ensembles), "\nEnsembles:", ensembles)
draw_dynamics(dynamic.time,
dynamic.output,
x_title="t",
y_title="y(t)",
separate=separate_representation)
return ensembles
def template_clustering(file,
number_clusters,
arg_order=0.999,
arg_collect_dynamic=True,
ccore_flag=False):
sample = read_sample(file)
network = hsyncnet(sample, number_clusters, ccore=ccore_flag)
(time, dynamic) = network.process(arg_order,
collect_dynamic=arg_collect_dynamic)
clusters = network.get_clusters()
if (arg_collect_dynamic == True):
draw_dynamics(time,
dynamic,
x_title="Time",
y_title="Phase",
y_lim=[0, 2 * 3.14])
draw_clusters(sample, clusters)
def template_segmentation_image(source,
map_som_size=[5, 5],
average_neighbors=5,
sync_order=0.998,
show_dyn=False,
show_som_map=False):
data = read_image(source)
network = syncsom(data, map_som_size[0], map_som_size[1])
(ticks, (dyn_time, dyn_phase)) = timedcall(network.process,
average_neighbors, show_dyn,
sync_order)
print("Sample: ", source, "\t\tExecution time: ", ticks, "\t\tWinners: ",
network.som_layer.get_winner_number(), "\n")
if (show_dyn is True):
draw_dynamics(dyn_time, dyn_phase)
clusters = network.get_clusters()
draw_image_mask_segments(source, clusters)
def template_clustering(file,
map_size,
trust_order,
sync_order=0.999,
show_dyn=False,
show_layer1=False,
show_layer2=False,
show_clusters=True):
# Read sample
sample = read_sample(file)
# Create network
network = syncsom(sample, map_size[0], map_size[1])
# Run processing
(ticks, (dyn_time, dyn_phase)) = timedcall(network.process, trust_order,
show_dyn, sync_order)
print("Sample: ", file, "\t\tExecution time: ", ticks, "\n")
# Show dynamic of the last layer.
if (show_dyn == True):
draw_dynamics(dyn_time,
dyn_phase,
x_title="Time",
y_title="Phase",
y_lim=[0, 2 * 3.14])
if (show_clusters == True):
clusters = network.get_som_clusters()
draw_clusters(network.som_layer.weights, clusters)
# Show network stuff.
if (show_layer1 == True):
network.show_som_layer()
if (show_layer2 == True):
network.show_sync_layer()
if (show_clusters == True):
clusters = network.get_clusters()
draw_clusters(sample, clusters)
def template_graph_coloring(filename,
alpha,
eps,
steps,
time,
title=None,
tolerance=0.1):
if (title is None): title = filename
graph = read_graph(filename)
network = hysteresisgcolor(graph.data, alpha, eps)
(t, dyn) = network.simulate(steps, time)
draw_dynamics(t, dyn, x_title="Time", y_title="State")
clusters = network.get_clusters(tolerance)
for index in range(0, len(clusters)):
print("Color #", index, ": ", clusters[index])
coloring_map = network.get_map_coloring(tolerance)
draw_graph(graph, coloring_map)
def template_graph_coloring(positive_weight,
negative_weight,
filename,
reduction=None,
title=None):
if (title is None): title = filename
print("\nGraph Coloring: ", title)
graph = read_graph(filename)
network = syncgcolor(graph.data, positive_weight, negative_weight,
reduction)
(t, dyn) = network.process(order=0.999,
solution=solve_type.FAST,
collect_dynamic=True)
draw_dynamics(t, dyn, x_title="Time", y_title="Phase", y_lim=[0, 2 * 3.14])
clusters = network.get_clusters()
for index in range(0, len(clusters)):
print("Color #", index, ": ", clusters[index])
coloring_map = network.get_map_coloring()
print("Number colors: ", max(coloring_map))
draw_graph(graph, coloring_map)
# Check validity of colors
for index_node in range(len(graph.data)):
color_neighbors = [
coloring_map[index] for index in range(len(graph.data[index_node]))
if graph.data[index_node][index] != 0 and index_node != index
]
#print(index_node, map_coloring[index_node], color_neighbors, assigned_colors, map_coloring, "\n\n");
if (coloring_map[index_node] in color_neighbors):
print("Warining: Incorrect coloring")
return
def template_segmentation_image(source, color_radius, object_radius,
noise_size, show_dyn):
data = read_image(source)
print("Pixel dimension: ", len(data[0]))
network = syncnet(data, color_radius, ccore=True)
print("Network has been created")
(ticks, (t, dyn)) = timedcall(network.process, 0.9995, solve_type.FAST,
show_dyn)
# (t, dyn) = network.process(0.998, solve_type.FAST, show_dyn);
print("Sample: ", source, "\t\tExecution time: ", ticks, "\n")
if (show_dyn is True):
draw_dynamics(t, dyn)
clusters = network.get_clusters()
real_clusters = [
cluster for cluster in clusters if len(cluster) > noise_size
]
draw_image_mask_segments(source, real_clusters)
if (object_radius is None):
return
# continue analysis
pointer_image = Image.open(source)
image_size = pointer_image.size
object_colored_clusters = []
object_colored_dynamics = []
total_dyn = []
for cluster in clusters:
coordinates = []
for index in cluster:
y = floor(index / image_size[0])
x = index - y * image_size[0]
coordinates.append([x, y])
print(coordinates)
# perform clustering analysis of the colored objects
if (network is not None):
del network
network = None
if (len(coordinates) < noise_size):
continue
network = syncnet(coordinates, object_radius, ccore=True)
(t, dyn) = network.process(0.999, solve_type.FAST, show_dyn)
if (show_dyn is True):
object_colored_dynamics.append((t, dyn))
object_clusters = network.get_clusters()
# decode it
real_description_clusters = []
for object_cluster in object_clusters:
real_description = []
for index_object in object_cluster:
real_description.append(cluster[index_object])
real_description_clusters.append(real_description)
if (len(real_description) > noise_size):
object_colored_clusters.append(real_description)
# draw_image_mask_segments(source, [ cluster ]);
# draw_image_mask_segments(source, real_description_clusters);
draw_image_mask_segments(source, object_colored_clusters)
if (show_dyn is True):
draw_dynamics_set(object_colored_dynamics, None, None, None,
[0, 2 * 3.14], False, False)
def template_segmentation_image(source, color_radius, object_radius, noise_size, show_dyn):
data = read_image(source);
print("Pixel dimension: ", len(data[0]));
network = syncnet(data, color_radius, ccore = True);
print("Network has been created");
(ticks, (t, dyn)) = timedcall(network.process, 0.9995, solve_type.FAST, show_dyn);
# (t, dyn) = network.process(0.998, solve_type.FAST, show_dyn);
print("Sample: ", source, "\t\tExecution time: ", ticks, "\n");
if (show_dyn is True):
draw_dynamics(t, dyn);
clusters = network.get_clusters();
real_clusters = [cluster for cluster in clusters if len(cluster) > noise_size];
draw_image_mask_segments(source, real_clusters);
if (object_radius is None):
return;
# continue analysis
pointer_image = Image.open(source);
image_size = pointer_image.size;
object_colored_clusters = [];
object_colored_dynamics = [];
total_dyn = [];
for cluster in clusters:
coordinates = [];
for index in cluster:
y = floor(index / image_size[0]);
x = index - y * image_size[0];
coordinates.append([x, y]);
print(coordinates);
# perform clustering analysis of the colored objects
if (network is not None):
del network;
network = None;
if (len(coordinates) < noise_size):
continue;
network = syncnet(coordinates, object_radius, ccore = True);
(t, dyn) = network.process(0.999, solve_type.FAST, show_dyn);
if (show_dyn is True):
object_colored_dynamics.append( (t, dyn) );
object_clusters = network.get_clusters();
# decode it
real_description_clusters = [];
for object_cluster in object_clusters:
real_description = [];
for index_object in object_cluster:
real_description.append(cluster[index_object]);
real_description_clusters.append(real_description);
if (len(real_description) > noise_size):
object_colored_clusters.append(real_description);
# draw_image_mask_segments(source, [ cluster ]);
# draw_image_mask_segments(source, real_description_clusters);
draw_image_mask_segments(source, object_colored_clusters);
if (show_dyn is True):
draw_dynamics_set(object_colored_dynamics, None, None, None, [0, 2 * 3.14], False, False);
def template_dynamic_hhn(num_osc, steps, time, stimulus = None, params = None, separate_representation = False):
net = hhn_network(num_osc, stimulus, params);
(t, dyn) = net.simulate(steps, time);
draw_dynamics(t, dyn, x_title = "Time", y_title = "V", separate = separate_representation);