def testAverageNeighborFourDistanceNegativeValues(self):
points = [[0.0, 0.0], [0.0, -1.0], [-1.0, -1.0], [-1.0, 0.0]]
assert average_neighbor_distance(points, 1) == 1.0
assert average_neighbor_distance(points, 2) == 1.0
assert self.float_comparasion(average_neighbor_distance(points, 3),
1.1381)
def process(self, order = 0.998, solution = solve_type.FAST, collect_dynamic = False):
"""!
@brief Performs clustering of input data set in line with input parameters.
@param[in] order (double): Level of local synchronization between oscillator that defines end of synchronization process, range [0..1].
@param[in] solution (solve_type) Type of solving differential equation.
@param[in] collect_dynamic (bool): If True - returns whole history of process synchronization otherwise - only final state (when process of clustering is over).
@return (tuple) Returns dynamic of the network as tuple of lists on each iteration (time, oscillator_phases) that depends on collect_dynamic parameter.
@see get_clusters()
"""
if (self.__ccore_network_pointer is not None):
analyser = wrapper.hsyncnet_process(self.__ccore_network_pointer, order, solution, collect_dynamic);
return syncnet_analyser(None, None, analyser);
number_neighbors = self.__initial_neighbors;
current_number_clusters = float('inf');
dyn_phase = [];
dyn_time = [];
radius = average_neighbor_distance(self._osc_loc, number_neighbors);
increase_step = int(len(self._osc_loc) * self.__increase_persent);
if (increase_step < 1):
increase_step = 1;
analyser = None;
while(current_number_clusters > self._number_clusters):
self._create_connections(radius);
analyser = self.simulate_dynamic(order, solution, collect_dynamic);
if (collect_dynamic == True):
if (len(dyn_phase) == 0):
self.__store_dynamic(dyn_phase, dyn_time, analyser, True);
self.__store_dynamic(dyn_phase, dyn_time, analyser, False);
clusters = analyser.allocate_sync_ensembles(0.05);
# Get current number of allocated clusters
current_number_clusters = len(clusters);
# Increase number of neighbors that should be used
number_neighbors += increase_step;
# Update connectivity radius and check if average function can be used anymore
radius = self.__calculate_radius(number_neighbors, radius);
if (collect_dynamic != True):
self.__store_dynamic(dyn_phase, dyn_time, analyser, False);
return syncnet_analyser(dyn_phase, dyn_time, None);
def process(self, order = 0.998, solution = solve_type.FAST, collect_dynamic = False):
"""!
@brief Performs clustering of input data set in line with input parameters.
@param[in] order (double): Level of local synchronization between oscillator that defines end of synchronization process, range [0..1].
@param[in] solution (solve_type) Type of solving differential equation.
@param[in] collect_dynamic (bool): If True - returns whole history of process synchronization otherwise - only final state (when process of clustering is over).
@return (tuple) Returns dynamic of the network as tuple of lists on each iteration (time, oscillator_phases) that depends on collect_dynamic parameter.
@see get_clusters()
"""
if (self.__ccore_network_pointer is not None):
analyser = wrapper.hsyncnet_process(self.__ccore_network_pointer, order, solution, collect_dynamic);
return syncnet_analyser(None, None, analyser);
number_neighbors = 0;
current_number_clusters = float('inf');
dyn_phase = [];
dyn_time = [];
radius = 0.0;
while(current_number_clusters > self._number_clusters):
self._create_connections(radius);
analyser = self.simulate_dynamic(order, solution, collect_dynamic);
if (collect_dynamic == True):
dyn_phase += analyser.output;
if (len(dyn_time) > 0):
point_time_last = dyn_time[len(dyn_time) - 1];
dyn_time += [time_point + point_time_last for time_point in analyser.time];
else:
dyn_time += analyser.time;
clusters = analyser.allocate_sync_ensembles(0.05);
# Get current number of allocated clusters
current_number_clusters = len(clusters);
# Increase number of neighbors that should be used
number_neighbors += 1;
# Update connectivity radius and check if average function can be used anymore
if (number_neighbors >= len(self._osc_loc)):
radius = radius * 0.1 + radius;
else:
radius = average_neighbor_distance(self._osc_loc, number_neighbors);
return syncnet_analyser(dyn_phase, dyn_time, None);
def __calculate_radius(self, number_neighbors, radius):
"""!
@brief Calculate new connectivity radius.
@param[in] number_neighbors (uint): Average amount of neighbors that should be connected by new radius.
@param[in] radius (double): Current connectivity radius.
@return New connectivity radius.
"""
if (number_neighbors >= len(self._osc_loc)):
return radius * self.__increase_persent + radius
return average_neighbor_distance(self._osc_loc, number_neighbors)
def __calculate_radius(self, number_neighbors, radius):
"""!
@brief Calculate new connectivity radius.
@param[in] number_neighbors (uint): Average amount of neighbors that should be connected by new radius.
@param[in] radius (double): Current connectivity radius.
@return New connectivity radius.
"""
if (number_neighbors >= len(self._osc_loc)):
return radius * self.__increase_persent + radius;
return average_neighbor_distance(self._osc_loc, number_neighbors);
def process(self, number_neighbours, collect_dynamic=False, order=0.999):
"""!
@brief Performs simulation of the oscillatory network.
@param[in] number_neighbours (uint): Number of neighbours that should be used for calculation average distance and creation connections between oscillators.
@param[in] collect_dynamic (bool): If True - returns whole dynamic of oscillatory network, otherwise returns only last values of dynamics.
@param[in] order (double): Order of process synchronization that should be considered as end of clustering, destributed 0..1.
@return (tuple) Dynamic of oscillatory network. If argument 'collect_dynamic' = True, than return dynamic for the whole simulation time,
otherwise returns only last values (last step of simulation) of dynamic.
@see get_som_clusters()
@see get_clusters()
"""
# train self-organization map.
self._som.train(self._data, 100)
# prepare to build list.
weights = list()
self._som_osc_table.clear()
# must be cleared, if it's used before.
for i in range(self._som.size):
if self._som.awards[i] > 0:
weights.append(self._som.weights[i])
self._som_osc_table.append(i)
# calculate trusted distance between objects.
radius = 0
if len(weights) >= number_neighbours:
radius = average_neighbor_distance(weights, number_neighbours)
else:
radius = 0
# create oscillatory neural network.
self._sync = syncnet(weights, radius, initial_phases=initial_type.EQUIPARTITION)
self._analyser = self._sync.process(order, collect_dynamic=collect_dynamic)
# Draw SOM clusters.
# clusters = self._sync.get_clusters();
# draw_clusters(weights, clusters);
# self._som.show_network(awards = False, belongs = True);
# return dynamic if it was requested.
return (self._analyser.time, self._analyser.output)
def __create_weights(self, stimulus):
"""!
@brief Create weights between neurons in line with stimulus.
@param[in] stimulus (list): External stimulus for the chaotic neural network.
"""
self.__average_distance = average_neighbor_distance(stimulus, self.__amount_neighbors)
self.__weights = [ [ 0.0 for _ in range(len(stimulus)) ] for _ in range(len(stimulus)) ]
self.__weights_summary = [ 0.0 for _ in range(self.__num_osc) ]
if self.__conn_type == type_conn.ALL_TO_ALL:
self.__create_weights_all_to_all(stimulus)
elif self.__conn_type == type_conn.TRIANGULATION_DELAUNAY:
self.__create_weights_delaunay_triangulation(stimulus)
def process(self, number_neighbours, collect_dynamic = False, order = 0.999):
"""!
@brief Performs simulation of the oscillatory network.
@param[in] number_neighbours (uint): Number of neighbours that should be used for calculation average distance and creation connections between oscillators.
@param[in] collect_dynamic (bool): If True - returns whole dynamic of oscillatory network, otherwise returns only last values of dynamics.
@param[in] order (double): Order of process synchronization that should be considered as end of clustering, destributed 0..1.
@return (tuple) Dynamic of oscillatory network. If argument 'collect_dynamic' = True, than return dynamic for the whole simulation time,
otherwise returns only last values (last step of simulation) of dynamic.
@see get_som_clusters()
@see get_clusters()
"""
# train self-organization map.
self._som.train(self._data, 100);
# prepare to build list.
weights = list();
self._som_osc_table.clear(); # must be cleared, if it's used before.
for i in range(self._som.size):
if (self._som.awards[i] > 0):
weights.append(self._som.weights[i]);
self._som_osc_table.append(i);
# calculate trusted distance between objects.
radius = 0;
if (len(weights) >= number_neighbours):
radius = average_neighbor_distance(weights, number_neighbours);
else:
radius = 0;
# create oscillatory neural network.
self._sync = syncnet(weights, radius, initial_phases = initial_type.EQUIPARTITION);
self._analyser = self._sync.process(order, collect_dynamic = collect_dynamic);
# Draw SOM clusters.
#clusters = self._sync.get_clusters();
#draw_clusters(weights, clusters);
#self._som.show_network(awards = False, belongs = True);
# return dynamic if it was requested.
return (self._analyser.time, self._analyser.output);
def process(self,
order=0.998,
solution=solve_type.FAST,
collect_dynamic=False):
"""!
@brief Performs clustering of input data set in line with input parameters.
@param[in] order (double): Level of local synchronization between oscillator that defines end of synchronization process, range [0..1].
@param[in] solution (solve_type) Type of solving differential equation.
@param[in] collect_dynamic (bool): If True - returns whole history of process synchronization otherwise - only final state (when process of clustering is over).
@return (tuple) Returns dynamic of the network as tuple of lists on each iteration (time, oscillator_phases) that depends on collect_dynamic parameter.
@see get_clusters()
"""
if (self.__ccore_network_pointer is not None):
analyser = wrapper.hsyncnet_process(self.__ccore_network_pointer,
order, solution,
collect_dynamic)
return syncnet_analyser(None, None, analyser)
number_neighbors = self.__initial_neighbors
current_number_clusters = float('inf')
dyn_phase = []
dyn_time = []
radius = average_neighbor_distance(self._osc_loc, number_neighbors)
increase_step = int(len(self._osc_loc) * self.__increase_persent)
if (increase_step < 1):
increase_step = 1
analyser = None
while (current_number_clusters > self._number_clusters):
self._create_connections(radius)
analyser = self.simulate_dynamic(order, solution, collect_dynamic)
if (collect_dynamic == True):
if (len(dyn_phase) == 0):
self.__store_dynamic(dyn_phase, dyn_time, analyser, True)
self.__store_dynamic(dyn_phase, dyn_time, analyser, False)
clusters = analyser.allocate_sync_ensembles(0.05)
# Get current number of allocated clusters
current_number_clusters = len(clusters)
# Increase number of neighbors that should be used
number_neighbors += increase_step
# Update connectivity radius and check if average function can be used anymore
radius = self.__calculate_radius(number_neighbors, radius)
if (collect_dynamic != True):
self.__store_dynamic(dyn_phase, dyn_time, analyser, False)
return syncnet_analyser(dyn_phase, dyn_time, None)
def testAverageNeighborFourDistance(self):
points = [[0.0, 0.0], [0.0, 1.0], [1.0, 1.0], [1.0, 0.0]];
assert average_neighbor_distance(points, 1) == 1.0;
assert average_neighbor_distance(points, 2) == 1.0;
assert self.float_comparasion(average_neighbor_distance(points, 3), 1.1381);
def testAverageNeighborFourDistanceNegativeValues(self):
points = [[0.0, 0.0], [0.0, -1.0], [-1.0, -1.0], [-1.0, 0.0]];
assert average_neighbor_distance(points, 1) == 1.0;
assert average_neighbor_distance(points, 2) == 1.0;
assert self.float_comparasion(average_neighbor_distance(points, 3), 1.1381);
def testAverageNeighborDistance(self):
points = [[0, 0], [0, 1], [1, 1], [1, 0]];
assert average_neighbor_distance(points, 1) == 1.0;
assert average_neighbor_distance(points, 2) == 1.0;
assert self.float_comparasion(average_neighbor_distance(points, 3), 1.1381);
