| @@ -15,17 +15,17 @@ class GEDEnv(object): | |||||
| def __init__(self): | def __init__(self): | ||||
| self.__initialized = False | |||||
| self.__new_graph_ids = [] | |||||
| self.__ged_data = GEDData() | |||||
| self._initialized = False | |||||
| self._new_graph_ids = [] | |||||
| self._ged_data = GEDData() | |||||
| # Variables needed for approximating ged_instance_. | # Variables needed for approximating ged_instance_. | ||||
| self.__lower_bounds = {} | |||||
| self.__upper_bounds = {} | |||||
| self.__runtimes = {} | |||||
| self.__node_maps = {} | |||||
| self.__original_to_internal_node_ids = [] | |||||
| self.__internal_to_original_node_ids = [] | |||||
| self.__ged_method = None | |||||
| self._lower_bounds = {} | |||||
| self._upper_bounds = {} | |||||
| self._runtimes = {} | |||||
| self._node_maps = {} | |||||
| self._original_to_internal_node_ids = [] | |||||
| self._internal_to_original_node_ids = [] | |||||
| self._ged_method = None | |||||
| def set_edit_cost(self, edit_cost, edit_cost_constants=[]): | def set_edit_cost(self, edit_cost, edit_cost_constants=[]): | ||||
| @@ -36,7 +36,7 @@ class GEDEnv(object): | |||||
| * @param[in] edit_cost_constants Constants passed to the constructor of the edit cost class selected by @p edit_costs. | * @param[in] edit_cost_constants Constants passed to the constructor of the edit cost class selected by @p edit_costs. | ||||
| */ | */ | ||||
| """ | """ | ||||
| self.__ged_data._set_edit_cost(edit_cost, edit_cost_constants) | |||||
| self._ged_data._set_edit_cost(edit_cost, edit_cost_constants) | |||||
| def add_graph(self, graph_name='', graph_class=''): | def add_graph(self, graph_name='', graph_class=''): | ||||
| @@ -49,17 +49,17 @@ class GEDEnv(object): | |||||
| */ | */ | ||||
| """ | """ | ||||
| # @todo: graphs are not uninitialized. | # @todo: graphs are not uninitialized. | ||||
| self.__initialized = False | |||||
| graph_id = self.__ged_data._num_graphs_without_shuffled_copies | |||||
| self.__ged_data._num_graphs_without_shuffled_copies += 1 | |||||
| self.__new_graph_ids.append(graph_id) | |||||
| self.__ged_data._graphs.append(nx.Graph()) | |||||
| self.__ged_data._graph_names.append(graph_name) | |||||
| self.__ged_data._graph_classes.append(graph_class) | |||||
| self.__original_to_internal_node_ids.append({}) | |||||
| self.__internal_to_original_node_ids.append({}) | |||||
| self.__ged_data._strings_to_internal_node_ids.append({}) | |||||
| self.__ged_data._internal_node_ids_to_strings.append({}) | |||||
| self._initialized = False | |||||
| graph_id = self._ged_data._num_graphs_without_shuffled_copies | |||||
| self._ged_data._num_graphs_without_shuffled_copies += 1 | |||||
| self._new_graph_ids.append(graph_id) | |||||
| self._ged_data._graphs.append(nx.Graph()) | |||||
| self._ged_data._graph_names.append(graph_name) | |||||
| self._ged_data._graph_classes.append(graph_class) | |||||
| self._original_to_internal_node_ids.append({}) | |||||
| self._internal_to_original_node_ids.append({}) | |||||
| self._ged_data._strings_to_internal_node_ids.append({}) | |||||
| self._ged_data._internal_node_ids_to_strings.append({}) | |||||
| return graph_id | return graph_id | ||||
| @@ -70,14 +70,14 @@ class GEDEnv(object): | |||||
| * @param[in] graph_id ID of graph that has to be cleared. | * @param[in] graph_id ID of graph that has to be cleared. | ||||
| */ | */ | ||||
| """ | """ | ||||
| if graph_id > self.__ged_data.num_graphs_without_shuffled_copies(): | |||||
| if graph_id > self._ged_data.num_graphs_without_shuffled_copies(): | |||||
| raise Exception('The graph', self.get_graph_name(graph_id), 'has not been added to the environment.') | raise Exception('The graph', self.get_graph_name(graph_id), 'has not been added to the environment.') | ||||
| self.__ged_data._graphs[graph_id].clear() | |||||
| self.__original_to_internal_node_ids[graph_id].clear() | |||||
| self.__internal_to_original_node_ids[graph_id].clear() | |||||
| self.__ged_data._strings_to_internal_node_ids[graph_id].clear() | |||||
| self.__ged_data._internal_node_ids_to_strings[graph_id].clear() | |||||
| self.__initialized = False | |||||
| self._ged_data._graphs[graph_id].clear() | |||||
| self._original_to_internal_node_ids[graph_id].clear() | |||||
| self._internal_to_original_node_ids[graph_id].clear() | |||||
| self._ged_data._strings_to_internal_node_ids[graph_id].clear() | |||||
| self._ged_data._internal_node_ids_to_strings[graph_id].clear() | |||||
| self._initialized = False | |||||
| def add_node(self, graph_id, node_id, node_label): | def add_node(self, graph_id, node_id, node_label): | ||||
| @@ -90,15 +90,15 @@ class GEDEnv(object): | |||||
| */ | */ | ||||
| """ | """ | ||||
| # @todo: check ids. | # @todo: check ids. | ||||
| self.__initialized = False | |||||
| internal_node_id = nx.number_of_nodes(self.__ged_data._graphs[graph_id]) | |||||
| self.__ged_data._graphs[graph_id].add_node(internal_node_id, label=node_label) | |||||
| self.__original_to_internal_node_ids[graph_id][node_id] = internal_node_id | |||||
| self.__internal_to_original_node_ids[graph_id][internal_node_id] = node_id | |||||
| self.__ged_data._strings_to_internal_node_ids[graph_id][str(node_id)] = internal_node_id | |||||
| self.__ged_data._internal_node_ids_to_strings[graph_id][internal_node_id] = str(node_id) | |||||
| self.__ged_data._node_label_to_id(node_label) | |||||
| label_id = self.__ged_data._node_label_to_id(node_label) | |||||
| self._initialized = False | |||||
| internal_node_id = nx.number_of_nodes(self._ged_data._graphs[graph_id]) | |||||
| self._ged_data._graphs[graph_id].add_node(internal_node_id, label=node_label) | |||||
| self._original_to_internal_node_ids[graph_id][node_id] = internal_node_id | |||||
| self._internal_to_original_node_ids[graph_id][internal_node_id] = node_id | |||||
| self._ged_data._strings_to_internal_node_ids[graph_id][str(node_id)] = internal_node_id | |||||
| self._ged_data._internal_node_ids_to_strings[graph_id][internal_node_id] = str(node_id) | |||||
| self._ged_data._node_label_to_id(node_label) | |||||
| label_id = self._ged_data._node_label_to_id(node_label) | |||||
| # @todo: ged_data_.graphs_[graph_id].set_label | # @todo: ged_data_.graphs_[graph_id].set_label | ||||
| @@ -114,10 +114,10 @@ class GEDEnv(object): | |||||
| */ | */ | ||||
| """ | """ | ||||
| # @todo: check everything. | # @todo: check everything. | ||||
| self.__initialized = False | |||||
| self._initialized = False | |||||
| # @todo: check ignore_duplicates. | # @todo: check ignore_duplicates. | ||||
| self.__ged_data._graphs[graph_id].add_edge(self.__original_to_internal_node_ids[graph_id][nd_from], self.__original_to_internal_node_ids[graph_id][nd_to], label=edge_label) | |||||
| label_id = self.__ged_data._edge_label_to_id(edge_label) | |||||
| self._ged_data._graphs[graph_id].add_edge(self._original_to_internal_node_ids[graph_id][nd_from], self._original_to_internal_node_ids[graph_id][nd_to], label=edge_label) | |||||
| label_id = self._ged_data._edge_label_to_id(edge_label) | |||||
| # @todo: ged_data_.graphs_[graph_id].set_label | # @todo: ged_data_.graphs_[graph_id].set_label | ||||
| @@ -182,30 +182,30 @@ class GEDEnv(object): | |||||
| init_type = OptionsStringMap.InitType[init_type] | init_type = OptionsStringMap.InitType[init_type] | ||||
| # Throw an exception if no edit costs have been selected. | # Throw an exception if no edit costs have been selected. | ||||
| if self.__ged_data._edit_cost is None: | |||||
| if self._ged_data._edit_cost is None: | |||||
| raise Exception('No edit costs have been selected. Call set_edit_cost() before calling init().') | raise Exception('No edit costs have been selected. Call set_edit_cost() before calling init().') | ||||
| # Return if the environment is initialized. | # Return if the environment is initialized. | ||||
| if self.__initialized: | |||||
| if self._initialized: | |||||
| return | return | ||||
| # Set initialization type. | # Set initialization type. | ||||
| self.__ged_data._init_type = init_type | |||||
| self._ged_data._init_type = init_type | |||||
| # @todo: Construct shuffled graph copies if necessary. | # @todo: Construct shuffled graph copies if necessary. | ||||
| # Re-initialize adjacency matrices (also previously initialized graphs must be re-initialized because of possible re-allocation). | # Re-initialize adjacency matrices (also previously initialized graphs must be re-initialized because of possible re-allocation). | ||||
| # @todo: setup_adjacency_matrix, don't know if neccessary. | # @todo: setup_adjacency_matrix, don't know if neccessary. | ||||
| self.__ged_data._max_num_nodes = np.max([nx.number_of_nodes(g) for g in self.__ged_data._graphs]) | |||||
| self.__ged_data._max_num_edges = np.max([nx.number_of_edges(g) for g in self.__ged_data._graphs]) | |||||
| self._ged_data._max_num_nodes = np.max([nx.number_of_nodes(g) for g in self._ged_data._graphs]) | |||||
| self._ged_data._max_num_edges = np.max([nx.number_of_edges(g) for g in self._ged_data._graphs]) | |||||
| # Initialize cost matrices if necessary. | # Initialize cost matrices if necessary. | ||||
| if self.__ged_data._eager_init(): | |||||
| if self._ged_data._eager_init(): | |||||
| pass # @todo: init_cost_matrices_: 1. Update node cost matrix if new node labels have been added to the environment; 2. Update edge cost matrix if new edge labels have been added to the environment. | pass # @todo: init_cost_matrices_: 1. Update node cost matrix if new node labels have been added to the environment; 2. Update edge cost matrix if new edge labels have been added to the environment. | ||||
| # Mark environment as initialized. | # Mark environment as initialized. | ||||
| self.__initialized = True | |||||
| self.__new_graph_ids.clear() | |||||
| self._initialized = True | |||||
| self._new_graph_ids.clear() | |||||
| def is_initialized(self): | def is_initialized(self): | ||||
| @@ -215,7 +215,7 @@ class GEDEnv(object): | |||||
| * @return True if the environment is initialized. | * @return True if the environment is initialized. | ||||
| */ | */ | ||||
| """ | """ | ||||
| return self.__initialized | |||||
| return self._initialized | |||||
| def get_init_type(self): | def get_init_type(self): | ||||
| @@ -225,16 +225,16 @@ class GEDEnv(object): | |||||
| * @return Initialization type. | * @return Initialization type. | ||||
| */ | */ | ||||
| """ | """ | ||||
| return self.__ged_data._init_type | |||||
| return self._ged_data._init_type | |||||
| def set_label_costs(self, node_label_costs=None, edge_label_costs=None): | def set_label_costs(self, node_label_costs=None, edge_label_costs=None): | ||||
| """Set the costs between labels. | """Set the costs between labels. | ||||
| """ | """ | ||||
| if node_label_costs is not None: | if node_label_costs is not None: | ||||
| self.__ged_data._node_label_costs = node_label_costs | |||||
| self._ged_data._node_label_costs = node_label_costs | |||||
| if edge_label_costs is not None: | if edge_label_costs is not None: | ||||
| self.__ged_data._edge_label_costs = edge_label_costs | |||||
| self._ged_data._edge_label_costs = edge_label_costs | |||||
| def set_method(self, method, options=''): | def set_method(self, method, options=''): | ||||
| @@ -245,67 +245,67 @@ class GEDEnv(object): | |||||
| * @param[in] options An options string of the form @"[--@<option@> @<arg@>] [...]@" passed to the selected method. | * @param[in] options An options string of the form @"[--@<option@> @<arg@>] [...]@" passed to the selected method. | ||||
| */ | */ | ||||
| """ | """ | ||||
| del self.__ged_method | |||||
| del self._ged_method | |||||
| if isinstance(method, str): | if isinstance(method, str): | ||||
| method = OptionsStringMap.GEDMethod[method] | method = OptionsStringMap.GEDMethod[method] | ||||
| if method == Options.GEDMethod.BRANCH: | if method == Options.GEDMethod.BRANCH: | ||||
| self.__ged_method = Branch(self.__ged_data) | |||||
| self._ged_method = Branch(self._ged_data) | |||||
| elif method == Options.GEDMethod.BRANCH_FAST: | elif method == Options.GEDMethod.BRANCH_FAST: | ||||
| self.__ged_method = BranchFast(self.__ged_data) | |||||
| self._ged_method = BranchFast(self._ged_data) | |||||
| elif method == Options.GEDMethod.BRANCH_FAST: | elif method == Options.GEDMethod.BRANCH_FAST: | ||||
| self.__ged_method = BranchFast(self.__ged_data) | |||||
| self._ged_method = BranchFast(self._ged_data) | |||||
| elif method == Options.GEDMethod.BRANCH_TIGHT: | elif method == Options.GEDMethod.BRANCH_TIGHT: | ||||
| self.__ged_method = BranchTight(self.__ged_data) | |||||
| self._ged_method = BranchTight(self._ged_data) | |||||
| elif method == Options.GEDMethod.BRANCH_UNIFORM: | elif method == Options.GEDMethod.BRANCH_UNIFORM: | ||||
| self.__ged_method = BranchUniform(self.__ged_data) | |||||
| self._ged_method = BranchUniform(self._ged_data) | |||||
| elif method == Options.GEDMethod.BRANCH_COMPACT: | elif method == Options.GEDMethod.BRANCH_COMPACT: | ||||
| self.__ged_method = BranchCompact(self.__ged_data) | |||||
| self._ged_method = BranchCompact(self._ged_data) | |||||
| elif method == Options.GEDMethod.PARTITION: | elif method == Options.GEDMethod.PARTITION: | ||||
| self.__ged_method = Partition(self.__ged_data) | |||||
| self._ged_method = Partition(self._ged_data) | |||||
| elif method == Options.GEDMethod.HYBRID: | elif method == Options.GEDMethod.HYBRID: | ||||
| self.__ged_method = Hybrid(self.__ged_data) | |||||
| self._ged_method = Hybrid(self._ged_data) | |||||
| elif method == Options.GEDMethod.RING: | elif method == Options.GEDMethod.RING: | ||||
| self.__ged_method = Ring(self.__ged_data) | |||||
| self._ged_method = Ring(self._ged_data) | |||||
| elif method == Options.GEDMethod.ANCHOR_AWARE_GED: | elif method == Options.GEDMethod.ANCHOR_AWARE_GED: | ||||
| self.__ged_method = AnchorAwareGED(self.__ged_data) | |||||
| self._ged_method = AnchorAwareGED(self._ged_data) | |||||
| elif method == Options.GEDMethod.WALKS: | elif method == Options.GEDMethod.WALKS: | ||||
| self.__ged_method = Walks(self.__ged_data) | |||||
| self._ged_method = Walks(self._ged_data) | |||||
| elif method == Options.GEDMethod.IPFP: | elif method == Options.GEDMethod.IPFP: | ||||
| self.__ged_method = IPFP(self.__ged_data) | |||||
| self._ged_method = IPFP(self._ged_data) | |||||
| elif method == Options.GEDMethod.BIPARTITE: | elif method == Options.GEDMethod.BIPARTITE: | ||||
| from gklearn.ged.methods import Bipartite | from gklearn.ged.methods import Bipartite | ||||
| self.__ged_method = Bipartite(self.__ged_data) | |||||
| self._ged_method = Bipartite(self._ged_data) | |||||
| elif method == Options.GEDMethod.SUBGRAPH: | elif method == Options.GEDMethod.SUBGRAPH: | ||||
| self.__ged_method = Subgraph(self.__ged_data) | |||||
| self._ged_method = Subgraph(self._ged_data) | |||||
| elif method == Options.GEDMethod.NODE: | elif method == Options.GEDMethod.NODE: | ||||
| self.__ged_method = Node(self.__ged_data) | |||||
| self._ged_method = Node(self._ged_data) | |||||
| elif method == Options.GEDMethod.RING_ML: | elif method == Options.GEDMethod.RING_ML: | ||||
| self.__ged_method = RingML(self.__ged_data) | |||||
| self._ged_method = RingML(self._ged_data) | |||||
| elif method == Options.GEDMethod.BIPARTITE_ML: | elif method == Options.GEDMethod.BIPARTITE_ML: | ||||
| self.__ged_method = BipartiteML(self.__ged_data) | |||||
| self._ged_method = BipartiteML(self._ged_data) | |||||
| elif method == Options.GEDMethod.REFINE: | elif method == Options.GEDMethod.REFINE: | ||||
| self.__ged_method = Refine(self.__ged_data) | |||||
| self._ged_method = Refine(self._ged_data) | |||||
| elif method == Options.GEDMethod.BP_BEAM: | elif method == Options.GEDMethod.BP_BEAM: | ||||
| self.__ged_method = BPBeam(self.__ged_data) | |||||
| self._ged_method = BPBeam(self._ged_data) | |||||
| elif method == Options.GEDMethod.SIMULATED_ANNEALING: | elif method == Options.GEDMethod.SIMULATED_ANNEALING: | ||||
| self.__ged_method = SimulatedAnnealing(self.__ged_data) | |||||
| self._ged_method = SimulatedAnnealing(self._ged_data) | |||||
| elif method == Options.GEDMethod.HED: | elif method == Options.GEDMethod.HED: | ||||
| self.__ged_method = HED(self.__ged_data) | |||||
| self._ged_method = HED(self._ged_data) | |||||
| elif method == Options.GEDMethod.STAR: | elif method == Options.GEDMethod.STAR: | ||||
| self.__ged_method = STAR(self.__ged_data) | |||||
| self._ged_method = STAR(self._ged_data) | |||||
| # #ifdef GUROBI | # #ifdef GUROBI | ||||
| elif method == Options.GEDMethod.F1: | elif method == Options.GEDMethod.F1: | ||||
| self.__ged_method = F1(self.__ged_data) | |||||
| self._ged_method = F1(self._ged_data) | |||||
| elif method == Options.GEDMethod.F2: | elif method == Options.GEDMethod.F2: | ||||
| self.__ged_method = F2(self.__ged_data) | |||||
| self._ged_method = F2(self._ged_data) | |||||
| elif method == Options.GEDMethod.COMPACT_MIP: | elif method == Options.GEDMethod.COMPACT_MIP: | ||||
| self.__ged_method = CompactMIP(self.__ged_data) | |||||
| self._ged_method = CompactMIP(self._ged_data) | |||||
| elif method == Options.GEDMethod.BLP_NO_EDGE_LABELS: | elif method == Options.GEDMethod.BLP_NO_EDGE_LABELS: | ||||
| self.__ged_method = BLPNoEdgeLabels(self.__ged_data) | |||||
| self._ged_method = BLPNoEdgeLabels(self._ged_data) | |||||
| self.__ged_method.set_options(options) | |||||
| self._ged_method.set_options(options) | |||||
| def run_method(self, g_id, h_id): | def run_method(self, g_id, h_id): | ||||
| @@ -316,34 +316,34 @@ class GEDEnv(object): | |||||
| * @param[in] h_id ID of an input graph that has been added to the environment. | * @param[in] h_id ID of an input graph that has been added to the environment. | ||||
| */ | */ | ||||
| """ | """ | ||||
| if g_id >= self.__ged_data.num_graphs(): | |||||
| if g_id >= self._ged_data.num_graphs(): | |||||
| raise Exception('The graph with ID', str(g_id), 'has not been added to the environment.') | raise Exception('The graph with ID', str(g_id), 'has not been added to the environment.') | ||||
| if h_id >= self.__ged_data.num_graphs(): | |||||
| if h_id >= self._ged_data.num_graphs(): | |||||
| raise Exception('The graph with ID', str(h_id), 'has not been added to the environment.') | raise Exception('The graph with ID', str(h_id), 'has not been added to the environment.') | ||||
| if not self.__initialized: | |||||
| if not self._initialized: | |||||
| raise Exception('The environment is uninitialized. Call init() after adding all graphs to the environment.') | raise Exception('The environment is uninitialized. Call init() after adding all graphs to the environment.') | ||||
| if self.__ged_method is None: | |||||
| if self._ged_method is None: | |||||
| raise Exception('No method has been set. Call set_method() before calling run().') | raise Exception('No method has been set. Call set_method() before calling run().') | ||||
| # Call selected GEDMethod and store results. | # Call selected GEDMethod and store results. | ||||
| if self.__ged_data.shuffled_graph_copies_available() and (g_id == h_id): | |||||
| self.__ged_method.run(g_id, self.__ged_data.id_shuffled_graph_copy(h_id)) # @todo: why shuffle? | |||||
| if self._ged_data.shuffled_graph_copies_available() and (g_id == h_id): | |||||
| self._ged_method.run(g_id, self._ged_data.id_shuffled_graph_copy(h_id)) # @todo: why shuffle? | |||||
| else: | else: | ||||
| self.__ged_method.run(g_id, h_id) | |||||
| self.__lower_bounds[(g_id, h_id)] = self.__ged_method.get_lower_bound() | |||||
| self.__upper_bounds[(g_id, h_id)] = self.__ged_method.get_upper_bound() | |||||
| self.__runtimes[(g_id, h_id)] = self.__ged_method.get_runtime() | |||||
| self.__node_maps[(g_id, h_id)] = self.__ged_method.get_node_map() | |||||
| self._ged_method.run(g_id, h_id) | |||||
| self._lower_bounds[(g_id, h_id)] = self._ged_method.get_lower_bound() | |||||
| self._upper_bounds[(g_id, h_id)] = self._ged_method.get_upper_bound() | |||||
| self._runtimes[(g_id, h_id)] = self._ged_method.get_runtime() | |||||
| self._node_maps[(g_id, h_id)] = self._ged_method.get_node_map() | |||||
| def init_method(self): | def init_method(self): | ||||
| """Initializes the method specified by call to set_method(). | """Initializes the method specified by call to set_method(). | ||||
| """ | """ | ||||
| if not self.__initialized: | |||||
| if not self._initialized: | |||||
| raise Exception('The environment is uninitialized. Call init() before calling init_method().') | raise Exception('The environment is uninitialized. Call init() before calling init_method().') | ||||
| if self.__ged_method is None: | |||||
| if self._ged_method is None: | |||||
| raise Exception('No method has been set. Call set_method() before calling init_method().') | raise Exception('No method has been set. Call set_method() before calling init_method().') | ||||
| self.__ged_method.init() | |||||
| self._ged_method.init() | |||||
| def get_num_node_labels(self): | def get_num_node_labels(self): | ||||
| @@ -354,7 +354,7 @@ class GEDEnv(object): | |||||
| * @note If @p 1 is returned, the nodes are unlabeled. | * @note If @p 1 is returned, the nodes are unlabeled. | ||||
| */ | */ | ||||
| """ | """ | ||||
| return len(self.__ged_data._node_labels) | |||||
| return len(self._ged_data._node_labels) | |||||
| def get_all_node_labels(self): | def get_all_node_labels(self): | ||||
| @@ -365,7 +365,7 @@ class GEDEnv(object): | |||||
| * @note If @p 1 is returned, the nodes are unlabeled. | * @note If @p 1 is returned, the nodes are unlabeled. | ||||
| */ | */ | ||||
| """ | """ | ||||
| return self.__ged_data._node_labels | |||||
| return self._ged_data._node_labels | |||||
| def get_node_label(self, label_id, to_dict=True): | def get_node_label(self, label_id, to_dict=True): | ||||
| @@ -379,8 +379,8 @@ class GEDEnv(object): | |||||
| if label_id < 1 or label_id > self.get_num_node_labels(): | if label_id < 1 or label_id > self.get_num_node_labels(): | ||||
| raise Exception('The environment does not contain a node label with ID', str(label_id), '.') | raise Exception('The environment does not contain a node label with ID', str(label_id), '.') | ||||
| if to_dict: | if to_dict: | ||||
| return dict(self.__ged_data._node_labels[label_id - 1]) | |||||
| return self.__ged_data._node_labels[label_id - 1] | |||||
| return dict(self._ged_data._node_labels[label_id - 1]) | |||||
| return self._ged_data._node_labels[label_id - 1] | |||||
| def get_num_edge_labels(self): | def get_num_edge_labels(self): | ||||
| @@ -391,7 +391,7 @@ class GEDEnv(object): | |||||
| * @note If @p 1 is returned, the edges are unlabeled. | * @note If @p 1 is returned, the edges are unlabeled. | ||||
| */ | */ | ||||
| """ | """ | ||||
| return len(self.__ged_data._edge_labels) | |||||
| return len(self._ged_data._edge_labels) | |||||
| def get_all_edge_labels(self): | def get_all_edge_labels(self): | ||||
| @@ -402,7 +402,7 @@ class GEDEnv(object): | |||||
| * @note If @p 1 is returned, the edges are unlabeled. | * @note If @p 1 is returned, the edges are unlabeled. | ||||
| */ | */ | ||||
| """ | """ | ||||
| return self.__ged_data._edge_labels | |||||
| return self._ged_data._edge_labels | |||||
| def get_edge_label(self, label_id, to_dict=True): | def get_edge_label(self, label_id, to_dict=True): | ||||
| @@ -416,8 +416,8 @@ class GEDEnv(object): | |||||
| if label_id < 1 or label_id > self.get_num_edge_labels(): | if label_id < 1 or label_id > self.get_num_edge_labels(): | ||||
| raise Exception('The environment does not contain an edge label with ID', str(label_id), '.') | raise Exception('The environment does not contain an edge label with ID', str(label_id), '.') | ||||
| if to_dict: | if to_dict: | ||||
| return dict(self.__ged_data._edge_labels[label_id - 1]) | |||||
| return self.__ged_data._edge_labels[label_id - 1] | |||||
| return dict(self._ged_data._edge_labels[label_id - 1]) | |||||
| return self._ged_data._edge_labels[label_id - 1] | |||||
| def get_upper_bound(self, g_id, h_id): | def get_upper_bound(self, g_id, h_id): | ||||
| @@ -429,9 +429,9 @@ class GEDEnv(object): | |||||
| * @return Upper bound computed by the last call to run_method() with arguments @p g_id and @p h_id. | * @return Upper bound computed by the last call to run_method() with arguments @p g_id and @p h_id. | ||||
| */ | */ | ||||
| """ | """ | ||||
| if (g_id, h_id) not in self.__upper_bounds: | |||||
| if (g_id, h_id) not in self._upper_bounds: | |||||
| raise Exception('Call run(' + str(g_id) + ',' + str(h_id) + ') before calling get_upper_bound(' + str(g_id) + ',' + str(h_id) + ').') | raise Exception('Call run(' + str(g_id) + ',' + str(h_id) + ') before calling get_upper_bound(' + str(g_id) + ',' + str(h_id) + ').') | ||||
| return self.__upper_bounds[(g_id, h_id)] | |||||
| return self._upper_bounds[(g_id, h_id)] | |||||
| def get_lower_bound(self, g_id, h_id): | def get_lower_bound(self, g_id, h_id): | ||||
| @@ -443,9 +443,9 @@ class GEDEnv(object): | |||||
| * @return Lower bound computed by the last call to run_method() with arguments @p g_id and @p h_id. | * @return Lower bound computed by the last call to run_method() with arguments @p g_id and @p h_id. | ||||
| */ | */ | ||||
| """ | """ | ||||
| if (g_id, h_id) not in self.__lower_bounds: | |||||
| if (g_id, h_id) not in self._lower_bounds: | |||||
| raise Exception('Call run(' + str(g_id) + ',' + str(h_id) + ') before calling get_lower_bound(' + str(g_id) + ',' + str(h_id) + ').') | raise Exception('Call run(' + str(g_id) + ',' + str(h_id) + ') before calling get_lower_bound(' + str(g_id) + ',' + str(h_id) + ').') | ||||
| return self.__lower_bounds[(g_id, h_id)] | |||||
| return self._lower_bounds[(g_id, h_id)] | |||||
| def get_runtime(self, g_id, h_id): | def get_runtime(self, g_id, h_id): | ||||
| @@ -457,9 +457,9 @@ class GEDEnv(object): | |||||
| * @return Runtime of last call to run_method() with arguments @p g_id and @p h_id. | * @return Runtime of last call to run_method() with arguments @p g_id and @p h_id. | ||||
| */ | */ | ||||
| """ | """ | ||||
| if (g_id, h_id) not in self.__runtimes: | |||||
| if (g_id, h_id) not in self._runtimes: | |||||
| raise Exception('Call run(' + str(g_id) + ',' + str(h_id) + ') before calling get_runtime(' + str(g_id) + ',' + str(h_id) + ').') | raise Exception('Call run(' + str(g_id) + ',' + str(h_id) + ') before calling get_runtime(' + str(g_id) + ',' + str(h_id) + ').') | ||||
| return self.__runtimes[(g_id, h_id)] | |||||
| return self._runtimes[(g_id, h_id)] | |||||
| def get_init_time(self): | def get_init_time(self): | ||||
| @@ -469,7 +469,7 @@ class GEDEnv(object): | |||||
| * @return Runtime of the last call to init_method(). | * @return Runtime of the last call to init_method(). | ||||
| */ | */ | ||||
| """ | """ | ||||
| return self.__ged_method.get_init_time() | |||||
| return self._ged_method.get_init_time() | |||||
| def get_node_map(self, g_id, h_id): | def get_node_map(self, g_id, h_id): | ||||
| @@ -481,9 +481,9 @@ class GEDEnv(object): | |||||
| * @return Node map computed by the last call to run_method() with arguments @p g_id and @p h_id. | * @return Node map computed by the last call to run_method() with arguments @p g_id and @p h_id. | ||||
| */ | */ | ||||
| """ | """ | ||||
| if (g_id, h_id) not in self.__node_maps: | |||||
| if (g_id, h_id) not in self._node_maps: | |||||
| raise Exception('Call run(' + str(g_id) + ',' + str(h_id) + ') before calling get_node_map(' + str(g_id) + ',' + str(h_id) + ').') | raise Exception('Call run(' + str(g_id) + ',' + str(h_id) + ') before calling get_node_map(' + str(g_id) + ',' + str(h_id) + ').') | ||||
| return self.__node_maps[(g_id, h_id)] | |||||
| return self._node_maps[(g_id, h_id)] | |||||
| def get_forward_map(self, g_id, h_id) : | def get_forward_map(self, g_id, h_id) : | ||||
| @@ -531,7 +531,7 @@ class GEDEnv(object): | |||||
| * @param[in,out] node_map Node map whose induced edit cost is to be computed. | * @param[in,out] node_map Node map whose induced edit cost is to be computed. | ||||
| */ | */ | ||||
| """ | """ | ||||
| self.__ged_data.compute_induced_cost(self.__ged_data._graphs[g_id], self.__ged_data._graphs[h_id], node_map) | |||||
| self._ged_data.compute_induced_cost(self._ged_data._graphs[g_id], self._ged_data._graphs[h_id], node_map) | |||||
| def get_nx_graph(self, graph_id): | def get_nx_graph(self, graph_id): | ||||
| @@ -569,7 +569,7 @@ class GEDEnv(object): | |||||
| .. seealso:: get_graph_internal_id(), get_graph_num_nodes(), get_graph_num_edges(), get_original_node_ids(), get_graph_edges(), get_graph_adjacence_matrix() | .. seealso:: get_graph_internal_id(), get_graph_num_nodes(), get_graph_num_edges(), get_original_node_ids(), get_graph_edges(), get_graph_adjacence_matrix() | ||||
| .. note:: These functions allow to collect all the graph's informations. | .. note:: These functions allow to collect all the graph's informations. | ||||
| """ | """ | ||||
| graph = self.__ged_data.graph(graph_id) | |||||
| graph = self._ged_data.graph(graph_id) | |||||
| node_labels = [] | node_labels = [] | ||||
| for n in graph.nodes(): | for n in graph.nodes(): | ||||
| node_labels.append(graph.nodes[n]['label']) | node_labels.append(graph.nodes[n]['label']) | ||||
| @@ -590,7 +590,7 @@ class GEDEnv(object): | |||||
| .. seealso::get_graph_internal_id(), get_graph_num_nodes(), get_graph_num_edges(), get_original_node_ids(), get_graph_node_labels(), get_graph_adjacence_matrix() | .. seealso::get_graph_internal_id(), get_graph_num_nodes(), get_graph_num_edges(), get_original_node_ids(), get_graph_node_labels(), get_graph_adjacence_matrix() | ||||
| .. note:: These functions allow to collect all the graph's informations. | .. note:: These functions allow to collect all the graph's informations. | ||||
| """ | """ | ||||
| graph = self.__ged_data.graph(graph_id) | |||||
| graph = self._ged_data.graph(graph_id) | |||||
| if to_dict: | if to_dict: | ||||
| edges = {} | edges = {} | ||||
| for n1, n2, attr in graph.edges(data=True): | for n1, n2, attr in graph.edges(data=True): | ||||
| @@ -608,7 +608,7 @@ class GEDEnv(object): | |||||
| * @return Name of the input graph. | * @return Name of the input graph. | ||||
| */ | */ | ||||
| """ | """ | ||||
| return self.__ged_data._graph_names[graph_id] | |||||
| return self._ged_data._graph_names[graph_id] | |||||
| def get_graph_num_nodes(self, graph_id): | def get_graph_num_nodes(self, graph_id): | ||||
| @@ -619,7 +619,7 @@ class GEDEnv(object): | |||||
| * @return Number of nodes in the graph. | * @return Number of nodes in the graph. | ||||
| */ | */ | ||||
| """ | """ | ||||
| return nx.number_of_nodes(self.__ged_data.graph(graph_id)) | |||||
| return nx.number_of_nodes(self._ged_data.graph(graph_id)) | |||||
| def get_original_node_ids(self, graph_id): | def get_original_node_ids(self, graph_id): | ||||
| @@ -634,11 +634,11 @@ class GEDEnv(object): | |||||
| .. seealso::get_graph_internal_id(), get_graph_num_nodes(), get_graph_num_edges(), get_graph_node_labels(), get_graph_edges(), get_graph_adjacence_matrix() | .. seealso::get_graph_internal_id(), get_graph_num_nodes(), get_graph_num_edges(), get_graph_node_labels(), get_graph_edges(), get_graph_adjacence_matrix() | ||||
| .. note:: These functions allow to collect all the graph's informations. | .. note:: These functions allow to collect all the graph's informations. | ||||
| """ | """ | ||||
| return [i for i in self.__internal_to_original_node_ids[graph_id].values()] | |||||
| return [i for i in self._internal_to_original_node_ids[graph_id].values()] | |||||
| def get_node_cost(self, node_label_1, node_label_2): | def get_node_cost(self, node_label_1, node_label_2): | ||||
| return self.__ged_data.node_cost(node_label_1, node_label_2) | |||||
| return self._ged_data.node_cost(node_label_1, node_label_2) | |||||
| def get_node_rel_cost(self, node_label_1, node_label_2): | def get_node_rel_cost(self, node_label_1, node_label_2): | ||||
| @@ -654,7 +654,7 @@ class GEDEnv(object): | |||||
| node_label_1 = tuple(sorted(node_label_1.items(), key=lambda kv: kv[0])) | node_label_1 = tuple(sorted(node_label_1.items(), key=lambda kv: kv[0])) | ||||
| if isinstance(node_label_2, dict): | if isinstance(node_label_2, dict): | ||||
| node_label_2 = tuple(sorted(node_label_2.items(), key=lambda kv: kv[0])) | node_label_2 = tuple(sorted(node_label_2.items(), key=lambda kv: kv[0])) | ||||
| return self.__ged_data._edit_cost.node_rel_cost_fun(node_label_1, node_label_2) # @todo: may need to use node_cost() instead (or change node_cost() and modify ged_method for pre-defined cost matrices.) | |||||
| return self._ged_data._edit_cost.node_rel_cost_fun(node_label_1, node_label_2) # @todo: may need to use node_cost() instead (or change node_cost() and modify ged_method for pre-defined cost matrices.) | |||||
| def get_node_del_cost(self, node_label): | def get_node_del_cost(self, node_label): | ||||
| @@ -667,7 +667,7 @@ class GEDEnv(object): | |||||
| """ | """ | ||||
| if isinstance(node_label, dict): | if isinstance(node_label, dict): | ||||
| node_label = tuple(sorted(node_label.items(), key=lambda kv: kv[0])) | node_label = tuple(sorted(node_label.items(), key=lambda kv: kv[0])) | ||||
| return self.__ged_data._edit_cost.node_del_cost_fun(node_label) | |||||
| return self._ged_data._edit_cost.node_del_cost_fun(node_label) | |||||
| def get_node_ins_cost(self, node_label): | def get_node_ins_cost(self, node_label): | ||||
| @@ -680,11 +680,11 @@ class GEDEnv(object): | |||||
| """ | """ | ||||
| if isinstance(node_label, dict): | if isinstance(node_label, dict): | ||||
| node_label = tuple(sorted(node_label.items(), key=lambda kv: kv[0])) | node_label = tuple(sorted(node_label.items(), key=lambda kv: kv[0])) | ||||
| return self.__ged_data._edit_cost.node_ins_cost_fun(node_label) | |||||
| return self._ged_data._edit_cost.node_ins_cost_fun(node_label) | |||||
| def get_edge_cost(self, edge_label_1, edge_label_2): | def get_edge_cost(self, edge_label_1, edge_label_2): | ||||
| return self.__ged_data.edge_cost(edge_label_1, edge_label_2) | |||||
| return self._ged_data.edge_cost(edge_label_1, edge_label_2) | |||||
| def get_edge_rel_cost(self, edge_label_1, edge_label_2): | def get_edge_rel_cost(self, edge_label_1, edge_label_2): | ||||
| @@ -700,7 +700,7 @@ class GEDEnv(object): | |||||
| edge_label_1 = tuple(sorted(edge_label_1.items(), key=lambda kv: kv[0])) | edge_label_1 = tuple(sorted(edge_label_1.items(), key=lambda kv: kv[0])) | ||||
| if isinstance(edge_label_2, dict): | if isinstance(edge_label_2, dict): | ||||
| edge_label_2 = tuple(sorted(edge_label_2.items(), key=lambda kv: kv[0])) | edge_label_2 = tuple(sorted(edge_label_2.items(), key=lambda kv: kv[0])) | ||||
| return self.__ged_data._edit_cost.edge_rel_cost_fun(edge_label_1, edge_label_2) | |||||
| return self._ged_data._edit_cost.edge_rel_cost_fun(edge_label_1, edge_label_2) | |||||
| def get_edge_del_cost(self, edge_label): | def get_edge_del_cost(self, edge_label): | ||||
| @@ -713,7 +713,7 @@ class GEDEnv(object): | |||||
| """ | """ | ||||
| if isinstance(edge_label, dict): | if isinstance(edge_label, dict): | ||||
| edge_label = tuple(sorted(edge_label.items(), key=lambda kv: kv[0])) | edge_label = tuple(sorted(edge_label.items(), key=lambda kv: kv[0])) | ||||
| return self.__ged_data._edit_cost.edge_del_cost_fun(edge_label) | |||||
| return self._ged_data._edit_cost.edge_del_cost_fun(edge_label) | |||||
| def get_edge_ins_cost(self, edge_label): | def get_edge_ins_cost(self, edge_label): | ||||
| @@ -726,8 +726,8 @@ class GEDEnv(object): | |||||
| """ | """ | ||||
| if isinstance(edge_label, dict): | if isinstance(edge_label, dict): | ||||
| edge_label = tuple(sorted(edge_label.items(), key=lambda kv: kv[0])) | edge_label = tuple(sorted(edge_label.items(), key=lambda kv: kv[0])) | ||||
| return self.__ged_data._edit_cost.edge_ins_cost_fun(edge_label) | |||||
| return self._ged_data._edit_cost.edge_ins_cost_fun(edge_label) | |||||
| def get_all_graph_ids(self): | def get_all_graph_ids(self): | ||||
| return [i for i in range(0, self.__ged_data._num_graphs_without_shuffled_copies)] | |||||
| return [i for i in range(0, self._ged_data._num_graphs_without_shuffled_copies)] | |||||