Add share memory trajectories

PyCTBN/PyCTBN/parameters_estimator.py

@@ -17,9 +17,10 @@ class ParametersEstimator:
     :_single_set_of_cims: the set of cims object that will hold the cims of the node
     """
 
-    def __init__(self, trajectories: Trajectory, net_graph: NetworkGraph):
+    def __init__(self, times, trajectories, net_graph: NetworkGraph):
         """Constructor Method
         """
+        self._times = times
         self._trajectories = trajectories
         self._net_graph = net_graph
         self._single_set_of_cims = None
@@ -45,13 +46,13 @@ class ParametersEstimator:
         node_indx = self._net_graph.get_node_indx(node_id)
         state_res_times = self._single_set_of_cims._state_residence_times
         transition_matrices = self._single_set_of_cims._transition_matrices
-        self.compute_state_res_time_for_node(node_indx, self._trajectories.times,
+        self.compute_state_res_time_for_node(node_indx, self._times,
-                                             self._trajectories.trajectory,
+                                             self._trajectories,
                                              self._net_graph.time_filtering,
                                              self._net_graph.time_scalar_indexing_strucure,
                                              state_res_times)
         self.compute_state_transitions_for_a_node(node_indx,
-                                                  self._trajectories.complete_trajectory,
+                                                  self._trajectories,
                                                   self._net_graph.transition_filtering,
                                                   self._net_graph.transition_scalar_indexing_structure,
                                                   transition_matrices)

PyCTBN/PyCTBN/structure_estimator.py

@@ -9,6 +9,7 @@ from networkx.readwrite import json_graph
 from scipy.stats import chi2 as chi2_dist
 from scipy.stats import f as f_dist
 import multiprocessing
+from multiprocessing import shared_memory
 
 
 from .cache import Cache
@@ -40,6 +41,15 @@ class StructureEstimator:
         """
         self._sample_path = sample_path
         self._nodes = np.array(self._sample_path.structure.nodes_labels)
+        self._shm_times = multiprocessing.shared_memory.SharedMemory(create=True,
+                                                                     size=self._sample_path.trajectories.times.nbytes)
+        self._shm_trajectories = multiprocessing.shared_memory.SharedMemory(create=True,
+                                                                            size=self._sample_path.trajectories.complete_trajectory.nbytes)
+        self._times = np.ndarray(self._sample_path.trajectories.times.shape, self._sample_path.trajectories.times.dtype, self._shm_times.buf)
+        self._times[:] = self._sample_path.trajectories.times[:]
+
+        self._trajectories = np.ndarray(self._sample_path.trajectories.complete_trajectory.shape, self._sample_path.trajectories.complete_trajectory.dtype, self._shm_trajectories.buf)
+        self._trajectories[:] = self._sample_path.trajectories.complete_trajectory[:]
         self._nodes_vals = self._sample_path.structure.nodes_values
         self._nodes_indxs = self._sample_path.structure.nodes_indexes
         self._complete_graph = self.build_complete_graph(self._sample_path.structure.nodes_labels)
@@ -112,7 +122,7 @@ class StructureEstimator:
             s1 = Structure(l1, indxs1, vals1, eds1, tot_vars_count)
             g1 = NetworkGraph(s1)
             g1.fast_init(test_child)
-            p1 = ParametersEstimator(self._sample_path.trajectories, g1)
+            p1 = ParametersEstimator(self._times, self._trajectories, g1)
             p1.fast_init(test_child)
             sofc1 = p1.compute_parameters_for_node(test_child)
             cache.put(set(p_set), sofc1)
@@ -130,7 +140,7 @@ class StructureEstimator:
             s2 = Structure(l2, indxs2, vals2, eds2, tot_vars_count)
             g2 = NetworkGraph(s2)
             g2.fast_init(test_child)
-            p2 = ParametersEstimator(self._sample_path.trajectories, g2)
+            p2 = ParametersEstimator(self._times, self._trajectories, g2)
             p2.fast_init(test_child)
             sofc2 = p2.compute_parameters_for_node(test_child)
             cache.put(set(p_set), sofc2)
@@ -247,7 +257,7 @@ class StructureEstimator:
         """Save the estimated Structure to a .json file in the path where the data are loaded from.
         The file is named as the input dataset but the `results_` word is appended to the results file.
         """
-        res = json_graph.node_link_data(self._result_graph_graph)
+        res = json_graph.node_link_data(self._result_graph)
         name = self._sample_path._importer.file_path.rsplit('/', 1)[-1] + str(self._sample_path._importer.dataset_id())
         name = 'results_' + name
         with open(name, 'w') as f: