Trajectory Generator

.gitignore

@@ -7,3 +7,4 @@ __pycache__
 **/results_data
 **/.scannerwork
 **/build
+test.py

PyCTBN/PyCTBN/estimators/parameters_estimator.py

@@ -33,7 +33,8 @@ class ParametersEstimator(object):
         """
         p_vals = self._net_graph._aggregated_info_about_nodes_parents[2]
         node_states_number = self._net_graph.get_states_number(node_id)
-        self._single_set_of_cims = SetOfCims(node_id, p_vals, node_states_number, self._net_graph.p_combs)
+        self._single_set_of_cims = SetOfCims(node_id = node_id, parents_states_number = p_vals, 
+            node_states_number = node_states_number, p_combs = self._net_graph.p_combs)
 
     def compute_parameters_for_node(self, node_id: str) -> SetOfCims:
         """Compute the CIMS of the node identified by the label ``node_id``.

PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py

@@ -11,12 +11,16 @@ class ConditionalIntensityMatrix(object):
     :type state_transition_matrix: numpy.ndArray
     :_cim: the actual cim of the node
     """
-    def __init__(self, state_residence_times: np.array, state_transition_matrix: np.array):
+    def __init__(self, state_residence_times: np.array = None, state_transition_matrix: np.array = None, 
+        cim: np.array = None):
         """Constructor Method
         """
         self._state_residence_times = state_residence_times
         self._state_transition_matrix = state_transition_matrix
-        self._cim = self.state_transition_matrix.astype(np.float64)
+        if cim is not None:
+            self._cim = cim
+        else:
+            self._cim = self.state_transition_matrix.astype(np.float64)
 
     def compute_cim_coefficients(self) -> None:
         """Compute the coefficients of the matrix _cim by using the following equality q_xx' = M[x, x'] / T[x].

PyCTBN/PyCTBN/structure_graph/set_of_cims.py

@@ -23,7 +23,8 @@ class SetOfCims(object):
     :_actual_cims: the cims of the node
     """
 
-    def __init__(self, node_id: str, parents_states_number: typing.List, node_states_number: int, p_combs: np.ndarray):
+    def __init__(self, node_id: str, parents_states_number: typing.List, node_states_number: int, p_combs: np.ndarray,
+        cims: np.ndarray = None):
         """Constructor Method
         """
         self._node_id = node_id
@@ -33,7 +34,11 @@ class SetOfCims(object):
         self._state_residence_times = None
         self._transition_matrices = None
         self._p_combs = p_combs
-        self.build_times_and_transitions_structures()
+
+        if cims is not None:
+            self._actual_cims = cims
+        else:
+            self.build_times_and_transitions_structures()
 
     def build_times_and_transitions_structures(self) -> None:
         """Initializes at the correct dimensions the state residence times matrix and the state transition matrices.
@@ -57,7 +62,7 @@ class SetOfCims(object):
         :type transition_matrices: numpy.ndArray
         """
         for state_res_time_vector, transition_matrix in zip(state_res_times, transition_matrices):
-            cim_to_add = ConditionalIntensityMatrix(state_res_time_vector, transition_matrix)
+            cim_to_add = ConditionalIntensityMatrix(state_residence_times = state_res_time_vector, state_transition_matrix = transition_matrix)
             cim_to_add.compute_cim_coefficients()
             self._actual_cims.append(cim_to_add)
         self._actual_cims = np.array(self._actual_cims)

PyCTBN/PyCTBN/structure_graph/trajectory_generator.py

@@ -0,0 +1,71 @@
+from ..utility.abstract_importer import AbstractImporter
+from .conditional_intensity_matrix import ConditionalIntensityMatrix
+from .set_of_cims import SetOfCims
+from .trajectory import Trajectory
+import numpy as np
+import pandas as pd
+import re
+from numpy import random
+
+class TrajectoryGenerator(object):
+    def __init__(self, importer: AbstractImporter):
+        self._importer = importer
+        self._importer.import_data(0)
+
+        self._vnames = self._importer._df_variables.iloc[:, 0].to_list()
+        
+        self._parents = {}
+        for v in self._vnames:
+            self._parents[v] = self._importer._df_structure.where(self._importer._df_structure["To"] == v).dropna()["From"].tolist()
+
+        self._cims = {}
+        sampled_cims = self._importer._raw_data[0]["dyn.cims"]
+        for v in sampled_cims.keys():
+            p_combs = []
+            v_cims = []
+            for comb in sampled_cims[v].keys():
+                p_combs.append(np.array(re.findall(r"=(\d)", comb)).astype("int"))
+                cim = pd.DataFrame(sampled_cims[v][comb]).to_numpy()      
+                v_cims.append(ConditionalIntensityMatrix(cim = cim))
+            
+            sof = SetOfCims(node_id = v, parents_states_number = [self._importer._df_variables.where(self._importer._df_variables["Name"] == p)["Value"] for p in self._parents[v]], 
+                node_states_number = self._importer._df_variables.where(self._importer._df_variables["Name"] == v)["Value"], p_combs = p_combs, cims = v_cims)
+            self._cims[v] = sof
+
+    def CTBN_Sample(self, t_end):
+        #Replace v_values with sigma (pandas dataframe)
+        t = 0
+        sigma = pd.DataFrame(columns = (["Time"] + self._vnames))
+        sigma.loc[len(sigma)] = [0] + [0 for v in self._vnames]
+        time = np.full(len(self._vnames), np.NaN)
+
+        while True:
+            for i in range(0, time.size):
+                if np.isnan(time[i]):
+                    # Probability to transition from current state v_values[i] to (1 - v_values[i])
+                    current_values = sigma.loc[len(sigma) - 1]
+                    cim = self._cims[self._vnames[i]].filter_cims_with_mask(np.array([True for p in self._parents[self._vnames[i]]]), 
+                        [current_values.at[p] for p in self._parents[self._vnames[i]]])[0].cim
+                    param = cim[current_values.at[self._vnames[i]]][1 - current_values.at[self._vnames[i]]]
+
+                    time[i] = t + random.exponential(scale = param)
+        
+            # next = index of the variable that will transition first
+            next = time.argmin()
+            t = time[next]
+
+            if t >= t_end:
+                return sigma
+            else:
+                new_row = pd.DataFrame(sigma[-1:].values, columns = sigma.columns)
+                new_row.loc[0].at[self._vnames[next]] = 1 - new_row.loc[0].at[self._vnames[next]]
+                new_row.loc[0].at["Time"] = round(t, 4)
+                sigma = sigma.append(new_row, ignore_index = True)
+
+                """ sup = sigma.loc[len(sigma) - 1]
+                sup.at[self._vnames[next]] = 1 - sup.at[self._vnames[next]]
+                sup.at["Time"] = round(t, 4)
+                sigma.loc[len(sigma)] = sup """
+
+                # undefine variable time
+                time[next] = np.NaN

PyCTBN/tests/structure_graph/test_cim.py

@@ -17,14 +17,16 @@ class TestConditionalIntensityMatrix(unittest.TestCase):
             cls.state_transition_matrix[i, i] = np.sum(cls.state_transition_matrix[i])
 
     def test_init(self):
-        c1 = ConditionalIntensityMatrix(self.state_res_times, self.state_transition_matrix)
+        c1 = ConditionalIntensityMatrix(state_residence_times = self.state_res_times, 
+            state_transition_matrix = self.state_transition_matrix)
         self.assertTrue(np.array_equal(self.state_res_times, c1.state_residence_times))
         self.assertTrue(np.array_equal(self.state_transition_matrix, c1.state_transition_matrix))
         self.assertEqual(c1.cim.dtype, np.float)
         self.assertEqual(self.state_transition_matrix.shape, c1.cim.shape)
 
     def test_compute_cim_coefficients(self):
-        c1 = ConditionalIntensityMatrix(self.state_res_times, self.state_transition_matrix)
+        c1 = ConditionalIntensityMatrix(state_residence_times = self.state_res_times, 
+            state_transition_matrix = self.state_transition_matrix)
         c2 = self.state_transition_matrix.astype(np.float)
         np.fill_diagonal(c2, c2.diagonal() * -1)
         for i in range(0, len(self.state_res_times)):
@@ -38,7 +40,8 @@ class TestConditionalIntensityMatrix(unittest.TestCase):
                 self.assertTrue(np.isclose(c1.cim[i, j], c2[i, j], 1e01, 1e-01))
 
     def test_repr(self):
-        c1 = ConditionalIntensityMatrix(self.state_res_times, self.state_transition_matrix)
+        c1 = ConditionalIntensityMatrix(state_residence_times = self.state_res_times, 
+            state_transition_matrix = self.state_transition_matrix)
         print(c1)
 
 

PyCTBN/tests/structure_graph/test_setofcims.py

@@ -49,7 +49,8 @@ class TestSetOfCims(unittest.TestCase):
 
     def test_filter_cims_with_mask(self):
         p_combs = self.build_p_comb_structure_for_a_node(self.possible_cardinalities)
-        sofc1 = SetOfCims('X', self.possible_cardinalities, 3, p_combs)
+        sofc1 = SetOfCims(node_id = 'X', parents_states_number = self.possible_cardinalities, node_states_number = 3, 
+            p_combs = p_combs)
         state_res_times_list = []
         transition_matrices_list = []
         for i in range(len(p_combs)):
@@ -73,7 +74,8 @@ class TestSetOfCims(unittest.TestCase):
     def aux_test_build_cims(self, node_id, p_values, node_states, p_combs):
         state_res_times_list = []
         transition_matrices_list = []
-        so1 = SetOfCims(node_id, p_values, node_states, p_combs)
+        so1 = SetOfCims(node_id = node_id, parents_states_number = p_values, node_states_number = node_states, 
+            p_combs = p_combs)
         for i in range(len(p_combs)):
             state_res_times = np.random.rand(1, node_states)[0]
             state_res_times = state_res_times * 1000
@@ -87,7 +89,8 @@ class TestSetOfCims(unittest.TestCase):
         self.assertIsNone(so1._state_residence_times)
 
     def aux_test_init(self, node_id, parents_states_number, node_states_number, p_combs):
-        sofcims = SetOfCims(node_id, parents_states_number, node_states_number, p_combs)
+        sofcims = SetOfCims(node_id = node_id, parents_states_number = parents_states_number, 
+            node_states_number = node_states_number, p_combs = p_combs)
         self.assertEqual(sofcims._node_id, node_id)
         self.assertTrue(np.array_equal(sofcims._p_combs, p_combs))
         self.assertTrue(np.array_equal(sofcims._parents_states_number, parents_states_number))

PyCTBN/tests/utility/test_cache.py

@@ -16,13 +16,13 @@ class TestCache(unittest.TestCase):
     def test_put(self):
         c1 = Cache()
         pset1 = {'X', 'Y'}
-        sofc1 = SetOfCims('Z', [], 3, np.array([]))
+        sofc1 = SetOfCims(node_id = 'Z', parents_states_number = [], node_states_number = 3, p_combs = np.array([]))
         c1.put(pset1, sofc1)
         self.assertEqual(1, len(c1._actual_cache))
         self.assertEqual(1, len(c1._list_of_sets_of_parents))
         self.assertEqual(sofc1, c1._actual_cache[0])
         pset2 = {'X'}
-        sofc2 = SetOfCims('Z', [], 3, np.array([]))
+        sofc2 = SetOfCims(node_id = 'Z', parents_states_number = [], node_states_number = 3, p_combs = np.array([]))
         c1.put(pset2, sofc2)
         self.assertEqual(2, len(c1._actual_cache))
         self.assertEqual(2, len(c1._list_of_sets_of_parents))
@@ -31,7 +31,7 @@ class TestCache(unittest.TestCase):
     def test_find(self):
         c1 = Cache()
         pset1 = {'X', 'Y'}
-        sofc1 = SetOfCims('Z', [], 3, np.array([]))
+        sofc1 = SetOfCims(node_id = 'Z', parents_states_number = [], node_states_number = 3, p_combs = np.array([]))
         c1.put(pset1, sofc1)
         self.assertEqual(1, len(c1._actual_cache))
         self.assertEqual(1, len(c1._list_of_sets_of_parents))