Refactor on docs; Add performance comparison

PyCTBN/PyCTBN/abstract_importer.py

@@ -12,15 +12,17 @@ class AbstractImporter(ABC):
     :_concatenated_samples: Dataframe containing the concatenation of all the processed trajectories
     :_df_structure: Dataframe containing the structure of the network (edges)
     :_df_variables: Dataframe containing the nodes cardinalities
-    :_sorter: A list containing the columns header (excluding the time column) of the `_concatenated_samples`
+    :_sorter: A list containing the columns header (excluding the time column) of the ``_concatenated_samples``
 
     .. warning::
-            The class members ``_df_variables`` and ``_df_structure`` HAVE to be properly constructed
-            as Pandas Dataframes with the following structure:
-            Header of _df_structure = [From_Node | To_Node]
-            Header of _df_variables = [Variable_Label | Variable_Cardinality]
-        .. note::
-            See :class:``JsonImporter`` for an example implementation
+        The class members ``_df_variables`` and ``_df_structure`` HAVE to be properly constructed
+        as Pandas Dataframes with the following structure:
+        Header of _df_structure = [From_Node | To_Node]
+        Header of _df_variables = [Variable_Label | Variable_Cardinality]
+
+    .. note::
+        See :class:``JsonImporter`` for an example implementation
+
     """
 
     def __init__(self, file_path: str):
@@ -32,7 +34,7 @@ class AbstractImporter(ABC):
         self._concatenated_samples = None
         self._sorter = None
         super().__init__()
-    
+
     @abstractmethod
     def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
         """Initializes the ``_sorter`` class member from a trajectory dataframe, exctracting the header of the frame

PyCTBN/PyCTBN/cache.py

@@ -1,6 +1,6 @@
 
 import typing
-#import set_of_cims as sofc
+
 from .set_of_cims import SetOfCims
 
 

PyCTBN/PyCTBN/json_importer.py

@@ -3,18 +3,13 @@ import json
 import typing
 import pandas as pd
 
-#import abstract_importer as ai
 from .abstract_importer import AbstractImporter
 
 
 class JsonImporter(AbstractImporter):
     """Implements the abstracts methods of AbstractImporter and adds all the necessary methods to process and prepare
-    the data in json extension with the following structure:
-    [0]
-        |_ dyn.cims
-        |_ dyn.str
-        |_ samples
-        |_ variabels
+    the data in json extension.
+
     :param file_path: the path of the file that contains tha data to be imported
     :type file_path: string
     :param samples_label: the reference key for the samples in the trajectories
@@ -41,6 +36,7 @@ class JsonImporter(AbstractImporter):
         .. note::
             This constructor calls also the method ``read_json_file()``, so after the construction of the object
             the class member ``_raw_data`` will contain the raw imported json data.
+
         """
         self._samples_label = samples_label
         self._structure_label = structure_label
@@ -139,7 +135,7 @@ class JsonImporter(AbstractImporter):
         return df_samples_list
 
     def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
-        """Implements the abstract method build_sorter of the :class:`AbstractImporter` for this dataset
+        """Implements the abstract method build_sorter of the :class:`AbstractImporter` for this dataset.
         """
         columns_header = list(sample_frame.columns.values)
         columns_header.remove(self._time_key)

PyCTBN/PyCTBN/network_graph.py

@@ -3,7 +3,6 @@ import typing
 import networkx as nx
 import numpy as np
 
-#import structure as st
 from .structure import Structure
 
 

PyCTBN/PyCTBN/parameters_estimator.py

@@ -1,15 +1,11 @@
 
 import numpy as np
 
-#import network_graph as ng
-#import trajectory as tr
-#import set_of_cims as sofc
 from .trajectory import Trajectory
 from .set_of_cims import SetOfCims
 from .network_graph import NetworkGraph
 
 
-
 class ParametersEstimator:
     """Has the task of computing the cims of particular node given the trajectories and the net structure
     in the graph ``_net_graph``.

PyCTBN/PyCTBN/sample_path.py

@@ -1,7 +1,4 @@
 
-#import abstract_importer as imp
-#import structure as st
-#import trajectory as tr
 from .abstract_importer import AbstractImporter
 from .structure import Structure
 from .trajectory import Trajectory

PyCTBN/PyCTBN/set_of_cims.py

@@ -1,7 +1,6 @@
 import typing
 import numpy as np
 
-#import conditional_intensity_matrix as cim
 from .conditional_intensity_matrix import ConditionalIntensityMatrix
 
 

PyCTBN/PyCTBN/structure_estimator.py

@@ -1,5 +1,4 @@
 
-
 from tqdm import tqdm
 import itertools
 import json
@@ -10,12 +9,6 @@ from networkx.readwrite import json_graph
 from scipy.stats import chi2 as chi2_dist
 from scipy.stats import f as f_dist
 
-#import cache as ch
-#import conditional_intensity_matrix as condim
-#import network_graph as ng
-#import parameters_estimator as pe
-#import sample_path as sp
-#import structure as st
 from .cache import Cache
 from .conditional_intensity_matrix import ConditionalIntensityMatrix
 from .network_graph import NetworkGraph
@@ -144,7 +137,7 @@ class StructureEstimator:
         :type cim1: ConditionalIntensityMatrix
         :param cim2: a cim belonging to the graph with test parent
         :type cim2: ConditionalIntensityMatrix
-        :return:True iff both tests do NOT reject the null hypothesis of indipendence. False otherwise.
+        :return: True iff both tests do NOT reject the null hypothesis of independence. False otherwise.
         :rtype: bool
         """
         M1 = cim1.state_transition_matrix
@@ -180,7 +173,6 @@ class StructureEstimator:
         :param tot_vars_count: the number of _nodes in the net
         :type tot_vars_count: int
         """
-        #print("##################TESTING VAR################", var_id)
         u = list(self._complete_graph.predecessors(var_id))
         child_states_numb = self._sample_path.structure.get_states_number(var_id)
         b = 0
@@ -228,8 +220,7 @@ class StructureEstimator:
 
     def save_results(self) -> None:
         """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 appendend to the results file.
-
+        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._complete_graph)
         name = self._sample_path._importer.file_path.rsplit('/', 1)[-1] + str(self._sample_path._importer.dataset_id())
@@ -237,4 +228,12 @@ class StructureEstimator:
         with open(name, 'w') as f:
             json.dump(res, f)
 
+    def adjacency_matrix(self) -> np.ndarray:
+        """Converts the estimated structrure ``_complete_graph`` to a boolean adjacency matrix representation.
+
+        :return: The adjacency matrix of the graph ``_complete_graph``
+        :rtype: numpy.ndArray
+        """
+        return nx.adj_matrix(self._complete_graph).toarray().astype(bool)
+
 

PyCTBN/deprecated/simple_cvs_importer.py

@@ -1,11 +1,10 @@
 import pandas as pd
 import glob
 import os
-
 import typing
 
-from .abstract_importer import AbstractImporter
-from .sample_path import SamplePath
+from PyCTBN.PyCTBN.abstract_importer import AbstractImporter
+from PyCTBN.PyCTBN.sample_path import SamplePath
 
 
 class CSVImporter(AbstractImporter):
@@ -45,7 +44,7 @@ class CSVImporter(AbstractImporter):
 
 
 def main():
-    read_files = glob.glob(os.path.join('../data', "*.csv"))
+    read_files = glob.glob(os.path.join('../../data', "*.csv"))
     print(read_files[0])
     csvimp = CSVImporter(read_files[0])
     s1 = SamplePath(csvimp)

PyCTBN/tests/original_ctpc_algorithm.py

@@ -9,7 +9,7 @@ from scipy.stats import chi2 as chi2_dist
 from scipy.stats import f as f_dist
 from tqdm import tqdm
 
-from .abstract_importer import AbstractImporter
+from PyCTBN.PyCTBN.abstract_importer import AbstractImporter
 
 
 class OriginalCTPCAlgorithm(AbstractImporter):

PyCTBN/tests/performance_comparisons.py

@@ -0,0 +1,70 @@
+import unittest
+import os
+import glob
+import numpy as np
+import pandas as pd
+import timeit
+
+from ..PyCTBN.sample_path import SamplePath
+from ..PyCTBN.structure_estimator import StructureEstimator
+from ..PyCTBN.json_importer import JsonImporter
+from PyCTBN.tests.original_ctpc_algorithm import OriginalCTPCAlgorithm
+
+
+class PerformanceComparisons(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        cls.read_files = glob.glob(os.path.join('./data', "*.json"))
+        cls.datasets_numb = None
+        cls.s1 = None
+        cls.importer = None
+        cls.original_algo = None
+        cls.original_times = []
+        cls.optimized_times = []
+        cls.results = []
+
+    def test_time_comparisons(self):
+        for file_path in self.read_files:
+            self.importer = JsonImporter(file_path, 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+            self.original_algo = OriginalCTPCAlgorithm(file_path, 'samples', 'dyn.str', 'variables',
+                                                       'Time', 'Name', self.importer._raw_data)
+            self.datasets_numb = self.original_algo.datasets_numb()
+            print("Testing on file: ", file_path, " with ", self.datasets_numb, " Datasets")
+            for indx in range(self.datasets_numb):
+                print("Running Test: ", indx)
+                self.aux_build_importer(indx)
+                self.aux_build_original_algo(indx)
+                se1 = StructureEstimator(self.s1, 0.1, 0.1)
+                opt_time = timeit.timeit(se1.ctpc_algorithm, number=1)
+                original_time = timeit.timeit(self.original_algo.cb_structure_algo, number=1)
+                opt_res = se1.adjacency_matrix()
+                original_res = self.original_algo.matrix
+                self.original_times.append(original_time)
+                self.optimized_times.append(opt_time)
+                self.results.append((original_res, opt_res))
+                self.assertTrue(np.array_equal(original_res, opt_res))
+            self.save_datas(self.original_times, self.optimized_times)
+            self.original_times[:] = []
+            self.optimized_times[:] = []
+
+    def aux_build_importer(self, indx):
+        self.importer.import_data(indx)
+        self.s1 = SamplePath(self.importer)
+        self.s1.build_trajectories()
+        self.s1.build_structure()
+
+    def aux_build_original_algo(self, indx):
+        self.original_algo.import_data(indx)
+        self.original_algo.prepare_trajectories(self.original_algo.df_samples_list, self.original_algo.variables)
+
+    def save_datas(self, original_list, opt_list):
+        df_results = pd.DataFrame({'orginal_execution_time': original_list, 'optimized_execution_time': opt_list})
+        name = self.importer.file_path.rsplit('/', 1)[-1]
+        name = name.split('.', 1)[0]
+        name = 'execution_times_' + name + '.csv'
+        df_results.to_csv(name, index=False)
+
+
+if __name__ == '__main__':
+    unittest.main()

documentation/PyCTBN.rst

@@ -0,0 +1,101 @@
+PyCTBN package
+==============
+
+Submodules
+----------
+
+PyCTBN.abstract\_importer module
+--------------------------------
+
+.. automodule:: PyCTBN.abstract_importer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.cache module
+-------------------
+
+.. automodule:: PyCTBN.cache
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.conditional\_intensity\_matrix module
+--------------------------------------------
+
+.. automodule:: PyCTBN.conditional_intensity_matrix
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.json\_importer module
+----------------------------
+
+.. automodule:: PyCTBN.json_importer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.network\_graph module
+----------------------------
+
+.. automodule:: PyCTBN.network_graph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.parameters\_estimator module
+-----------------------------------
+
+.. automodule:: PyCTBN.parameters_estimator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.sample\_path module
+--------------------------
+
+.. automodule:: PyCTBN.sample_path
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.set\_of\_cims module
+---------------------------
+
+.. automodule:: PyCTBN.set_of_cims
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.structure module
+-----------------------
+
+.. automodule:: PyCTBN.structure
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.structure\_estimator module
+----------------------------------
+
+.. automodule:: PyCTBN.structure_estimator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.trajectory module
+------------------------
+
+.. automodule:: PyCTBN.trajectory
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: PyCTBN
+   :members:
+   :undoc-members:
+   :show-inheritance:

documentation/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 0c64bed84aa4ce76aedaca18241d82e7
+config: 5ff9615d2690725079f899e2857b650e
 tags: 645f666f9bcd5a90fca523b33c5a78b7

documentation/_build/html/_sources/PyCTBN.rst.txt

@@ -0,0 +1,101 @@
+PyCTBN package
+==============
+
+Submodules
+----------
+
+PyCTBN.abstract\_importer module
+--------------------------------
+
+.. automodule:: PyCTBN.abstract_importer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.cache module
+-------------------
+
+.. automodule:: PyCTBN.cache
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.conditional\_intensity\_matrix module
+--------------------------------------------
+
+.. automodule:: PyCTBN.conditional_intensity_matrix
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.json\_importer module
+----------------------------
+
+.. automodule:: PyCTBN.json_importer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.network\_graph module
+----------------------------
+
+.. automodule:: PyCTBN.network_graph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.parameters\_estimator module
+-----------------------------------
+
+.. automodule:: PyCTBN.parameters_estimator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.sample\_path module
+--------------------------
+
+.. automodule:: PyCTBN.sample_path
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.set\_of\_cims module
+---------------------------
+
+.. automodule:: PyCTBN.set_of_cims
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.structure module
+-----------------------
+
+.. automodule:: PyCTBN.structure
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.structure\_estimator module
+----------------------------------
+
+.. automodule:: PyCTBN.structure_estimator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+PyCTBN.trajectory module
+------------------------
+
+.. automodule:: PyCTBN.trajectory
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: PyCTBN
+   :members:
+   :undoc-members:
+   :show-inheritance:

documentation/_build/html/_sources/examples.rst.txt

@@ -0,0 +1,123 @@
+Examples
+=============
+
+Installation/Usage:
+*******************
+
+
+Implementing your own data importer
+***********************************
+.. code-block:: python
+
+    """This example demonstrates the implementation of a simple data importer the extends the class abstract importer to import data in csv format.
+    The net in exam has three ternary nodes.
+    """
+
+    from .abstract_importer import AbstractImporter
+
+    class CSVImporter(AbstractImporter):
+
+        def __init__(self, file_path):
+            self._df_samples_list = None
+            super(CSVImporter, self).__init__(file_path)
+
+        def import_data(self):
+            self.read_csv_file()
+            self._sorter = self.build_sorter(self._df_samples_list[0])
+            self.import_variables()
+            self.import_structure()
+            self.compute_row_delta_in_all_samples_frames(self._df_samples_list)
+
+        def read_csv_file(self):
+            df = pd.read_csv(self._file_path)
+            df.drop(df.columns[[0]], axis=1, inplace=True)
+            self._df_samples_list = [df]
+
+        def import_variables(self):
+            values_list = [3 for var in self._sorter]
+            # initialize dict of lists
+            data = {'Name':self._sorter, 'Value':values_list}
+            # Create the pandas DataFrame
+            self._df_variables = pd.DataFrame(data)
+
+        def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
+            return list(sample_frame.columns)[1:]
+
+        def import_structure(self):
+            data = {'From':['X','Y','Z'], 'To':['Z','Z','Y']}
+            self._df_structure = pd.DataFrame(data)
+
+        def dataset_id(self) -> object:
+            pass
+
+Parameters Estimation Example
+*****************************
+
+.. code-block:: python
+
+    from PyCTBN.PyCTBN.json_importer import JsonImporter
+    from PyCTBN.PyCTBN.sample_path import SamplePath
+    from PyCTBN.PyCTBN.network_graph import NetworkGraph
+    from PyCTBN.PyCTBN.parameters_estimator import ParametersEstimator
+
+
+    def main():
+        read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir
+        #import data
+        importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        importer.import_data(0)
+        #Create a SamplePath Obj passing an already filled AbstractImporter object
+        s1 = SamplePath(importer)
+        #Build The trajectries and the structural infos
+        s1.build_trajectories()
+        s1.build_structure()
+        print(s1.structure.edges)
+        print(s1.structure.nodes_values)
+        #From The Structure Object build the Graph
+        g = NetworkGraph(s1.structure)
+        #Select a node you want to estimate the parameters
+        node = g.nodes[2]
+        print("Node", node)
+        #Init the _graph specifically for THIS node
+        g.fast_init(node)
+        #Use SamplePath and Grpah to create a ParametersEstimator Object
+        p1 = ParametersEstimator(s1.trajectories, g)
+        #Init the peEst specifically for THIS node
+        p1.fast_init(node)
+        #Compute the parameters
+        sofc1 = p1.compute_parameters_for_node(node)
+        #The est CIMS are inside the resultant SetOfCIms Obj
+        print(sofc1.actual_cims)
+
+Structure Estimation Example
+****************************
+
+.. code-block:: python
+
+    from PyCTBN.PyCTBN.json_importer import JsonImporter
+    from PyCTBN.PyCTBN.sample_path import SamplePath
+    from PyCTBN.PyCTBN.structure_estimator import StructureEstimator
+    
+    def structure_estimation_example():
+
+        # read the json files in ./data path
+        read_files = glob.glob(os.path.join('./data', "*.json"))
+        # initialize a JsonImporter object for the first file
+        importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        # import the data at index 0 of the outer json array
+        importer.import_data(0)
+        # construct a SamplePath Object passing a filled AbstractImporter
+        s1 = SamplePath(importer)
+        # build the trajectories
+        s1.build_trajectories()
+        # build the real structure
+        s1.build_structure()
+        # construct a StructureEstimator object
+        se1 = StructureEstimator(s1, 0.1, 0.1)
+        # call the ctpc algorithm
+        se1.ctpc_algorithm()
+        # the adjacency matrix of the estimated structure
+        print(se1.adjacency_matrix())
+        # save results to a json file
+        se1.save_results()
+

documentation/_build/html/_sources/index.rst.txt

@@ -1,5 +1,5 @@
 .. PyCTBN documentation master file, created by
-   sphinx-quickstart on Mon Nov 30 16:37:03 2020.
+   sphinx-quickstart on Mon Dec  7 15:11:12 2020.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
@@ -10,7 +10,8 @@ Welcome to PyCTBN's documentation!
    :maxdepth: 2
    :caption: Contents:
 
-
+   PyCTBN
+   examples
 
 Indices and tables
 ==================

documentation/_build/html/_sources/modules.rst.txt

@@ -0,0 +1,7 @@
+PyCTBN
+======
+
+.. toctree::
+   :maxdepth: 4
+
+   PyCTBN

documentation/_build/html/_sources/rst/abstract_importer.rst.txt

@@ -1,7 +0,0 @@
-abstract\_importer module
-=========================
-
-.. automodule:: abstract_importer
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/rst/cache.rst.txt

@@ -1,7 +0,0 @@
-cache module
-============
-
-.. automodule:: cache
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/rst/conditional_intensity_matrix.rst.txt

@@ -1,7 +0,0 @@
-conditional\_intensity\_matrix module
-=====================================
-
-.. automodule:: conditional_intensity_matrix
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/rst/json_importer.rst.txt

@@ -1,7 +0,0 @@
-json\_importer module
-=====================
-
-.. automodule:: json_importer
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/rst/modules.rst.txt

@@ -1,17 +0,0 @@
-scripts
-=======
-
-.. toctree::
-   :maxdepth: 4
-
-   abstract_importer
-   cache
-   conditional_intensity_matrix
-   json_importer
-   network_graph
-   parameters_estimator
-   sample_path
-   set_of_cims
-   structure
-   structure_estimator
-   trajectory

documentation/_build/html/_sources/rst/network_graph.rst.txt

@@ -1,7 +0,0 @@
-network\_graph module
-=====================
-
-.. automodule:: network_graph
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/rst/parameters_estimator.rst.txt

@@ -1,7 +0,0 @@
-parameters\_estimator module
-============================
-
-.. automodule:: parameters_estimator
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/rst/sample_path.rst.txt

@@ -1,7 +0,0 @@
-sample\_path module
-===================
-
-.. automodule:: sample_path
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/rst/set_of_cims.rst.txt

@@ -1,7 +0,0 @@
-set\_of\_cims module
-====================
-
-.. automodule:: set_of_cims
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/rst/structure.rst.txt

@@ -1,7 +0,0 @@
-structure module
-================
-
-.. automodule:: structure
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/rst/structure_estimator.rst.txt

@@ -1,7 +0,0 @@
-structure\_estimator module
-===========================
-
-.. automodule:: structure_estimator
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/rst/trajectory.rst.txt

@@ -1,7 +0,0 @@
-trajectory module
-=================
-
-.. automodule:: trajectory
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '',
+    VERSION: '1.0',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

documentation/_build/html/_static/pygments.css

@@ -1,2 +1,7 @@
+pre { line-height: 125%; }
+td.linenos pre { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+td.linenos pre.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
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 .highlight .hll { background-color: #ffffcc }
-.highlight  { background: #ffffff; }
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documentation/_build/html/examples.html

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+          
+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+</ul>
+</li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Examples</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#installation-usage">Installation/Usage:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#implementing-your-own-data-importer">Implementing your own data importer</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#parameters-estimation-example">Parameters Estimation Example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#structure-estimation-example">Structure Estimation Example</a></li>
+</ul>
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+</ul>
+
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+	    <div id="content" class="hfeed entry-container hentry">
+  <div class="section" id="examples">
+<h1>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="installation-usage">
+<h2>Installation/Usage:<a class="headerlink" href="#installation-usage" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="implementing-your-own-data-importer">
+<h2>Implementing your own data importer<a class="headerlink" href="#implementing-your-own-data-importer" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="sd">&quot;&quot;&quot;This example demonstrates the implementation of a simple data importer the extends the class abstract importer to import data in csv format.</span>
+<span class="sd">The net in exam has three ternary nodes.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">from</span> <span class="nn">.abstract_importer</span> <span class="kn">import</span> <span class="n">AbstractImporter</span>
+
+<span class="k">class</span> <span class="nc">CSVImporter</span><span class="p">(</span><span class="n">AbstractImporter</span><span class="p">):</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">file_path</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_df_samples_list</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">CSVImporter</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">file_path</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">import_data</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">read_csv_file</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_sorter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">build_sorter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df_samples_list</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">import_variables</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">import_structure</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">compute_row_delta_in_all_samples_frames</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df_samples_list</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">read_csv_file</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_file_path</span><span class="p">)</span>
+        <span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">[[</span><span class="mi">0</span><span class="p">]],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_df_samples_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">df</span><span class="p">]</span>
+
+    <span class="k">def</span> <span class="nf">import_variables</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">values_list</span> <span class="o">=</span> <span class="p">[</span><span class="mi">3</span> <span class="k">for</span> <span class="n">var</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sorter</span><span class="p">]</span>
+        <span class="c1"># initialize dict of lists</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;Name&#39;</span><span class="p">:</span><span class="bp">self</span><span class="o">.</span><span class="n">_sorter</span><span class="p">,</span> <span class="s1">&#39;Value&#39;</span><span class="p">:</span><span class="n">values_list</span><span class="p">}</span>
+        <span class="c1"># Create the pandas DataFrame</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_df_variables</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">build_sorter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sample_frame</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">List</span><span class="p">:</span>
+        <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">sample_frame</span><span class="o">.</span><span class="n">columns</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]</span>
+
+    <span class="k">def</span> <span class="nf">import_structure</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;From&#39;</span><span class="p">:[</span><span class="s1">&#39;X&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">,</span><span class="s1">&#39;Z&#39;</span><span class="p">],</span> <span class="s1">&#39;To&#39;</span><span class="p">:[</span><span class="s1">&#39;Z&#39;</span><span class="p">,</span><span class="s1">&#39;Z&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">]}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_df_structure</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">dataset_id</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">object</span><span class="p">:</span>
+        <span class="k">pass</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="parameters-estimation-example">
+<h2>Parameters Estimation Example<a class="headerlink" href="#parameters-estimation-example" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">PyCTBN.PyCTBN.json_importer</span> <span class="kn">import</span> <span class="n">JsonImporter</span>
+<span class="kn">from</span> <span class="nn">PyCTBN.PyCTBN.sample_path</span> <span class="kn">import</span> <span class="n">SamplePath</span>
+<span class="kn">from</span> <span class="nn">PyCTBN.PyCTBN.network_graph</span> <span class="kn">import</span> <span class="n">NetworkGraph</span>
+<span class="kn">from</span> <span class="nn">PyCTBN.PyCTBN.parameters_estimator</span> <span class="kn">import</span> <span class="n">ParametersEstimator</span>
+
+
+<span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
+    <span class="n">read_files</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;./data&#39;</span><span class="p">,</span> <span class="s2">&quot;*.json&quot;</span><span class="p">))</span> <span class="c1">#Take all json files in this dir</span>
+    <span class="c1">#import data</span>
+    <span class="n">importer</span> <span class="o">=</span> <span class="n">JsonImporter</span><span class="p">(</span><span class="n">read_files</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;samples&#39;</span><span class="p">,</span> <span class="s1">&#39;dyn.str&#39;</span><span class="p">,</span> <span class="s1">&#39;variables&#39;</span><span class="p">,</span> <span class="s1">&#39;Time&#39;</span><span class="p">,</span> <span class="s1">&#39;Name&#39;</span><span class="p">)</span>
+    <span class="n">importer</span><span class="o">.</span><span class="n">import_data</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+    <span class="c1">#Create a SamplePath Obj passing an already filled AbstractImporter object</span>
+    <span class="n">s1</span> <span class="o">=</span> <span class="n">SamplePath</span><span class="p">(</span><span class="n">importer</span><span class="p">)</span>
+    <span class="c1">#Build The trajectries and the structural infos</span>
+    <span class="n">s1</span><span class="o">.</span><span class="n">build_trajectories</span><span class="p">()</span>
+    <span class="n">s1</span><span class="o">.</span><span class="n">build_structure</span><span class="p">()</span>
+    <span class="nb">print</span><span class="p">(</span><span class="n">s1</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">edges</span><span class="p">)</span>
+    <span class="nb">print</span><span class="p">(</span><span class="n">s1</span><span class="o">.</span><span class="n">structure</span><span class="o">.</span><span class="n">nodes_values</span><span class="p">)</span>
+    <span class="c1">#From The Structure Object build the Graph</span>
+    <span class="n">g</span> <span class="o">=</span> <span class="n">NetworkGraph</span><span class="p">(</span><span class="n">s1</span><span class="o">.</span><span class="n">structure</span><span class="p">)</span>
+    <span class="c1">#Select a node you want to estimate the parameters</span>
+    <span class="n">node</span> <span class="o">=</span> <span class="n">g</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Node&quot;</span><span class="p">,</span> <span class="n">node</span><span class="p">)</span>
+    <span class="c1">#Init the _graph specifically for THIS node</span>
+    <span class="n">g</span><span class="o">.</span><span class="n">fast_init</span><span class="p">(</span><span class="n">node</span><span class="p">)</span>
+    <span class="c1">#Use SamplePath and Grpah to create a ParametersEstimator Object</span>
+    <span class="n">p1</span> <span class="o">=</span> <span class="n">ParametersEstimator</span><span class="p">(</span><span class="n">s1</span><span class="o">.</span><span class="n">trajectories</span><span class="p">,</span> <span class="n">g</span><span class="p">)</span>
+    <span class="c1">#Init the peEst specifically for THIS node</span>
+    <span class="n">p1</span><span class="o">.</span><span class="n">fast_init</span><span class="p">(</span><span class="n">node</span><span class="p">)</span>
+    <span class="c1">#Compute the parameters</span>
+    <span class="n">sofc1</span> <span class="o">=</span> <span class="n">p1</span><span class="o">.</span><span class="n">compute_parameters_for_node</span><span class="p">(</span><span class="n">node</span><span class="p">)</span>
+    <span class="c1">#The est CIMS are inside the resultant SetOfCIms Obj</span>
+    <span class="nb">print</span><span class="p">(</span><span class="n">sofc1</span><span class="o">.</span><span class="n">actual_cims</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="structure-estimation-example">
+<h2>Structure Estimation Example<a class="headerlink" href="#structure-estimation-example" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">PyCTBN.PyCTBN.json_importer</span> <span class="kn">import</span> <span class="n">JsonImporter</span>
+<span class="kn">from</span> <span class="nn">PyCTBN.PyCTBN.sample_path</span> <span class="kn">import</span> <span class="n">SamplePath</span>
+<span class="kn">from</span> <span class="nn">PyCTBN.PyCTBN.structure_estimator</span> <span class="kn">import</span> <span class="n">StructureEstimator</span>
+
+<span class="k">def</span> <span class="nf">structure_estimation_example</span><span class="p">():</span>
+
+    <span class="c1"># read the json files in ./data path</span>
+    <span class="n">read_files</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;./data&#39;</span><span class="p">,</span> <span class="s2">&quot;*.json&quot;</span><span class="p">))</span>
+    <span class="c1"># initialize a JsonImporter object for the first file</span>
+    <span class="n">importer</span> <span class="o">=</span> <span class="n">JsonImporter</span><span class="p">(</span><span class="n">read_files</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;samples&#39;</span><span class="p">,</span> <span class="s1">&#39;dyn.str&#39;</span><span class="p">,</span> <span class="s1">&#39;variables&#39;</span><span class="p">,</span> <span class="s1">&#39;Time&#39;</span><span class="p">,</span> <span class="s1">&#39;Name&#39;</span><span class="p">)</span>
+    <span class="c1"># import the data at index 0 of the outer json array</span>
+    <span class="n">importer</span><span class="o">.</span><span class="n">import_data</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+    <span class="c1"># construct a SamplePath Object passing a filled AbstractImporter</span>
+    <span class="n">s1</span> <span class="o">=</span> <span class="n">SamplePath</span><span class="p">(</span><span class="n">importer</span><span class="p">)</span>
+    <span class="c1"># build the trajectories</span>
+    <span class="n">s1</span><span class="o">.</span><span class="n">build_trajectories</span><span class="p">()</span>
+    <span class="c1"># build the real structure</span>
+    <span class="n">s1</span><span class="o">.</span><span class="n">build_structure</span><span class="p">()</span>
+    <span class="c1"># construct a StructureEstimator object</span>
+    <span class="n">se1</span> <span class="o">=</span> <span class="n">StructureEstimator</span><span class="p">(</span><span class="n">s1</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">)</span>
+    <span class="c1"># call the ctpc algorithm</span>
+    <span class="n">se1</span><span class="o">.</span><span class="n">ctpc_algorithm</span><span class="p">()</span>
+    <span class="c1"># the adjacency matrix of the estimated structure</span>
+    <span class="nb">print</span><span class="p">(</span><span class="n">se1</span><span class="o">.</span><span class="n">adjacency_matrix</span><span class="p">())</span>
+    <span class="c1"># save results to a json file</span>
+    <span class="n">se1</span><span class="o">.</span><span class="n">save_results</span><span class="p">()</span>
+</pre></div>
+</div>
+</div>
+</div>
+
+
+	    </div>
+            <footer>
+  
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+      
+        <a href="PyCTBN.html" class="btn btn-neutral" title="PyCTBN package"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2020, Alessandro Bregoli, Filippo Martini.
+    </p>
+  </div>
+
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/jucacrispim/sphinx_pdj_theme">theme</a> provided by <a href="http://poraodojuca.net">Porão do Juca</a>.
+
+</footer>
+	</div>
+	</div>
+	  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'1.0',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js">
+
+    </script>
+    <script type="text/javascript" src="_static/underscore.js">
+
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+    <script type="text/javascript" src="_static/doctools.js">
+
+    </script>
+    <script type="text/javascript" src="_static/language_data.js">
+
+    </script>
+
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+   <script type="text/javascript"
+           src="_static/js/theme.js"></script>
+
+   <script type="text/javascript"
+           src="_static/js/pdj.js"></script>
+
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+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
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+</html>

documentation/_build/html/genindex.html

@@ -8,7 +8,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
   
-  <title>Index &mdash; PyCTBN  documentation</title>
+  <title>Index &mdash; PyCTBN 1.0 documentation</title>
   
 
   
@@ -26,7 +26,7 @@
         <link rel="index" title="Index"
               href="#"/>
         <link rel="search" title="Search" href="search.html"/>
-    <link rel="top" title="PyCTBN  documentation" href="index.html"/>
+    <link rel="top" title="PyCTBN 1.0 documentation" href="index.html"/>
 
     <meta http-equiv="content-type" content="text/html; charset=utf-8" />
     <meta http-equiv="cache-control" content="public" />
@@ -58,8 +58,33 @@
 	
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"></div>
+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#installation-usage">Installation/Usage:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#implementing-your-own-data-importer">Implementing your own data importer</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#parameters-estimation-example">Parameters Estimation Example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#structure-estimation-example">Structure Estimation Example</a></li>
+</ul>
+</li>
+</ul>
+
           
         
 
@@ -124,22 +149,17 @@
 <h2 id="A">A</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li>
-    abstract_importer
-
-      <ul>
-        <li><a href="rst/abstract_importer.html#module-abstract_importer">module</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter">AbstractImporter (class in PyCTBN.abstract_importer)</a>
 </li>
-      </ul></li>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter">AbstractImporter (class in abstract_importer)</a>
+      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.actual_cims">actual_cims() (PyCTBN.set_of_cims.SetOfCims property)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/set_of_cims.html#set_of_cims.SetOfCims.actual_cims">actual_cims() (set_of_cims.SetOfCims property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.add_edges">add_edges() (PyCTBN.network_graph.NetworkGraph method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.add_edges">add_edges() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.add_nodes">add_nodes() (PyCTBN.network_graph.NetworkGraph method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.add_nodes">add_nodes() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.adjacency_matrix">adjacency_matrix() (PyCTBN.structure_estimator.StructureEstimator method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -147,35 +167,35 @@
 <h2 id="B">B</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/set_of_cims.html#set_of_cims.SetOfCims.build_cims">build_cims() (set_of_cims.SetOfCims method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.build_cims">build_cims() (PyCTBN.set_of_cims.SetOfCims method)</a>
 </li>
-      <li><a href="rst/structure_estimator.html#structure_estimator.StructureEstimator.build_complete_graph">build_complete_graph() (structure_estimator.StructureEstimator method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.build_complete_graph">build_complete_graph() (PyCTBN.structure_estimator.StructureEstimator method)</a>
 </li>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.build_list_of_samples_array">build_list_of_samples_array() (abstract_importer.AbstractImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.build_list_of_samples_array">build_list_of_samples_array() (PyCTBN.abstract_importer.AbstractImporter method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.build_p_comb_structure_for_a_node">build_p_comb_structure_for_a_node() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.build_p_comb_structure_for_a_node">build_p_comb_structure_for_a_node() (PyCTBN.network_graph.NetworkGraph method)</a>
 </li>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.build_sorter">build_sorter() (abstract_importer.AbstractImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.build_sorter">build_sorter() (PyCTBN.abstract_importer.AbstractImporter method)</a>
 
       <ul>
-        <li><a href="rst/json_importer.html#json_importer.JsonImporter.build_sorter">(json_importer.JsonImporter method)</a>
+        <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.build_sorter">(PyCTBN.json_importer.JsonImporter method)</a>
 </li>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/sample_path.html#sample_path.SamplePath.build_structure">build_structure() (sample_path.SamplePath method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath.build_structure">build_structure() (PyCTBN.sample_path.SamplePath method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.build_time_columns_filtering_for_a_node">build_time_columns_filtering_for_a_node() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.build_time_columns_filtering_for_a_node">build_time_columns_filtering_for_a_node() (PyCTBN.network_graph.NetworkGraph method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.build_time_scalar_indexing_structure_for_a_node">build_time_scalar_indexing_structure_for_a_node() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.build_time_scalar_indexing_structure_for_a_node">build_time_scalar_indexing_structure_for_a_node() (PyCTBN.network_graph.NetworkGraph method)</a>
 </li>
-      <li><a href="rst/set_of_cims.html#set_of_cims.SetOfCims.build_times_and_transitions_structures">build_times_and_transitions_structures() (set_of_cims.SetOfCims method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.build_times_and_transitions_structures">build_times_and_transitions_structures() (PyCTBN.set_of_cims.SetOfCims method)</a>
 </li>
-      <li><a href="rst/sample_path.html#sample_path.SamplePath.build_trajectories">build_trajectories() (sample_path.SamplePath method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath.build_trajectories">build_trajectories() (PyCTBN.sample_path.SamplePath method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.build_transition_filtering_for_a_node">build_transition_filtering_for_a_node() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.build_transition_filtering_for_a_node">build_transition_filtering_for_a_node() (PyCTBN.network_graph.NetworkGraph method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.build_transition_scalar_indexing_structure_for_a_node">build_transition_scalar_indexing_structure_for_a_node() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.build_transition_scalar_indexing_structure_for_a_node">build_transition_scalar_indexing_structure_for_a_node() (PyCTBN.network_graph.NetworkGraph method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -183,53 +203,39 @@
 <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li>
-    cache
-
-      <ul>
-        <li><a href="rst/cache.html#module-cache">module</a>
-</li>
-      </ul></li>
-      <li><a href="rst/cache.html#cache.Cache">Cache (class in cache)</a>
+      <li><a href="PyCTBN.html#PyCTBN.cache.Cache">Cache (class in PyCTBN.cache)</a>
 </li>
-      <li><a href="rst/conditional_intensity_matrix.html#conditional_intensity_matrix.ConditionalIntensityMatrix.cim">cim() (conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix.cim">cim() (PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
 </li>
-      <li><a href="rst/cache.html#cache.Cache.clear">clear() (cache.Cache method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.cache.Cache.clear">clear() (PyCTBN.cache.Cache method)</a>
 </li>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.clear_concatenated_frame">clear_concatenated_frame() (abstract_importer.AbstractImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.clear_concatenated_frame">clear_concatenated_frame() (PyCTBN.abstract_importer.AbstractImporter method)</a>
 </li>
-      <li><a href="rst/json_importer.html#json_importer.JsonImporter.clear_data_frame_list">clear_data_frame_list() (json_importer.JsonImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.clear_data_frame_list">clear_data_frame_list() (PyCTBN.json_importer.JsonImporter method)</a>
 </li>
-      <li><a href="rst/structure_estimator.html#structure_estimator.StructureEstimator.complete_test">complete_test() (structure_estimator.StructureEstimator method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.complete_test">complete_test() (PyCTBN.structure_estimator.StructureEstimator method)</a>
 </li>
-      <li><a href="rst/trajectory.html#trajectory.Trajectory.complete_trajectory">complete_trajectory() (trajectory.Trajectory property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.trajectory.Trajectory.complete_trajectory">complete_trajectory() (PyCTBN.trajectory.Trajectory property)</a>
 </li>
-      <li><a href="rst/conditional_intensity_matrix.html#conditional_intensity_matrix.ConditionalIntensityMatrix.compute_cim_coefficients">compute_cim_coefficients() (conditional_intensity_matrix.ConditionalIntensityMatrix method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix.compute_cim_coefficients">compute_cim_coefficients() (PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/parameters_estimator.html#parameters_estimator.ParametersEstimator.compute_parameters_for_node">compute_parameters_for_node() (parameters_estimator.ParametersEstimator method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.parameters_estimator.ParametersEstimator.compute_parameters_for_node">compute_parameters_for_node() (PyCTBN.parameters_estimator.ParametersEstimator method)</a>
 </li>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.compute_row_delta_in_all_samples_frames">compute_row_delta_in_all_samples_frames() (abstract_importer.AbstractImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.compute_row_delta_in_all_samples_frames">compute_row_delta_in_all_samples_frames() (PyCTBN.abstract_importer.AbstractImporter method)</a>
 </li>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.compute_row_delta_sigle_samples_frame">compute_row_delta_sigle_samples_frame() (abstract_importer.AbstractImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.compute_row_delta_sigle_samples_frame">compute_row_delta_sigle_samples_frame() (PyCTBN.abstract_importer.AbstractImporter method)</a>
 </li>
-      <li><a href="rst/parameters_estimator.html#parameters_estimator.ParametersEstimator.compute_state_res_time_for_node">compute_state_res_time_for_node() (parameters_estimator.ParametersEstimator method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.parameters_estimator.ParametersEstimator.compute_state_res_time_for_node">compute_state_res_time_for_node() (PyCTBN.parameters_estimator.ParametersEstimator method)</a>
 </li>
-      <li><a href="rst/parameters_estimator.html#parameters_estimator.ParametersEstimator.compute_state_transitions_for_a_node">compute_state_transitions_for_a_node() (parameters_estimator.ParametersEstimator method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.parameters_estimator.ParametersEstimator.compute_state_transitions_for_a_node">compute_state_transitions_for_a_node() (PyCTBN.parameters_estimator.ParametersEstimator method)</a>
 </li>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.concatenated_samples">concatenated_samples() (abstract_importer.AbstractImporter property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.concatenated_samples">concatenated_samples() (PyCTBN.abstract_importer.AbstractImporter property)</a>
 </li>
-      <li>
-    conditional_intensity_matrix
-
-      <ul>
-        <li><a href="rst/conditional_intensity_matrix.html#module-conditional_intensity_matrix">module</a>
+      <li><a href="PyCTBN.html#PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix">ConditionalIntensityMatrix (class in PyCTBN.conditional_intensity_matrix)</a>
 </li>
-      </ul></li>
-      <li><a href="rst/conditional_intensity_matrix.html#conditional_intensity_matrix.ConditionalIntensityMatrix">ConditionalIntensityMatrix (class in conditional_intensity_matrix)</a>
-</li>
-      <li><a href="rst/structure_estimator.html#structure_estimator.StructureEstimator.ctpc_algorithm">ctpc_algorithm() (structure_estimator.StructureEstimator method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.ctpc_algorithm">ctpc_algorithm() (PyCTBN.structure_estimator.StructureEstimator method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -237,10 +243,10 @@
 <h2 id="D">D</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.dataset_id">dataset_id() (abstract_importer.AbstractImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.dataset_id">dataset_id() (PyCTBN.abstract_importer.AbstractImporter method)</a>
 
       <ul>
-        <li><a href="rst/json_importer.html#json_importer.JsonImporter.dataset_id">(json_importer.JsonImporter method)</a>
+        <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.dataset_id">(PyCTBN.json_importer.JsonImporter method)</a>
 </li>
       </ul></li>
   </ul></td>
@@ -249,10 +255,10 @@
 <h2 id="E">E</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.edges">edges() (network_graph.NetworkGraph property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.edges">edges() (PyCTBN.network_graph.NetworkGraph property)</a>
 
       <ul>
-        <li><a href="rst/structure.html#structure.Structure.edges">(structure.Structure property)</a>
+        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.edges">(PyCTBN.structure.Structure property)</a>
 </li>
       </ul></li>
   </ul></td>
@@ -261,19 +267,19 @@
 <h2 id="F">F</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.fast_init">fast_init() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.fast_init">fast_init() (PyCTBN.network_graph.NetworkGraph method)</a>
 
       <ul>
-        <li><a href="rst/parameters_estimator.html#parameters_estimator.ParametersEstimator.fast_init">(parameters_estimator.ParametersEstimator method)</a>
+        <li><a href="PyCTBN.html#PyCTBN.parameters_estimator.ParametersEstimator.fast_init">(PyCTBN.parameters_estimator.ParametersEstimator method)</a>
 </li>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.file_path">file_path() (abstract_importer.AbstractImporter property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.file_path">file_path() (PyCTBN.abstract_importer.AbstractImporter property)</a>
 </li>
-      <li><a href="rst/set_of_cims.html#set_of_cims.SetOfCims.filter_cims_with_mask">filter_cims_with_mask() (set_of_cims.SetOfCims method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.filter_cims_with_mask">filter_cims_with_mask() (PyCTBN.set_of_cims.SetOfCims method)</a>
 </li>
-      <li><a href="rst/cache.html#cache.Cache.find">find() (cache.Cache method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.cache.Cache.find">find() (PyCTBN.cache.Cache method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -281,34 +287,34 @@
 <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/structure_estimator.html#structure_estimator.StructureEstimator.generate_possible_sub_sets_of_size">generate_possible_sub_sets_of_size() (structure_estimator.StructureEstimator method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.generate_possible_sub_sets_of_size">generate_possible_sub_sets_of_size() (PyCTBN.structure_estimator.StructureEstimator method)</a>
 </li>
-      <li><a href="rst/set_of_cims.html#set_of_cims.SetOfCims.get_cims_number">get_cims_number() (set_of_cims.SetOfCims method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.get_cims_number">get_cims_number() (PyCTBN.set_of_cims.SetOfCims method)</a>
 </li>
-      <li><a href="rst/structure.html#structure.Structure.get_node_id">get_node_id() (structure.Structure method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure.Structure.get_node_id">get_node_id() (PyCTBN.structure.Structure method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.get_node_indx">get_node_indx() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.get_node_indx">get_node_indx() (PyCTBN.network_graph.NetworkGraph method)</a>
 
       <ul>
-        <li><a href="rst/structure.html#structure.Structure.get_node_indx">(structure.Structure method)</a>
+        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.get_node_indx">(PyCTBN.structure.Structure method)</a>
 </li>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.get_ordered_by_indx_set_of_parents">get_ordered_by_indx_set_of_parents() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.get_ordered_by_indx_set_of_parents">get_ordered_by_indx_set_of_parents() (PyCTBN.network_graph.NetworkGraph method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.get_parents_by_id">get_parents_by_id() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.get_parents_by_id">get_parents_by_id() (PyCTBN.network_graph.NetworkGraph method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.get_positional_node_indx">get_positional_node_indx() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.get_positional_node_indx">get_positional_node_indx() (PyCTBN.network_graph.NetworkGraph method)</a>
 
       <ul>
-        <li><a href="rst/structure.html#structure.Structure.get_positional_node_indx">(structure.Structure method)</a>
+        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.get_positional_node_indx">(PyCTBN.structure.Structure method)</a>
 </li>
       </ul></li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.get_states_number">get_states_number() (network_graph.NetworkGraph method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.get_states_number">get_states_number() (PyCTBN.network_graph.NetworkGraph method)</a>
 
       <ul>
-        <li><a href="rst/structure.html#structure.Structure.get_states_number">(structure.Structure method)</a>
+        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.get_states_number">(PyCTBN.structure.Structure method)</a>
 </li>
       </ul></li>
   </ul></td>
@@ -317,23 +323,19 @@
 <h2 id="I">I</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.import_data">import_data() (abstract_importer.AbstractImporter method)</a>
-
-      <ul>
-        <li><a href="rst/json_importer.html#json_importer.JsonImporter.import_data">(json_importer.JsonImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.import_data">import_data() (PyCTBN.json_importer.JsonImporter method)</a>
 </li>
-      </ul></li>
-      <li><a href="rst/json_importer.html#json_importer.JsonImporter.import_sampled_cims">import_sampled_cims() (json_importer.JsonImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.import_sampled_cims">import_sampled_cims() (PyCTBN.json_importer.JsonImporter method)</a>
+</li>
+      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.import_structure">import_structure() (PyCTBN.json_importer.JsonImporter method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/json_importer.html#json_importer.JsonImporter.import_structure">import_structure() (json_importer.JsonImporter method)</a>
-</li>
-      <li><a href="rst/json_importer.html#json_importer.JsonImporter.import_trajectories">import_trajectories() (json_importer.JsonImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.import_trajectories">import_trajectories() (PyCTBN.json_importer.JsonImporter method)</a>
 </li>
-      <li><a href="rst/json_importer.html#json_importer.JsonImporter.import_variables">import_variables() (json_importer.JsonImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.import_variables">import_variables() (PyCTBN.json_importer.JsonImporter method)</a>
 </li>
-      <li><a href="rst/structure_estimator.html#structure_estimator.StructureEstimator.independence_test">independence_test() (structure_estimator.StructureEstimator method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.independence_test">independence_test() (PyCTBN.structure_estimator.StructureEstimator method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -341,16 +343,7 @@
 <h2 id="J">J</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li>
-    json_importer
-
-      <ul>
-        <li><a href="rst/json_importer.html#module-json_importer">module</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/json_importer.html#json_importer.JsonImporter">JsonImporter (class in json_importer)</a>
+      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter">JsonImporter (class in PyCTBN.json_importer)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -362,27 +355,29 @@
     module
 
       <ul>
-        <li><a href="rst/abstract_importer.html#module-abstract_importer">abstract_importer</a>
+        <li><a href="PyCTBN.html#module-PyCTBN">PyCTBN</a>
 </li>
-        <li><a href="rst/cache.html#module-cache">cache</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer</a>
 </li>
-        <li><a href="rst/conditional_intensity_matrix.html#module-conditional_intensity_matrix">conditional_intensity_matrix</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache</a>
 </li>
-        <li><a href="rst/json_importer.html#module-json_importer">json_importer</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix</a>
 </li>
-        <li><a href="rst/network_graph.html#module-network_graph">network_graph</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer</a>
 </li>
-        <li><a href="rst/parameters_estimator.html#module-parameters_estimator">parameters_estimator</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph</a>
 </li>
-        <li><a href="rst/sample_path.html#module-sample_path">sample_path</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator</a>
 </li>
-        <li><a href="rst/set_of_cims.html#module-set_of_cims">set_of_cims</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path</a>
 </li>
-        <li><a href="rst/structure.html#module-structure">structure</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims</a>
 </li>
-        <li><a href="rst/structure_estimator.html#module-structure_estimator">structure_estimator</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure</a>
 </li>
-        <li><a href="rst/trajectory.html#module-trajectory">trajectory</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator</a>
+</li>
+        <li><a href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory</a>
 </li>
       </ul></li>
   </ul></td>
@@ -391,34 +386,27 @@
 <h2 id="N">N</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li>
-    network_graph
-
-      <ul>
-        <li><a href="rst/network_graph.html#module-network_graph">module</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph">NetworkGraph (class in PyCTBN.network_graph)</a>
 </li>
-      </ul></li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph">NetworkGraph (class in network_graph)</a>
-</li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.nodes">nodes() (network_graph.NetworkGraph property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.nodes">nodes() (PyCTBN.network_graph.NetworkGraph property)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.nodes_indexes">nodes_indexes() (network_graph.NetworkGraph property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.nodes_indexes">nodes_indexes() (PyCTBN.network_graph.NetworkGraph property)</a>
 
       <ul>
-        <li><a href="rst/structure.html#structure.Structure.nodes_indexes">(structure.Structure property)</a>
+        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.nodes_indexes">(PyCTBN.structure.Structure property)</a>
 </li>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/structure.html#structure.Structure.nodes_labels">nodes_labels() (structure.Structure property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure.Structure.nodes_labels">nodes_labels() (PyCTBN.structure.Structure property)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.nodes_values">nodes_values() (network_graph.NetworkGraph property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.nodes_values">nodes_values() (PyCTBN.network_graph.NetworkGraph property)</a>
 
       <ul>
-        <li><a href="rst/structure.html#structure.Structure.nodes_values">(structure.Structure property)</a>
+        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.nodes_values">(PyCTBN.structure.Structure property)</a>
 </li>
       </ul></li>
-      <li><a href="rst/json_importer.html#json_importer.JsonImporter.normalize_trajectories">normalize_trajectories() (json_importer.JsonImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.normalize_trajectories">normalize_trajectories() (PyCTBN.json_importer.JsonImporter method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -426,11 +414,11 @@
 <h2 id="O">O</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/structure_estimator.html#structure_estimator.StructureEstimator.one_iteration_of_CTPC_algorithm">one_iteration_of_CTPC_algorithm() (structure_estimator.StructureEstimator method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.one_iteration_of_CTPC_algorithm">one_iteration_of_CTPC_algorithm() (PyCTBN.structure_estimator.StructureEstimator method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/json_importer.html#json_importer.JsonImporter.one_level_normalizing">one_level_normalizing() (json_importer.JsonImporter method)</a>
+      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.one_level_normalizing">one_level_normalizing() (PyCTBN.json_importer.JsonImporter method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -438,127 +426,169 @@
 <h2 id="P">P</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.p_combs">p_combs() (network_graph.NetworkGraph property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.p_combs">p_combs() (PyCTBN.network_graph.NetworkGraph property)</a>
 
       <ul>
-        <li><a href="rst/set_of_cims.html#set_of_cims.SetOfCims.p_combs">(set_of_cims.SetOfCims property)</a>
+        <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.p_combs">(PyCTBN.set_of_cims.SetOfCims property)</a>
 </li>
       </ul></li>
+      <li><a href="PyCTBN.html#PyCTBN.parameters_estimator.ParametersEstimator">ParametersEstimator (class in PyCTBN.parameters_estimator)</a>
+</li>
+      <li><a href="PyCTBN.html#PyCTBN.cache.Cache.put">put() (PyCTBN.cache.Cache method)</a>
+</li>
       <li>
-    parameters_estimator
+    PyCTBN
 
       <ul>
-        <li><a href="rst/parameters_estimator.html#module-parameters_estimator">module</a>
+        <li><a href="PyCTBN.html#module-PyCTBN">module</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/parameters_estimator.html#parameters_estimator.ParametersEstimator">ParametersEstimator (class in parameters_estimator)</a>
-</li>
-      <li><a href="rst/cache.html#cache.Cache.put">put() (cache.Cache method)</a>
-</li>
-  </ul></td>
-</tr></table>
+      <li>
+    PyCTBN.abstract_importer
 
-<h2 id="R">R</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/json_importer.html#json_importer.JsonImporter.read_json_file">read_json_file() (json_importer.JsonImporter method)</a>
+      <ul>
+        <li><a href="PyCTBN.html#module-PyCTBN.abstract_importer">module</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="S">S</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
+      </ul></li>
       <li>
-    sample_path
+    PyCTBN.cache
 
       <ul>
-        <li><a href="rst/sample_path.html#module-sample_path">module</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.cache">module</a>
 </li>
       </ul></li>
-      <li><a href="rst/sample_path.html#sample_path.SamplePath">SamplePath (class in sample_path)</a>
-</li>
-      <li><a href="rst/structure_estimator.html#structure_estimator.StructureEstimator.save_results">save_results() (structure_estimator.StructureEstimator method)</a>
-</li>
       <li>
-    set_of_cims
+    PyCTBN.conditional_intensity_matrix
 
       <ul>
-        <li><a href="rst/set_of_cims.html#module-set_of_cims">module</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">module</a>
 </li>
       </ul></li>
-      <li><a href="rst/set_of_cims.html#set_of_cims.SetOfCims">SetOfCims (class in set_of_cims)</a>
-</li>
-      <li><a href="rst/trajectory.html#trajectory.Trajectory.size">size() (trajectory.Trajectory method)</a>
-</li>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.sorter">sorter() (abstract_importer.AbstractImporter property)</a>
+      <li>
+    PyCTBN.json_importer
+
+      <ul>
+        <li><a href="PyCTBN.html#module-PyCTBN.json_importer">module</a>
 </li>
+      </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/conditional_intensity_matrix.html#conditional_intensity_matrix.ConditionalIntensityMatrix.state_residence_times">state_residence_times() (conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
+      <li>
+    PyCTBN.network_graph
+
+      <ul>
+        <li><a href="PyCTBN.html#module-PyCTBN.network_graph">module</a>
 </li>
-      <li><a href="rst/conditional_intensity_matrix.html#conditional_intensity_matrix.ConditionalIntensityMatrix.state_transition_matrix">state_transition_matrix() (conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
+      </ul></li>
+      <li>
+    PyCTBN.parameters_estimator
+
+      <ul>
+        <li><a href="PyCTBN.html#module-PyCTBN.parameters_estimator">module</a>
 </li>
+      </ul></li>
       <li>
-    structure
+    PyCTBN.sample_path
 
       <ul>
-        <li><a href="rst/structure.html#module-structure">module</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.sample_path">module</a>
 </li>
       </ul></li>
-      <li><a href="rst/structure.html#structure.Structure">Structure (class in structure)</a>
+      <li>
+    PyCTBN.set_of_cims
+
+      <ul>
+        <li><a href="PyCTBN.html#module-PyCTBN.set_of_cims">module</a>
 </li>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.structure">structure() (abstract_importer.AbstractImporter property)</a>
+      </ul></li>
+      <li>
+    PyCTBN.structure
 
       <ul>
-        <li><a href="rst/sample_path.html#sample_path.SamplePath.structure">(sample_path.SamplePath property)</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.structure">module</a>
 </li>
       </ul></li>
       <li>
-    structure_estimator
+    PyCTBN.structure_estimator
 
       <ul>
-        <li><a href="rst/structure_estimator.html#module-structure_estimator">module</a>
+        <li><a href="PyCTBN.html#module-PyCTBN.structure_estimator">module</a>
 </li>
       </ul></li>
-      <li><a href="rst/structure_estimator.html#structure_estimator.StructureEstimator">StructureEstimator (class in structure_estimator)</a>
+      <li>
+    PyCTBN.trajectory
+
+      <ul>
+        <li><a href="PyCTBN.html#module-PyCTBN.trajectory">module</a>
 </li>
+      </ul></li>
   </ul></td>
 </tr></table>
 
-<h2 id="T">T</h2>
+<h2 id="R">R</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.time_filtering">time_filtering() (network_graph.NetworkGraph property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.read_json_file">read_json_file() (PyCTBN.json_importer.JsonImporter method)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.time_scalar_indexing_strucure">time_scalar_indexing_strucure() (network_graph.NetworkGraph property)</a>
+  </ul></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath">SamplePath (class in PyCTBN.sample_path)</a>
 </li>
-      <li><a href="rst/trajectory.html#trajectory.Trajectory.times">times() (trajectory.Trajectory property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.save_results">save_results() (PyCTBN.structure_estimator.StructureEstimator method)</a>
 </li>
-      <li><a href="rst/sample_path.html#sample_path.SamplePath.total_variables_count">total_variables_count() (sample_path.SamplePath property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims">SetOfCims (class in PyCTBN.set_of_cims)</a>
 </li>
-      <li><a href="rst/structure.html#structure.Structure.total_variables_number">total_variables_number() (structure.Structure property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.trajectory.Trajectory.size">size() (PyCTBN.trajectory.Trajectory method)</a>
 </li>
-      <li><a href="rst/sample_path.html#sample_path.SamplePath.trajectories">trajectories() (sample_path.SamplePath property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.sorter">sorter() (PyCTBN.abstract_importer.AbstractImporter property)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li>
-    trajectory
+      <li><a href="PyCTBN.html#PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix.state_residence_times">state_residence_times() (PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
+</li>
+      <li><a href="PyCTBN.html#PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix.state_transition_matrix">state_transition_matrix() (PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
+</li>
+      <li><a href="PyCTBN.html#PyCTBN.structure.Structure">Structure (class in PyCTBN.structure)</a>
+</li>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.structure">structure() (PyCTBN.abstract_importer.AbstractImporter property)</a>
 
       <ul>
-        <li><a href="rst/trajectory.html#module-trajectory">module</a>
+        <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath.structure">(PyCTBN.sample_path.SamplePath property)</a>
 </li>
       </ul></li>
-      <li><a href="rst/trajectory.html#trajectory.Trajectory">Trajectory (class in trajectory)</a>
+      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator">StructureEstimator (class in PyCTBN.structure_estimator)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.time_filtering">time_filtering() (PyCTBN.network_graph.NetworkGraph property)</a>
+</li>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.time_scalar_indexing_strucure">time_scalar_indexing_strucure() (PyCTBN.network_graph.NetworkGraph property)</a>
+</li>
+      <li><a href="PyCTBN.html#PyCTBN.trajectory.Trajectory.times">times() (PyCTBN.trajectory.Trajectory property)</a>
+</li>
+      <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath.total_variables_count">total_variables_count() (PyCTBN.sample_path.SamplePath property)</a>
+</li>
+      <li><a href="PyCTBN.html#PyCTBN.structure.Structure.total_variables_number">total_variables_number() (PyCTBN.structure.Structure property)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath.trajectories">trajectories() (PyCTBN.sample_path.SamplePath property)</a>
+</li>
+      <li><a href="PyCTBN.html#PyCTBN.trajectory.Trajectory">Trajectory (class in PyCTBN.trajectory)</a>
 </li>
-      <li><a href="rst/trajectory.html#trajectory.Trajectory.trajectory">trajectory() (trajectory.Trajectory property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.trajectory.Trajectory.trajectory">trajectory() (PyCTBN.trajectory.Trajectory property)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.transition_filtering">transition_filtering() (network_graph.NetworkGraph property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.transition_filtering">transition_filtering() (PyCTBN.network_graph.NetworkGraph property)</a>
 </li>
-      <li><a href="rst/network_graph.html#network_graph.NetworkGraph.transition_scalar_indexing_structure">transition_scalar_indexing_structure() (network_graph.NetworkGraph property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.transition_scalar_indexing_structure">transition_scalar_indexing_structure() (PyCTBN.network_graph.NetworkGraph property)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -566,7 +596,7 @@
 <h2 id="V">V</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="rst/abstract_importer.html#abstract_importer.AbstractImporter.variables">variables() (abstract_importer.AbstractImporter property)</a>
+      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.variables">variables() (PyCTBN.abstract_importer.AbstractImporter property)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -581,7 +611,7 @@
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2020, Filippo Martini.
+        &copy; Copyright 2020, Alessandro Bregoli, Filippo Martini.
     </p>
   </div>
 
@@ -595,7 +625,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'',
+            VERSION:'1.0',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',
             HAS_SOURCE:  true

documentation/_build/html/index.html

@@ -8,7 +8,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
   
-  <title>Welcome to PyCTBN’s documentation! &mdash; PyCTBN  documentation</title>
+  <title>Welcome to PyCTBN’s documentation! &mdash; PyCTBN 1.0 documentation</title>
   
 
   
@@ -26,7 +26,8 @@
         <link rel="index" title="Index"
               href="genindex.html"/>
         <link rel="search" title="Search" href="search.html"/>
-    <link rel="top" title="PyCTBN  documentation" href="#"/>
+    <link rel="top" title="PyCTBN 1.0 documentation" href="#"/>
+        <link rel="next" title="PyCTBN package" href="PyCTBN.html"/>
 
     <meta http-equiv="content-type" content="text/html; charset=utf-8" />
     <meta http-equiv="cache-control" content="public" />
@@ -58,12 +59,33 @@
 	
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Welcome to PyCTBN’s documentation!</a></li>
-<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
 </ul>
-</div>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#installation-usage">Installation/Usage:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#implementing-your-own-data-importer">Implementing your own data importer</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#parameters-estimation-example">Parameters Estimation Example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#structure-estimation-example">Structure Estimation Example</a></li>
+</ul>
+</li>
+</ul>
+
           
         
 
@@ -105,6 +127,32 @@
   <div class="section" id="welcome-to-pyctbn-s-documentation">
 <h1>Welcome to PyCTBN’s documentation!<a class="headerlink" href="#welcome-to-pyctbn-s-documentation" title="Permalink to this headline">¶</a></h1>
 <div class="toctree-wrapper compound">
+<p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#installation-usage">Installation/Usage:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#implementing-your-own-data-importer">Implementing your own data importer</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#parameters-estimation-example">Parameters Estimation Example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#structure-estimation-example">Structure Estimation Example</a></li>
+</ul>
+</li>
+</ul>
 </div>
 </div>
 <div class="section" id="indices-and-tables">
@@ -120,12 +168,19 @@
 	    </div>
             <footer>
   
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="PyCTBN.html" class="btn btn-neutral float-right" title="PyCTBN package">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+    </div>
+  
 
   <hr/>
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2020, Filippo Martini.
+        &copy; Copyright 2020, Alessandro Bregoli, Filippo Martini.
     </p>
   </div>
 
@@ -139,7 +194,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'',
+            VERSION:'1.0',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',
             HAS_SOURCE:  true

documentation/_build/html/modules.html

@@ -0,0 +1,210 @@
+
+
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
+<html xml:lang="" lang="" version="-//W3C//DTD XHTML 1.1//EN" xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+  
+  <title>PyCTBN &mdash; PyCTBN 1.0 documentation</title>
+  
+
+  
+
+  
+
+    <link href='https://fonts.googleapis.com/css?family=Lato:400,700,400italic,700italic|Roboto+Slab:400,700|Inconsolata:400,700' rel='stylesheet' type='text/css'/>
+    <link rel="stylesheet" href="_static/css/pdj.css" type="text/css" />
+
+  
+
+  
+
+  
+        <link rel="index" title="Index"
+              href="genindex.html"/>
+        <link rel="search" title="Search" href="search.html"/>
+    <link rel="top" title="PyCTBN 1.0 documentation" href="index.html"/>
+
+    <meta http-equiv="content-type" content="text/html; charset=utf-8" />
+    <meta http-equiv="cache-control" content="public" />
+    <meta name="robots" content="follow, all" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <!-- Add jQuery library -->
+    <script type="text/javascript" src="http://code.jquery.com/jquery-latest.min.js"></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
+
+  </head>
+
+  <body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        <a href="index.html" class="fa fa-home"> PyCTBN </a>
+        <div role="search">
+	  <form id ="rtd-search-form" class="wy-form"
+		action="search.html" method="get">
+	    <input type="text" name="q" placeholder="Search docs" />
+	    <input type="hidden" name="check_keywords" value="yes" />
+	    <input type="hidden" name="area" value="default" />
+	  </form>
+	</div>
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+	
+          
+          
+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#installation-usage">Installation/Usage:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#implementing-your-own-data-importer">Implementing your own data importer</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#parameters-estimation-example">Parameters Estimation Example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#structure-estimation-example">Structure Estimation Example</a></li>
+</ul>
+</li>
+</ul>
+
+          
+        
+
+      </div>
+      &nbsp;
+    </nav>
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      <nav class="wy-nav-top" id="barra-mobile" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+        <a href="#">Porão do Juca</a>
+      </nav>
+
+      <div class="wy-nav-content">
+	<div class="fundo-claro">
+	</div>
+	<div class="fundo-escuro">
+	</div>
+
+        <div class="rst-content">
+          <div role="navigation" aria-label="breadcrumbs navigation">
+	    
+	    <!-- <ul class="wy-breadcrumbs"> -->
+	    <!--   <li><a href="#">Docs</a> &raquo;</li> -->
+
+	    <!--   <li>Features</li> -->
+	    <!--   <li class="wy-breadcrumbs-aside"> -->
+
+	    <!-- 	<a href="_sources/index.txt" rel="nofollow"> View page source</a> -->
+
+	    <!--   </li> -->
+	    <!-- </ul> -->
+	    <!-- <hr/> -->
+	  </div>
+
+          <div role="main" class="">
+
+	    <div id="content" class="hfeed entry-container hentry">
+  <div class="section" id="pyctbn">
+<h1>PyCTBN<a class="headerlink" href="#pyctbn" title="Permalink to this headline">¶</a></h1>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+
+
+	    </div>
+            <footer>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2020, Alessandro Bregoli, Filippo Martini.
+    </p>
+  </div>
+
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/jucacrispim/sphinx_pdj_theme">theme</a> provided by <a href="http://poraodojuca.net">Porão do Juca</a>.
+
+</footer>
+	</div>
+	</div>
+	  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'1.0',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js">
+
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+    <script type="text/javascript" src="_static/underscore.js">
+
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+    <script type="text/javascript" src="_static/doctools.js">
+
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+
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+  
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+   <script type="text/javascript"
+           src="_static/js/theme.js"></script>
+
+   <script type="text/javascript"
+           src="_static/js/pdj.js"></script>
+
+  
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+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+  </body>
+</html>

documentation/_build/html/py-modindex.html

@@ -8,7 +8,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
   
-  <title>Python Module Index &mdash; PyCTBN  documentation</title>
+  <title>Python Module Index &mdash; PyCTBN 1.0 documentation</title>
   
 
   
@@ -26,13 +26,9 @@
         <link rel="index" title="Index"
               href="genindex.html"/>
         <link rel="search" title="Search" href="search.html"/>
-    <link rel="top" title="PyCTBN  documentation" href="index.html"/>
+    <link rel="top" title="PyCTBN 1.0 documentation" href="index.html"/>
 
 
-    <script>
-      DOCUMENTATION_OPTIONS.COLLAPSE_INDEX = true;
-    </script>
-
 
 
     <meta http-equiv="content-type" content="text/html; charset=utf-8" />
@@ -65,8 +61,33 @@
 	
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"></div>
+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#installation-usage">Installation/Usage:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#implementing-your-own-data-importer">Implementing your own data importer</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#parameters-estimation-example">Parameters Estimation Example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#structure-estimation-example">Structure Estimation Example</a></li>
+</ul>
+</li>
+</ul>
+
           
         
 
@@ -109,91 +130,73 @@
    <h1>Python Module Index</h1>
 
    <div class="modindex-jumpbox">
-   <a href="#cap-a"><strong>a</strong></a> | 
-   <a href="#cap-c"><strong>c</strong></a> | 
-   <a href="#cap-j"><strong>j</strong></a> | 
-   <a href="#cap-n"><strong>n</strong></a> | 
-   <a href="#cap-p"><strong>p</strong></a> | 
-   <a href="#cap-s"><strong>s</strong></a> | 
-   <a href="#cap-t"><strong>t</strong></a>
+   <a href="#cap-p"><strong>p</strong></a>
    </div>
 
    <table class="indextable modindextable">
      <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
-     <tr class="cap" id="cap-a"><td></td><td>
-       <strong>a</strong></td><td></td></tr>
+     <tr class="cap" id="cap-p"><td></td><td>
+       <strong>p</strong></td><td></td></tr>
      <tr>
-       <td></td>
+       <td><img src="_static/minus.png" class="toggler"
+              id="toggle-1" style="display: none" alt="-" /></td>
        <td>
-       <a href="rst/abstract_importer.html#module-abstract_importer"><code class="xref">abstract_importer</code></a></td><td>
+       <a href="PyCTBN.html#module-PyCTBN"><code class="xref">PyCTBN</code></a></td><td>
        <em></em></td></tr>
-     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
-     <tr class="cap" id="cap-c"><td></td><td>
-       <strong>c</strong></td><td></td></tr>
-     <tr>
+     <tr class="cg-1">
        <td></td>
-       <td>
-       <a href="rst/cache.html#module-cache"><code class="xref">cache</code></a></td><td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.abstract_importer"><code class="xref">PyCTBN.abstract_importer</code></a></td><td>
        <em></em></td></tr>
-     <tr>
+     <tr class="cg-1">
        <td></td>
-       <td>
-       <a href="rst/conditional_intensity_matrix.html#module-conditional_intensity_matrix"><code class="xref">conditional_intensity_matrix</code></a></td><td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.cache"><code class="xref">PyCTBN.cache</code></a></td><td>
        <em></em></td></tr>
-     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
-     <tr class="cap" id="cap-j"><td></td><td>
-       <strong>j</strong></td><td></td></tr>
-     <tr>
+     <tr class="cg-1">
        <td></td>
-       <td>
-       <a href="rst/json_importer.html#module-json_importer"><code class="xref">json_importer</code></a></td><td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix"><code class="xref">PyCTBN.conditional_intensity_matrix</code></a></td><td>
        <em></em></td></tr>
-     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
-     <tr class="cap" id="cap-n"><td></td><td>
-       <strong>n</strong></td><td></td></tr>
-     <tr>
+     <tr class="cg-1">
        <td></td>
-       <td>
-       <a href="rst/network_graph.html#module-network_graph"><code class="xref">network_graph</code></a></td><td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.json_importer"><code class="xref">PyCTBN.json_importer</code></a></td><td>
        <em></em></td></tr>
-     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
-     <tr class="cap" id="cap-p"><td></td><td>
-       <strong>p</strong></td><td></td></tr>
-     <tr>
+     <tr class="cg-1">
        <td></td>
-       <td>
-       <a href="rst/parameters_estimator.html#module-parameters_estimator"><code class="xref">parameters_estimator</code></a></td><td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.network_graph"><code class="xref">PyCTBN.network_graph</code></a></td><td>
        <em></em></td></tr>
-     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
-     <tr class="cap" id="cap-s"><td></td><td>
-       <strong>s</strong></td><td></td></tr>
-     <tr>
+     <tr class="cg-1">
        <td></td>
-       <td>
-       <a href="rst/sample_path.html#module-sample_path"><code class="xref">sample_path</code></a></td><td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.parameters_estimator"><code class="xref">PyCTBN.parameters_estimator</code></a></td><td>
        <em></em></td></tr>
-     <tr>
+     <tr class="cg-1">
        <td></td>
-       <td>
-       <a href="rst/set_of_cims.html#module-set_of_cims"><code class="xref">set_of_cims</code></a></td><td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.sample_path"><code class="xref">PyCTBN.sample_path</code></a></td><td>
        <em></em></td></tr>
-     <tr>
+     <tr class="cg-1">
        <td></td>
-       <td>
-       <a href="rst/structure.html#module-structure"><code class="xref">structure</code></a></td><td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.set_of_cims"><code class="xref">PyCTBN.set_of_cims</code></a></td><td>
        <em></em></td></tr>
-     <tr>
+     <tr class="cg-1">
        <td></td>
-       <td>
-       <a href="rst/structure_estimator.html#module-structure_estimator"><code class="xref">structure_estimator</code></a></td><td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.structure"><code class="xref">PyCTBN.structure</code></a></td><td>
        <em></em></td></tr>
-     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
-     <tr class="cap" id="cap-t"><td></td><td>
-       <strong>t</strong></td><td></td></tr>
-     <tr>
+     <tr class="cg-1">
        <td></td>
-       <td>
-       <a href="rst/trajectory.html#module-trajectory"><code class="xref">trajectory</code></a></td><td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.structure_estimator"><code class="xref">PyCTBN.structure_estimator</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="PyCTBN.html#module-PyCTBN.trajectory"><code class="xref">PyCTBN.trajectory</code></a></td><td>
        <em></em></td></tr>
    </table>
 
@@ -206,7 +209,7 @@
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2020, Filippo Martini.
+        &copy; Copyright 2020, Alessandro Bregoli, Filippo Martini.
     </p>
   </div>
 
@@ -220,7 +223,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
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-            VERSION:'',
+            VERSION:'1.0',
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             HAS_SOURCE:  true

documentation/_build/html/rst/abstract_importer.html

@@ -1,333 +0,0 @@
-
-
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
-<html xml:lang="" lang="" version="-//W3C//DTD XHTML 1.1//EN" xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta charset="utf-8">
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-  
-  <title>abstract_importer module &mdash; PyCTBN  documentation</title>
-  
-
-  
-
-  
-
-    <link href='https://fonts.googleapis.com/css?family=Lato:400,700,400italic,700italic|Roboto+Slab:400,700|Inconsolata:400,700' rel='stylesheet' type='text/css'/>
-    <link rel="stylesheet" href="../_static/css/pdj.css" type="text/css" />
-
-  
-
-  
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-  
-        <link rel="index" title="Index"
-              href="../genindex.html"/>
-        <link rel="search" title="Search" href="../search.html"/>
-    <link rel="top" title="PyCTBN  documentation" href="../index.html"/>
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-	
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-<li><a class="reference internal" href="#">abstract_importer module</a></li>
-</ul>
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-
-	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="module-abstract_importer">
-<span id="abstract-importer-module"></span><h1>abstract_importer module<a class="headerlink" href="#module-abstract_importer" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="abstract_importer.AbstractImporter">
-<em class="property">class </em><code class="sig-prename descclassname">abstract_importer.</code><code class="sig-name descname">AbstractImporter</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">file_path</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span><a class="headerlink" href="#abstract_importer.AbstractImporter" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">abc.ABC</span></code></p>
-<p>Abstract class that exposes all the necessary methods to process the trajectories and the net structure.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>file_path</strong> (<em>str</em>) – the file path</p>
-</dd>
-<dt class="field-even">_concatenated_samples</dt>
-<dd class="field-even"><p>Dataframe containing the concatenation of all the processed trajectories</p>
-</dd>
-<dt class="field-odd">_df_structure</dt>
-<dd class="field-odd"><p>Dataframe containing the structure of the network (edges)</p>
-</dd>
-<dt class="field-even">_df_variables</dt>
-<dd class="field-even"><p>Dataframe containing the nodes cardinalities</p>
-</dd>
-<dt class="field-odd">_sorter</dt>
-<dd class="field-odd"><p>A list containing the columns header (excluding the time column) of the <cite>_concatenated_samples</cite></p>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="abstract_importer.AbstractImporter.build_list_of_samples_array">
-<code class="sig-name descname">build_list_of_samples_array</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">data_frame</span><span class="p">:</span> <span class="n">pandas.core.frame.DataFrame</span></em><span class="sig-paren">)</span> &#x2192; List<a class="headerlink" href="#abstract_importer.AbstractImporter.build_list_of_samples_array" title="Permalink to this definition">¶</a></dt>
-<dd><p>Builds a List containing the columns of data_frame and converts them to a numpy array.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>data_frame</strong> (<em>pandas.Dataframe</em>) – the dataframe from which the columns have to be extracted and converted</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>the resulting list of numpy arrays</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>List</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="abstract_importer.AbstractImporter.build_sorter">
-<em class="property">abstract </em><code class="sig-name descname">build_sorter</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">sample_frame</span><span class="p">:</span> <span class="n">pandas.core.frame.DataFrame</span></em><span class="sig-paren">)</span> &#x2192; List<a class="headerlink" href="#abstract_importer.AbstractImporter.build_sorter" title="Permalink to this definition">¶</a></dt>
-<dd><p>Initializes the <code class="docutils literal notranslate"><span class="pre">_sorter</span></code> class member from a trajectory dataframe, exctracting the header of the frame
-and keeping ONLY the variables symbolic labels, cutting out the time label in the header.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>sample_frame</strong> (<em>pandas.DataFrame</em>) – The dataframe from which extract the header</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A list containing the processed header.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>List</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="abstract_importer.AbstractImporter.clear_concatenated_frame">
-<code class="sig-name descname">clear_concatenated_frame</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#abstract_importer.AbstractImporter.clear_concatenated_frame" title="Permalink to this definition">¶</a></dt>
-<dd><p>Removes all values in the dataframe concatenated_samples.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="abstract_importer.AbstractImporter.compute_row_delta_in_all_samples_frames">
-<code class="sig-name descname">compute_row_delta_in_all_samples_frames</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">df_samples_list</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#abstract_importer.AbstractImporter.compute_row_delta_in_all_samples_frames" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calls the method <code class="docutils literal notranslate"><span class="pre">compute_row_delta_sigle_samples_frame</span></code> on every dataframe present in the list
-<code class="docutils literal notranslate"><span class="pre">df_samples_list</span></code>.
-Concatenates the result in the dataframe <code class="docutils literal notranslate"><span class="pre">concatanated_samples</span></code></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>df_samples_list</strong> (<em>List</em>) – the datframe’s list to be processed and concatenated</p>
-</dd>
-</dl>
-<div class="admonition warning">
-<p class="admonition-title">Warning</p>
-<p>The Dataframe sample_frame has to follow the column structure of this header:
-Header of sample_frame = [Time | Variable values]
-The class member self._sorter HAS to be properly INITIALIZED (See class members definition doc)</p>
-</div>
-<div class="admonition note">
-<p class="admonition-title">Note</p>
-<p>After the call of this method the class member <code class="docutils literal notranslate"><span class="pre">concatanated_samples</span></code> will contain all processed
-and merged trajectories</p>
-</div>
-</dd></dl>
-
-<dl class="py method">
-<dt id="abstract_importer.AbstractImporter.compute_row_delta_sigle_samples_frame">
-<code class="sig-name descname">compute_row_delta_sigle_samples_frame</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">sample_frame</span><span class="p">:</span> <span class="n">pandas.core.frame.DataFrame</span></em>, <em class="sig-param"><span class="n">columns_header</span><span class="p">:</span> <span class="n">List</span></em>, <em class="sig-param"><span class="n">shifted_cols_header</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; pandas.core.frame.DataFrame<a class="headerlink" href="#abstract_importer.AbstractImporter.compute_row_delta_sigle_samples_frame" title="Permalink to this definition">¶</a></dt>
-<dd><p>Computes the difference between each value present in th time column.
-Copies and shift by one position up all the values present in the remaining columns.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sample_frame</strong> (<em>pandas.Dataframe</em>) – the traj to be processed</p></li>
-<li><p><strong>columns_header</strong> (<em>List</em>) – the original header of sample_frame</p></li>
-<li><p><strong>shifted_cols_header</strong> (<em>List</em>) – a copy of columns_header with changed names of the contents</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The processed dataframe</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>pandas.Dataframe</p>
-</dd>
-</dl>
-<div class="admonition warning">
-<p class="admonition-title">Warning</p>
-<p>the Dataframe <code class="docutils literal notranslate"><span class="pre">sample_frame</span></code> has to follow the column structure of this header:
-Header of sample_frame = [Time | Variable values]</p>
-</div>
-</dd></dl>
-
-<dl class="py method">
-<dt id="abstract_importer.AbstractImporter.concatenated_samples">
-<em class="property">property </em><code class="sig-name descname">concatenated_samples</code><a class="headerlink" href="#abstract_importer.AbstractImporter.concatenated_samples" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="abstract_importer.AbstractImporter.dataset_id">
-<em class="property">abstract </em><code class="sig-name descname">dataset_id</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; object<a class="headerlink" href="#abstract_importer.AbstractImporter.dataset_id" title="Permalink to this definition">¶</a></dt>
-<dd><p>If the original dataset contains multiple dataset, this method returns a unique id to identify the current
-dataset</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="abstract_importer.AbstractImporter.file_path">
-<em class="property">property </em><code class="sig-name descname">file_path</code><a class="headerlink" href="#abstract_importer.AbstractImporter.file_path" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
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-<em class="property">abstract </em><code class="sig-name descname">import_data</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#abstract_importer.AbstractImporter.import_data" title="Permalink to this definition">¶</a></dt>
-<dd><p>Imports all the trajectories, variables cardinalities, and net edges.</p>
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-as Pandas Dataframes with the following structure:
-Header of _df_structure = [From_Node | To_Node]
-Header of _df_variables = [Variable_Label | Variable_Cardinality]</p>
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-<p>See :class:<code class="docutils literal notranslate"><span class="pre">JsonImporter</span></code> for an example of implementation of this method.</p>
-</div>
-</dd></dl>
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documentation/_build/html/rst/cache.html

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-<li><a class="reference internal" href="#">cache module</a></li>
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-  <div class="section" id="module-cache">
-<span id="cache-module"></span><h1>cache module<a class="headerlink" href="#module-cache" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="cache.Cache">
-<em class="property">class </em><code class="sig-prename descclassname">cache.</code><code class="sig-name descname">Cache</code><a class="headerlink" href="#cache.Cache" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>This class acts as a cache of <code class="docutils literal notranslate"><span class="pre">SetOfCims</span></code> objects for a node.</p>
-<dl class="field-list simple">
-<dt class="field-odd">_list_of_sets_of_parents</dt>
-<dd class="field-odd"><p>a list of <code class="docutils literal notranslate"><span class="pre">Sets</span></code> objects of the parents to which the cim in cache at SAME
-index is related</p>
-</dd>
-<dt class="field-even">_actual_cache</dt>
-<dd class="field-even"><p>a list of setOfCims objects</p>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="cache.Cache.clear">
-<code class="sig-name descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#cache.Cache.clear" title="Permalink to this definition">¶</a></dt>
-<dd><p>Clear the contents both of <code class="docutils literal notranslate"><span class="pre">_actual_cache</span></code> and <code class="docutils literal notranslate"><span class="pre">_list_of_sets_of_parents</span></code>.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="cache.Cache.find">
-<code class="sig-name descname">find</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">parents_comb</span><span class="p">:</span> <span class="n">Set</span></em><span class="sig-paren">)</span> &#x2192; <a class="reference internal" href="set_of_cims.html#set_of_cims.SetOfCims" title="set_of_cims.SetOfCims">set_of_cims.SetOfCims</a><a class="headerlink" href="#cache.Cache.find" title="Permalink to this definition">¶</a></dt>
-<dd><p>Tries to find in cache given the symbolic parents combination <code class="docutils literal notranslate"><span class="pre">parents_comb</span></code> the <code class="docutils literal notranslate"><span class="pre">SetOfCims</span></code>
-related to that <code class="docutils literal notranslate"><span class="pre">parents_comb</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>parents_comb</strong> (<em>Set</em>) – the parents related to that <code class="docutils literal notranslate"><span class="pre">SetOfCims</span></code></p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A <code class="docutils literal notranslate"><span class="pre">SetOfCims</span></code> object if the <code class="docutils literal notranslate"><span class="pre">parents_comb</span></code> index is found in <code class="docutils literal notranslate"><span class="pre">_list_of_sets_of_parents</span></code>.
-None otherwise.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="set_of_cims.html#set_of_cims.SetOfCims" title="set_of_cims.SetOfCims">SetOfCims</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="cache.Cache.put">
-<code class="sig-name descname">put</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">parents_comb</span><span class="p">:</span> <span class="n">Set</span></em>, <em class="sig-param"><span class="n">socim</span><span class="p">:</span> <span class="n"><a class="reference internal" href="set_of_cims.html#set_of_cims.SetOfCims" title="set_of_cims.SetOfCims">set_of_cims.SetOfCims</a></span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#cache.Cache.put" title="Permalink to this definition">¶</a></dt>
-<dd><p>Place in cache the <code class="docutils literal notranslate"><span class="pre">SetOfCims</span></code> object, and the related symbolic index <code class="docutils literal notranslate"><span class="pre">parents_comb</span></code> in
-<code class="docutils literal notranslate"><span class="pre">_list_of_sets_of_parents</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>parents_comb</strong> (<em>Set</em>) – the symbolic set index</p></li>
-<li><p><strong>socim</strong> (<a class="reference internal" href="set_of_cims.html#set_of_cims.SetOfCims" title="set_of_cims.SetOfCims"><em>SetOfCims</em></a>) – the related SetOfCims object</p></li>
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documentation/_build/html/rst/conditional_intensity_matrix.html

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-  <div class="section" id="module-conditional_intensity_matrix">
-<span id="conditional-intensity-matrix-module"></span><h1>conditional_intensity_matrix module<a class="headerlink" href="#module-conditional_intensity_matrix" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="conditional_intensity_matrix.ConditionalIntensityMatrix">
-<em class="property">class </em><code class="sig-prename descclassname">conditional_intensity_matrix.</code><code class="sig-name descname">ConditionalIntensityMatrix</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">state_residence_times</span><span class="p">:</span> <span class="n">numpy.array</span></em>, <em class="sig-param"><span class="n">state_transition_matrix</span><span class="p">:</span> <span class="n">numpy.array</span></em><span class="sig-paren">)</span><a class="headerlink" href="#conditional_intensity_matrix.ConditionalIntensityMatrix" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Abstracts the Conditional Intesity matrix of a node as aggregation of the state residence times vector
-and state transition matrix and the actual CIM matrix.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>state_residence_times</strong> (<em>numpy.array</em>) – state residence times vector</p></li>
-<li><p><strong>state_transition_matrix</strong> (<em>numpy.ndArray</em>) – the transitions count matrix</p></li>
-</ul>
-</dd>
-<dt class="field-even">_cim</dt>
-<dd class="field-even"><p>the actual cim of the node</p>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="conditional_intensity_matrix.ConditionalIntensityMatrix.cim">
-<em class="property">property </em><code class="sig-name descname">cim</code><a class="headerlink" href="#conditional_intensity_matrix.ConditionalIntensityMatrix.cim" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="conditional_intensity_matrix.ConditionalIntensityMatrix.compute_cim_coefficients">
-<code class="sig-name descname">compute_cim_coefficients</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#conditional_intensity_matrix.ConditionalIntensityMatrix.compute_cim_coefficients" title="Permalink to this definition">¶</a></dt>
-<dd><p>Compute the coefficients of the matrix _cim by using the following equality q_xx’ = M[x, x’] / T[x].
-The class member <code class="docutils literal notranslate"><span class="pre">_cim</span></code> will contain the computed cim</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="conditional_intensity_matrix.ConditionalIntensityMatrix.state_residence_times">
-<em class="property">property </em><code class="sig-name descname">state_residence_times</code><a class="headerlink" href="#conditional_intensity_matrix.ConditionalIntensityMatrix.state_residence_times" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="conditional_intensity_matrix.ConditionalIntensityMatrix.state_transition_matrix">
-<em class="property">property </em><code class="sig-name descname">state_transition_matrix</code><a class="headerlink" href="#conditional_intensity_matrix.ConditionalIntensityMatrix.state_transition_matrix" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
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-  <div class="section" id="module-json_importer">
-<span id="json-importer-module"></span><h1>json_importer module<a class="headerlink" href="#module-json_importer" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="json_importer.JsonImporter">
-<em class="property">class </em><code class="sig-prename descclassname">json_importer.</code><code class="sig-name descname">JsonImporter</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">file_path</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">samples_label</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">structure_label</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">variables_label</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">time_key</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">variables_key</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">array_indx</span><span class="p">:</span> <span class="n">int</span></em><span class="sig-paren">)</span><a class="headerlink" href="#json_importer.JsonImporter" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference internal" href="abstract_importer.html#abstract_importer.AbstractImporter" title="abstract_importer.AbstractImporter"><code class="xref py py-class docutils literal notranslate"><span class="pre">abstract_importer.AbstractImporter</span></code></a></p>
-<p>Implements the abstracts methods of AbstractImporter and adds all the necessary methods to process and prepare the data in json ext.
-with the following structure:
-[0]</p>
-<blockquote>
-<div><p><a href="#id1"><span class="problematic" id="id2">|</span></a>_ dyn.cims
-<a href="#id3"><span class="problematic" id="id4">|</span></a>_ dyn.str
-<a href="#id5"><span class="problematic" id="id6">|</span></a>_ samples
-<a href="#id7"><span class="problematic" id="id8">|</span></a>_ variabels</p>
-</div></blockquote>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>file_path</strong> (<em>string</em>) – the path of the file that contains tha data to be imported</p></li>
-<li><p><strong>samples_label</strong> (<em>string</em>) – the reference key for the samples in the trajectories</p></li>
-<li><p><strong>structure_label</strong> (<em>string</em>) – the reference key for the structure of the network data</p></li>
-<li><p><strong>variables_label</strong> (<em>string</em>) – the reference key for the cardinalites of the nodes data</p></li>
-<li><p><strong>time_key</strong> (<em>string</em>) – the key used to identify the timestamps in each trajectory</p></li>
-<li><p><strong>variables_key</strong> (<em>string</em>) – the key used to identify the names of the variables in the net</p></li>
-<li><p><strong>array_indx</strong> (<em>int</em>) – the index of the outer JsonArray to exctract the data from</p></li>
-</ul>
-</dd>
-<dt class="field-even">_df_samples_list</dt>
-<dd class="field-even"><p>a Dataframe list in which every dataframe contains a trajectory</p>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="json_importer.JsonImporter.build_sorter">
-<code class="sig-name descname">build_sorter</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">sample_frame</span><span class="p">:</span> <span class="n">pandas.core.frame.DataFrame</span></em><span class="sig-paren">)</span> &#x2192; List<a class="headerlink" href="#json_importer.JsonImporter.build_sorter" title="Permalink to this definition">¶</a></dt>
-<dd><p>Implements the abstract method build_sorter of the <code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractImporter</span></code> for this dataset</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="json_importer.JsonImporter.clear_data_frame_list">
-<code class="sig-name descname">clear_data_frame_list</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#json_importer.JsonImporter.clear_data_frame_list" title="Permalink to this definition">¶</a></dt>
-<dd><p>Removes all values present in the dataframes in the list <code class="docutils literal notranslate"><span class="pre">_df_samples_list</span></code>.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="json_importer.JsonImporter.dataset_id">
-<code class="sig-name descname">dataset_id</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; object<a class="headerlink" href="#json_importer.JsonImporter.dataset_id" title="Permalink to this definition">¶</a></dt>
-<dd><p>If the original dataset contains multiple dataset, this method returns a unique id to identify the current
-dataset</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="json_importer.JsonImporter.import_data">
-<code class="sig-name descname">import_data</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#json_importer.JsonImporter.import_data" title="Permalink to this definition">¶</a></dt>
-<dd><p>Implements the abstract method of <code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractImporter</span></code></p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="json_importer.JsonImporter.import_sampled_cims">
-<code class="sig-name descname">import_sampled_cims</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">raw_data</span><span class="p">:</span> <span class="n">List</span></em>, <em class="sig-param"><span class="n">indx</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">cims_key</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; Dict<a class="headerlink" href="#json_importer.JsonImporter.import_sampled_cims" title="Permalink to this definition">¶</a></dt>
-<dd><p>Imports the synthetic CIMS in the dataset in a dictionary, using variables labels
-as keys for the set of CIMS of a particular node.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>raw_data</strong> (<em>List</em>) – List of Dicts</p></li>
-<li><p><strong>indx</strong> (<em>int</em>) – The index of the array from which the data have to be extracted</p></li>
-<li><p><strong>cims_key</strong> (<em>string</em>) – the key where the json object cims are placed</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>a dictionary containing the sampled CIMS for all the variables in the net</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>Dictionary</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="json_importer.JsonImporter.import_structure">
-<code class="sig-name descname">import_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">raw_data</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; pandas.core.frame.DataFrame<a class="headerlink" href="#json_importer.JsonImporter.import_structure" title="Permalink to this definition">¶</a></dt>
-<dd><p>Imports in a dataframe the data in the list raw_data at the key <code class="docutils literal notranslate"><span class="pre">_structure_label</span></code></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>raw_data</strong> (<em>List</em>) – List of Dicts</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Dataframe containg the starting node a ending node of every arc of the network</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>pandas.Dataframe</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="json_importer.JsonImporter.import_trajectories">
-<code class="sig-name descname">import_trajectories</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">raw_data</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; List<a class="headerlink" href="#json_importer.JsonImporter.import_trajectories" title="Permalink to this definition">¶</a></dt>
-<dd><p>Imports the trajectories from the list of dicts <code class="docutils literal notranslate"><span class="pre">raw_data</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>raw_data</strong> (<em>List</em>) – List of Dicts</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>List of dataframes containing all the trajectories</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>List</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="json_importer.JsonImporter.import_variables">
-<code class="sig-name descname">import_variables</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">raw_data</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; pandas.core.frame.DataFrame<a class="headerlink" href="#json_importer.JsonImporter.import_variables" title="Permalink to this definition">¶</a></dt>
-<dd><p>Imports the data in <code class="docutils literal notranslate"><span class="pre">raw_data</span></code> at the key <code class="docutils literal notranslate"><span class="pre">_variables_label</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>raw_data</strong> (<em>List</em>) – List of Dicts</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Datframe containg the variables simbolic labels and their cardinalities</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>pandas.Dataframe</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="json_importer.JsonImporter.normalize_trajectories">
-<code class="sig-name descname">normalize_trajectories</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">raw_data</span><span class="p">:</span> <span class="n">List</span></em>, <em class="sig-param"><span class="n">indx</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">trajectories_key</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; List<a class="headerlink" href="#json_importer.JsonImporter.normalize_trajectories" title="Permalink to this definition">¶</a></dt>
-<dd><p>Extracts the trajectories in <code class="docutils literal notranslate"><span class="pre">raw_data</span></code> at the index <code class="docutils literal notranslate"><span class="pre">index</span></code> at the key <code class="docutils literal notranslate"><span class="pre">trajectories</span> <span class="pre">key</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>raw_data</strong> (<em>List</em>) – List of Dicts</p></li>
-<li><p><strong>indx</strong> (<em>int</em>) – The index of the array from which the data have to be extracted</p></li>
-<li><p><strong>trajectories_key</strong> (<em>string</em>) – the key of the trajectories objects</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A list of daframes containg the trajectories</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>List</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="json_importer.JsonImporter.one_level_normalizing">
-<code class="sig-name descname">one_level_normalizing</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">raw_data</span><span class="p">:</span> <span class="n">List</span></em>, <em class="sig-param"><span class="n">indx</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">key</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; pandas.core.frame.DataFrame<a class="headerlink" href="#json_importer.JsonImporter.one_level_normalizing" title="Permalink to this definition">¶</a></dt>
-<dd><p>Extracts the one-level nested data in the list <code class="docutils literal notranslate"><span class="pre">raw_data</span></code> at the index <code class="docutils literal notranslate"><span class="pre">indx</span></code> at the key <code class="docutils literal notranslate"><span class="pre">key</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>raw_data</strong> (<em>List</em>) – List of Dicts</p></li>
-<li><p><strong>indx</strong> (<em>int</em>) – The index of the array from which the data have to be extracted</p></li>
-<li><p><strong>key</strong> (<em>string</em>) – the key for the Dicts from which exctract data</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A normalized dataframe</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>pandas.Datframe</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="json_importer.JsonImporter.read_json_file">
-<code class="sig-name descname">read_json_file</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; List<a class="headerlink" href="#json_importer.JsonImporter.read_json_file" title="Permalink to this definition">¶</a></dt>
-<dd><p>Reads the JSON file in the path self.filePath</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The contents of the json file</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p>List</p>
-</dd>
-</dl>
-</dd></dl>
-
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-  <div class="section" id="module-network_graph">
-<span id="network-graph-module"></span><h1>network_graph module<a class="headerlink" href="#module-network_graph" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="network_graph.NetworkGraph">
-<em class="property">class </em><code class="sig-prename descclassname">network_graph.</code><code class="sig-name descname">NetworkGraph</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">graph_struct</span><span class="p">:</span> <span class="n"><a class="reference internal" href="structure.html#structure.Structure" title="structure.Structure">structure.Structure</a></span></em><span class="sig-paren">)</span><a class="headerlink" href="#network_graph.NetworkGraph" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Abstracts the infos contained in the Structure class in the form of a directed graph.
-Has the task of creating all the necessary filtering and indexing structures for parameters estimation</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>graph_struct</strong> (<a class="reference internal" href="structure.html#structure.Structure" title="structure.Structure"><em>Structure</em></a>) – the <code class="docutils literal notranslate"><span class="pre">Structure</span></code> object from which infos about the net will be extracted</p>
-</dd>
-<dt class="field-even">_graph</dt>
-<dd class="field-even"><p>directed graph</p>
-</dd>
-<dt class="field-odd">_aggregated_info_about_nodes_parents</dt>
-<dd class="field-odd"><p>a structure that contains all the necessary infos
-about every parents of the node of which all the indexing and filtering structures will be constructed.</p>
-</dd>
-<dt class="field-even">_time_scalar_indexing_structure</dt>
-<dd class="field-even"><p>the indexing structure for state res time estimation</p>
-</dd>
-<dt class="field-odd">_transition_scalar_indexing_structure</dt>
-<dd class="field-odd"><p>the indexing structure for transition computation</p>
-</dd>
-<dt class="field-even">_time_filtering</dt>
-<dd class="field-even"><p>the columns filtering structure used in the computation of the state res times</p>
-</dd>
-<dt class="field-odd">_transition_filtering</dt>
-<dd class="field-odd"><p>the columns filtering structure used in the computation of the transition
-from one state to another</p>
-</dd>
-<dt class="field-even">_p_combs_structure</dt>
-<dd class="field-even"><p>all the possible parents states combination for the node of interest</p>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.add_edges">
-<code class="sig-name descname">add_edges</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">list_of_edges</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#network_graph.NetworkGraph.add_edges" title="Permalink to this definition">¶</a></dt>
-<dd><p>Add the edges to the <code class="docutils literal notranslate"><span class="pre">_graph</span></code> contained in the list <code class="docutils literal notranslate"><span class="pre">list_of_edges</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>list_of_edges</strong> (<em>List</em>) – the list containing of tuples containing the edges</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.add_nodes">
-<code class="sig-name descname">add_nodes</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">list_of_nodes</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#network_graph.NetworkGraph.add_nodes" title="Permalink to this definition">¶</a></dt>
-<dd><p>Adds the nodes to the <code class="docutils literal notranslate"><span class="pre">_graph</span></code> contained in the list of nodes <code class="docutils literal notranslate"><span class="pre">list_of_nodes</span></code>.
-Sets all the properties that identify a nodes (index, positional index, cardinality)</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>list_of_nodes</strong> (<em>List</em>) – the nodes to add to <code class="docutils literal notranslate"><span class="pre">_graph</span></code></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.build_p_comb_structure_for_a_node">
-<code class="sig-name descname">build_p_comb_structure_for_a_node</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">parents_values</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; numpy.ndarray<a class="headerlink" href="#network_graph.NetworkGraph.build_p_comb_structure_for_a_node" title="Permalink to this definition">¶</a></dt>
-<dd><p>Builds the combinatorial structure that contains the combinations of all the values contained in
-<code class="docutils literal notranslate"><span class="pre">parents_values</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>parents_values</strong> (<em>List</em>) – the cardinalities of the nodes</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A numpy matrix containing a grid of the combinations</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>numpy.ndArray</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.build_time_columns_filtering_for_a_node">
-<code class="sig-name descname">build_time_columns_filtering_for_a_node</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_indx</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">p_indxs</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; numpy.ndarray<a class="headerlink" href="#network_graph.NetworkGraph.build_time_columns_filtering_for_a_node" title="Permalink to this definition">¶</a></dt>
-<dd><p>Builds the necessary structure to filter the desired columns indicated by <code class="docutils literal notranslate"><span class="pre">node_indx</span></code> and <code class="docutils literal notranslate"><span class="pre">p_indxs</span></code>
-in the dataset.
-This structute will be used in the computation of the state res times.
-:param node_indx: the index of the node
-:type node_indx: int
-:param p_indxs: the indexes of the node’s parents
-:type p_indxs: List
-:return: The filtering structure for times estimation
-:rtype: numpy.ndArray</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.build_time_scalar_indexing_structure_for_a_node">
-<code class="sig-name descname">build_time_scalar_indexing_structure_for_a_node</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">parents_vals</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; numpy.ndarray<a class="headerlink" href="#network_graph.NetworkGraph.build_time_scalar_indexing_structure_for_a_node" title="Permalink to this definition">¶</a></dt>
-<dd><p>Builds an indexing structure for the computation of state residence times values.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>node_id</strong> (<em>string</em>) – the node label</p></li>
-<li><p><strong>parents_vals</strong> (<em>List</em>) – the caridinalites of the node’s parents</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The time indexing structure</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>numpy.ndArray</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.build_transition_filtering_for_a_node">
-<code class="sig-name descname">build_transition_filtering_for_a_node</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_indx</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">p_indxs</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; numpy.ndarray<a class="headerlink" href="#network_graph.NetworkGraph.build_transition_filtering_for_a_node" title="Permalink to this definition">¶</a></dt>
-<dd><p>Builds the necessary structure to filter the desired columns indicated by <code class="docutils literal notranslate"><span class="pre">node_indx</span></code> and <code class="docutils literal notranslate"><span class="pre">p_indxs</span></code>
-in the dataset.
-This structure will be used in the computation of the state transitions values.
-:param node_indx: the index of the node
-:type node_indx: int
-:param p_indxs: the indexes of the node’s parents
-:type p_indxs: List
-:return: The filtering structure for transitions estimation
-:rtype: numpy.ndArray</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.build_transition_scalar_indexing_structure_for_a_node">
-<code class="sig-name descname">build_transition_scalar_indexing_structure_for_a_node</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">parents_vals</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; numpy.ndarray<a class="headerlink" href="#network_graph.NetworkGraph.build_transition_scalar_indexing_structure_for_a_node" title="Permalink to this definition">¶</a></dt>
-<dd><p>Builds an indexing structure for the computation of state transitions values.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>node_id</strong> (<em>string</em>) – the node label</p></li>
-<li><p><strong>parents_vals</strong> (<em>List</em>) – the caridinalites of the node’s parents</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The transition indexing structure</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>numpy.ndArray</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.edges">
-<em class="property">property </em><code class="sig-name descname">edges</code><a class="headerlink" href="#network_graph.NetworkGraph.edges" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.fast_init">
-<code class="sig-name descname">fast_init</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#network_graph.NetworkGraph.fast_init" title="Permalink to this definition">¶</a></dt>
-<dd><p>Initializes all the necessary structures for parameters estimation of the node identified by the label
-node_id</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>node_id</strong> (<em>string</em>) – the label of the node</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.get_node_indx">
-<code class="sig-name descname">get_node_indx</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span></em><span class="sig-paren">)</span> &#x2192; int<a class="headerlink" href="#network_graph.NetworkGraph.get_node_indx" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.get_ordered_by_indx_set_of_parents">
-<code class="sig-name descname">get_ordered_by_indx_set_of_parents</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; Tuple<a class="headerlink" href="#network_graph.NetworkGraph.get_ordered_by_indx_set_of_parents" title="Permalink to this definition">¶</a></dt>
-<dd><p>Builds the aggregated structure that holds all the infos relative to the parent set of the node, namely
-(parents_labels, parents_indexes, parents_cardinalities).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>node</strong> (<em>string</em>) – the label of the node</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>a tuple containing all the parent set infos</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>Tuple</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.get_parents_by_id">
-<code class="sig-name descname">get_parents_by_id</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span></em><span class="sig-paren">)</span> &#x2192; List<a class="headerlink" href="#network_graph.NetworkGraph.get_parents_by_id" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a list of labels of the parents of the node <code class="docutils literal notranslate"><span class="pre">node_id</span></code></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>node_id</strong> (<em>string</em>) – the node label</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>a List of labels of the parents</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>List</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.get_positional_node_indx">
-<code class="sig-name descname">get_positional_node_indx</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span></em><span class="sig-paren">)</span> &#x2192; int<a class="headerlink" href="#network_graph.NetworkGraph.get_positional_node_indx" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.get_states_number">
-<code class="sig-name descname">get_states_number</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span></em><span class="sig-paren">)</span> &#x2192; int<a class="headerlink" href="#network_graph.NetworkGraph.get_states_number" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.nodes">
-<em class="property">property </em><code class="sig-name descname">nodes</code><a class="headerlink" href="#network_graph.NetworkGraph.nodes" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="network_graph.NetworkGraph.nodes_indexes">
-<em class="property">property </em><code class="sig-name descname">nodes_indexes</code><a class="headerlink" href="#network_graph.NetworkGraph.nodes_indexes" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
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-<dt id="network_graph.NetworkGraph.nodes_values">
-<em class="property">property </em><code class="sig-name descname">nodes_values</code><a class="headerlink" href="#network_graph.NetworkGraph.nodes_values" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
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-<em class="property">property </em><code class="sig-name descname">p_combs</code><a class="headerlink" href="#network_graph.NetworkGraph.p_combs" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
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-<dt id="network_graph.NetworkGraph.time_filtering">
-<em class="property">property </em><code class="sig-name descname">time_filtering</code><a class="headerlink" href="#network_graph.NetworkGraph.time_filtering" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
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-<em class="property">property </em><code class="sig-name descname">time_scalar_indexing_strucure</code><a class="headerlink" href="#network_graph.NetworkGraph.time_scalar_indexing_strucure" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
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-<dd></dd></dl>
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documentation/_build/html/rst/parameters_estimator.html

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-  <div class="section" id="module-parameters_estimator">
-<span id="parameters-estimator-module"></span><h1>parameters_estimator module<a class="headerlink" href="#module-parameters_estimator" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="parameters_estimator.ParametersEstimator">
-<em class="property">class </em><code class="sig-prename descclassname">parameters_estimator.</code><code class="sig-name descname">ParametersEstimator</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">trajectories</span><span class="p">:</span> <span class="n"><a class="reference internal" href="trajectory.html#trajectory.Trajectory" title="trajectory.Trajectory">trajectory.Trajectory</a></span></em>, <em class="sig-param"><span class="n">net_graph</span><span class="p">:</span> <span class="n"><a class="reference internal" href="network_graph.html#network_graph.NetworkGraph" title="network_graph.NetworkGraph">network_graph.NetworkGraph</a></span></em><span class="sig-paren">)</span><a class="headerlink" href="#parameters_estimator.ParametersEstimator" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Has the task of computing the cims of particular node given the trajectories and the net structure
-in the graph <code class="docutils literal notranslate"><span class="pre">_net_graph</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>trajectories</strong> (<a class="reference internal" href="trajectory.html#trajectory.Trajectory" title="trajectory.Trajectory"><em>Trajectory</em></a>) – the trajectories</p></li>
-<li><p><strong>net_graph</strong> (<a class="reference internal" href="network_graph.html#network_graph.NetworkGraph" title="network_graph.NetworkGraph"><em>NetworkGraph</em></a>) – the net structure</p></li>
-</ul>
-</dd>
-<dt class="field-even">_single_set_of_cims</dt>
-<dd class="field-even"><p>the set of cims object that will hold the cims of the node</p>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="parameters_estimator.ParametersEstimator.compute_parameters_for_node">
-<code class="sig-name descname">compute_parameters_for_node</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; <a class="reference internal" href="set_of_cims.html#set_of_cims.SetOfCims" title="set_of_cims.SetOfCims">set_of_cims.SetOfCims</a><a class="headerlink" href="#parameters_estimator.ParametersEstimator.compute_parameters_for_node" title="Permalink to this definition">¶</a></dt>
-<dd><p>Compute the CIMS of the node identified by the label <code class="docutils literal notranslate"><span class="pre">node_id</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>node_id</strong> (<em>string</em>) – the node label</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A SetOfCims object filled with the computed CIMS</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="set_of_cims.html#set_of_cims.SetOfCims" title="set_of_cims.SetOfCims">SetOfCims</a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="parameters_estimator.ParametersEstimator.compute_state_res_time_for_node">
-<code class="sig-name descname">compute_state_res_time_for_node</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_indx</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">times</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">trajectory</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">cols_filter</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">scalar_indexes_struct</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">T</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#parameters_estimator.ParametersEstimator.compute_state_res_time_for_node" title="Permalink to this definition">¶</a></dt>
-<dd><p>Compute the state residence times for a node and fill the matrix <code class="docutils literal notranslate"><span class="pre">T</span></code> with the results</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>node_indx</strong> (<em>int</em>) – the index of the node</p></li>
-<li><p><strong>times</strong> (<em>numpy.array</em>) – the times deltas vector</p></li>
-<li><p><strong>trajectory</strong> (<em>numpy.ndArray</em>) – the trajectory</p></li>
-<li><p><strong>cols_filter</strong> (<em>numpy.array</em>) – the columns filtering structure</p></li>
-<li><p><strong>scalar_indexes_struct</strong> (<em>numpy.array</em>) – the indexing structure</p></li>
-<li><p><strong>T</strong> (<em>numpy.ndArray</em>) – the state residence times vectors</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="parameters_estimator.ParametersEstimator.compute_state_transitions_for_a_node">
-<code class="sig-name descname">compute_state_transitions_for_a_node</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_indx</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">trajectory</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">cols_filter</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">scalar_indexing</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">M</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em><span class="sig-paren">)</span><a class="headerlink" href="#parameters_estimator.ParametersEstimator.compute_state_transitions_for_a_node" title="Permalink to this definition">¶</a></dt>
-<dd><p>Compute the state residence times for a node and fill the matrices <code class="docutils literal notranslate"><span class="pre">M</span></code> with the results.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>node_indx</strong> (<em>int</em>) – the index of the node</p></li>
-<li><p><strong>trajectory</strong> (<em>numpy.ndArray</em>) – the trajectory</p></li>
-<li><p><strong>cols_filter</strong> (<em>numpy.array</em>) – the columns filtering structure</p></li>
-<li><p><strong>scalar_indexing</strong> (<em>numpy.array</em>) – the indexing structure</p></li>
-<li><p><strong>M</strong> (<em>numpy.ndArray</em>) – the state transitions matrices</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="parameters_estimator.ParametersEstimator.fast_init">
-<code class="sig-name descname">fast_init</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#parameters_estimator.ParametersEstimator.fast_init" title="Permalink to this definition">¶</a></dt>
-<dd><p>Initializes all the necessary structures for the parameters estimation for the node <code class="docutils literal notranslate"><span class="pre">node_id</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>node_id</strong> (<em>string</em>) – the node label</p>
-</dd>
-</dl>
-</dd></dl>
-
-</dd></dl>
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-  <div class="section" id="module-sample_path">
-<span id="sample-path-module"></span><h1>sample_path module<a class="headerlink" href="#module-sample_path" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="sample_path.SamplePath">
-<em class="property">class </em><code class="sig-prename descclassname">sample_path.</code><code class="sig-name descname">SamplePath</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">importer</span><span class="p">:</span> <span class="n"><a class="reference internal" href="abstract_importer.html#abstract_importer.AbstractImporter" title="abstract_importer.AbstractImporter">abstract_importer.AbstractImporter</a></span></em><span class="sig-paren">)</span><a class="headerlink" href="#sample_path.SamplePath" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Aggregates all the informations about the trajectories, the real structure of the sampled net and variables
-cardinalites. Has the task of creating the objects <code class="docutils literal notranslate"><span class="pre">Trajectory</span></code> and <code class="docutils literal notranslate"><span class="pre">Structure</span></code> that will
-contain the mentioned data.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>importer</strong> (<a class="reference internal" href="abstract_importer.html#abstract_importer.AbstractImporter" title="abstract_importer.AbstractImporter"><em>AbstractImporter</em></a>) – the Importer objects that will import ad process data</p>
-</dd>
-<dt class="field-even">_trajectories</dt>
-<dd class="field-even"><p>the <code class="docutils literal notranslate"><span class="pre">Trajectory</span></code> object that will contain all the concatenated trajectories</p>
-</dd>
-<dt class="field-odd">_structure</dt>
-<dd class="field-odd"><p>the <code class="docutils literal notranslate"><span class="pre">Structure</span></code> Object that will contain all the structurral infos about the net</p>
-</dd>
-<dt class="field-even">_total_variables_count</dt>
-<dd class="field-even"><p>the number of variables in the net</p>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="sample_path.SamplePath.build_structure">
-<code class="sig-name descname">build_structure</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#sample_path.SamplePath.build_structure" title="Permalink to this definition">¶</a></dt>
-<dd><p>Builds the <code class="docutils literal notranslate"><span class="pre">Structure</span></code> object that aggregates all the infos about the net.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="sample_path.SamplePath.build_trajectories">
-<code class="sig-name descname">build_trajectories</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#sample_path.SamplePath.build_trajectories" title="Permalink to this definition">¶</a></dt>
-<dd><p>Builds the Trajectory object that will contain all the trajectories.
-Clears all the unused dataframes in <code class="docutils literal notranslate"><span class="pre">_importer</span></code> Object</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="sample_path.SamplePath.structure">
-<em class="property">property </em><code class="sig-name descname">structure</code><a class="headerlink" href="#sample_path.SamplePath.structure" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="sample_path.SamplePath.total_variables_count">
-<em class="property">property </em><code class="sig-name descname">total_variables_count</code><a class="headerlink" href="#sample_path.SamplePath.total_variables_count" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="sample_path.SamplePath.trajectories">
-<em class="property">property </em><code class="sig-name descname">trajectories</code><a class="headerlink" href="#sample_path.SamplePath.trajectories" title="Permalink to this definition">¶</a></dt>
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documentation/_build/html/rst/set_of_cims.html

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-  <div class="section" id="module-set_of_cims">
-<span id="set-of-cims-module"></span><h1>set_of_cims module<a class="headerlink" href="#module-set_of_cims" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="set_of_cims.SetOfCims">
-<em class="property">class </em><code class="sig-prename descclassname">set_of_cims.</code><code class="sig-name descname">SetOfCims</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">parents_states_number</span><span class="p">:</span> <span class="n">List</span></em>, <em class="sig-param"><span class="n">node_states_number</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">p_combs</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em><span class="sig-paren">)</span><a class="headerlink" href="#set_of_cims.SetOfCims" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Aggregates all the CIMS of the node identified by the label _node_id.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>node_id</strong> – the node label</p></li>
-<li><p><strong>parents_states_number</strong> (<em>List</em>) – the cardinalities of the parents</p></li>
-<li><p><strong>node_states_number</strong> (<em>int</em>) – the caridinality of the node</p></li>
-<li><p><strong>p_combs</strong> (<em>numpy.ndArray</em>) – the p_comb structure bound to this node</p></li>
-</ul>
-</dd>
-<dt class="field-even">_state_residence_time</dt>
-<dd class="field-even"><p>matrix containing all the state residence time vectors for the node</p>
-</dd>
-<dt class="field-odd">_transition_matrices</dt>
-<dd class="field-odd"><p>matrix containing all the transition matrices for the node</p>
-</dd>
-<dt class="field-even">_actual_cims</dt>
-<dd class="field-even"><p>the cims of the node</p>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="set_of_cims.SetOfCims.actual_cims">
-<em class="property">property </em><code class="sig-name descname">actual_cims</code><a class="headerlink" href="#set_of_cims.SetOfCims.actual_cims" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="set_of_cims.SetOfCims.build_cims">
-<code class="sig-name descname">build_cims</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">state_res_times</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">transition_matrices</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#set_of_cims.SetOfCims.build_cims" title="Permalink to this definition">¶</a></dt>
-<dd><p>Build the <code class="docutils literal notranslate"><span class="pre">ConditionalIntensityMatrix</span></code> objects given the state residence times and transitions matrices.
-Compute the cim coefficients.The class member <code class="docutils literal notranslate"><span class="pre">_actual_cims</span></code> will contain the computed cims.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>state_res_times</strong> (<em>numpy.ndArray</em>) – the state residence times matrix</p></li>
-<li><p><strong>transition_matrices</strong> (<em>numpy.ndArray</em>) – the transition matrices</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="set_of_cims.SetOfCims.build_times_and_transitions_structures">
-<code class="sig-name descname">build_times_and_transitions_structures</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#set_of_cims.SetOfCims.build_times_and_transitions_structures" title="Permalink to this definition">¶</a></dt>
-<dd><p>Initializes at the correct dimensions the state residence times matrix and the state transition matrices.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="set_of_cims.SetOfCims.filter_cims_with_mask">
-<code class="sig-name descname">filter_cims_with_mask</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">mask_arr</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">comb</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; numpy.ndarray<a class="headerlink" href="#set_of_cims.SetOfCims.filter_cims_with_mask" title="Permalink to this definition">¶</a></dt>
-<dd><p>Filter the cims contained in the array <code class="docutils literal notranslate"><span class="pre">_actual_cims</span></code> given the boolean mask <code class="docutils literal notranslate"><span class="pre">mask_arr</span></code> and the index
-<code class="docutils literal notranslate"><span class="pre">comb</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mask_arr</strong> (<em>numpy.array</em>) – the boolean mask that indicates which parent to consider</p></li>
-<li><p><strong>comb</strong> (<em>numpy.array</em>) – the state/s of the filtered parents</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Array of <code class="docutils literal notranslate"><span class="pre">ConditionalIntensityMatrix</span></code> objects</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>numpy.array</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="set_of_cims.SetOfCims.get_cims_number">
-<code class="sig-name descname">get_cims_number</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#set_of_cims.SetOfCims.get_cims_number" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="set_of_cims.SetOfCims.p_combs">
-<em class="property">property </em><code class="sig-name descname">p_combs</code><a class="headerlink" href="#set_of_cims.SetOfCims.p_combs" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
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documentation/_build/html/rst/structure.html

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-  <div class="section" id="module-structure">
-<span id="structure-module"></span><h1>structure module<a class="headerlink" href="#module-structure" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="structure.Structure">
-<em class="property">class </em><code class="sig-prename descclassname">structure.</code><code class="sig-name descname">Structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">nodes_labels_list</span><span class="p">:</span> <span class="n">List</span></em>, <em class="sig-param"><span class="n">nodes_indexes_arr</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">nodes_vals_arr</span><span class="p">:</span> <span class="n">numpy.ndarray</span></em>, <em class="sig-param"><span class="n">edges_list</span><span class="p">:</span> <span class="n">List</span></em>, <em class="sig-param"><span class="n">total_variables_number</span><span class="p">:</span> <span class="n">int</span></em><span class="sig-paren">)</span><a class="headerlink" href="#structure.Structure" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Contains all the infos about the network structure(nodes labels, nodes caridinalites, edges, indexes)</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>nodes_labels_list</strong> (<em>List</em>) – the symbolic names of the variables</p></li>
-<li><p><strong>nodes_indexes_arr</strong> (<em>numpy.ndArray</em>) – the indexes of the nodes</p></li>
-<li><p><strong>nodes_vals_arr</strong> (<em>numpy.ndArray</em>) – the cardinalites of the nodes</p></li>
-<li><p><strong>edges_list</strong> (<em>List</em>) – the edges of the network</p></li>
-<li><p><strong>total_variables_number</strong> (<em>int</em>) – the total number of variables in the net</p></li>
-</ul>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="structure.Structure.edges">
-<em class="property">property </em><code class="sig-name descname">edges</code><a class="headerlink" href="#structure.Structure.edges" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="structure.Structure.get_node_id">
-<code class="sig-name descname">get_node_id</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_indx</span><span class="p">:</span> <span class="n">int</span></em><span class="sig-paren">)</span> &#x2192; str<a class="headerlink" href="#structure.Structure.get_node_id" title="Permalink to this definition">¶</a></dt>
-<dd><p>Given the <code class="docutils literal notranslate"><span class="pre">node_index</span></code> returns the node label.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>node_indx</strong> (<em>int</em>) – the node index</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>the node label</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>string</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="structure.Structure.get_node_indx">
-<code class="sig-name descname">get_node_indx</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; int<a class="headerlink" href="#structure.Structure.get_node_indx" title="Permalink to this definition">¶</a></dt>
-<dd><p>Given the <code class="docutils literal notranslate"><span class="pre">node_index</span></code> returns the node label.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>node_id</strong> (<em>string</em>) – the node label</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>the node index</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>int</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="structure.Structure.get_positional_node_indx">
-<code class="sig-name descname">get_positional_node_indx</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_id</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; int<a class="headerlink" href="#structure.Structure.get_positional_node_indx" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="structure.Structure.get_states_number">
-<code class="sig-name descname">get_states_number</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; int<a class="headerlink" href="#structure.Structure.get_states_number" title="Permalink to this definition">¶</a></dt>
-<dd><p>Given the node label <code class="docutils literal notranslate"><span class="pre">node</span></code> returns the cardinality of the node.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>node</strong> (<em>string</em>) – the node label</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>the node cardinality</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>int</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="structure.Structure.nodes_indexes">
-<em class="property">property </em><code class="sig-name descname">nodes_indexes</code><a class="headerlink" href="#structure.Structure.nodes_indexes" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="structure.Structure.nodes_labels">
-<em class="property">property </em><code class="sig-name descname">nodes_labels</code><a class="headerlink" href="#structure.Structure.nodes_labels" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="structure.Structure.nodes_values">
-<em class="property">property </em><code class="sig-name descname">nodes_values</code><a class="headerlink" href="#structure.Structure.nodes_values" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="structure.Structure.total_variables_number">
-<em class="property">property </em><code class="sig-name descname">total_variables_number</code><a class="headerlink" href="#structure.Structure.total_variables_number" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
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-  <div class="section" id="module-structure_estimator">
-<span id="structure-estimator-module"></span><h1>structure_estimator module<a class="headerlink" href="#module-structure_estimator" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="structure_estimator.StructureEstimator">
-<em class="property">class </em><code class="sig-prename descclassname">structure_estimator.</code><code class="sig-name descname">StructureEstimator</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">sample_path</span><span class="p">:</span> <span class="n"><a class="reference internal" href="sample_path.html#sample_path.SamplePath" title="sample_path.SamplePath">sample_path.SamplePath</a></span></em>, <em class="sig-param"><span class="n">exp_test_alfa</span><span class="p">:</span> <span class="n">float</span></em>, <em class="sig-param"><span class="n">chi_test_alfa</span><span class="p">:</span> <span class="n">float</span></em><span class="sig-paren">)</span><a class="headerlink" href="#structure_estimator.StructureEstimator" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Has the task of estimating the network structure given the trajectories in <code class="docutils literal notranslate"><span class="pre">samplepath</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sample_path</strong> (<a class="reference internal" href="sample_path.html#sample_path.SamplePath" title="sample_path.SamplePath"><em>SamplePath</em></a>) – the _sample_path object containing the trajectories and the real structure</p></li>
-<li><p><strong>exp_test_alfa</strong> (<em>float</em>) – the significance level for the exponential Hp test</p></li>
-<li><p><strong>chi_test_alfa</strong> (<em>float</em>) – the significance level for the chi Hp test</p></li>
-</ul>
-</dd>
-<dt class="field-even">_nodes</dt>
-<dd class="field-even"><p>the nodes labels</p>
-</dd>
-<dt class="field-odd">_nodes_vals</dt>
-<dd class="field-odd"><p>the nodes cardinalities</p>
-</dd>
-<dt class="field-even">_nodes_indxs</dt>
-<dd class="field-even"><p>the nodes indexes</p>
-</dd>
-<dt class="field-odd">_complete_graph</dt>
-<dd class="field-odd"><p>the complete directed graph built using the nodes labels in <code class="docutils literal notranslate"><span class="pre">_nodes</span></code></p>
-</dd>
-<dt class="field-even">_cache</dt>
-<dd class="field-even"><p>the Cache object</p>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="structure_estimator.StructureEstimator.build_complete_graph">
-<code class="sig-name descname">build_complete_graph</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">node_ids</span><span class="p">:</span> <span class="n">List</span></em><span class="sig-paren">)</span> &#x2192; networkx.classes.digraph.DiGraph<a class="headerlink" href="#structure_estimator.StructureEstimator.build_complete_graph" title="Permalink to this definition">¶</a></dt>
-<dd><p>Builds a complete directed graph (no self loops) given the nodes labels in the list <code class="docutils literal notranslate"><span class="pre">node_ids</span></code>:</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>node_ids</strong> (<em>List</em>) – the list of nodes labels</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>a complete Digraph Object</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>networkx.DiGraph</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="structure_estimator.StructureEstimator.complete_test">
-<code class="sig-name descname">complete_test</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">test_parent</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">test_child</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">parent_set</span><span class="p">:</span> <span class="n">List</span></em>, <em class="sig-param"><span class="n">child_states_numb</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">tot_vars_count</span><span class="p">:</span> <span class="n">int</span></em><span class="sig-paren">)</span> &#x2192; bool<a class="headerlink" href="#structure_estimator.StructureEstimator.complete_test" title="Permalink to this definition">¶</a></dt>
-<dd><p>Performs a complete independence test on the directed graphs G1 = {test_child U parent_set}
-G2 = {G1 U test_parent} (added as an additional parent of the test_child).
-Generates all the necessary structures and datas to perform the tests.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>test_parent</strong> (<em>string</em>) – the node label of the test parent</p></li>
-<li><p><strong>test_child</strong> (<em>string</em>) – the node label of the child</p></li>
-<li><p><strong>parent_set</strong> (<em>List</em>) – the common parent set</p></li>
-<li><p><strong>child_states_numb</strong> (<em>int</em>) – the cardinality of the <code class="docutils literal notranslate"><span class="pre">test_child</span></code></p></li>
-<li><p><strong>tot_vars_count</strong> (<em>int</em>) – the total number of variables in the net</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>True iff test_child and test_parent are independent given the sep_set parent_set. False otherwise</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>bool</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="structure_estimator.StructureEstimator.ctpc_algorithm">
-<code class="sig-name descname">ctpc_algorithm</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#structure_estimator.StructureEstimator.ctpc_algorithm" title="Permalink to this definition">¶</a></dt>
-<dd><p>Compute the CTPC algorithm over the entire net.</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="structure_estimator.StructureEstimator.generate_possible_sub_sets_of_size">
-<code class="sig-name descname">generate_possible_sub_sets_of_size</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">u</span><span class="p">:</span> <span class="n">List</span></em>, <em class="sig-param"><span class="n">size</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">parent_label</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; Iterator<a class="headerlink" href="#structure_estimator.StructureEstimator.generate_possible_sub_sets_of_size" title="Permalink to this definition">¶</a></dt>
-<dd><p>Creates a list containing all possible subsets of the list <code class="docutils literal notranslate"><span class="pre">u</span></code> of size <code class="docutils literal notranslate"><span class="pre">size</span></code>,
-that do not contains a the node identified by <code class="docutils literal notranslate"><span class="pre">parent_label</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>u</strong> (<em>List</em>) – the list of nodes</p></li>
-<li><p><strong>size</strong> (<em>int</em>) – the size of the subsets</p></li>
-<li><p><strong>parent_label</strong> (<em>string</em>) – the node to exclude in the subsets generation</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>an Iterator Object containing a list of lists</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p>Iterator</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="structure_estimator.StructureEstimator.independence_test">
-<code class="sig-name descname">independence_test</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">child_states_numb</span><span class="p">:</span> <span class="n">int</span></em>, <em class="sig-param"><span class="n">cim1</span><span class="p">:</span> <span class="n"><a class="reference internal" href="conditional_intensity_matrix.html#conditional_intensity_matrix.ConditionalIntensityMatrix" title="conditional_intensity_matrix.ConditionalIntensityMatrix">conditional_intensity_matrix.ConditionalIntensityMatrix</a></span></em>, <em class="sig-param"><span class="n">cim2</span><span class="p">:</span> <span class="n"><a class="reference internal" href="conditional_intensity_matrix.html#conditional_intensity_matrix.ConditionalIntensityMatrix" title="conditional_intensity_matrix.ConditionalIntensityMatrix">conditional_intensity_matrix.ConditionalIntensityMatrix</a></span></em><span class="sig-paren">)</span> &#x2192; bool<a class="headerlink" href="#structure_estimator.StructureEstimator.independence_test" title="Permalink to this definition">¶</a></dt>
-<dd><p>Compute the actual independence test using two cims.
-It is performed first the exponential test and if the null hypothesis is not rejected,
-it is performed also the chi_test.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>child_states_numb</strong> (<em>int</em>) – the cardinality of the test child</p></li>
-<li><p><strong>cim1</strong> (<a class="reference internal" href="conditional_intensity_matrix.html#conditional_intensity_matrix.ConditionalIntensityMatrix" title="conditional_intensity_matrix.ConditionalIntensityMatrix"><em>ConditionalIntensityMatrix</em></a>) – a cim belonging to the graph without test parent</p></li>
-<li><p><strong>cim2</strong> (<a class="reference internal" href="conditional_intensity_matrix.html#conditional_intensity_matrix.ConditionalIntensityMatrix" title="conditional_intensity_matrix.ConditionalIntensityMatrix"><em>ConditionalIntensityMatrix</em></a>) – a cim belonging to the graph with test parent</p></li>
-</ul>
-</dd>
-</dl>
-<p>:return:True iff both tests do NOT reject the null hypothesis of indipendence. False otherwise.
-:rtype: bool</p>
-</dd></dl>
-
-<dl class="py method">
-<dt id="structure_estimator.StructureEstimator.one_iteration_of_CTPC_algorithm">
-<code class="sig-name descname">one_iteration_of_CTPC_algorithm</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">var_id</span><span class="p">:</span> <span class="n">str</span></em>, <em class="sig-param"><span class="n">tot_vars_count</span><span class="p">:</span> <span class="n">int</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#structure_estimator.StructureEstimator.one_iteration_of_CTPC_algorithm" title="Permalink to this definition">¶</a></dt>
-<dd><p>Performs an iteration of the CTPC algorithm using the node <code class="docutils literal notranslate"><span class="pre">var_id</span></code> as <code class="docutils literal notranslate"><span class="pre">test_child</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>var_id</strong> (<em>string</em>) – the node label of the test child</p></li>
-<li><p><strong>tot_vars_count</strong> (<em>int</em>) – the number of _nodes in the net</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt id="structure_estimator.StructureEstimator.save_results">
-<code class="sig-name descname">save_results</code><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#structure_estimator.StructureEstimator.save_results" title="Permalink to this definition">¶</a></dt>
-<dd><p>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 <a href="#id1"><span class="problematic" id="id2">results_</span></a> word is appendend to the results file.</p>
-</dd></dl>
-
-</dd></dl>
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-    <script type="text/javascript" src="../_static/doctools.js">
-
-    </script>
-    <script type="text/javascript" src="../_static/language_data.js">
-
-    </script>
-
-  
-
-   <script type="text/javascript"
-           src="../_static/js/theme.js"></script>
-
-   <script type="text/javascript"
-           src="../_static/js/pdj.js"></script>
-
-  
-  
-  <script type="text/javascript">
-      jQuery(function () {
-          SphinxRtdTheme.StickyNav.enable();
-      });
-  </script>
-   
-
-  </body>
-</html>

documentation/_build/html/rst/trajectory.html

@@ -1,210 +0,0 @@
-
-
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
-<html xml:lang="" lang="" version="-//W3C//DTD XHTML 1.1//EN" xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta charset="utf-8">
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-  
-  <title>trajectory module &mdash; PyCTBN  documentation</title>
-  
-
-  
-
-  
-
-    <link href='https://fonts.googleapis.com/css?family=Lato:400,700,400italic,700italic|Roboto+Slab:400,700|Inconsolata:400,700' rel='stylesheet' type='text/css'/>
-    <link rel="stylesheet" href="../_static/css/pdj.css" type="text/css" />
-
-  
-
-  
-
-  
-        <link rel="index" title="Index"
-              href="../genindex.html"/>
-        <link rel="search" title="Search" href="../search.html"/>
-    <link rel="top" title="PyCTBN  documentation" href="../index.html"/>
-
-    <meta http-equiv="content-type" content="text/html; charset=utf-8" />
-    <meta http-equiv="cache-control" content="public" />
-    <meta name="robots" content="follow, all" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <!-- Add jQuery library -->
-    <script type="text/javascript" src="http://code.jquery.com/jquery-latest.min.js"></script>
-    <script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
-
-  </head>
-
-  <body class="wy-body-for-nav" role="document">
-
-  <div class="wy-grid-for-nav">
-    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
-      <div class="wy-side-nav-search">
-        <a href="../index.html" class="fa fa-home"> PyCTBN </a>
-        <div role="search">
-	  <form id ="rtd-search-form" class="wy-form"
-		action="../search.html" method="get">
-	    <input type="text" name="q" placeholder="Search docs" />
-	    <input type="hidden" name="check_keywords" value="yes" />
-	    <input type="hidden" name="area" value="default" />
-	  </form>
-	</div>
-      </div>
-
-      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-	
-          
-          
-              <!-- Local TOC -->
-              <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">trajectory module</a></li>
-</ul>
-</div>
-          
-        
-
-      </div>
-      &nbsp;
-    </nav>
-    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
-
-      <nav class="wy-nav-top" id="barra-mobile" role="navigation" aria-label="top navigation">
-        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-        <a href="#">Porão do Juca</a>
-      </nav>
-
-      <div class="wy-nav-content">
-	<div class="fundo-claro">
-	</div>
-	<div class="fundo-escuro">
-	</div>
-
-        <div class="rst-content">
-          <div role="navigation" aria-label="breadcrumbs navigation">
-	    
-	    <!-- <ul class="wy-breadcrumbs"> -->
-	    <!--   <li><a href="#">Docs</a> &raquo;</li> -->
-
-	    <!--   <li>Features</li> -->
-	    <!--   <li class="wy-breadcrumbs-aside"> -->
-
-	    <!-- 	<a href="_sources/index.txt" rel="nofollow"> View page source</a> -->
-
-	    <!--   </li> -->
-	    <!-- </ul> -->
-	    <!-- <hr/> -->
-	  </div>
-
-          <div role="main" class="">
-
-	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="module-trajectory">
-<span id="trajectory-module"></span><h1>trajectory module<a class="headerlink" href="#module-trajectory" title="Permalink to this headline">¶</a></h1>
-<dl class="py class">
-<dt id="trajectory.Trajectory">
-<em class="property">class </em><code class="sig-prename descclassname">trajectory.</code><code class="sig-name descname">Trajectory</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">list_of_columns</span><span class="p">:</span> <span class="n">List</span></em>, <em class="sig-param"><span class="n">original_cols_number</span><span class="p">:</span> <span class="n">int</span></em><span class="sig-paren">)</span><a class="headerlink" href="#trajectory.Trajectory" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Abstracts the infos about a complete set of trajectories, represented as a numpy array of doubles (the time deltas)
-and a numpy matrix of ints (the changes of states).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>list_of_columns</strong> (<em>List</em>) – the list containing the times array and values matrix</p></li>
-<li><p><strong>original_cols_number</strong> (<em>int</em>) – total number of cols in the data</p></li>
-</ul>
-</dd>
-<dt class="field-even">_actual_trajectory</dt>
-<dd class="field-even"><p>the trajectory containing also the duplicated/shifted values</p>
-</dd>
-<dt class="field-odd">_times</dt>
-<dd class="field-odd"><p>the array containing the time deltas</p>
-</dd>
-</dl>
-<dl class="py method">
-<dt id="trajectory.Trajectory.complete_trajectory">
-<em class="property">property </em><code class="sig-name descname">complete_trajectory</code><a class="headerlink" href="#trajectory.Trajectory.complete_trajectory" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="trajectory.Trajectory.size">
-<code class="sig-name descname">size</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trajectory.Trajectory.size" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="trajectory.Trajectory.times">
-<em class="property">property </em><code class="sig-name descname">times</code><a class="headerlink" href="#trajectory.Trajectory.times" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt id="trajectory.Trajectory.trajectory">
-<em class="property">property </em><code class="sig-name descname">trajectory</code><a class="headerlink" href="#trajectory.Trajectory.trajectory" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-</dd></dl>
-
-</div>
-
-
-	    </div>
-            <footer>
-  
-
-  <hr/>
-
-  <div role="contentinfo">
-    <p>
-        &copy; Copyright 2020, Filippo Martini.
-    </p>
-  </div>
-
-  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/jucacrispim/sphinx_pdj_theme">theme</a> provided by <a href="http://poraodojuca.net">Porão do Juca</a>.
-
-</footer>
-	</div>
-	</div>
-	  
-
-    <script type="text/javascript">
-        var DOCUMENTATION_OPTIONS = {
-            URL_ROOT:'../',
-            VERSION:'',
-            COLLAPSE_INDEX:false,
-            FILE_SUFFIX:'.html',
-            HAS_SOURCE:  true
-        };
-    </script>
-    <script type="text/javascript" src="../_static/jquery.js">
-
-    </script>
-    <script type="text/javascript" src="../_static/underscore.js">
-
-    </script>
-    <script type="text/javascript" src="../_static/doctools.js">
-
-    </script>
-    <script type="text/javascript" src="../_static/language_data.js">
-
-    </script>
-
-  
-
-   <script type="text/javascript"
-           src="../_static/js/theme.js"></script>
-
-   <script type="text/javascript"
-           src="../_static/js/pdj.js"></script>
-
-  
-  
-  <script type="text/javascript">
-      jQuery(function () {
-          SphinxRtdTheme.StickyNav.enable();
-      });
-  </script>
-   
-
-  </body>
-</html>

documentation/_build/html/search.html

@@ -8,7 +8,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
   
-  <title>Search &mdash; PyCTBN  documentation</title>
+  <title>Search &mdash; PyCTBN 1.0 documentation</title>
   
 
   
@@ -26,7 +26,7 @@
         <link rel="index" title="Index"
               href="genindex.html"/>
         <link rel="search" title="Search" href="#"/>
-    <link rel="top" title="PyCTBN  documentation" href="index.html"/>
+    <link rel="top" title="PyCTBN 1.0 documentation" href="index.html"/>
 
     <meta http-equiv="content-type" content="text/html; charset=utf-8" />
     <meta http-equiv="cache-control" content="public" />
@@ -58,8 +58,33 @@
 	
           
           
-              <!-- Local TOC -->
-              <div class="local-toc"></div>
+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#installation-usage">Installation/Usage:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#implementing-your-own-data-importer">Implementing your own data importer</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#parameters-estimation-example">Parameters Estimation Example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#structure-estimation-example">Structure Estimation Example</a></li>
+</ul>
+</li>
+</ul>
+
           
         
 
@@ -120,7 +145,7 @@
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2020, Filippo Martini.
+        &copy; Copyright 2020, Alessandro Bregoli, Filippo Martini.
     </p>
   </div>
 
@@ -134,7 +159,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'',
+            VERSION:'1.0',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',
             HAS_SOURCE:  true

documentation/conf.py

@@ -12,15 +12,18 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../PyCTBN/PyCTBN'))
+sys.path.insert(0, os.path.abspath('../PyCTBN/'))
 print(sys.path)
 
 
 # -- Project information -----------------------------------------------------
 
 project = 'PyCTBN'
-copyright = '2020, Filippo Martini'
-author = 'Filippo Martini'
+copyright = '2020, Alessandro Bregoli, Filippo Martini'
+author = 'Alessandro Bregoli, Filippo Martini'
+
+# The full version, including alpha/beta/rc tags
+release = '1.0'
 
 
 # -- General configuration ---------------------------------------------------
@@ -28,7 +31,8 @@ author = 'Filippo Martini'
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc']
+extensions = ['sphinx.ext.autodoc'
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

documentation/examples.rst

@@ -0,0 +1,123 @@
+Examples
+=============
+
+Installation/Usage:
+*******************
+
+
+Implementing your own data importer
+***********************************
+.. code-block:: python
+
+    """This example demonstrates the implementation of a simple data importer the extends the class abstract importer to import data in csv format.
+    The net in exam has three ternary nodes.
+    """
+
+    from .abstract_importer import AbstractImporter
+
+    class CSVImporter(AbstractImporter):
+
+        def __init__(self, file_path):
+            self._df_samples_list = None
+            super(CSVImporter, self).__init__(file_path)
+
+        def import_data(self):
+            self.read_csv_file()
+            self._sorter = self.build_sorter(self._df_samples_list[0])
+            self.import_variables()
+            self.import_structure()
+            self.compute_row_delta_in_all_samples_frames(self._df_samples_list)
+
+        def read_csv_file(self):
+            df = pd.read_csv(self._file_path)
+            df.drop(df.columns[[0]], axis=1, inplace=True)
+            self._df_samples_list = [df]
+
+        def import_variables(self):
+            values_list = [3 for var in self._sorter]
+            # initialize dict of lists
+            data = {'Name':self._sorter, 'Value':values_list}
+            # Create the pandas DataFrame
+            self._df_variables = pd.DataFrame(data)
+
+        def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
+            return list(sample_frame.columns)[1:]
+
+        def import_structure(self):
+            data = {'From':['X','Y','Z'], 'To':['Z','Z','Y']}
+            self._df_structure = pd.DataFrame(data)
+
+        def dataset_id(self) -> object:
+            pass
+
+Parameters Estimation Example
+*****************************
+
+.. code-block:: python
+
+    from PyCTBN.PyCTBN.json_importer import JsonImporter
+    from PyCTBN.PyCTBN.sample_path import SamplePath
+    from PyCTBN.PyCTBN.network_graph import NetworkGraph
+    from PyCTBN.PyCTBN.parameters_estimator import ParametersEstimator
+
+
+    def main():
+        read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir
+        #import data
+        importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        importer.import_data(0)
+        #Create a SamplePath Obj passing an already filled AbstractImporter object
+        s1 = SamplePath(importer)
+        #Build The trajectries and the structural infos
+        s1.build_trajectories()
+        s1.build_structure()
+        print(s1.structure.edges)
+        print(s1.structure.nodes_values)
+        #From The Structure Object build the Graph
+        g = NetworkGraph(s1.structure)
+        #Select a node you want to estimate the parameters
+        node = g.nodes[2]
+        print("Node", node)
+        #Init the _graph specifically for THIS node
+        g.fast_init(node)
+        #Use SamplePath and Grpah to create a ParametersEstimator Object
+        p1 = ParametersEstimator(s1.trajectories, g)
+        #Init the peEst specifically for THIS node
+        p1.fast_init(node)
+        #Compute the parameters
+        sofc1 = p1.compute_parameters_for_node(node)
+        #The est CIMS are inside the resultant SetOfCIms Obj
+        print(sofc1.actual_cims)
+
+Structure Estimation Example
+****************************
+
+.. code-block:: python
+
+    from PyCTBN.PyCTBN.json_importer import JsonImporter
+    from PyCTBN.PyCTBN.sample_path import SamplePath
+    from PyCTBN.PyCTBN.structure_estimator import StructureEstimator
+    
+    def structure_estimation_example():
+
+        # read the json files in ./data path
+        read_files = glob.glob(os.path.join('./data', "*.json"))
+        # initialize a JsonImporter object for the first file
+        importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        # import the data at index 0 of the outer json array
+        importer.import_data(0)
+        # construct a SamplePath Object passing a filled AbstractImporter
+        s1 = SamplePath(importer)
+        # build the trajectories
+        s1.build_trajectories()
+        # build the real structure
+        s1.build_structure()
+        # construct a StructureEstimator object
+        se1 = StructureEstimator(s1, 0.1, 0.1)
+        # call the ctpc algorithm
+        se1.ctpc_algorithm()
+        # the adjacency matrix of the estimated structure
+        print(se1.adjacency_matrix())
+        # save results to a json file
+        se1.save_results()
+

documentation/index.rst

@@ -1,5 +1,5 @@
 .. PyCTBN documentation master file, created by
-   sphinx-quickstart on Mon Nov 30 16:37:03 2020.
+   sphinx-quickstart on Mon Dec  7 15:11:12 2020.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
@@ -10,7 +10,8 @@ Welcome to PyCTBN's documentation!
    :maxdepth: 2
    :caption: Contents:
 
-
+   PyCTBN
+   examples
 
 Indices and tables
 ==================

documentation/modules.rst

@@ -0,0 +1,7 @@
+PyCTBN
+======
+
+.. toctree::
+   :maxdepth: 4
+
+   PyCTBN

documentation/rst/abstract_importer.rst

@@ -1,48 +0,0 @@
-abstract\_importer module
-=========================
-
-.. automodule:: abstract_importer
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-An example of a simple CSV Importer
-===================================
-Suppose you have a csv dataset containing only the trajectories, three variables labels and cardinalites.
-Then the resulting importer that inherit and extends AbstractImpoter would be:
-
-.. code_block:: python
-   class CSVImporter(AbstractImporter):
-
-    def __init__(self, file_path):
-        self._df_samples_list = None
-        super(CSVImporter, self).__init__(file_path)
-
-    def import_data(self):
-        self.read_csv_file()
-        self._sorter = self.build_sorter(self._df_samples_list[0])
-        self.import_variables()
-        self.import_structure()
-        self.compute_row_delta_in_all_samples_frames(self._df_samples_list)
-
-    def read_csv_file(self):
-        df = pd.read_csv(self._file_path)
-        df.drop(df.columns[[0]], axis=1, inplace=True)
-        self._df_samples_list = [df]
-
-    def import_variables(self):
-        values_list = [3 for var in self._sorter]
-        # initialize dict of lists
-        data = {'Name':self._sorter, 'Value':values_list}
-        # Create the pandas DataFrame
-        self._df_variables = pd.DataFrame(data)
-
-    def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
-        return list(sample_frame.columns)[1:]
-
-    def import_structure(self):
-        data = {'From':['X','Y','Z'], 'To':['Z','Z','Y']}
-        self._df_structure = pd.DataFrame(data)
-
-    def dataset_id(self) -> object:
-        pass

documentation/rst/cache.rst

@@ -1,7 +0,0 @@
-cache module
-============
-
-.. automodule:: cache
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/rst/conditional_intensity_matrix.rst

@@ -1,7 +0,0 @@
-conditional\_intensity\_matrix module
-=====================================
-
-.. automodule:: conditional_intensity_matrix
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/rst/json_importer.rst

@@ -1,7 +0,0 @@
-json\_importer module
-=====================
-
-.. automodule:: json_importer
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/rst/modules.rst

@@ -1,17 +0,0 @@
-scripts
-=======
-
-.. toctree::
-   :maxdepth: 4
-
-   abstract_importer
-   cache
-   conditional_intensity_matrix
-   json_importer
-   network_graph
-   parameters_estimator
-   sample_path
-   set_of_cims
-   structure
-   structure_estimator
-   trajectory

documentation/rst/network_graph.rst

@@ -1,7 +0,0 @@
-network\_graph module
-=====================
-
-.. automodule:: network_graph
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/rst/parameters_estimator.rst

@@ -1,7 +0,0 @@
-parameters\_estimator module
-============================
-
-.. automodule:: parameters_estimator
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/rst/sample_path.rst

@@ -1,7 +0,0 @@
-sample\_path module
-===================
-
-.. automodule:: sample_path
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/rst/set_of_cims.rst

@@ -1,7 +0,0 @@
-set\_of\_cims module
-====================
-
-.. automodule:: set_of_cims
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/rst/structure.rst

@@ -1,7 +0,0 @@
-structure module
-================
-
-.. automodule:: structure
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/rst/structure_estimator.rst

@@ -1,7 +0,0 @@
-structure\_estimator module
-===========================
-
-.. automodule:: structure_estimator
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/rst/trajectory.rst

@@ -1,7 +0,0 @@
-trajectory module
-=================
-
-.. automodule:: trajectory
-   :members:
-   :undoc-members:
-   :show-inheritance:

parameters_estimation_example.py

@@ -0,0 +1,42 @@
+
+import os
+import glob
+
+
+from PyCTBN.PyCTBN.json_importer import JsonImporter
+from PyCTBN.PyCTBN.sample_path import SamplePath
+from PyCTBN.PyCTBN.network_graph import NetworkGraph
+from PyCTBN.PyCTBN.parameters_estimator import ParametersEstimator
+
+
+def main():
+    read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir
+    #import data
+    importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+    importer.import_data(0)
+    #Create a SamplePath Obj
+    s1 = SamplePath(importer)
+    #Build The trajectries and the structural infos
+    s1.build_trajectories()
+    s1.build_structure()
+    print(s1.structure.edges)
+    print(s1.structure.nodes_values)
+    #From The Structure Object build the Graph
+    g = NetworkGraph(s1.structure)
+    #Select a node you want to estimate the parameters
+    node = g.nodes[2]
+    print("Node", node)
+    #Init the _graph specifically for THIS node
+    g.fast_init(node)
+    #Use SamplePath and Grpah to create a ParametersEstimator Object
+    p1 = ParametersEstimator(s1.trajectories, g)
+    #Init the peEst specifically for THIS node
+    p1.fast_init(node)
+    #Compute the parameters
+    sofc1 = p1.compute_parameters_for_node(node)
+    #The est CIMS are inside the resultant SetOfCIms Obj
+    print(sofc1.actual_cims)
+
+
+if __name__ == "__main__":
+    main()

setup.py

@@ -9,8 +9,9 @@ setup(name='PyCTBN',
       description='A Continuous Time Bayesian Networks Library',
       packages=find_packages(exclude=['tests', 'data']),
       install_requires=[
-          'numpy', 'pandas', 'networkx'],
+          'numpy', 'pandas', 'networkx', 'scipy', 'tqdm'],
       dependency_links=['https://github.com/numpy/numpy', 'https://github.com/pandas-dev/pandas',
-                        'https://github.com/networkx/networkx'],
+                        'https://github.com/networkx/networkx', 'https://github.com/scipy/scipy',
+                        'https://github.com/tqdm/tqdm'],
       long_description=open('README.md').read(),
       zip_safe=False)

structure_estimation_example.py

@@ -0,0 +1,30 @@
+import os
+import glob
+
+from PyCTBN.PyCTBN.json_importer import JsonImporter
+from PyCTBN.PyCTBN.sample_path import SamplePath
+from PyCTBN.PyCTBN.structure_estimator import StructureEstimator
+
+
+def structure_estimation_example():
+
+    # read the json files in ./data path
+    read_files = glob.glob(os.path.join('./data', "*.json"))
+    # initialize a JsonImporter object for the first file
+    importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+    # import the data at index 0 of the outer json array
+    importer.import_data(0)
+    # construct a SamplePath Object passing a filled AbstractImporter
+    s1 = SamplePath(importer)
+    # build the trajectories
+    s1.build_trajectories()
+    # build the real structure
+    s1.build_structure()
+    # construct a StructureEstimator object
+    se1 = StructureEstimator(s1, 0.1, 0.1)
+    # call the ctpc algorithm
+    se1.ctpc_algorithm()
+    # the adjacency matrix of the estimated structure
+    print(se1.adjacency_matrix())
+    # save results to a json file
+    se1.save_results()

venv/bin/Activate.ps1

@@ -0,0 +1,241 @@
+<#
+.Synopsis
+Activate a Python virtual environment for the current PowerShell session.
+
+.Description
+Pushes the python executable for a virtual environment to the front of the
+$Env:PATH environment variable and sets the prompt to signify that you are
+in a Python virtual environment. Makes use of the command line switches as
+well as the `pyvenv.cfg` file values present in the virtual environment.
+
+.Parameter VenvDir
+Path to the directory that contains the virtual environment to activate. The
+default value for this is the parent of the directory that the Activate.ps1
+script is located within.
+
+.Parameter Prompt
+The prompt prefix to display when this virtual environment is activated. By
+default, this prompt is the name of the virtual environment folder (VenvDir)
+surrounded by parentheses and followed by a single space (ie. '(.venv) ').
+
+.Example
+Activate.ps1
+Activates the Python virtual environment that contains the Activate.ps1 script.
+
+.Example
+Activate.ps1 -Verbose
+Activates the Python virtual environment that contains the Activate.ps1 script,
+and shows extra information about the activation as it executes.
+
+.Example
+Activate.ps1 -VenvDir C:\Users\MyUser\Common\.venv
+Activates the Python virtual environment located in the specified location.
+
+.Example
+Activate.ps1 -Prompt "MyPython"
+Activates the Python virtual environment that contains the Activate.ps1 script,
+and prefixes the current prompt with the specified string (surrounded in
+parentheses) while the virtual environment is active.
+
+.Notes
+On Windows, it may be required to enable this Activate.ps1 script by setting the
+execution policy for the user. You can do this by issuing the following PowerShell
+command:
+
+PS C:\> Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser
+
+For more information on Execution Policies: 
+https://go.microsoft.com/fwlink/?LinkID=135170
+
+#>
+Param(
+    [Parameter(Mandatory = $false)]
+    [String]
+    $VenvDir,
+    [Parameter(Mandatory = $false)]
+    [String]
+    $Prompt
+)
+
+<# Function declarations --------------------------------------------------- #>
+
+<#
+.Synopsis
+Remove all shell session elements added by the Activate script, including the
+addition of the virtual environment's Python executable from the beginning of
+the PATH variable.
+
+.Parameter NonDestructive
+If present, do not remove this function from the global namespace for the
+session.
+
+#>
+function global:deactivate ([switch]$NonDestructive) {
+    # Revert to original values
+
+    # The prior prompt:
+    if (Test-Path -Path Function:_OLD_VIRTUAL_PROMPT) {
+        Copy-Item -Path Function:_OLD_VIRTUAL_PROMPT -Destination Function:prompt
+        Remove-Item -Path Function:_OLD_VIRTUAL_PROMPT
+    }
+
+    # The prior PYTHONHOME:
+    if (Test-Path -Path Env:_OLD_VIRTUAL_PYTHONHOME) {
+        Copy-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME -Destination Env:PYTHONHOME
+        Remove-Item -Path Env:_OLD_VIRTUAL_PYTHONHOME
+    }
+
+    # The prior PATH:
+    if (Test-Path -Path Env:_OLD_VIRTUAL_PATH) {
+        Copy-Item -Path Env:_OLD_VIRTUAL_PATH -Destination Env:PATH
+        Remove-Item -Path Env:_OLD_VIRTUAL_PATH
+    }
+
+    # Just remove the VIRTUAL_ENV altogether:
+    if (Test-Path -Path Env:VIRTUAL_ENV) {
+        Remove-Item -Path env:VIRTUAL_ENV
+    }
+
+    # Just remove the _PYTHON_VENV_PROMPT_PREFIX altogether:
+    if (Get-Variable -Name "_PYTHON_VENV_PROMPT_PREFIX" -ErrorAction SilentlyContinue) {
+        Remove-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Scope Global -Force
+    }
+
+    # Leave deactivate function in the global namespace if requested:
+    if (-not $NonDestructive) {
+        Remove-Item -Path function:deactivate
+    }
+}
+
+<#
+.Description
+Get-PyVenvConfig parses the values from the pyvenv.cfg file located in the
+given folder, and returns them in a map.
+
+For each line in the pyvenv.cfg file, if that line can be parsed into exactly
+two strings separated by `=` (with any amount of whitespace surrounding the =)
+then it is considered a `key = value` line. The left hand string is the key,
+the right hand is the value.
+
+If the value starts with a `'` or a `"` then the first and last character is
+stripped from the value before being captured.
+
+.Parameter ConfigDir
+Path to the directory that contains the `pyvenv.cfg` file.
+#>
+function Get-PyVenvConfig(
+    [String]
+    $ConfigDir
+) {
+    Write-Verbose "Given ConfigDir=$ConfigDir, obtain values in pyvenv.cfg"
+
+    # Ensure the file exists, and issue a warning if it doesn't (but still allow the function to continue).
+    $pyvenvConfigPath = Join-Path -Resolve -Path $ConfigDir -ChildPath 'pyvenv.cfg' -ErrorAction Continue
+
+    # An empty map will be returned if no config file is found.
+    $pyvenvConfig = @{ }
+
+    if ($pyvenvConfigPath) {
+
+        Write-Verbose "File exists, parse `key = value` lines"
+        $pyvenvConfigContent = Get-Content -Path $pyvenvConfigPath
+
+        $pyvenvConfigContent | ForEach-Object {
+            $keyval = $PSItem -split "\s*=\s*", 2
+            if ($keyval[0] -and $keyval[1]) {
+                $val = $keyval[1]
+
+                # Remove extraneous quotations around a string value.
+                if ("'""".Contains($val.Substring(0, 1))) {
+                    $val = $val.Substring(1, $val.Length - 2)
+                }
+
+                $pyvenvConfig[$keyval[0]] = $val
+                Write-Verbose "Adding Key: '$($keyval[0])'='$val'"
+            }
+        }
+    }
+    return $pyvenvConfig
+}
+
+
+<# Begin Activate script --------------------------------------------------- #>
+
+# Determine the containing directory of this script
+$VenvExecPath = Split-Path -Parent $MyInvocation.MyCommand.Definition
+$VenvExecDir = Get-Item -Path $VenvExecPath
+
+Write-Verbose "Activation script is located in path: '$VenvExecPath'"
+Write-Verbose "VenvExecDir Fullname: '$($VenvExecDir.FullName)"
+Write-Verbose "VenvExecDir Name: '$($VenvExecDir.Name)"
+
+# Set values required in priority: CmdLine, ConfigFile, Default
+# First, get the location of the virtual environment, it might not be
+# VenvExecDir if specified on the command line.
+if ($VenvDir) {
+    Write-Verbose "VenvDir given as parameter, using '$VenvDir' to determine values"
+}
+else {
+    Write-Verbose "VenvDir not given as a parameter, using parent directory name as VenvDir."
+    $VenvDir = $VenvExecDir.Parent.FullName.TrimEnd("\\/")
+    Write-Verbose "VenvDir=$VenvDir"
+}
+
+# Next, read the `pyvenv.cfg` file to determine any required value such
+# as `prompt`.
+$pyvenvCfg = Get-PyVenvConfig -ConfigDir $VenvDir
+
+# Next, set the prompt from the command line, or the config file, or
+# just use the name of the virtual environment folder.
+if ($Prompt) {
+    Write-Verbose "Prompt specified as argument, using '$Prompt'"
+}
+else {
+    Write-Verbose "Prompt not specified as argument to script, checking pyvenv.cfg value"
+    if ($pyvenvCfg -and $pyvenvCfg['prompt']) {
+        Write-Verbose "  Setting based on value in pyvenv.cfg='$($pyvenvCfg['prompt'])'"
+        $Prompt = $pyvenvCfg['prompt'];
+    }
+    else {
+        Write-Verbose "  Setting prompt based on parent's directory's name. (Is the directory name passed to venv module when creating the virutal environment)"
+        Write-Verbose "  Got leaf-name of $VenvDir='$(Split-Path -Path $venvDir -Leaf)'"
+        $Prompt = Split-Path -Path $venvDir -Leaf
+    }
+}
+
+Write-Verbose "Prompt = '$Prompt'"
+Write-Verbose "VenvDir='$VenvDir'"
+
+# Deactivate any currently active virtual environment, but leave the
+# deactivate function in place.
+deactivate -nondestructive
+
+# Now set the environment variable VIRTUAL_ENV, used by many tools to determine
+# that there is an activated venv.
+$env:VIRTUAL_ENV = $VenvDir
+
+if (-not $Env:VIRTUAL_ENV_DISABLE_PROMPT) {
+
+    Write-Verbose "Setting prompt to '$Prompt'"
+
+    # Set the prompt to include the env name
+    # Make sure _OLD_VIRTUAL_PROMPT is global
+    function global:_OLD_VIRTUAL_PROMPT { "" }
+    Copy-Item -Path function:prompt -Destination function:_OLD_VIRTUAL_PROMPT
+    New-Variable -Name _PYTHON_VENV_PROMPT_PREFIX -Description "Python virtual environment prompt prefix" -Scope Global -Option ReadOnly -Visibility Public -Value $Prompt
+
+    function global:prompt {
+        Write-Host -NoNewline -ForegroundColor Green "($_PYTHON_VENV_PROMPT_PREFIX) "
+        _OLD_VIRTUAL_PROMPT
+    }
+}
+
+# Clear PYTHONHOME
+if (Test-Path -Path Env:PYTHONHOME) {
+    Copy-Item -Path Env:PYTHONHOME -Destination Env:_OLD_VIRTUAL_PYTHONHOME
+    Remove-Item -Path Env:PYTHONHOME
+}
+
+# Add the venv to the PATH
+Copy-Item -Path Env:PATH -Destination Env:_OLD_VIRTUAL_PATH
+$Env:PATH = "$VenvExecDir$([System.IO.Path]::PathSeparator)$Env:PATH"

venv/bin/activate

@@ -0,0 +1,66 @@
+# This file must be used with "source bin/activate" *from bash*
+# you cannot run it directly
+
+deactivate () {
+    # reset old environment variables
+    if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then
+        PATH="${_OLD_VIRTUAL_PATH:-}"
+        export PATH
+        unset _OLD_VIRTUAL_PATH
+    fi
+    if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then
+        PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}"
+        export PYTHONHOME
+        unset _OLD_VIRTUAL_PYTHONHOME
+    fi
+
+    # This should detect bash and zsh, which have a hash command that must
+    # be called to get it to forget past commands.  Without forgetting
+    # past commands the $PATH changes we made may not be respected
+    if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then
+        hash -r 2> /dev/null
+    fi
+
+    if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then
+        PS1="${_OLD_VIRTUAL_PS1:-}"
+        export PS1
+        unset _OLD_VIRTUAL_PS1
+    fi
+
+    unset VIRTUAL_ENV
+    if [ ! "${1:-}" = "nondestructive" ] ; then
+    # Self destruct!
+        unset -f deactivate
+    fi
+}
+
+# unset irrelevant variables
+deactivate nondestructive
+
+VIRTUAL_ENV="/Users/Zalum/Desktop/Tesi/PyCTBN/venv"
+export VIRTUAL_ENV
+
+_OLD_VIRTUAL_PATH="$PATH"
+PATH="$VIRTUAL_ENV/bin:$PATH"
+export PATH
+
+# unset PYTHONHOME if set
+# this will fail if PYTHONHOME is set to the empty string (which is bad anyway)
+# could use `if (set -u; : $PYTHONHOME) ;` in bash
+if [ -n "${PYTHONHOME:-}" ] ; then
+    _OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}"
+    unset PYTHONHOME
+fi
+
+if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then
+    _OLD_VIRTUAL_PS1="${PS1:-}"
+    PS1="(venv) ${PS1:-}"
+    export PS1
+fi
+
+# This should detect bash and zsh, which have a hash command that must
+# be called to get it to forget past commands.  Without forgetting
+# past commands the $PATH changes we made may not be respected
+if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then
+    hash -r 2> /dev/null
+fi

venv/bin/activate.csh

@@ -0,0 +1,25 @@
+# This file must be used with "source bin/activate.csh" *from csh*.
+# You cannot run it directly.
+# Created by Davide Di Blasi <davidedb@gmail.com>.
+# Ported to Python 3.3 venv by Andrew Svetlov <andrew.svetlov@gmail.com>
+
+alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; test "\!:*" != "nondestructive" && unalias deactivate'
+
+# Unset irrelevant variables.
+deactivate nondestructive
+
+setenv VIRTUAL_ENV "/Users/Zalum/Desktop/Tesi/PyCTBN/venv"
+
+set _OLD_VIRTUAL_PATH="$PATH"
+setenv PATH "$VIRTUAL_ENV/bin:$PATH"
+
+
+set _OLD_VIRTUAL_PROMPT="$prompt"
+
+if (! "$?VIRTUAL_ENV_DISABLE_PROMPT") then
+    set prompt = "(venv) $prompt"
+endif
+
+alias pydoc python -m pydoc
+
+rehash

venv/bin/activate.fish

@@ -0,0 +1,64 @@
+# This file must be used with "source <venv>/bin/activate.fish" *from fish*
+# (https://fishshell.com/); you cannot run it directly.
+
+function deactivate  -d "Exit virtual environment and return to normal shell environment"
+    # reset old environment variables
+    if test -n "$_OLD_VIRTUAL_PATH"
+        set -gx PATH $_OLD_VIRTUAL_PATH
+        set -e _OLD_VIRTUAL_PATH
+    end
+    if test -n "$_OLD_VIRTUAL_PYTHONHOME"
+        set -gx PYTHONHOME $_OLD_VIRTUAL_PYTHONHOME
+        set -e _OLD_VIRTUAL_PYTHONHOME
+    end
+
+    if test -n "$_OLD_FISH_PROMPT_OVERRIDE"
+        functions -e fish_prompt
+        set -e _OLD_FISH_PROMPT_OVERRIDE
+        functions -c _old_fish_prompt fish_prompt
+        functions -e _old_fish_prompt
+    end
+
+    set -e VIRTUAL_ENV
+    if test "$argv[1]" != "nondestructive"
+        # Self-destruct!
+        functions -e deactivate
+    end
+end
+
+# Unset irrelevant variables.
+deactivate nondestructive
+
+set -gx VIRTUAL_ENV "/Users/Zalum/Desktop/Tesi/PyCTBN/venv"
+
+set -gx _OLD_VIRTUAL_PATH $PATH
+set -gx PATH "$VIRTUAL_ENV/bin" $PATH
+
+# Unset PYTHONHOME if set.
+if set -q PYTHONHOME
+    set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME
+    set -e PYTHONHOME
+end
+
+if test -z "$VIRTUAL_ENV_DISABLE_PROMPT"
+    # fish uses a function instead of an env var to generate the prompt.
+
+    # Save the current fish_prompt function as the function _old_fish_prompt.
+    functions -c fish_prompt _old_fish_prompt
+
+    # With the original prompt function renamed, we can override with our own.
+    function fish_prompt
+        # Save the return status of the last command.
+        set -l old_status $status
+
+        # Output the venv prompt; color taken from the blue of the Python logo.
+        printf "%s%s%s" (set_color 4B8BBE) "(venv) " (set_color normal)
+
+        # Restore the return status of the previous command.
+        echo "exit $old_status" | .
+        # Output the original/"old" prompt.
+        _old_fish_prompt
+    end
+
+    set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV"
+end

venv/bin/easy_install

@@ -0,0 +1,8 @@
+#!/Users/Zalum/Desktop/Tesi/PyCTBN/venv/bin/python
+# -*- coding: utf-8 -*-
+import re
+import sys
+from setuptools.command.easy_install import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

venv/bin/easy_install-3.9

@@ -0,0 +1,8 @@
+#!/Users/Zalum/Desktop/Tesi/PyCTBN/venv/bin/python
+# -*- coding: utf-8 -*-
+import re
+import sys
+from setuptools.command.easy_install import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

venv/bin/f2py

@@ -0,0 +1,8 @@
+#!/Users/Zalum/Desktop/Tesi/PyCTBN/venv/bin/python
+# -*- coding: utf-8 -*-
+import re
+import sys
+from numpy.f2py.f2py2e import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

venv/bin/f2py3

@@ -0,0 +1,8 @@
+#!/Users/Zalum/Desktop/Tesi/PyCTBN/venv/bin/python
+# -*- coding: utf-8 -*-
+import re
+import sys
+from numpy.f2py.f2py2e import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

venv/bin/f2py3.9

@@ -0,0 +1,8 @@
+#!/Users/Zalum/Desktop/Tesi/PyCTBN/venv/bin/python
+# -*- coding: utf-8 -*-
+import re
+import sys
+from numpy.f2py.f2py2e import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

venv/bin/pip

@@ -0,0 +1,8 @@
+#!/Users/Zalum/Desktop/Tesi/PyCTBN/venv/bin/python
+# -*- coding: utf-8 -*-
+import re
+import sys
+from pip._internal.cli.main import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

venv/bin/pip3

@@ -0,0 +1,8 @@
+#!/Users/Zalum/Desktop/Tesi/PyCTBN/venv/bin/python
+# -*- coding: utf-8 -*-
+import re
+import sys
+from pip._internal.cli.main import main
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())