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parallel_struct_est
Filippo Martini 4 years ago
parent d4a079268a
commit ccc562a1a6
32 changed files with 8 additions and 3928 deletions
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  1. 9
      .gitignore
  2. BIN
      CTBN_project_dominio.pdf
  3. 41
      basic_main.py
  4. 0
      main_package/.scannerwork/.sonar_lock
  5. 6
      main_package/.scannerwork/report-task.txt
  6. 0
      main_package/PyCTBN/__init__.py
  7. 149
      main_package/PyCTBN/abstract_importer.py
  8. 54
      main_package/PyCTBN/cache.py
  9. 42
      main_package/PyCTBN/conditional_intensity_matrix.py
  10. 25
      main_package/PyCTBN/deprecated/sets_of_cims_container.py
  11. 169
      main_package/PyCTBN/json_importer.py
  12. 297
      main_package/PyCTBN/network_graph.py
  13. 495
      main_package/PyCTBN/original_ctpc_algorithm.py
  14. 143
      main_package/PyCTBN/parameters_estimator.py
  15. 69
      main_package/PyCTBN/sample_path.py
  16. 94
      main_package/PyCTBN/set_of_cims.py
  17. 62
      main_package/PyCTBN/simple_cvs_importer.py
  18. 98
      main_package/PyCTBN/structure.py
  19. 240
      main_package/PyCTBN/structure_estimator.py
  20. 46
      main_package/PyCTBN/trajectory.py
  21. 0
      main_package/tests/__init__.py
  22. 963
      main_package/tests/coverage.xml
  23. 57
      main_package/tests/test_cache.py
  24. 46
      main_package/tests/test_cim.py
  25. 175
      main_package/tests/test_json_importer.py
  26. 187
      main_package/tests/test_networkgraph.py
  27. 67
      main_package/tests/test_parameters_estimator.py
  28. 39
      main_package/tests/test_sample_path.py
  29. 133
      main_package/tests/test_setofcims.py
  30. 81
      main_package/tests/test_structure.py
  31. 103
      main_package/tests/test_structure_estimator.py
  32. 46
      main_package/tests/test_trajectory.py

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.gitignore vendored
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__pycache__
.vscode
*.csv
*.json
.idea
*.pyc
.coverage
./data/
./venv/
./PyCTBN/.scannerwork

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CTBN_project_dominio.pdf
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41
basic_main.py
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import os
import glob
from PyCTBN.json_importer import JsonImporter
from PyCTBN.sample_path import SamplePath
from PyCTBN.network_graph import NetworkGraph
from 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()

0
main_package/.scannerwork/.sonar_lock
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6
main_package/.scannerwork/report-task.txt
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projectKey=Ctbn_Project
serverUrl=http://localhost:9000
serverVersion=8.4.1.35646
dashboardUrl=http://localhost:9000/dashboard?id=Ctbn_Project
ceTaskId=AXPs4gCNB9mzoAo2hiLI
ceTaskUrl=http://localhost:9000/api/ce/task?id=AXPs4gCNB9mzoAo2hiLI

0
main_package/PyCTBN/__init__.py
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149
main_package/PyCTBN/abstract_importer.py
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from abc import ABC, abstractmethod
import pandas as pd
import typing
class AbstractImporter(ABC):
"""Abstract class that exposes all the necessary methods to process the trajectories and the net structure.
:param file_path: the file path
:type file_path: str
:_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`
"""
def __init__(self, file_path: str):
"""Constructor
"""
self._file_path = file_path
self._df_variables = None
self._df_structure = None
self._concatenated_samples = None
self._sorter = None
super().__init__()
@abstractmethod
def import_data(self) -> None:
"""Imports all the trajectories, variables cardinalities, and net edges.
.. 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 of implementation of this method.
"""
pass
@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
and keeping ONLY the variables symbolic labels, cutting out the time label in the header.
:param sample_frame: The dataframe from which extract the header
:type sample_frame: pandas.DataFrame
:return: A list containing the processed header.
:rtype: List
"""
pass
def compute_row_delta_sigle_samples_frame(self, sample_frame: pd.DataFrame,
columns_header: typing.List, shifted_cols_header: typing.List) \
-> pd.DataFrame:
"""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.
:param sample_frame: the traj to be processed
:type sample_frame: pandas.Dataframe
:param columns_header: the original header of sample_frame
:type columns_header: List
:param shifted_cols_header: a copy of columns_header with changed names of the contents
:type shifted_cols_header: List
:return: The processed dataframe
:rtype: pandas.Dataframe
.. warning::
the Dataframe ``sample_frame`` has to follow the column structure of this header:
Header of sample_frame = [Time | Variable values]
"""
sample_frame.iloc[:, 0] = sample_frame.iloc[:, 0].diff().shift(-1)
shifted_cols = sample_frame[columns_header].shift(-1).fillna(0).astype('int32')
shifted_cols.columns = shifted_cols_header
sample_frame = sample_frame.assign(**shifted_cols)
sample_frame.drop(sample_frame.tail(1).index, inplace=True)
return sample_frame
def compute_row_delta_in_all_samples_frames(self, df_samples_list: typing.List) -> None:
"""Calls the method ``compute_row_delta_sigle_samples_frame`` on every dataframe present in the list
``df_samples_list``.
Concatenates the result in the dataframe ``concatanated_samples``
:param df_samples_list: the datframe's list to be processed and concatenated
:type df_samples_list: List
.. warning::
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)
.. note::
After the call of this method the class member ``concatanated_samples`` will contain all processed
and merged trajectories
"""
if not self._sorter:
raise RuntimeError("The class member self._sorter has to be INITIALIZED!")
shifted_cols_header = [s + "S" for s in self._sorter]
compute_row_delta = self.compute_row_delta_sigle_samples_frame
proc_samples_list = [compute_row_delta(sample, self._sorter, shifted_cols_header)
for sample in df_samples_list]
self._concatenated_samples = pd.concat(proc_samples_list)
complete_header = self._sorter[:]
complete_header.insert(0,'Time')
complete_header.extend(shifted_cols_header)
self._concatenated_samples = self._concatenated_samples[complete_header]
def build_list_of_samples_array(self, data_frame: pd.DataFrame) -> typing.List:
"""Builds a List containing the columns of data_frame and converts them to a numpy array.
:param data_frame: the dataframe from which the columns have to be extracted and converted
:type data_frame: pandas.Dataframe
:return: the resulting list of numpy arrays
:rtype: List
"""
columns_list = [data_frame[column].to_numpy() for column in data_frame]
return columns_list
def clear_concatenated_frame(self) -> None:
"""Removes all values in the dataframe concatenated_samples.
"""
self._concatenated_samples = self._concatenated_samples.iloc[0:0]
@abstractmethod
def dataset_id(self) -> object:
"""If the original dataset contains multiple dataset, this method returns a unique id to identify the current
dataset
"""
pass
@property
def concatenated_samples(self) -> pd.DataFrame:
return self._concatenated_samples
@property
def variables(self) -> pd.DataFrame:
return self._df_variables
@property
def structure(self) -> pd.DataFrame:
return self._df_structure
@property
def sorter(self) -> typing.List:
return self._sorter
@property
def file_path(self) -> str:
return self._file_path

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main_package/PyCTBN/cache.py
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import typing
#import set_of_cims as sofc
from .set_of_cims import SetOfCims
class Cache:
"""This class acts as a cache of ``SetOfCims`` objects for a node.
:_list_of_sets_of_parents: a list of ``Sets`` objects of the parents to which the cim in cache at SAME
index is related
:_actual_cache: a list of setOfCims objects
"""
def __init__(self):
"""Constructor Method
"""
self._list_of_sets_of_parents = []
self._actual_cache = []
def find(self, parents_comb: typing.Set) -> SetOfCims:
"""
Tries to find in cache given the symbolic parents combination ``parents_comb`` the ``SetOfCims``
related to that ``parents_comb``.
:param parents_comb: the parents related to that ``SetOfCims``
:type parents_comb: Set
:return: A ``SetOfCims`` object if the ``parents_comb`` index is found in ``_list_of_sets_of_parents``.
None otherwise.
:rtype: SetOfCims
"""
try:
result = self._actual_cache[self._list_of_sets_of_parents.index(parents_comb)]
return result
except ValueError:
return None
def put(self, parents_comb: typing.Set, socim: SetOfCims) -> None:
"""Place in cache the ``SetOfCims`` object, and the related symbolic index ``parents_comb`` in
``_list_of_sets_of_parents``.
:param parents_comb: the symbolic set index
:type parents_comb: Set
:param socim: the related SetOfCims object
:type socim: SetOfCims
"""
self._list_of_sets_of_parents.append(parents_comb)
self._actual_cache.append(socim)
def clear(self) -> None:
"""Clear the contents both of ``_actual_cache`` and ``_list_of_sets_of_parents``.
"""
del self._list_of_sets_of_parents[:]
del self._actual_cache[:]

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main_package/PyCTBN/conditional_intensity_matrix.py
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import numpy as np
class ConditionalIntensityMatrix:
"""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.
:param state_residence_times: state residence times vector
:type state_residence_times: numpy.array
:param state_transition_matrix: the transitions count matrix
:type state_transition_matrix: numpy.ndArray
:_cim: the actual cim of the node
"""
def __init__(self, state_residence_times: np.array, state_transition_matrix: np.array):
"""Constructor Method
"""
self._state_residence_times = state_residence_times
self._state_transition_matrix = state_transition_matrix
self._cim = self.state_transition_matrix.astype(np.float64)
def compute_cim_coefficients(self) -> None:
"""Compute the coefficients of the matrix _cim by using the following equality q_xx' = M[x, x'] / T[x].
The class member ``_cim`` will contain the computed cim
"""
np.fill_diagonal(self._cim, self._cim.diagonal() * -1)
self._cim = ((self._cim.T + 1) / (self._state_residence_times + 1)).T
@property
def state_residence_times(self) -> np.ndarray:
return self._state_residence_times
@property
def state_transition_matrix(self) -> np.ndarray:
return self._state_transition_matrix
@property
def cim(self) -> np.ndarray:
return self._cim
def __repr__(self):
return 'CIM:\n' + str(self.cim)

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main_package/PyCTBN/deprecated/sets_of_cims_container.py
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import set_of_cims as socim
class SetsOfCimsContainer:
"""
Aggrega un insieme di oggetti SetOfCims
"""
def __init__(self, list_of_keys, states_number_per_node, list_of_parents_states_number, p_combs_list):
self.sets_of_cims = None
self.init_cims_structure(list_of_keys, states_number_per_node, list_of_parents_states_number, p_combs_list)
#self.states_per_variable = states_number
def init_cims_structure(self, keys, states_number_per_node, list_of_parents_states_number, p_combs_list):
"""for indx, key in enumerate(keys):
self.sets_of_cims.append(
socim.SetOfCims(key, list_of_parents_states_number[indx], states_number_per_node[indx]))"""
self.sets_of_cims = [socim.SetOfCims(pair[1], list_of_parents_states_number[pair[0]], states_number_per_node[pair[0]], p_combs_list[pair[0]])
for pair in enumerate(keys)]
def get_set_of_cims(self, node_indx):
return self.sets_of_cims[node_indx]
def get_cims_of_node(self, node_indx, cim_indx):
return self.sets_of_cims[node_indx].get_cim(cim_indx)

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main_package/PyCTBN/json_importer.py
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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 ext.
with the following structure:
[0]
|_ dyn.cims
|_ dyn.str
|_ samples
|_ variabels
: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
:type samples_label: string
:param structure_label: the reference key for the structure of the network data
:type structure_label: string
:param variables_label: the reference key for the cardinalites of the nodes data
:type variables_label: string
:param time_key: the key used to identify the timestamps in each trajectory
:type time_key: string
:param variables_key: the key used to identify the names of the variables in the net
:type variables_key: string
:param array_indx: the index of the outer JsonArray to exctract the data from
:type array_indx: int
:_df_samples_list: a Dataframe list in which every dataframe contains a trajectory
"""
def __init__(self, file_path: str, samples_label: str, structure_label: str, variables_label: str, time_key: str,
variables_key: str, array_indx: int):
"""Constructor method
"""
self._samples_label = samples_label
self._structure_label = structure_label
self._variables_label = variables_label
self._time_key = time_key
self._variables_key = variables_key
self._df_samples_list = None
self._array_indx = array_indx
super(JsonImporter, self).__init__(file_path)
def import_data(self) -> None:
"""Implements the abstract method of :class:`AbstractImporter`
"""
raw_data = self.read_json_file()
self._df_samples_list = self.import_trajectories(raw_data)
self._sorter = self.build_sorter(self._df_samples_list[0])
self.compute_row_delta_in_all_samples_frames(self._df_samples_list)
self.clear_data_frame_list()
self._df_structure = self.import_structure(raw_data)
self._df_variables = self.import_variables(raw_data)
def import_trajectories(self, raw_data: typing.List) -> typing.List:
"""Imports the trajectories from the list of dicts ``raw_data``.
:param raw_data: List of Dicts
:type raw_data: List
:return: List of dataframes containing all the trajectories
:rtype: List
"""
return self.normalize_trajectories(raw_data, self._array_indx, self._samples_label)
def import_structure(self, raw_data: typing.List) -> pd.DataFrame:
"""Imports in a dataframe the data in the list raw_data at the key ``_structure_label``
:param raw_data: List of Dicts
:type raw_data: List
:return: Dataframe containg the starting node a ending node of every arc of the network
:rtype: pandas.Dataframe
"""
return self.one_level_normalizing(raw_data, self._array_indx, self._structure_label)
def import_variables(self, raw_data: typing.List) -> pd.DataFrame:
"""Imports the data in ``raw_data`` at the key ``_variables_label``.
:param raw_data: List of Dicts
:type raw_data: List
:return: Datframe containg the variables simbolic labels and their cardinalities
:rtype: pandas.Dataframe
"""
return self.one_level_normalizing(raw_data, self._array_indx, self._variables_label)
def read_json_file(self) -> typing.List:
"""Reads the JSON file in the path self.filePath
:return: The contents of the json file
:rtype: List
"""
with open(self._file_path) as f:
data = json.load(f)
return data
def one_level_normalizing(self, raw_data: typing.List, indx: int, key: str) -> pd.DataFrame:
"""Extracts the one-level nested data in the list ``raw_data`` at the index ``indx`` at the key ``key``.
:param raw_data: List of Dicts
:type raw_data: List
:param indx: The index of the array from which the data have to be extracted
:type indx: int
:param key: the key for the Dicts from which exctract data
:type key: string
:return: A normalized dataframe
:rtype: pandas.Datframe
"""
return pd.DataFrame(raw_data[indx][key])
def normalize_trajectories(self, raw_data: typing.List, indx: int, trajectories_key: str) -> typing.List:
"""
Extracts the trajectories in ``raw_data`` at the index ``index`` at the key ``trajectories key``.
:param raw_data: List of Dicts
:type raw_data: List
:param indx: The index of the array from which the data have to be extracted
:type indx: int
:param trajectories_key: the key of the trajectories objects
:type trajectories_key: string
:return: A list of daframes containg the trajectories
:rtype: List
"""
dataframe = pd.DataFrame
smps = raw_data[indx][trajectories_key]
df_samples_list = [dataframe(sample) for sample in smps]
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
"""
columns_header = list(sample_frame.columns.values)
columns_header.remove(self._time_key)
return columns_header
def clear_data_frame_list(self) -> None:
"""Removes all values present in the dataframes in the list ``_df_samples_list``.
"""
for indx in range(len(self._df_samples_list)):
self._df_samples_list[indx] = self._df_samples_list[indx].iloc[0:0]
def dataset_id(self) -> object:
return self._array_indx
def import_sampled_cims(self, raw_data: typing.List, indx: int, cims_key: str) -> typing.Dict:
"""Imports the synthetic CIMS in the dataset in a dictionary, using variables labels
as keys for the set of CIMS of a particular node.
:param raw_data: List of Dicts
:type raw_data: List
:param indx: The index of the array from which the data have to be extracted
:type indx: int
:param cims_key: the key where the json object cims are placed
:type cims_key: string
:return: a dictionary containing the sampled CIMS for all the variables in the net
:rtype: Dictionary
"""
cims_for_all_vars = {}
for var in raw_data[indx][cims_key]:
sampled_cims_list = []
cims_for_all_vars[var] = sampled_cims_list
for p_comb in raw_data[indx][cims_key][var]:
cims_for_all_vars[var].append(pd.DataFrame(raw_data[indx][cims_key][var][p_comb]).to_numpy())
return cims_for_all_vars

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main_package/PyCTBN/network_graph.py
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import typing
import networkx as nx
import numpy as np
#import structure as st
from .structure import Structure
class NetworkGraph:
"""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
:param graph_struct: the ``Structure`` object from which infos about the net will be extracted
:type graph_struct: Structure
:_graph: directed graph
:_aggregated_info_about_nodes_parents: 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.
:_time_scalar_indexing_structure: the indexing structure for state res time estimation
:_transition_scalar_indexing_structure: the indexing structure for transition computation
:_time_filtering: the columns filtering structure used in the computation of the state res times
:_transition_filtering: the columns filtering structure used in the computation of the transition
from one state to another
:_p_combs_structure: all the possible parents states combination for the node of interest
"""
def __init__(self, graph_struct: Structure):
"""Constructor Method
"""
self._graph_struct = graph_struct
self._graph = nx.DiGraph()
self._aggregated_info_about_nodes_parents = None
self._time_scalar_indexing_structure = None
self._transition_scalar_indexing_structure = None
self._time_filtering = None
self._transition_filtering = None
self._p_combs_structure = None
def fast_init(self, node_id: str) -> None:
"""Initializes all the necessary structures for parameters estimation of the node identified by the label
node_id
:param node_id: the label of the node
:type node_id: string
"""
self.add_nodes(self._graph_struct.nodes_labels)
self.add_edges(self._graph_struct.edges)
self._aggregated_info_about_nodes_parents = self.get_ordered_by_indx_set_of_parents(node_id)
p_indxs = self._aggregated_info_about_nodes_parents[1]
p_vals = self._aggregated_info_about_nodes_parents[2]
self._time_scalar_indexing_structure = self.build_time_scalar_indexing_structure_for_a_node(node_id,
p_vals)
self._transition_scalar_indexing_structure = self.build_transition_scalar_indexing_structure_for_a_node(node_id,
p_vals)
node_indx = self.get_node_indx(node_id)
self._time_filtering = self.build_time_columns_filtering_for_a_node(node_indx, p_indxs)
self._transition_filtering = self.build_transition_filtering_for_a_node(node_indx, p_indxs)
self._p_combs_structure = self.build_p_comb_structure_for_a_node(p_vals)
def add_nodes(self, list_of_nodes: typing.List) -> None:
"""Adds the nodes to the ``_graph`` contained in the list of nodes ``list_of_nodes``.
Sets all the properties that identify a nodes (index, positional index, cardinality)
:param list_of_nodes: the nodes to add to ``_graph``
:type list_of_nodes: List
"""
nodes_indxs = self._graph_struct.nodes_indexes
nodes_vals = self._graph_struct.nodes_values
pos = 0
for id, node_indx, node_val in zip(list_of_nodes, nodes_indxs, nodes_vals):
self._graph.add_node(id, indx=node_indx, val=node_val, pos_indx=pos)
pos += 1
def add_edges(self, list_of_edges: typing.List) -> None:
"""Add the edges to the ``_graph`` contained in the list ``list_of_edges``.
:param list_of_edges: the list containing of tuples containing the edges
:type list_of_edges: List
"""
self._graph.add_edges_from(list_of_edges)
def get_ordered_by_indx_set_of_parents(self, node: str) -> typing.Tuple:
"""Builds the aggregated structure that holds all the infos relative to the parent set of the node, namely
(parents_labels, parents_indexes, parents_cardinalities).
:param node: the label of the node
:type node: string
:return: a tuple containing all the parent set infos
:rtype: Tuple
"""
parents = self.get_parents_by_id(node)
nodes = self._graph_struct.nodes_labels
d = {v: i for i, v in enumerate(nodes)}
sorted_parents = sorted(parents, key=lambda v: d[v])
get_node_indx = self.get_node_indx
p_indxes = [get_node_indx(node) for node in sorted_parents]
p_values = [self.get_states_number(node) for node in sorted_parents]
return (sorted_parents, p_indxes, p_values)
def build_time_scalar_indexing_structure_for_a_node(self, node_id: str, parents_vals: typing.List) -> np.ndarray:
"""Builds an indexing structure for the computation of state residence times values.
:param node_id: the node label
:type node_id: string
:param parents_vals: the caridinalites of the node's parents
:type parents_vals: List
:return: The time indexing structure
:rtype: numpy.ndArray
"""
T_vector = np.array([self.get_states_number(node_id)])
T_vector = np.append(T_vector, parents_vals)
T_vector = T_vector.cumprod().astype(np.int)
return T_vector
def build_transition_scalar_indexing_structure_for_a_node(self, node_id: str, parents_vals: typing.List) \
-> np.ndarray:
"""Builds an indexing structure for the computation of state transitions values.
:param node_id: the node label
:type node_id: string
:param parents_vals: the caridinalites of the node's parents
:type parents_vals: List
:return: The transition indexing structure
:rtype: numpy.ndArray
"""
node_states_number = self.get_states_number(node_id)
M_vector = np.array([node_states_number,
node_states_number])
M_vector = np.append(M_vector, parents_vals)
M_vector = M_vector.cumprod().astype(np.int)
return M_vector
def build_time_columns_filtering_for_a_node(self, node_indx: int, p_indxs: typing.List) -> np.ndarray:
"""
Builds the necessary structure to filter the desired columns indicated by ``node_indx`` and ``p_indxs``
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
"""
return np.append(np.array([node_indx], dtype=np.int), p_indxs).astype(np.int)
def build_transition_filtering_for_a_node(self, node_indx: int, p_indxs: typing.List) -> np.ndarray:
"""Builds the necessary structure to filter the desired columns indicated by ``node_indx`` and ``p_indxs``
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
"""
nodes_number = self._graph_struct.total_variables_number
return np.array([node_indx + nodes_number, node_indx, *p_indxs], dtype=np.int)
def build_p_comb_structure_for_a_node(self, parents_values: typing.List) -> np.ndarray:
"""
Builds the combinatorial structure that contains the combinations of all the values contained in
``parents_values``.
:param parents_values: the cardinalities of the nodes
:type parents_values: List
:return: A numpy matrix containing a grid of the combinations
:rtype: numpy.ndArray
"""
tmp = []
for val in parents_values:
tmp.append([x for x in range(val)])
if len(parents_values) > 0:
parents_comb = np.array(np.meshgrid(*tmp)).T.reshape(-1, len(parents_values))
if len(parents_values) > 1:
tmp_comb = parents_comb[:, 1].copy()
parents_comb[:, 1] = parents_comb[:, 0].copy()
parents_comb[:, 0] = tmp_comb
else:
parents_comb = np.array([[]], dtype=np.int)
return parents_comb
def get_parents_by_id(self, node_id) -> typing.List:
"""Returns a list of labels of the parents of the node ``node_id``
:param node_id: the node label
:type node_id: string
:return: a List of labels of the parents
:rtype: List
"""
return list(self._graph.predecessors(node_id))
def get_states_number(self, node_id) -> int:
return self._graph.nodes[node_id]['val']
def get_node_indx(self, node_id) -> int:
return nx.get_node_attributes(self._graph, 'indx')[node_id]
def get_positional_node_indx(self, node_id) -> int:
return self._graph.nodes[node_id]['pos_indx']
@property
def nodes(self) -> typing.List:
return self._graph_struct.nodes_labels
@property
def edges(self) -> typing.List:
return list(self._graph.edges)
@property
def nodes_indexes(self) -> np.ndarray:
return self._graph_struct.nodes_indexes
@property
def nodes_values(self) -> np.ndarray:
return self._graph_struct.nodes_values
@property
def time_scalar_indexing_strucure(self) -> np.ndarray:
return self._time_scalar_indexing_structure
@property
def time_filtering(self) -> np.ndarray:
return self._time_filtering
@property
def transition_scalar_indexing_structure(self) -> np.ndarray:
return self._transition_scalar_indexing_structure
@property
def transition_filtering(self) -> np.ndarray:
return self._transition_filtering
@property
def p_combs(self) -> np.ndarray:
return self._p_combs_structure
"""
##############These Methods are actually unused but could become useful in the near future################
def init_graph(self):
self.add_nodes(self._nodes_labels)
self.add_edges(self._graph_struct.edges)
self._aggregated_info_about_nodes_parents = self.get_ord_set_of_par_of_all_nodes()
self._fancy_indexing = self.build_fancy_indexing_structure(0)
self.build_scalar_indexing_structures()
self.build_time_columns_filtering_structure()
self.build_transition_columns_filtering_structure()
self._p_combs_structure = self.build_p_combs_structure()
def build_time_columns_filtering_structure(self):
nodes_indxs = self._nodes_indexes
self._time_filtering = [np.append(np.array([node_indx], dtype=np.int), p_indxs).astype(np.int)
for node_indx, p_indxs in zip(nodes_indxs, self._fancy_indexing)]
def build_transition_columns_filtering_structure(self):
nodes_number = self._graph_struct.total_variables_number
nodes_indxs = self._nodes_indexes
self._transition_filtering = [np.array([node_indx + nodes_number, node_indx, *p_indxs], dtype=np.int)
for node_indx, p_indxs in zip(nodes_indxs,
self._fancy_indexing)]
def build_scalar_indexing_structures(self):
parents_values_for_all_nodes = self.get_ordered_by_indx_parents_values_for_all_nodes()
build_transition_scalar_indexing_structure_for_a_node = \
self.build_transition_scalar_indexing_structure_for_a_node
build_time_scalar_indexing_structure_for_a_node = self.build_time_scalar_indexing_structure_for_a_node
aggr = [(build_transition_scalar_indexing_structure_for_a_node(node_id, p_vals),
build_time_scalar_indexing_structure_for_a_node(node_id, p_vals))
for node_id, p_vals in
zip(self._nodes_labels,
parents_values_for_all_nodes)]
self._transition_scalar_indexing_structure = [i[0] for i in aggr]
self._time_scalar_indexing_structure = [i[1] for i in aggr]
def build_p_combs_structure(self):
parents_values_for_all_nodes = self.get_ordered_by_indx_parents_values_for_all_nodes()
p_combs_struct = [self.build_p_comb_structure_for_a_node(p_vals) for p_vals in parents_values_for_all_nodes]
return p_combs_struct
def get_ord_set_of_par_of_all_nodes(self):
get_ordered_by_indx_set_of_parents = self.get_ordered_by_indx_set_of_parents
result = [get_ordered_by_indx_set_of_parents(node) for node in self._nodes_labels]
return result
def get_ordered_by_indx_parents_values_for_all_nodes(self):
pars_values = [i[2] for i in self._aggregated_info_about_nodes_parents]
return pars_values
def build_fancy_indexing_structure(self, start_indx):
if start_indx > 0:
pass
else:
fancy_indx = [i[1] for i in self._aggregated_info_about_nodes_parents]
return fancy_indx
"""

495
main_package/PyCTBN/original_ctpc_algorithm.py
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@ -1,495 +0,0 @@
import glob
import json
import os
from itertools import combinations
import typing
import numpy as np
import pandas as pd
from line_profiler import LineProfiler
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
class OriginalCTPCAlgorithm(AbstractImporter):
"""
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]
|_ dyn.cims
|_ dyn.str
|_ samples
|_ variabels
:_file_path: the path of the file that contains tha data to be imported
:_samples_label: the reference key for the samples in the trajectories
:_structure_label: the reference key for the structure of the network data
:_variables_label: the reference key for the cardinalites of the nodes data
:_time_key: the key used to identify the timestamps in each trajectory
:_variables_key: the key used to identify the names of the variables in the net
:_df_samples_list: a Dataframe list in which every df contains a trajectory
"""
def dataset_id(self) -> object:
pass
def __init__(self, file_path: str, samples_label: str, structure_label: str, variables_label: str, time_key: str,
variables_key: str, array_indx: int):
"""
Parameters:
file_path: the path of the file that contains tha data to be imported
:_samples_label: the reference key for the samples in the trajectories
:_structure_label: the reference key for the structure of the network data
:_variables_label: the reference key for the cardinalites of the nodes data
:_time_key: the key used to identify the timestamps in each trajectory
:_variables_key: the key used to identify the names of the variables in the net
"""
self.samples_label = samples_label
self.structure_label = structure_label
self.variables_label = variables_label
self.time_key = time_key
self.variables_key = variables_key
self.df_samples_list = None
self.trajectories = None
self._array_indx = array_indx
self.matrix = None
super(OriginalCTPCAlgorithm, self).__init__(file_path)
def import_data(self):
"""
Imports and prepares all data present needed for subsequent processing.
Parameters:
:void
Returns:
_void
"""
raw_data = self.read_json_file()
self.df_samples_list = self.import_trajectories(raw_data)
self._sorter = self.build_sorter(self.df_samples_list[0])
#self.compute_row_delta_in_all_samples_frames(self._df_samples_list)
#self.clear_data_frame_list()
self._df_structure = self.import_structure(raw_data)
self._df_variables = self.import_variables(raw_data, self._sorter)
def import_trajectories(self, raw_data: typing.List):
"""
Imports the trajectories in the list of dicts raw_data.
Parameters:
:raw_data: List of Dicts
Returns:
:List of dataframes containing all the trajectories
"""
return self.normalize_trajectories(raw_data, self._array_indx, self.samples_label)
def import_structure(self, raw_data: typing.List) -> pd.DataFrame:
"""
Imports in a dataframe the data in the list raw_data at the key _structure_label
Parameters:
:raw_data: the data
Returns:
:Daframe containg the starting node a ending node of every arc of the network
"""
return self.one_level_normalizing(raw_data, self._array_indx, self.structure_label)
def import_variables(self, raw_data: typing.List, sorter: typing.List) -> pd.DataFrame:
"""
Imports the data in raw_data at the key _variables_label.
Sorts the row of the dataframe df_variables using the list sorter.
Parameters:
:raw_data: the data
:sorter: the header of the dataset containing only variables symbolic labels
Returns:
:Datframe containg the variables simbolic labels and their cardinalities
"""
return self.one_level_normalizing(raw_data, self._array_indx, self.variables_label)
#TODO Usando come Pre-requisito l'ordinamento del frame _df_variables uguale a quello presente in
#TODO self _sorter questo codice risulta inutile
"""self._df_variables[self._variables_key] = self._df_variables[self._variables_key].astype("category")
self._df_variables[self._variables_key] = self._df_variables[self._variables_key].cat.set_categories(sorter)
self._df_variables = self._df_variables.sort_values([self._variables_key])
self._df_variables.reset_index(inplace=True)
self._df_variables.drop('index', axis=1, inplace=True)
#print("Var Frame", self._df_variables)
"""
def read_json_file(self) -> typing.List:
"""
Reads the JSON file in the path self.filePath
Parameters:
:void
Returns:
:data: the contents of the json file
"""
with open(self._file_path) as f:
data = json.load(f)
return data
def one_level_normalizing(self, raw_data: typing.List, indx: int, key: str) -> pd.DataFrame:
"""
Extracts the one-level nested data in the list raw_data at the index indx at the key key
Parameters:
:raw_data: List of Dicts
:indx: The index of the array from which the data have to be extracted
:key: the key for the Dicts from which exctract data
Returns:
:a normalized dataframe:
"""
return pd.DataFrame(raw_data[indx][key])
def normalize_trajectories(self, raw_data: typing.List, indx: int, trajectories_key: str):
"""
Extracts the traj in raw_data at the index index at the key trajectories key.
Parameters:
:raw_data: the data
:indx: the index of the array from which extract data
:trajectories_key: the key of the trajectories objects
Returns:
:A list of daframes containg the trajectories
"""
dataframe = pd.DataFrame
smps = raw_data[indx][trajectories_key]
df_samples_list = [dataframe(sample) for sample in smps]
return df_samples_list
#columns_header = list(self._df_samples_list[0].columns.values)
#columns_header.remove(self._time_key)
#self._sorter = columns_header
def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
"""
Implements the abstract method build_sorter for this dataset
"""
columns_header = list(sample_frame.columns.values)
columns_header.remove(self.time_key)
return columns_header
def clear_data_frame_list(self):
"""
Removes all values present in the dataframes in the list _df_samples_list
Parameters:
:void
Returns:
:void
"""
for indx in range(len(self.df_samples_list)):
self.df_samples_list[indx] = self.df_samples_list[indx].iloc[0:0]
def prepare_trajectories(self, trajectories, variables):
"""
Riformula le traiettorie per rendere più efficiente la fase di computazione delle cim
Parameters
-------------
trajectories: [pandas.DataFrame]
Un array di pandas dataframe contenente tutte le traiettorie. Ogni array avrà una
colonna per il timestamp (sempre la prima) e n colonne una per ogni variabili
presente nella rete.
variables: pandas.DataFrame
Pandas dataframe contenente due colonne: il nome della variabile e cardinalità
della variabile
"""
dimensions = np.array([x.shape[0] - 1 for x in trajectories], dtype=np.int)
ret_array = np.zeros([dimensions.sum(), trajectories[0].shape[1] * 2])
cum_dim = np.zeros(len(trajectories) + 1, dtype=np.int)
cum_dim[1:] = dimensions.cumsum()
dimensions.cumsum()
for it in range(len(trajectories)):
tmp = trajectories[it].to_numpy()
dim = tmp.shape[1]
ret_array[cum_dim[it]:cum_dim[it + 1], 0:dim] = tmp[:-1]
ret_array[cum_dim[it]:cum_dim[it + 1], dim] = np.diff(tmp[:, 0])
ret_array[cum_dim[it]:cum_dim[it + 1], dim + 1:] = np.roll(tmp[:, 1:], -1, axis=0)[:-1]
self.trajectories = ret_array
#self.variables = variables
@staticmethod
def _compute_cim(trajectories, child_id, parents_id, T_vector, M_vector, parents_comb, M, T):
"""Funzione interna per calcolare le CIM
Parameters:
-----------
trajectories: np.array
Array contenente le traiettorie. (self.trajectories)
child_id: int
Indice del nodo di cui si vogliono calcolare le cim
parents:id: [int]
Array degli indici dei genitori nel nodo child_id
T_vector: np.array
Array numpy per l'indicizzazione dell'array T
M_vector: np.array
Array numpy per l'indicizzazione dell'array M
parents_comb: [(int)]
Array di tuple contenenti tutte le possibili combinazioni dei genitori di child_id
M: np.array
Array numpy contenente la statistica sufficiente M
T: np.array
Array numpy contenente la statistica sufficiente T
Returns:
---------
CIM: np.array
Array numpy contenente le CIM
"""
#print(T)
diag_indices = np.array([x * M.shape[1] + x % M.shape[1] for x in range(M.shape[0] * M.shape[1])],
dtype=np.int64)
#print(diag_indices)
T_filter = np.array([child_id, *parents_id], dtype=np.int) + 1
#print("TFilter",T_filter)
#print("TVector", T_vector)
#print("Trajectories", trajectories)
#print("Actual TVect",T_vector / T_vector[0])
#print("Masked COlumns", trajectories[:, T_filter]) # Colonne non shiftate dei values
#print("Masked Multiplied COlumns",trajectories[:, T_filter] * (T_vector / T_vector[0]) )
#print("Summing",np.sum(trajectories[:, T_filter] * (T_vector / T_vector[0]), axis=1))
#print("Deltas",trajectories[:, int(trajectories.shape[1] / 2)]) # i delta times
assert np.sum(trajectories[:, T_filter] * (T_vector / T_vector[0]), axis=1).size == \
trajectories[:, int(trajectories.shape[1] / 2)].size
#print(T_vector[-1])
T[:] = np.bincount(np.sum(trajectories[:, T_filter] * T_vector / T_vector[0], axis=1).astype(np.int), \
trajectories[:, int(trajectories.shape[1] / 2)], minlength=T_vector[-1]).reshape(-1,
T.shape[1])
#print("Shape", T.shape[1])
#print(np.bincount(np.sum(trajectories[:, T_filter] * T_vector / T_vector[0], axis=1).astype(np.int), \
#trajectories[:, int(trajectories.shape[1] / 2)], minlength=T_vector[-1]))
###### Transitions #######
#print("Shifted Node column", trajectories[:, int(trajectories.shape[1] / 2) + 1 + child_id].astype(np.int))
#print("Step 2", trajectories[:, int(trajectories.shape[1] / 2) + 1 + child_id].astype(np.int) >= 0)
trj_tmp = trajectories[trajectories[:, int(trajectories.shape[1] / 2) + 1 + child_id].astype(np.int) >= 0]
#print("Trj Temp", trj_tmp)
M_filter = np.array([child_id, child_id, *parents_id], dtype=np.int) + 1
#print("MFilter", M_filter)
M_filter[0] += int(trj_tmp.shape[1] / 2)
#print("MFilter", M_filter)
#print("MVector", M_vector)
#print("Division", M_vector / M_vector[0])
#print("Masked Traj temp", (trj_tmp[:, M_filter]))
#print("Masked Multiplied Traj temp", trj_tmp[:, M_filter] * M_vector / M_vector[0])
#print("Summing", np.sum(trj_tmp[:, M_filter] * M_vector / M_vector[0], axis=1))
#print(M.shape[2])
M[:] = np.bincount(np.sum(trj_tmp[:, M_filter] * M_vector / M_vector[0], axis=1).astype(np.int), \
minlength=M_vector[-1]).reshape(-1, M.shape[1], M.shape[2])
#print("M!!!!!!!", M)
M_raveled = M.ravel()
#print("Raveled", M_raveled)
M_raveled[diag_indices] = 0
M_raveled[diag_indices] = np.sum(M, axis=2).ravel()
#print("Raveled", M_raveled)
q = (M.ravel()[diag_indices].reshape(-1, M.shape[1]) + 1) / (T + 1)
theta = (M + 1) / (M.ravel()[diag_indices].reshape(-1, M.shape[2], 1) + 1)
negate_main_diag = np.ones((M.shape[1], M.shape[2]))
np.fill_diagonal(negate_main_diag, -1)
theta = np.multiply(theta, negate_main_diag)
return theta * q.reshape(-1, M.shape[2], 1)
def compute_cim(self, child_id, parents_id):
"""Metodo utilizzato per calcolare le CIM di un nodo dati i suoi genitori
Parameters:
-----------
child_id: int
Indice del nodo di cui si vogliono calcolare le cim
parents:id: [int]
Array degli indici dei genitori nel nodo child_id
Return:
----------
Restituisce una tupla contenente:
parents_comb: [(int)]
Array di tuple contenenti tutte le possibili combinazioni dei genitori di child_id
M: np.array
Array numpy contenente la statistica sufficiente M
T: np.array
Array numpy contenente la statistica sufficiente T
CIM: np.array
Array numpy contenente le CIM
"""
tmp = []
child_id = int(child_id)
parents_id = np.array(parents_id, dtype=np.int)
parents_id.sort()
#print("Parents id",parents_id)
#breakpoint()
for idx in parents_id:
tmp.append([x for x in range(self.variables.loc[idx, "Value"])])
#print("TIMP", tmp)
if len(parents_id) > 0:
parents_comb = np.array(np.meshgrid(*tmp)).T.reshape(-1, len(parents_id))
#print(np.argsort(parents_comb))
#print("PArents COmb", parents_comb)
if len(parents_id) > 1:
tmp_comb = parents_comb[:, 1].copy()
#print(tmp_comb)
parents_comb[:, 1] = parents_comb[:, 0].copy()
parents_comb[:, 0] = tmp_comb
else:
parents_comb = np.array([[]], dtype=np.int)
#print("PARENTS COMB ", parents_comb)
M = np.zeros([max(1, parents_comb.shape[0]), \
self.variables.loc[child_id, "Value"], \
self.variables.loc[child_id, "Value"]], dtype=np.int)
#print(M)
T = np.zeros([max(1, parents_comb.shape[0]), \
self.variables.loc[child_id, "Value"]], dtype=np.float)
#print(T)
#print("T Vector")
#print(child_id)
T_vector = np.array([self.variables.iloc[child_id, 1].astype(np.int)])
#print(T_vector)
#for x in parents_id:
#print(self.variables.iloc[x, 1])
T_vector = np.append(T_vector, [self.variables.iloc[x, 1] for x in parents_id])
#print(T_vector)
T_vector = T_vector.cumprod().astype(np.int)
#print(T_vector)
#print("M Vector")
M_vector = np.array([self.variables.iloc[child_id, 1], self.variables.iloc[child_id, 1].astype(np.int)])
#print(M_vector)
M_vector = np.append(M_vector, [self.variables.iloc[x, 1] for x in parents_id])
#for x in parents_id:
#print(self.variables.iloc[x, 1])
M_vector = M_vector.cumprod().astype(np.int)
#print("MVECTOR", M_vector)
CIM = self._compute_cim(self.trajectories, child_id, parents_id, T_vector, M_vector, parents_comb, M, T)
return parents_comb, M, T, CIM
def independence_test(self, to_var, from_var, sep_set, alpha_exp, alpha_chi2, thumb_threshold):
#print("To var", to_var)
#print("From var", from_var)
#print("sep set", sep_set)
parents = np.array(sep_set)
parents = np.append(parents, from_var)
parents.sort()
#print("PARENTS", parents)
parents_no_from_mask = parents != from_var
#print("Parents Comb NO Mask", parents_no_from_mask)
parents_comb_from, M_from, T_from, CIM_from = self.compute_cim(to_var, parents)
#print("Parents Comb From", parents_comb_from)
#print("C2:", CIM_from)
if self.variables.loc[to_var, "Value"] > 2:
df = (self.variables.loc[to_var, "Value"] - 1) ** 2
df = df * (self.variables.loc[from_var, "Value"])
for v in sep_set:
df = df * (self.variables.loc[v, "Value"])
if np.all(np.sum(np.diagonal(M_from, axis1=1, axis2=2), axis=1) / df < thumb_threshold):
return False
#print("Before CHi quantile", self.variables.loc[to_var, "Value"] - 1)
chi_2_quantile = chi2_dist.ppf(1 - alpha_chi2, self.variables.loc[to_var, "Value"] - 1)
#print("Chi Quantile", chi_2_quantile)
parents_comb, M, T, CIM = self.compute_cim(to_var, parents[parents_no_from_mask])
#print("C1", CIM)
for comb_id in range(parents_comb.shape[0]):
# Bad code, inefficient
#print("COMB ID", comb_id)
if parents.shape[0] > 1:
#print("STEP 0", parents_comb_from[:, parents_no_from_mask])
#print("STEP 1", np.all(parents_comb_from[:, parents_no_from_mask] == parents_comb[comb_id], axis=1))
#print("STEP 2", np.argwhere(
#np.all(parents_comb_from[:, parents_no_from_mask] == parents_comb[comb_id], axis=1)).ravel())
tmp_parents_comb_from_ids = np.argwhere(
np.all(parents_comb_from[:, parents_no_from_mask] == parents_comb[comb_id], axis=1)).ravel()
else:
tmp_parents_comb_from_ids = np.array([x for x in range(parents_comb_from.shape[0])])
#print("TMP PAR COMB IDSSSS:", tmp_parents_comb_from_ids)
for comb_from_id in tmp_parents_comb_from_ids:
#print("COMB ID FROM", comb_from_id)
diag = np.diag(CIM[comb_id])
diag_from = np.diag(CIM_from[comb_from_id])
#print("Diag C2", diag_from)
#print("Diag C1", diag)
r1 = np.diag(M[comb_id])
r2 = np.diag(M_from[comb_from_id])
stats = diag_from / diag
#print("Exponential Test", stats, r1, r2)
for id_diag in range(diag.shape[0]):
if stats[id_diag] < f_dist.ppf(alpha_exp / 2, r1[id_diag], r2[id_diag]) or \
stats[id_diag] > f_dist.ppf(1 - alpha_exp / 2, r1[id_diag], r2[id_diag]):
return False
if diag.shape[0] > 2:
# https://www.itl.nist.gov/div898/software/dataplot/refman1/auxillar/chi2samp.htm
K_from = np.sqrt(M[comb_id].diagonal() / M_from[comb_from_id].diagonal())
K = np.sqrt(M_from[comb_from_id].diagonal() / M[comb_id].diagonal())
#print("K From", K_from)
#print("K ", K)
M_no_diag = M[comb_id][~np.eye(diag.shape[0], dtype=np.bool)].reshape(diag.shape[0], -1)
M_from_no_diag = M_from[comb_from_id][~np.eye(diag.shape[0], dtype=np.bool)].reshape(diag.shape[0],
-1)
#print("M No Diag", M_no_diag)
#print("M From No Diag", M_from_no_diag)
chi_stats = np.sum((np.power((M_no_diag.T * K).T - (M_from_no_diag.T * K_from).T, 2) \
/ (M_no_diag + M_from_no_diag)), axis=1)
#print("Chi stats", chi_stats)
#print("Chi Quantile", chi_2_quantile)
if np.any(chi_stats > chi_2_quantile):
return False
return True
def cb_structure_algo(self, alpha_exp=0.1, alpha_chi2=0.1, thumb_threshold=25):
adj_matrix = np.ones((self.variables.shape[0], self.variables.shape[0]), dtype=np.bool)
np.fill_diagonal(adj_matrix, False)
for to_var in tqdm(range(self.variables.shape[0])):
n = 0
tested_variables = np.argwhere(adj_matrix[:, to_var]).ravel()
while n < tested_variables.shape[0]:
for from_var in tested_variables:
if from_var not in tested_variables:
continue
if n >= tested_variables.shape[0]:
break
sep_set_vars = tested_variables[tested_variables != from_var]
for comb in combinations(sep_set_vars, n):
if self.independence_test(to_var, from_var, comb, alpha_exp, alpha_chi2, thumb_threshold):
#print("######REMOVING EDGE #############", from_var, to_var)
adj_matrix[from_var, to_var] = False
tested_variables = np.argwhere(adj_matrix[:, to_var]).ravel()
break
n += 1
#print("MATRIZ:", adj_matrix)
self.matrix = adj_matrix

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main_package/PyCTBN/parameters_estimator.py
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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``.
:param trajectories: the trajectories
:type trajectories: Trajectory
:param net_graph: the net structure
:type net_graph: NetworkGraph
:_single_set_of_cims: the set of cims object that will hold the cims of the node
"""
def __init__(self, trajectories: Trajectory, net_graph: NetworkGraph):
"""Constructor Method
"""
self._trajectories = trajectories
self._net_graph = net_graph
self._single_set_of_cims = None
def fast_init(self, node_id: str) -> None:
"""Initializes all the necessary structures for the parameters estimation for the node ``node_id``.
:param node_id: the node label
:type node_id: string
"""
p_vals = self._net_graph._aggregated_info_about_nodes_parents[2]
node_states_number = self._net_graph.get_states_number(node_id)
self._single_set_of_cims = SetOfCims(node_id, p_vals, node_states_number, self._net_graph.p_combs)
def compute_parameters_for_node(self, node_id: str) -> SetOfCims:
"""Compute the CIMS of the node identified by the label ``node_id``.
:param node_id: the node label
:type node_id: string
:return: A SetOfCims object filled with the computed CIMS
:rtype: SetOfCims
"""
node_indx = self._net_graph.get_node_indx(node_id)
state_res_times = self._single_set_of_cims._state_residence_times
transition_matrices = self._single_set_of_cims._transition_matrices
self.compute_state_res_time_for_node(node_indx, self._trajectories.times,
self._trajectories.trajectory,
self._net_graph.time_filtering,
self._net_graph.time_scalar_indexing_strucure,
state_res_times)
self.compute_state_transitions_for_a_node(node_indx,
self._trajectories.complete_trajectory,
self._net_graph.transition_filtering,
self._net_graph.transition_scalar_indexing_structure,
transition_matrices)
self._single_set_of_cims.build_cims(state_res_times, transition_matrices)
return self._single_set_of_cims
def compute_state_res_time_for_node(self, node_indx: int, times: np.ndarray, trajectory: np.ndarray,
cols_filter: np.ndarray, scalar_indexes_struct: np.ndarray,
T: np.ndarray) -> None:
"""Compute the state residence times for a node and fill the matrix ``T`` with the results
:param node_indx: the index of the node
:type node_indx: int
:param times: the times deltas vector
:type times: numpy.array
:param trajectory: the trajectory
:type trajectory: numpy.ndArray
:param cols_filter: the columns filtering structure
:type cols_filter: numpy.array
:param scalar_indexes_struct: the indexing structure
:type scalar_indexes_struct: numpy.array
:param T: the state residence times vectors
:type T: numpy.ndArray
"""
T[:] = np.bincount(np.sum(trajectory[:, cols_filter] * scalar_indexes_struct / scalar_indexes_struct[0], axis=1)
.astype(np.int), \
times,
minlength=scalar_indexes_struct[-1]).reshape(-1, T.shape[1])
def compute_state_transitions_for_a_node(self, node_indx: int, trajectory: np.ndarray, cols_filter: np.ndarray,
scalar_indexing: np.ndarray, M: np.ndarray):
"""Compute the state residence times for a node and fill the matrices ``M`` with the results.
:param node_indx: the index of the node
:type node_indx: int
:param trajectory: the trajectory
:type trajectory: numpy.ndArray
:param cols_filter: the columns filtering structure
:type cols_filter: numpy.array
:param scalar_indexing: the indexing structure
:type scalar_indexing: numpy.array
:param M: the state transitions matrices
:type M: numpy.ndArray
"""
diag_indices = np.array([x * M.shape[1] + x % M.shape[1] for x in range(M.shape[0] * M.shape[1])],
dtype=np.int64)
trj_tmp = trajectory[trajectory[:, int(trajectory.shape[1] / 2) + node_indx].astype(np.int) >= 0]
M[:] = np.bincount(np.sum(trj_tmp[:, cols_filter] * scalar_indexing / scalar_indexing[0], axis=1).astype(np.int),
minlength=scalar_indexing[-1]).reshape(-1, M.shape[1], M.shape[2])
M_raveled = M.ravel()
M_raveled[diag_indices] = 0
M_raveled[diag_indices] = np.sum(M, axis=2).ravel()
"""
##############These Methods are actually unused but could become useful in the near future################
def init_sets_cims_container(self):
self.sets_of_cims_struct = acims.SetsOfCimsContainer(self._net_graph.nodes,
self._net_graph.nodes_values,
self._net_graph.
get_ordered_by_indx_parents_values_for_all_nodes(),
self._net_graph.p_combs)
def compute_parameters(self):
for indx, aggr in enumerate(zip(self._net_graph.nodes, self.sets_of_cims_struct.sets_of_cims)):
self.compute_state_res_time_for_node(self._net_graph.get_node_indx(aggr[0]), self.sample_path.trajectories.times,
self.sample_path.trajectories.trajectory,
self._net_graph.time_filtering[indx],
self._net_graph.time_scalar_indexing_strucure[indx],
aggr[1]._state_residence_times)
self.compute_state_transitions_for_a_node(self._net_graph.get_node_indx(aggr[0]),
self.sample_path.trajectories.complete_trajectory,
self._net_graph.transition_filtering[indx],
self._net_graph.transition_scalar_indexing_structure[indx],
aggr[1]._transition_matrices)
aggr[1].build_cims(aggr[1]._state_residence_times, aggr[1]._transition_matrices)
"""

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main_package/PyCTBN/sample_path.py
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#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
class SamplePath:
"""Aggregates all the informations about the trajectories, the real structure of the sampled net and variables
cardinalites. Has the task of creating the objects ``Trajectory`` and ``Structure`` that will
contain the mentioned data.
:param importer: the Importer objects that will import ad process data
:type importer: AbstractImporter
:_trajectories: the ``Trajectory`` object that will contain all the concatenated trajectories
:_structure: the ``Structure`` Object that will contain all the structurral infos about the net
:_total_variables_count: the number of variables in the net
"""
def __init__(self, importer: AbstractImporter):
"""Constructor Method
"""
self._importer = importer
self._trajectories = None
self._structure = None
self._total_variables_count = None
self._importer.import_data()
def build_trajectories(self) -> None:
"""Builds the Trajectory object that will contain all the trajectories.
Clears all the unused dataframes in ``_importer`` Object
"""
self._trajectories = \
Trajectory(self._importer.build_list_of_samples_array(self._importer.concatenated_samples),
len(self._importer.sorter) + 1)
self._importer.clear_concatenated_frame()
def build_structure(self) -> None:
"""
Builds the ``Structure`` object that aggregates all the infos about the net.
"""
if self._importer.sorter != self._importer.variables.iloc[:, 0].to_list():
raise RuntimeError("The Dataset columns order have to match the order of labels in the variables Frame!")
self._total_variables_count = len(self._importer.sorter)
labels = self._importer.variables.iloc[:, 0].to_list()
indxs = self._importer.variables.index.to_numpy()
vals = self._importer.variables.iloc[:, 1].to_numpy()
edges = list(self._importer.structure.to_records(index=False))
self._structure = Structure(labels, indxs, vals, edges,
self._total_variables_count)
@property
def trajectories(self) -> Trajectory:
return self._trajectories
@property
def structure(self) -> Structure:
return self._structure
@property
def total_variables_count(self):
return self._total_variables_count

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main_package/PyCTBN/set_of_cims.py
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import typing
import numpy as np
#import conditional_intensity_matrix as cim
from .conditional_intensity_matrix import ConditionalIntensityMatrix
class SetOfCims:
"""Aggregates all the CIMS of the node identified by the label _node_id.
:param node_id: the node label
:type node_ind: string
:param parents_states_number: the cardinalities of the parents
:type parents_states_number: List
:param node_states_number: the caridinality of the node
:type node_states_number: int
:param p_combs: the p_comb structure bound to this node
:type p_combs: numpy.ndArray
:_state_residence_time: matrix containing all the state residence time vectors for the node
:_transition_matrices: matrix containing all the transition matrices for the node
:_actual_cims: the cims of the node
"""
def __init__(self, node_id: str, parents_states_number: typing.List, node_states_number: int, p_combs: np.ndarray):
"""Constructor Method
"""
self._node_id = node_id
self._parents_states_number = parents_states_number
self._node_states_number = node_states_number
self._actual_cims = []
self._state_residence_times = None
self._transition_matrices = None
self._p_combs = p_combs
self.build_times_and_transitions_structures()
def build_times_and_transitions_structures(self) -> None:
"""Initializes at the correct dimensions the state residence times matrix and the state transition matrices.
"""
if not self._parents_states_number:
self._state_residence_times = np.zeros((1, self._node_states_number), dtype=np.float)
self._transition_matrices = np.zeros((1, self._node_states_number, self._node_states_number), dtype=np.int)
else:
self._state_residence_times = \
np.zeros((np.prod(self._parents_states_number), self._node_states_number), dtype=np.float)
self._transition_matrices = np.zeros([np.prod(self._parents_states_number), self._node_states_number,
self._node_states_number], dtype=np.int)
def build_cims(self, state_res_times: np.ndarray, transition_matrices: np.ndarray) -> None:
"""Build the ``ConditionalIntensityMatrix`` objects given the state residence times and transitions matrices.
Compute the cim coefficients.The class member ``_actual_cims`` will contain the computed cims.
:param state_res_times: the state residence times matrix
:type state_res_times: numpy.ndArray
:param transition_matrices: the transition matrices
:type transition_matrices: numpy.ndArray
"""
for state_res_time_vector, transition_matrix in zip(state_res_times, transition_matrices):
cim_to_add = ConditionalIntensityMatrix(state_res_time_vector, transition_matrix)
cim_to_add.compute_cim_coefficients()
self._actual_cims.append(cim_to_add)
self._actual_cims = np.array(self._actual_cims)
self._transition_matrices = None
self._state_residence_times = None
def filter_cims_with_mask(self, mask_arr: np.ndarray, comb: typing.List) -> np.ndarray:
"""Filter the cims contained in the array ``_actual_cims`` given the boolean mask ``mask_arr`` and the index
``comb``.
:param mask_arr: the boolean mask that indicates which parent to consider
:type mask_arr: numpy.array
:param comb: the state/s of the filtered parents
:type comb: numpy.array
:return: Array of ``ConditionalIntensityMatrix`` objects
:rtype: numpy.array
"""
if mask_arr.size <= 1:
return self._actual_cims
else:
flat_indxs = np.argwhere(np.all(self._p_combs[:, mask_arr] == comb, axis=1)).ravel()
return self._actual_cims[flat_indxs]
@property
def actual_cims(self) -> np.ndarray:
return self._actual_cims
@property
def p_combs(self) -> np.ndarray:
return self._p_combs
def get_cims_number(self):
return len(self._actual_cims)

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main_package/PyCTBN/simple_cvs_importer.py
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import pandas as pd
import glob
import os
import typing
#import abstract_importer as ai
#import sample_path as sp
from .abstract_importer import AbstractImporter
from .sample_path import SamplePath
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
def main():
read_files = glob.glob(os.path.join('../data', "*.csv"))
print(read_files[0])
csvimp = CSVImporter(read_files[0])
s1 = SamplePath(csvimp)
s1.build_trajectories()
s1.build_structure()
print(s1.structure)
print(s1.trajectories)
if __name__ == "__main__":
main()

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main_package/PyCTBN/structure.py
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import typing as ty
import numpy as np
class Structure:
"""Contains all the infos about the network structure(nodes labels, nodes caridinalites, edges, indexes)
:param nodes_labels_list: the symbolic names of the variables
:type nodes_labels_list: List
:param nodes_indexes_arr: the indexes of the nodes
:type nodes_indexes_arr: numpy.ndArray
:param nodes_vals_arr: the cardinalites of the nodes
:type nodes_vals_arr: numpy.ndArray
:param edges_list: the edges of the network
:type edges_list: List
:param total_variables_number: the total number of variables in the net
:type total_variables_number: int
"""
def __init__(self, nodes_labels_list: ty.List, nodes_indexes_arr: np.ndarray, nodes_vals_arr: np.ndarray,
edges_list: ty.List, total_variables_number: int):
"""Constructor Method
"""
self._nodes_labels_list = nodes_labels_list
self._nodes_indexes_arr = nodes_indexes_arr
self._nodes_vals_arr = nodes_vals_arr
self._edges_list = edges_list
self._total_variables_number = total_variables_number
@property
def edges(self) -> ty.List:
return self._edges_list
@property
def nodes_labels(self) -> ty.List:
return self._nodes_labels_list
@property
def nodes_indexes(self) -> np.ndarray:
return self._nodes_indexes_arr
@property
def nodes_values(self) -> np.ndarray:
return self._nodes_vals_arr
@property
def total_variables_number(self) -> int:
return self._total_variables_number
def get_node_id(self, node_indx: int) -> str:
"""Given the ``node_index`` returns the node label.
:param node_indx: the node index
:type node_indx: int
:return: the node label
:rtype: string
"""
return self._nodes_labels_list[node_indx]
def get_node_indx(self, node_id: str) -> int:
"""Given the ``node_index`` returns the node label.
:param node_id: the node label
:type node_id: string
:return: the node index
:rtype: int
"""
pos_indx = self._nodes_labels_list.index(node_id)
return self._nodes_indexes_arr[pos_indx]
def get_positional_node_indx(self, node_id: str) -> int:
return self._nodes_labels_list.index(node_id)
def get_states_number(self, node: str) -> int:
"""Given the node label ``node`` returns the cardinality of the node.
:param node: the node label
:type node: string
:return: the node cardinality
:rtype: int
"""
pos_indx = self._nodes_labels_list.index(node)
return self._nodes_vals_arr[pos_indx]
def __repr__(self):
return "Variables:\n" + str(self._nodes_labels_list) +"\nValues:\n"+ str(self._nodes_vals_arr) +\
"\nEdges: \n" + str(self._edges_list)
def __eq__(self, other):
"""Overrides the default implementation"""
if isinstance(other, Structure):
return set(self._nodes_labels_list) == set(other._nodes_labels_list) and \
np.array_equal(self._nodes_vals_arr, other._nodes_vals_arr) and \
np.array_equal(self._nodes_indexes_arr, other._nodes_indexes_arr) and \
self._edges_list == other._edges_list
return NotImplemented

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from tqdm import tqdm
import itertools
import json
import typing
import networkx as nx
import numpy as np
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
from .parameters_estimator import ParametersEstimator
from .sample_path import SamplePath
from .structure import Structure
class StructureEstimator:
"""Has the task of estimating the network structure given the trajectories in ``samplepath``.
:param sample_path: the _sample_path object containing the trajectories and the real structure
:type sample_path: SamplePath
:param exp_test_alfa: the significance level for the exponential Hp test
:type exp_test_alfa: float
:param chi_test_alfa: the significance level for the chi Hp test
:type chi_test_alfa: float
:_nodes: the nodes labels
:_nodes_vals: the nodes cardinalities
:_nodes_indxs: the nodes indexes
:_complete_graph: the complete directed graph built using the nodes labels in ``_nodes``
:_cache: the Cache object
"""
def __init__(self, sample_path: SamplePath, exp_test_alfa: float, chi_test_alfa: float):
"""Constructor Method
"""
self._sample_path = sample_path
self._nodes = np.array(self._sample_path.structure.nodes_labels)
self._nodes_vals = self._sample_path.structure.nodes_values
self._nodes_indxs = self._sample_path.structure.nodes_indexes
self._complete_graph = self.build_complete_graph(self._sample_path.structure.nodes_labels)
self._exp_test_sign = exp_test_alfa
self._chi_test_alfa = chi_test_alfa
self._cache = Cache()
def build_complete_graph(self, node_ids: typing.List) -> nx.DiGraph:
"""Builds a complete directed graph (no self loops) given the nodes labels in the list ``node_ids``:
:param node_ids: the list of nodes labels
:type node_ids: List
:return: a complete Digraph Object
:rtype: networkx.DiGraph
"""
complete_graph = nx.DiGraph()
complete_graph.add_nodes_from(node_ids)
complete_graph.add_edges_from(itertools.permutations(node_ids, 2))
return complete_graph
def complete_test(self, test_parent: str, test_child: str, parent_set: typing.List, child_states_numb: int,
tot_vars_count: int) -> bool:
"""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.
:param test_parent: the node label of the test parent
:type test_parent: string
:param test_child: the node label of the child
:type test_child: string
:param parent_set: the common parent set
:type parent_set: List
:param child_states_numb: the cardinality of the ``test_child``
:type child_states_numb: int
:param tot_vars_count: the total number of variables in the net
:type tot_vars_count: int
:return: True iff test_child and test_parent are independent given the sep_set parent_set. False otherwise
:rtype: bool
"""
p_set = parent_set[:]
complete_info = parent_set[:]
complete_info.append(test_child)
parents = np.array(parent_set)
parents = np.append(parents, test_parent)
sorted_parents = self._nodes[np.isin(self._nodes, parents)]
cims_filter = sorted_parents != test_parent
sofc1 = self._cache.find(set(p_set))
if not sofc1:
bool_mask1 = np.isin(self._nodes, complete_info)
l1 = list(self._nodes[bool_mask1])
indxs1 = self._nodes_indxs[bool_mask1]
vals1 = self._nodes_vals[bool_mask1]
eds1 = list(itertools.product(parent_set,test_child))
s1 = Structure(l1, indxs1, vals1, eds1, tot_vars_count)
g1 = NetworkGraph(s1)
g1.fast_init(test_child)
p1 = ParametersEstimator(self._sample_path.trajectories, g1)
p1.fast_init(test_child)
sofc1 = p1.compute_parameters_for_node(test_child)
self._cache.put(set(p_set), sofc1)
sofc2 = None
p_set.insert(0, test_parent)
if p_set:
sofc2 = self._cache.find(set(p_set))
if not sofc2:
complete_info.append(test_parent)
bool_mask2 = np.isin(self._nodes, complete_info)
l2 = list(self._nodes[bool_mask2])
indxs2 = self._nodes_indxs[bool_mask2]
vals2 = self._nodes_vals[bool_mask2]
eds2 = list(itertools.product(p_set, test_child))
s2 = Structure(l2, indxs2, vals2, eds2, tot_vars_count)
g2 = NetworkGraph(s2)
g2.fast_init(test_child)
p2 = ParametersEstimator(self._sample_path.trajectories, g2)
p2.fast_init(test_child)
sofc2 = p2.compute_parameters_for_node(test_child)
self._cache.put(set(p_set), sofc2)
for cim1, p_comb in zip(sofc1.actual_cims, sofc1.p_combs):
cond_cims = sofc2.filter_cims_with_mask(cims_filter, p_comb)
for cim2 in cond_cims:
if not self.independence_test(child_states_numb, cim1, cim2):
return False
return True
def independence_test(self, child_states_numb: int, cim1: ConditionalIntensityMatrix,
cim2: ConditionalIntensityMatrix) -> bool:
"""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.
:param child_states_numb: the cardinality of the test child
:type child_states_numb: int
:param cim1: a cim belonging to the graph without test parent
: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.
:rtype: bool
"""
M1 = cim1.state_transition_matrix
M2 = cim2.state_transition_matrix
r1s = M1.diagonal()
r2s = M2.diagonal()
C1 = cim1.cim
C2 = cim2.cim
F_stats = C2.diagonal() / C1.diagonal()
exp_alfa = self._exp_test_sign
for val in range(0, child_states_numb):
if F_stats[val] < f_dist.ppf(exp_alfa / 2, r1s[val], r2s[val]) or \
F_stats[val] > f_dist.ppf(1 - exp_alfa / 2, r1s[val], r2s[val]):
return False
M1_no_diag = M1[~np.eye(M1.shape[0], dtype=bool)].reshape(M1.shape[0], -1)
M2_no_diag = M2[~np.eye(M2.shape[0], dtype=bool)].reshape(
M2.shape[0], -1)
chi_2_quantile = chi2_dist.ppf(1 - self._chi_test_alfa, child_states_numb - 1)
Ks = np.sqrt(r1s / r2s)
Ls = np.sqrt(r2s / r1s)
for val in range(0, child_states_numb):
Chi = np.sum(np.power(Ks[val] * M2_no_diag[val] - Ls[val] *M1_no_diag[val], 2) /
(M1_no_diag[val] + M2_no_diag[val]))
if Chi > chi_2_quantile:
return False
return True
def one_iteration_of_CTPC_algorithm(self, var_id: str, tot_vars_count: int) -> None:
"""Performs an iteration of the CTPC algorithm using the node ``var_id`` as ``test_child``.
:param var_id: the node label of the test child
:type var_id: string
: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
while b < len(u):
parent_indx = 0
while parent_indx < len(u):
removed = False
S = self.generate_possible_sub_sets_of_size(u, b, u[parent_indx])
test_parent = u[parent_indx]
for parents_set in S:
if self.complete_test(test_parent, var_id, parents_set, child_states_numb, tot_vars_count):
self._complete_graph.remove_edge(test_parent, var_id)
u.remove(test_parent)
removed = True
break
if not removed:
parent_indx += 1
b += 1
self._cache.clear()
def generate_possible_sub_sets_of_size(self, u: typing.List, size: int, parent_label: str) -> \
typing.Iterator:
"""Creates a list containing all possible subsets of the list ``u`` of size ``size``,
that do not contains a the node identified by ``parent_label``.
:param u: the list of nodes
:type u: List
:param size: the size of the subsets
:type size: int
:param parent_label: the node to exclude in the subsets generation
:type parent_label: string
:return: an Iterator Object containing a list of lists
:rtype: Iterator
"""
list_without_test_parent = u[:]
list_without_test_parent.remove(parent_label)
return map(list, itertools.combinations(list_without_test_parent, size))
def ctpc_algorithm(self) -> None:
"""Compute the CTPC algorithm over the entire net.
"""
ctpc_algo = self.one_iteration_of_CTPC_algorithm
total_vars_numb = self._sample_path.total_variables_count
[ctpc_algo(n, total_vars_numb) for n in tqdm(self._nodes)]
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.
"""
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())
name = 'results_' + name
with open(name, 'w') as f:
json.dump(res, f)

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main_package/PyCTBN/trajectory.py
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@ -1,46 +0,0 @@
import numpy as np
import typing
class Trajectory:
""" 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).
:param list_of_columns: the list containing the times array and values matrix
:type list_of_columns: List
:param original_cols_number: total number of cols in the data
:type original_cols_number: int
:_actual_trajectory: the trajectory containing also the duplicated/shifted values
:_times: the array containing the time deltas
"""
def __init__(self, list_of_columns: typing.List, original_cols_number: int):
"""Constructor Method
"""
if type(list_of_columns[0][0]) != np.float64:
raise TypeError('The first array in the list has to be Times')
self._original_cols_number = original_cols_number
self._actual_trajectory = np.array(list_of_columns[1:], dtype=np.int).T
self._times = np.array(list_of_columns[0], dtype=np.float)
@property
def trajectory(self) -> np.ndarray:
return self._actual_trajectory[:, :self._original_cols_number]
@property
def complete_trajectory(self) -> np.ndarray:
return self._actual_trajectory
@property
def times(self):
return self._times
def size(self):
return self._actual_trajectory.shape[0]
def __repr__(self):
return "Complete Trajectory Rows: " + str(self.size()) + "\n" + self.complete_trajectory.__repr__() + \
"\nTimes Rows:" + str(self.times.size) + "\n" + self.times.__repr__()

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57
main_package/tests/test_cache.py
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import unittest
import numpy as np
from ..PyCTBN.cache import Cache
from ..PyCTBN.set_of_cims import SetOfCims
class TestCache(unittest.TestCase):
def test_init(self):
c1 = Cache()
self.assertFalse(c1._list_of_sets_of_parents)
self.assertFalse(c1._actual_cache)
def test_put(self):
c1 = Cache()
pset1 = {'X', 'Y'}
sofc1 = SetOfCims('Z', [], 3, np.array([]))
c1.put(pset1, sofc1)
self.assertEqual(1, len(c1._actual_cache))
self.assertEqual(1, len(c1._list_of_sets_of_parents))
self.assertEqual(sofc1, c1._actual_cache[0])
pset2 = {'X'}
sofc2 = SetOfCims('Z', [], 3, np.array([]))
c1.put(pset2, sofc2)
self.assertEqual(2, len(c1._actual_cache))
self.assertEqual(2, len(c1._list_of_sets_of_parents))
self.assertEqual(sofc2, c1._actual_cache[1])
def test_find(self):
c1 = Cache()
pset1 = {'X', 'Y'}
sofc1 = SetOfCims('Z', [], 3, np.array([]))
c1.put(pset1, sofc1)
self.assertEqual(1, len(c1._actual_cache))
self.assertEqual(1, len(c1._list_of_sets_of_parents))
self.assertIsInstance(c1.find(pset1), SetOfCims)
self.assertEqual(sofc1, c1.find(pset1))
self.assertIsInstance(c1.find({'Y', 'X'}), SetOfCims)
self.assertEqual(sofc1, c1.find({'Y', 'X'}))
self.assertIsNone(c1.find({'X'}))
def test_clear(self):
c1 = Cache()
pset1 = {'X', 'Y'}
sofc1 = SetOfCims('Z', [], 3, np.array([]))
c1.put(pset1, sofc1)
self.assertEqual(1, len(c1._actual_cache))
self.assertEqual(1, len(c1._list_of_sets_of_parents))
c1.clear()
self.assertFalse(c1._list_of_sets_of_parents)
self.assertFalse(c1._actual_cache)
if __name__ == '__main__':
unittest.main()

46
main_package/tests/test_cim.py
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import unittest
import numpy as np
from ..PyCTBN.conditional_intensity_matrix import ConditionalIntensityMatrix
class TestConditionalIntensityMatrix(unittest.TestCase):
@classmethod
def setUpClass(cls) -> None:
cls.state_res_times = np.random.rand(1, 3)[0]
cls.state_res_times = cls.state_res_times * 1000
cls.state_transition_matrix = np.random.randint(1, 10000, (3, 3))
for i in range(0, len(cls.state_res_times)):
cls.state_transition_matrix[i, i] = 0
cls.state_transition_matrix[i, i] = np.sum(cls.state_transition_matrix[i])
def test_init(self):
c1 = ConditionalIntensityMatrix(self.state_res_times, self.state_transition_matrix)
self.assertTrue(np.array_equal(self.state_res_times, c1.state_residence_times))
self.assertTrue(np.array_equal(self.state_transition_matrix, c1.state_transition_matrix))
self.assertEqual(c1.cim.dtype, np.float)
self.assertEqual(self.state_transition_matrix.shape, c1.cim.shape)
def test_compute_cim_coefficients(self):
c1 = ConditionalIntensityMatrix(self.state_res_times, self.state_transition_matrix)
c2 = self.state_transition_matrix.astype(np.float)
np.fill_diagonal(c2, c2.diagonal() * -1)
for i in range(0, len(self.state_res_times)):
for j in range(0, len(self.state_res_times)):
c2[i, j] = (c2[i, j] + 1) / (self.state_res_times[i] + 1)
c1.compute_cim_coefficients()
for i in range(0, len(c1.state_residence_times)):
self.assertTrue(np.isclose(np.sum(c1.cim[i]), 0.0, 1e-02, 1e-01))
for i in range(0, len(self.state_res_times)):
for j in range(0, len(self.state_res_times)):
self.assertTrue(np.isclose(c1.cim[i, j], c2[i, j], 1e-02, 1e-01))
def test_repr(self):
c1 = ConditionalIntensityMatrix(self.state_res_times, self.state_transition_matrix)
print(c1)
if __name__ == '__main__':
unittest.main()

175
main_package/tests/test_json_importer.py
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import unittest
import os
import glob
import numpy as np
import pandas as pd
import json
from ..PyCTBN.json_importer import JsonImporter
class TestJsonImporter(unittest.TestCase):
@classmethod
def setUpClass(cls) -> None:
cls.read_files = glob.glob(os.path.join('./data', "*.json"))
#print(os.path.join('../data'))
def test_init(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
self.assertEqual(j1._samples_label, 'samples')
self.assertEqual(j1._structure_label, 'dyn.str')
self.assertEqual(j1._variables_label, 'variables')
self.assertEqual(j1._time_key, 'Time')
self.assertEqual(j1._variables_key, 'Name')
self.assertEqual(j1._file_path, self.read_files[0])
self.assertIsNone(j1._df_samples_list)
self.assertIsNone(j1.variables)
self.assertIsNone(j1.structure)
self.assertIsNone(j1.concatenated_samples)
self.assertIsNone(j1.sorter)
def test_read_json_file_found(self):
data_set = {"key1": [1, 2, 3], "key2": [4, 5, 6]}
with open('data.json', 'w') as f:
json.dump(data_set, f)
path = os.getcwd()
path = path + '/data.json'
j1 = JsonImporter(path, '', '', '', '', '', 0)
imported_data = j1.read_json_file()
self.assertTrue(self.ordered(data_set) == self.ordered(imported_data))
os.remove('data.json')
def test_read_json_file_not_found(self):
path = os.getcwd()
path = path + '/data.json'
j1 = JsonImporter(path, '', '', '', '', '', 0)
self.assertRaises(FileNotFoundError, j1.read_json_file)
def test_normalize_trajectories(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
raw_data = j1.read_json_file()
#print(raw_data)
df_samples_list = j1.normalize_trajectories(raw_data, 0, j1._samples_label)
self.assertEqual(len(df_samples_list), len(raw_data[0][j1._samples_label]))
#self.assertEqual(list(j1._df_samples_list[0].columns.values)[1:], j1.sorter)
def test_normalize_trajectories_wrong_indx(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
raw_data = j1.read_json_file()
self.assertRaises(IndexError, j1.normalize_trajectories, raw_data, 474, j1._samples_label)
def test_normalize_trajectories_wrong_key(self):
j1 = JsonImporter(self.read_files[0], 'sample', 'dyn.str', 'variables', 'Time', 'Name', 0)
raw_data = j1.read_json_file()
self.assertRaises(KeyError, j1.normalize_trajectories, raw_data, 0, j1._samples_label)
def test_compute_row_delta_single_samples_frame(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
raw_data = j1.read_json_file()
j1._df_samples_list = j1.import_trajectories(raw_data)
sample_frame = j1._df_samples_list[0]
original_copy = sample_frame.copy()
columns_header = list(sample_frame.columns.values)
shifted_cols_header = [s + "S" for s in columns_header[1:]]
new_sample_frame = j1.compute_row_delta_sigle_samples_frame(sample_frame, columns_header[1:],
shifted_cols_header)
self.assertEqual(len(list(sample_frame.columns.values)) + len(shifted_cols_header),
len(list(new_sample_frame.columns.values)))
self.assertEqual(sample_frame.shape[0] - 1, new_sample_frame.shape[0])
for indx, row in new_sample_frame.iterrows():
self.assertAlmostEqual(row['Time'],
original_copy.iloc[indx + 1]['Time'] - original_copy.iloc[indx]['Time'])
for indx, row in new_sample_frame.iterrows():
np.array_equal(np.array(row[columns_header[1:]],dtype=int),
np.array(original_copy.iloc[indx][columns_header[1:]],dtype=int))
np.array_equal(np.array(row[shifted_cols_header], dtype=int),
np.array(original_copy.iloc[indx + 1][columns_header[1:]], dtype=int))
def test_compute_row_delta_in_all_frames(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
raw_data = j1.read_json_file()
j1._df_samples_list = j1.import_trajectories(raw_data)
j1._sorter = j1.build_sorter(j1._df_samples_list[0])
j1.compute_row_delta_in_all_samples_frames(j1._df_samples_list)
self.assertEqual(list(j1._df_samples_list[0].columns.values),
list(j1.concatenated_samples.columns.values)[:len(list(j1._df_samples_list[0].columns.values))])
self.assertEqual(list(j1.concatenated_samples.columns.values)[0], j1._time_key)
def test_clear_data_frame_list(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
raw_data = j1.read_json_file()
j1._df_samples_list = j1.import_trajectories(raw_data)
j1._sorter = j1.build_sorter(j1._df_samples_list[0])
j1.compute_row_delta_in_all_samples_frames(j1._df_samples_list)
j1.clear_data_frame_list()
for df in j1._df_samples_list:
self.assertTrue(df.empty)
def test_clear_concatenated_frame(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
j1.import_data()
j1.clear_concatenated_frame()
self.assertTrue(j1.concatenated_samples.empty)
def test_build_list_of_samples_array(self):
data_set = {"key1": [1, 2, 3], "key2": [4.1, 5.2, 6.3]}
with open('data.json', 'w') as f:
json.dump(data_set, f)
path = os.getcwd()
path = path + '/data.json'
j1 = JsonImporter(path, '', '', '', '', '', 0)
raw_data = j1.read_json_file()
frame = pd.DataFrame(raw_data)
col_list = j1.build_list_of_samples_array(frame)
forced_list = []
for key in data_set:
forced_list.append(np.array(data_set[key]))
for a1, a2 in zip(col_list, forced_list):
self.assertTrue(np.array_equal(a1, a2))
os.remove('data.json')
def test_import_variables(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
sorter = ['X', 'Y', 'Z']
raw_data = [{'variables':{"Name": ['X', 'Y', 'Z'], "value": [3, 3, 3]}}]
df_var = j1.import_variables(raw_data)
self.assertEqual(list(df_var[j1._variables_key]), sorter)
def test_import_structure(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
raw_data = [{"dyn.str":[{"From":"X","To":"Z"},{"From":"Y","To":"Z"},{"From":"Z","To":"Y"}]}]
df_struct = j1.import_structure(raw_data)
#print(raw_data[0]['dyn.str'][0].items())
self.assertIsInstance(df_struct, pd.DataFrame)
def test_import_sampled_cims(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
raw_data = j1.read_json_file()
j1._df_samples_list = j1.import_trajectories(raw_data)
j1._sorter = j1.build_sorter(j1._df_samples_list[0])
cims = j1.import_sampled_cims(raw_data, 0, 'dyn.cims')
#j1.import_variables(raw_data, j1.sorter)
self.assertEqual(list(cims.keys()), j1.sorter)
def test_import_data(self):
j1 = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 2)
j1.import_data()
self.assertEqual(list(j1.variables[j1._variables_key]),
list(j1.concatenated_samples.columns.values[1:len(j1.variables[j1._variables_key]) + 1]))
print(j1.variables)
print(j1.structure)
print(j1.concatenated_samples)
def ordered(self, obj):
if isinstance(obj, dict):
return sorted((k, self.ordered(v)) for k, v in obj.items())
if isinstance(obj, list):
return sorted(self.ordered(x) for x in obj)
else:
return obj
if __name__ == '__main__':
unittest.main()

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main_package/tests/test_networkgraph.py
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import unittest
import glob
import os
import networkx as nx
import numpy as np
import itertools
from ..PyCTBN.sample_path import SamplePath
from ..PyCTBN.network_graph import NetworkGraph
from ..PyCTBN.json_importer import JsonImporter
class TestNetworkGraph(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.read_files = glob.glob(os.path.join('./data', "*.json"))
cls.importer = JsonImporter(cls.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
cls.s1 = SamplePath(cls.importer)
cls.s1.build_trajectories()
cls.s1.build_structure()
def test_init(self):
g1 = NetworkGraph(self.s1.structure)
self.assertEqual(self.s1.structure, g1._graph_struct)
self.assertIsInstance(g1._graph, nx.DiGraph)
self.assertIsNone(g1.time_scalar_indexing_strucure)
self.assertIsNone(g1.transition_scalar_indexing_structure)
self.assertIsNone(g1.transition_filtering)
self.assertIsNone(g1.p_combs)
def test_add_nodes(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_nodes(self.s1.structure.nodes_labels)
for n1, n2 in zip(g1.nodes, self.s1.structure.nodes_labels):
self.assertEqual(n1, n2)
def test_add_edges(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_edges(self.s1.structure.edges)
for e in self.s1.structure.edges:
self.assertIn(tuple(e), g1.edges)
def test_fast_init(self):
g1 = NetworkGraph(self.s1.structure)
for node in self.s1.structure.nodes_labels:
g1.fast_init(node)
self.assertIsNotNone(g1._graph.nodes)
self.assertIsNotNone(g1._graph.edges)
self.assertIsInstance(g1._time_scalar_indexing_structure, np.ndarray)
self.assertIsInstance(g1._transition_scalar_indexing_structure, np.ndarray)
self.assertIsInstance(g1._time_filtering, np.ndarray)
self.assertIsInstance(g1._transition_filtering, np.ndarray)
self.assertIsInstance(g1._p_combs_structure, np.ndarray)
self.assertIsInstance(g1._aggregated_info_about_nodes_parents, tuple)
def test_get_ordered_by_indx_set_of_parents(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_nodes(self.s1.structure.nodes_labels)
g1.add_edges(self.s1.structure.edges)
for node in self.s1.structure.nodes_labels:
aggr_info = g1.get_ordered_by_indx_set_of_parents(node)
for indx in range(len(aggr_info[0]) - 1 ):
self.assertLess(g1.get_node_indx(aggr_info[0][indx]), g1.get_node_indx(aggr_info[0][indx + 1]))
for par, par_indx in zip(aggr_info[0], aggr_info[1]):
self.assertEqual(g1.get_node_indx(par), par_indx)
for par, par_val in zip(aggr_info[0], aggr_info[2]):
self.assertEqual(g1._graph_struct.get_states_number(par), par_val)
def test_build_time_scalar_indexing_structure_for_a_node(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_nodes(self.s1.structure.nodes_labels)
g1.add_edges(self.s1.structure.edges)
for node in self.s1.structure.nodes_labels:
aggr_info = g1.get_ordered_by_indx_set_of_parents(node)
self.aux_build_time_scalar_indexing_structure_for_a_node(g1, node, aggr_info[1],
aggr_info[0], aggr_info[2])
def aux_build_time_scalar_indexing_structure_for_a_node(self, graph, node_id, parents_indxs, parents_labels, parents_vals):
time_scalar_indexing = graph.build_time_scalar_indexing_structure_for_a_node(node_id, parents_vals)
self.assertEqual(len(time_scalar_indexing), len(parents_indxs) + 1)
merged_list = parents_labels[:]
merged_list.insert(0, node_id)
vals_list = []
for node in merged_list:
vals_list.append(graph.get_states_number(node))
t_vec = np.array(vals_list)
t_vec = t_vec.cumprod()
self.assertTrue(np.array_equal(time_scalar_indexing, t_vec))
def test_build_transition_scalar_indexing_structure_for_a_node(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_nodes(self.s1.structure.nodes_labels)
g1.add_edges(self.s1.structure.edges)
for node in self.s1.structure.nodes_labels:
aggr_info = g1.get_ordered_by_indx_set_of_parents(node)
self.aux_build_transition_scalar_indexing_structure_for_a_node(g1, node, aggr_info[1],
aggr_info[0], aggr_info[2])
def aux_build_transition_scalar_indexing_structure_for_a_node(self, graph, node_id, parents_indxs, parents_labels,
parents_values):
transition_scalar_indexing = graph.build_transition_scalar_indexing_structure_for_a_node(node_id,
parents_values)
self.assertEqual(len(transition_scalar_indexing), len(parents_indxs) + 2)
merged_list = parents_labels[:]
merged_list.insert(0, node_id)
merged_list.insert(0, node_id)
vals_list = []
for node_id in merged_list:
vals_list.append(graph.get_states_number(node_id))
m_vec = np.array([vals_list])
m_vec = m_vec.cumprod()
self.assertTrue(np.array_equal(transition_scalar_indexing, m_vec))
def test_build_time_columns_filtering_structure_for_a_node(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_nodes(self.s1.structure.nodes_labels)
g1.add_edges(self.s1.structure.edges)
for node in self.s1.structure.nodes_labels:
aggr_info = g1.get_ordered_by_indx_set_of_parents(node)
self.aux_build_time_columns_filtering_structure_for_a_node(g1, node, aggr_info[1])
def aux_build_time_columns_filtering_structure_for_a_node(self, graph, node_id, p_indxs):
graph.build_time_columns_filtering_for_a_node(graph.get_node_indx(node_id), p_indxs)
single_filter = []
single_filter.append(graph.get_node_indx(node_id))
single_filter.extend(p_indxs)
self.assertTrue(np.array_equal(graph.build_time_columns_filtering_for_a_node(graph.get_node_indx(node_id),
p_indxs),np.array(single_filter)))
def test_build_transition_columns_filtering_structure(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_nodes(self.s1.structure.nodes_labels)
g1.add_edges(self.s1.structure.edges)
for node in self.s1.structure.nodes_labels:
aggr_info = g1.get_ordered_by_indx_set_of_parents(node)
self.aux_build_time_columns_filtering_structure_for_a_node(g1, node, aggr_info[1])
def aux_build_transition_columns_filtering_structure(self, graph, node_id, p_indxs):
single_filter = []
single_filter.append(graph.get_node_indx(node_id) + graph._graph_struct.total_variables_number)
single_filter.append(graph.get_node_indx(node_id))
single_filter.extend(p_indxs)
self.assertTrue(np.array_equal(graph.build_transition_filtering_for_a_node(graph.get_node_indx(node_id),
p_indxs), np.array(single_filter)))
def test_build_p_combs_structure(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_nodes(self.s1.structure.nodes_labels)
g1.add_edges(self.s1.structure.edges)
for node in self.s1.structure.nodes_labels:
aggr_info = g1.get_ordered_by_indx_set_of_parents(node)
self.aux_build_p_combs_structure(g1, aggr_info[2])
def aux_build_p_combs_structure(self, graph, p_vals):
p_combs = graph.build_p_comb_structure_for_a_node(p_vals)
p_possible_vals = []
for val in p_vals:
vals = [v for v in range(val)]
p_possible_vals.extend(vals)
comb_struct = set(itertools.product(p_possible_vals,repeat=len(p_vals)))
for comb in comb_struct:
self.assertIn(np.array(comb), p_combs)
def test_get_parents_by_id(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_nodes(self.s1.structure.nodes_labels)
g1.add_edges(self.s1.structure.edges)
for node in g1.nodes:
self.assertListEqual(g1.get_parents_by_id(node), list(g1._graph.predecessors(node)))
def test_get_states_number(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_nodes(self.s1.structure.nodes_labels)
g1.add_edges(self.s1.structure.edges)
for node, val in zip(g1.nodes, g1.nodes_values):
self.assertEqual(val, g1.get_states_number(node))
def test_get_node_indx(self):
g1 = NetworkGraph(self.s1.structure)
g1.add_nodes(self.s1.structure.nodes_labels)
g1.add_edges(self.s1.structure.edges)
for node, indx in zip(g1.nodes, g1.nodes_indexes):
self.assertEqual(indx, g1.get_node_indx(node))
if __name__ == '__main__':
unittest.main()

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main_package/tests/test_parameters_estimator.py
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import unittest
import numpy as np
import glob
import os
from ..PyCTBN.network_graph import NetworkGraph
from ..PyCTBN.sample_path import SamplePath
from ..PyCTBN.set_of_cims import SetOfCims
from ..PyCTBN.parameters_estimator import ParametersEstimator
from ..PyCTBN.json_importer import JsonImporter
class TestParametersEstimatior(unittest.TestCase):
@classmethod
def setUpClass(cls) -> None:
cls.read_files = glob.glob(os.path.join('./data', "*.json"))
cls.array_indx = 0
cls.importer = JsonImporter(cls.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name',
cls.array_indx)
cls.s1 = SamplePath(cls.importer)
cls.s1.build_trajectories()
cls.s1.build_structure()
print(cls.s1.structure.edges)
print(cls.s1.structure.nodes_values)
def test_fast_init(self):
for node in self.s1.structure.nodes_labels:
g = NetworkGraph(self.s1.structure)
g.fast_init(node)
p1 = ParametersEstimator(self.s1.trajectories, g)
self.assertEqual(p1._trajectories, self.s1.trajectories)
self.assertEqual(p1._net_graph, g)
self.assertIsNone(p1._single_set_of_cims)
p1.fast_init(node)
self.assertIsInstance(p1._single_set_of_cims, SetOfCims)
def test_compute_parameters_for_node(self):
for indx, node in enumerate(self.s1.structure.nodes_labels):
print(node)
g = NetworkGraph(self.s1.structure)
g.fast_init(node)
p1 = ParametersEstimator(self.s1.trajectories, g)
p1.fast_init(node)
sofc1 = p1.compute_parameters_for_node(node)
sampled_cims = self.aux_import_sampled_cims('dyn.cims')
sc = list(sampled_cims.values())
self.equality_of_cims_of_node(sc[indx], sofc1._actual_cims)
def equality_of_cims_of_node(self, sampled_cims, estimated_cims):
self.assertEqual(len(sampled_cims), len(estimated_cims))
for c1, c2 in zip(sampled_cims, estimated_cims):
self.cim_equality_test(c1, c2.cim)
def cim_equality_test(self, cim1, cim2):
for r1, r2 in zip(cim1, cim2):
self.assertTrue(np.all(np.isclose(r1, r2, 1e-01, 1e-01) == True))
def aux_import_sampled_cims(self, cims_label):
i1 = JsonImporter(self.read_files[0], '', '', '', '', '', self.array_indx)
raw_data = i1.read_json_file()
return i1.import_sampled_cims(raw_data, self.array_indx, cims_label)
if __name__ == '__main__':
unittest.main()

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main_package/tests/test_sample_path.py
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import unittest
import glob
import os
from ..PyCTBN.json_importer import JsonImporter
from ..PyCTBN.sample_path import SamplePath
from ..PyCTBN.trajectory import Trajectory
from ..PyCTBN.structure import Structure
class TestSamplePath(unittest.TestCase):
@classmethod
def setUpClass(cls) -> None:
cls.read_files = glob.glob(os.path.join('./data', "*.json"))
cls.importer = JsonImporter(cls.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
def test_init(self):
s1 = SamplePath(self.importer)
self.assertIsNone(s1.trajectories)
self.assertIsNone(s1.structure)
self.assertFalse(s1._importer.concatenated_samples.empty)
self.assertIsNone(s1._total_variables_count)
def test_build_trajectories(self):
s1 = SamplePath(self.importer)
s1.build_trajectories()
self.assertIsInstance(s1.trajectories, Trajectory)
def test_build_structure(self):
s1 = SamplePath(self.importer)
s1.build_structure()
self.assertIsInstance(s1.structure, Structure)
self.assertEqual(s1._total_variables_count, len(s1._importer.sorter))
if __name__ == '__main__':
unittest.main()

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main_package/tests/test_setofcims.py
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import unittest
import numpy as np
import itertools
from ..PyCTBN.set_of_cims import SetOfCims
class TestSetOfCims(unittest.TestCase):
@classmethod
def setUpClass(cls) -> None:
cls.node_id = 'X'
cls.possible_cardinalities = [2, 3]
cls.possible_states = [[0,1], [0, 1, 2]]
cls.node_states_number = range(2, 4)
def test_init(self):
# empty parent set
for sn in self.node_states_number:
p_combs = self.build_p_comb_structure_for_a_node([])
self.aux_test_init(self.node_id, [], sn, p_combs)
# one parent
for sn in self.node_states_number:
for p in itertools.product(self.possible_cardinalities, repeat=1):
p_combs = self.build_p_comb_structure_for_a_node(list(p))
self.aux_test_init(self.node_id, list(p), sn, p_combs)
#two parents
for sn in self.node_states_number:
for p in itertools.product(self.possible_cardinalities, repeat=2):
p_combs = self.build_p_comb_structure_for_a_node(list(p))
self.aux_test_init(self.node_id, list(p), sn, p_combs)
def test_build_cims(self):
# empty parent set
for sn in self.node_states_number:
p_combs = self.build_p_comb_structure_for_a_node([])
self.aux_test_build_cims(self.node_id, [], sn, p_combs)
# one parent
for sn in self.node_states_number:
for p in itertools.product(self.possible_cardinalities, repeat=1):
p_combs = self.build_p_comb_structure_for_a_node(list(p))
self.aux_test_build_cims(self.node_id, list(p), sn, p_combs)
#two parents
for sn in self.node_states_number:
for p in itertools.product(self.possible_cardinalities, repeat=2):
p_combs = self.build_p_comb_structure_for_a_node(list(p))
self.aux_test_build_cims(self.node_id, list(p), sn, p_combs)
def test_filter_cims_with_mask(self):
p_combs = self.build_p_comb_structure_for_a_node(self.possible_cardinalities)
sofc1 = SetOfCims('X', self.possible_cardinalities, 3, p_combs)
state_res_times_list = []
transition_matrices_list = []
for i in range(len(p_combs)):
state_res_times = np.random.rand(1, 3)[0]
state_res_times = state_res_times * 1000
state_transition_matrix = np.random.randint(1, 10000, (3, 3))
state_res_times_list.append(state_res_times)
transition_matrices_list.append(state_transition_matrix)
sofc1.build_cims(np.array(state_res_times_list), np.array(transition_matrices_list))
for length_of_mask in range(3):
for mask in list(itertools.permutations([True, False],r=length_of_mask)):
m = np.array(mask)
for parent_value in range(self.possible_cardinalities[0]):
cims = sofc1.filter_cims_with_mask(m, [parent_value])
if length_of_mask == 0 or length_of_mask == 1:
self.assertTrue(np.array_equal(sofc1._actual_cims, cims))
else:
indxs = self.another_filtering_method(p_combs, m, [parent_value])
self.assertTrue(np.array_equal(cims, sofc1._actual_cims[indxs]))
def aux_test_build_cims(self, node_id, p_values, node_states, p_combs):
state_res_times_list = []
transition_matrices_list = []
so1 = SetOfCims(node_id, p_values, node_states, p_combs)
for i in range(len(p_combs)):
state_res_times = np.random.rand(1, node_states)[0]
state_res_times = state_res_times * 1000
state_transition_matrix = np.random.randint(1, 10000, (node_states, node_states))
state_res_times_list.append(state_res_times)
transition_matrices_list.append(state_transition_matrix)
so1.build_cims(np.array(state_res_times_list), np.array(transition_matrices_list))
self.assertEqual(len(state_res_times_list), so1.get_cims_number())
self.assertIsInstance(so1._actual_cims, np.ndarray)
self.assertIsNone(so1._transition_matrices)
self.assertIsNone(so1._state_residence_times)
def aux_test_init(self, node_id, parents_states_number, node_states_number, p_combs):
sofcims = SetOfCims(node_id, parents_states_number, node_states_number, p_combs)
self.assertEqual(sofcims._node_id, node_id)
self.assertTrue(np.array_equal(sofcims._p_combs, p_combs))
self.assertTrue(np.array_equal(sofcims._parents_states_number, parents_states_number))
self.assertEqual(sofcims._node_states_number, node_states_number)
self.assertFalse(sofcims._actual_cims)
self.assertEqual(sofcims._state_residence_times.shape[0], np.prod(np.array(parents_states_number)))
self.assertEqual(len(sofcims._state_residence_times[0]), node_states_number)
self.assertEqual(sofcims._transition_matrices.shape[0], np.prod(np.array(parents_states_number)))
self.assertEqual(len(sofcims._transition_matrices[0][0]), node_states_number)
def build_p_comb_structure_for_a_node(self, parents_values):
"""
Builds the combinatory structure that contains the combinations of all the values contained in parents_values.
Parameters:
parents_values: the cardinalities of the nodes
Returns:
a numpy matrix containing a grid of the combinations
"""
tmp = []
for val in parents_values:
tmp.append([x for x in range(val)])
if len(parents_values) > 0:
parents_comb = np.array(np.meshgrid(*tmp)).T.reshape(-1, len(parents_values))
if len(parents_values) > 1:
tmp_comb = parents_comb[:, 1].copy()
parents_comb[:, 1] = parents_comb[:, 0].copy()
parents_comb[:, 0] = tmp_comb
else:
parents_comb = np.array([[]], dtype=np.int)
return parents_comb
def another_filtering_method(self,p_combs, mask, parent_value):
masked_combs = p_combs[:, mask]
indxs = []
for indx, val in enumerate(masked_combs):
if val == parent_value:
indxs.append(indx)
return np.array(indxs)
if __name__ == '__main__':
unittest.main()

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main_package/tests/test_structure.py
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import unittest
import numpy as np
from ..PyCTBN.structure import Structure
class TestStructure(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.labels = ['X','Y','Z']
cls.indxs = np.array([0,1,2])
cls.vals = np.array([3,3,3])
cls.edges = [('X','Z'),('Y','Z'), ('Z','Y')]
cls.vars_numb = len(cls.labels)
def test_init(self):
s1 = Structure(self.labels, self.indxs, self.vals, self.edges, self.vars_numb)
self.assertListEqual(self.labels,s1.nodes_labels)
self.assertIsInstance(s1.nodes_indexes, np.ndarray)
self.assertTrue(np.array_equal(self.indxs, s1.nodes_indexes))
self.assertIsInstance(s1.nodes_values, np.ndarray)
self.assertTrue(np.array_equal(self.vals, s1.nodes_values))
self.assertListEqual(self.edges, s1.edges)
self.assertEqual(self.vars_numb, s1.total_variables_number)
def test_get_node_id(self):
s1 = Structure(self.labels, self.indxs, self.vals, self.edges, self.vars_numb)
for indx, var in enumerate(self.labels):
self.assertEqual(var, s1.get_node_id(indx))
def test_get_node_indx(self):
l2 = self.labels[:]
l2.remove('Y')
i2 = self.indxs.copy()
np.delete(i2, 1)
v2 = self.vals.copy()
np.delete(v2, 1)
e2 = [('X','Z')]
n2 = self.vars_numb - 1
s1 = Structure(l2, i2, v2, e2, n2)
for indx, var in zip(i2, l2):
self.assertEqual(indx, s1.get_node_indx(var))
def test_get_positional_node_indx(self):
l2 = self.labels[:]
l2.remove('Y')
i2 = self.indxs.copy()
np.delete(i2, 1)
v2 = self.vals.copy()
np.delete(v2, 1)
e2 = [('X', 'Z')]
n2 = self.vars_numb - 1
s1 = Structure(l2, i2, v2, e2, n2)
for indx, var in enumerate(s1.nodes_labels):
self.assertEqual(indx, s1.get_positional_node_indx(var))
def test_get_states_number(self):
l2 = self.labels[:]
l2.remove('Y')
i2 = self.indxs.copy()
np.delete(i2, 1)
v2 = self.vals.copy()
np.delete(v2, 1)
e2 = [('X', 'Z')]
n2 = self.vars_numb - 1
s1 = Structure(l2, i2, v2, e2, n2)
for val, node in zip(v2, l2):
self.assertEqual(val, s1.get_states_number(node))
def test_equality(self):
s1 = Structure(self.labels, self.indxs, self.vals, self.edges, self.vars_numb)
s2 = Structure(self.labels, self.indxs, self.vals, self.edges, self.vars_numb)
self.assertEqual(s1, s2)
def test_repr(self):
s1 = Structure(self.labels, self.indxs, self.vals, self.edges, self.vars_numb)
print(s1)
if __name__ == '__main__':
unittest.main()

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main_package/tests/test_structure_estimator.py
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import glob
import math
import os
import unittest
import networkx as nx
import numpy as np
import psutil
from line_profiler import LineProfiler
import timeit
from ..PyCTBN.cache import Cache
from ..PyCTBN.sample_path import SamplePath
from ..PyCTBN.structure_estimator import StructureEstimator
from ..PyCTBN.json_importer import JsonImporter
class TestStructureEstimator(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.read_files = glob.glob(os.path.join('./data', "*.json"))
cls.importer = JsonImporter(cls.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name', 0)
cls.s1 = SamplePath(cls.importer)
cls.s1.build_trajectories()
cls.s1.build_structure()
def test_init(self):
exp_alfa = 0.1
chi_alfa = 0.1
se1 = StructureEstimator(self.s1, exp_alfa, chi_alfa)
self.assertEqual(self.s1, se1._sample_path)
self.assertTrue(np.array_equal(se1._nodes, np.array(self.s1.structure.nodes_labels)))
self.assertTrue(np.array_equal(se1._nodes_indxs, self.s1.structure.nodes_indexes))
self.assertTrue(np.array_equal(se1._nodes_vals, self.s1.structure.nodes_values))
self.assertEqual(se1._exp_test_sign, exp_alfa)
self.assertEqual(se1._chi_test_alfa, chi_alfa)
self.assertIsInstance(se1._complete_graph, nx.DiGraph)
self.assertIsInstance(se1._cache, Cache)
def test_build_complete_graph(self):
exp_alfa = 0.1
chi_alfa = 0.1
nodes_numb = len(self.s1.structure.nodes_labels)
se1 = StructureEstimator(self.s1, exp_alfa, chi_alfa)
cg = se1.build_complete_graph(self.s1.structure.nodes_labels)
self.assertEqual(len(cg.edges), nodes_numb*(nodes_numb - 1))
for node in self.s1.structure.nodes_labels:
no_self_loops = self.s1.structure.nodes_labels[:]
no_self_loops.remove(node)
for n2 in no_self_loops:
self.assertIn((node, n2), cg.edges)
def test_generate_possible_sub_sets_of_size(self):
exp_alfa = 0.1
chi_alfa = 0.1
nodes_numb = len(self.s1.structure.nodes_labels)
se1 = StructureEstimator(self.s1, exp_alfa, chi_alfa)
for node in self.s1.structure.nodes_labels:
for b in range(nodes_numb):
sets = se1.generate_possible_sub_sets_of_size(self.s1.structure.nodes_labels, b, node)
sets2 = se1.generate_possible_sub_sets_of_size(self.s1.structure.nodes_labels, b, node)
self.assertEqual(len(list(sets)), math.floor(math.factorial(nodes_numb - 1) /
(math.factorial(b)*math.factorial(nodes_numb -1 - b))))
for sset in sets2:
self.assertFalse(node in sset)
def test_time(self):
se1 = StructureEstimator(self.s1, 0.1, 0.1)
lp = LineProfiler()
#lp.add_function(se1.complete_test)
#lp.add_function(se1.one_iteration_of_CTPC_algorithm)
#lp.add_function(se1.independence_test)
lp_wrapper = lp(se1.ctpc_algorithm)
lp_wrapper()
lp.print_stats()
#print("Last time", lp.dump_stats())
#print("Exec Time", timeit.timeit(se1.ctpc_algorithm, number=1))
print(se1._complete_graph.edges)
print(self.s1.structure.edges)
for ed in self.s1.structure.edges:
self.assertIn(tuple(ed), se1._complete_graph.edges)
tuples_edges = [tuple(rec) for rec in self.s1.structure.edges]
spurious_edges = []
for ed in se1._complete_graph.edges:
if not(ed in tuples_edges):
spurious_edges.append(ed)
print("Spurious Edges:",spurious_edges)
print("Adj Matrix:", nx.adj_matrix(se1._complete_graph).toarray().astype(bool))
#se1.save_results()
def test_memory(self):
se1 = StructureEstimator(self.s1, 0.1, 0.1)
se1.ctpc_algorithm()
current_process = psutil.Process(os.getpid())
mem = current_process.memory_info().rss
print("Average Memory Usage in MB:", mem / 10**6)
if __name__ == '__main__':
unittest.main()

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main_package/tests/test_trajectory.py
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import unittest
import numpy as np
from ..PyCTBN.trajectory import Trajectory
class TestTrajectory(unittest.TestCase):
def test_init(self):
cols_list = [np.array([1.2,1.3,.14]), np.arange(1,4), np.arange(4,7)]
t1 = Trajectory(cols_list, len(cols_list) - 2)
self.assertTrue(np.array_equal(cols_list[0], t1.times))
self.assertTrue(np.array_equal(np.ravel(t1.complete_trajectory[:, : 1]), cols_list[1]))
self.assertTrue(np.array_equal(np.ravel(t1.complete_trajectory[:, 1: 2]), cols_list[2]))
self.assertEqual(len(cols_list) - 1, t1.complete_trajectory.shape[1])
self.assertEqual(t1.size(), t1.times.size)
def test_init_first_array_not_float_type(self):
cols_list = [np.arange(1, 4), np.arange(4, 7), np.array([1.2, 1.3, .14])]
self.assertRaises(TypeError, Trajectory, cols_list, len(cols_list))
def test_complete_trajectory(self):
cols_list = [np.array([1.2, 1.3, .14]), np.arange(1, 4), np.arange(4, 7)]
t1 = Trajectory(cols_list, len(cols_list) - 2)
complete = np.column_stack((cols_list[1], cols_list[2]))
self.assertTrue(np.array_equal(t1.complete_trajectory, complete))
def test_trajectory(self):
cols_list = [np.array([1.2, 1.3, .14]), np.arange(1, 4), np.arange(4, 7)]
t1 = Trajectory(cols_list, len(cols_list) - 2)
self.assertTrue(np.array_equal(cols_list[1], t1.trajectory.ravel()))
def test_times(self):
cols_list = [np.array([1.2, 1.3, .14]), np.arange(1, 4), np.arange(4, 7)]
t1 = Trajectory(cols_list, len(cols_list) - 2)
self.assertTrue(np.array_equal(cols_list[0], t1.times))
def test_repr(self):
cols_list = [np.array([1.2, 1.3, .14]), np.arange(1, 4), np.arange(4, 7)]
t1 = Trajectory(cols_list, len(cols_list) - 2)
print(t1)
if __name__ == '__main__':
unittest.main()