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Fix import issue in tests ;Add a basic main example

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parallel_struct_est
philpMartin 4 years ago
parent 813c2943bd
commit 8e1666a607
24 changed files with 1058 additions and 43 deletions
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  1. 0
      main_package/.scannerwork/.sonar_lock
  2. 6
      main_package/.scannerwork/report-task.txt
  3. 39
      main_package/basic_main.py
  4. 1
      main_package/classes/abstract_sample_path.py
  5. 1
      main_package/classes/cache.py
  6. 8
      main_package/classes/json_importer.py
  7. 5
      main_package/classes/network_graph.py
  8. 7
      main_package/classes/parameters_estimator.py
  9. 2
      main_package/classes/sample_path.py
  10. 4
      main_package/classes/set_of_cims.py
  11. 1
      main_package/classes/structure.py
  12. 18
      main_package/classes/structure_estimator.py
  13. 963
      main_package/tests/coverage.xml
  14. 2
      main_package/tests/test_cache.py
  15. 2
      main_package/tests/test_cim.py
  16. 4
      main_package/tests/test_json_importer.py
  17. 3
      main_package/tests/test_networkgraph.py
  18. 3
      main_package/tests/test_parameters_estimator.py
  19. 2
      main_package/tests/test_sample_path.py
  20. 2
      main_package/tests/test_setofcims.py
  21. 5
      main_package/tests/test_sets_of_cims_container.py
  22. 2
      main_package/tests/test_structure.py
  23. 19
      main_package/tests/test_structure_estimator.py
  24. 2
      main_package/tests/test_trajectory.py

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

39
main_package/basic_main.py
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import glob
import os
import sys
sys.path.append("./classes/")
import network_graph as ng
import sample_path as sp
import set_of_cims as sofc
import parameters_estimator as pe
import json_importer as ji
def main():
read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir
#import data
importer = ji.JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
#Create a SamplePath Obj
s1 = sp.SamplePath(importer)
#Build The trajectries and the structural infos
s1.build_trajectories()
s1.build_structure()
#From The Structure Object build the Graph
g = ng.NetworkGraph(s1.structure)
#Select a node you want to estimate the parameters
node = g.nodes[1]
#Init the graph specifically for THIS node
g.fast_init(node)
#Use SamplePath and Grpah to create a ParametersEstimator Object
p1 = pe.ParametersEstimator(s1, 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()

1
main_package/classes/abstract_sample_path.py
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from abc import ABC, abstractmethod from abc import ABC, abstractmethod
import abstract_importer as ai import abstract_importer as ai

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main_package/classes/cache.py
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import typing import typing
import set_of_cims as sofc import set_of_cims as sofc

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main_package/classes/json_importer.py
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import pandas as pd
import json import json
import typing import typing
from abstract_importer import AbstractImporter
import pandas as pd
import abstract_importer as ai
class JsonImporter(AbstractImporter): class JsonImporter(ai.AbstractImporter):
""" """
Implements the Interface AbstractImporter and adds all the necessary methods to process and prepare the data in json ext. Implements the Interface AbstractImporter and adds all the necessary methods to process and prepare the data in json ext.
with the following structure: with the following structure:

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main_package/classes/network_graph.py
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import typing
import networkx as nx import networkx as nx
import numpy as np import numpy as np
import typing
class NetworkGraph: class NetworkGraph:
@ -21,7 +22,7 @@ class NetworkGraph:
:_transition_scalar_indexing_structure: the indexing structure for transition computation :_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 :_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 :_transition_filtering: the columns filtering structure used in the computation of the transition from one state to another
:self._p_combs_structure: all the possibile parents states combination for every node in the net :self._p_combs_structure: all the possible parents states combination for every node in the net
""" """
def __init__(self, graph_struct): def __init__(self, graph_struct):

7
main_package/classes/parameters_estimator.py
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import numpy as np import numpy as np
import sets_of_cims_container as acims
import set_of_cims as sofc
import sample_path as sp
import network_graph as ng import network_graph as ng
import sample_path as sp
import set_of_cims as sofc
import sets_of_cims_container as acims
class ParametersEstimator: class ParametersEstimator:

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main_package/classes/sample_path.py
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import abstract_sample_path as asam import abstract_sample_path as asam
import json_importer as imp import json_importer as imp
import trajectory as tr
import structure as st import structure as st
import trajectory as tr
class SamplePath(asam.AbstractSamplePath): class SamplePath(asam.AbstractSamplePath):

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main_package/classes/set_of_cims.py
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import numpy as np
import typing import typing
import numpy as np
import conditional_intensity_matrix as cim import conditional_intensity_matrix as cim

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main_package/classes/structure.py
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import typing as ty import typing as ty
import numpy as np import numpy as np

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main_package/classes/structure_estimator.py
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import numpy as np
import itertools import itertools
import networkx as nx
from networkx.readwrite import json_graph
import json import json
import typing import typing
from scipy.stats import f as f_dist
from scipy.stats import chi2 as chi2_dist
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 sample_path as sp import cache as ch
import structure as st
import network_graph as ng
import conditional_intensity_matrix as condim import conditional_intensity_matrix as condim
import network_graph as ng
import parameters_estimator as pe import parameters_estimator as pe
import cache as ch import sample_path as sp
import structure as st
class StructureEstimator: class StructureEstimator:

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2
main_package/tests/test_cache.py
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@ -1,5 +1,5 @@
import sys import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/") sys.path.append("../classes/")
import unittest import unittest
import numpy as np import numpy as np

2
main_package/tests/test_cim.py
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@ -1,5 +1,5 @@
import sys import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/") sys.path.append("../classes/")
import unittest import unittest
import numpy as np import numpy as np

4
main_package/tests/test_json_importer.py
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@ -1,5 +1,5 @@
import sys import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/") sys.path.append("../classes/")
import unittest import unittest
import os import os
import glob import glob
@ -7,8 +7,6 @@ import numpy as np
import pandas as pd import pandas as pd
import json_importer as ji import json_importer as ji
from line_profiler import LineProfiler
import json import json

3
main_package/tests/test_networkgraph.py
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@ -1,12 +1,11 @@
import sys import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/") sys.path.append("../classes/")
import unittest import unittest
import glob import glob
import os import os
import networkx as nx import networkx as nx
import numpy as np import numpy as np
import itertools import itertools
from line_profiler import LineProfiler
import sample_path as sp import sample_path as sp
import network_graph as ng import network_graph as ng

3
main_package/tests/test_parameters_estimator.py
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@ -1,10 +1,9 @@
import sys import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/") sys.path.append("../classes/")
import unittest import unittest
import numpy as np import numpy as np
import glob import glob
import os import os
from line_profiler import LineProfiler
import network_graph as ng import network_graph as ng
import sample_path as sp import sample_path as sp

2
main_package/tests/test_sample_path.py
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@ -1,5 +1,5 @@
import sys import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/") sys.path.append("../classes/")
import unittest import unittest
import glob import glob
import os import os

2
main_package/tests/test_setofcims.py
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@ -1,5 +1,5 @@
import sys import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/") sys.path.append("../classes/")
import unittest import unittest
import numpy as np import numpy as np
import itertools import itertools

5
main_package/tests/test_sets_of_cims_container.py
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@ -1,7 +1,8 @@
import sys
sys.path.append("../classes/")
import unittest import unittest
import sets_of_cims_container as scc
import set_of_cims as sc import set_of_cims as sc
import sets_of_cims_container as scc
class TestSetsOfCimsContainer(unittest.TestCase): class TestSetsOfCimsContainer(unittest.TestCase):

2
main_package/tests/test_structure.py
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@ -1,5 +1,5 @@
import sys import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/") sys.path.append("../classes/")
import unittest import unittest
import numpy as np import numpy as np
import structure as st import structure as st

19
main_package/tests/test_structure_estimator.py
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@ -1,24 +1,25 @@
import sys import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/") sys.path.append("../classes/")
import unittest
import numpy as np
import networkx as nx
import glob import glob
import os
import math import math
from line_profiler import LineProfiler import os
import unittest
import networkx as nx
import numpy as np
import psutil import psutil
from line_profiler import LineProfiler
import json_importer as ji import cache as ch
import sample_path as sp import sample_path as sp
import structure_estimator as se import structure_estimator as se
import cache as ch import json_importer as ji
class TestStructureEstimator(unittest.TestCase): class TestStructureEstimator(unittest.TestCase):
@classmethod @classmethod
def setUpClass(cls) -> None: def setUpClass(cls):
cls.read_files = glob.glob(os.path.join('../data', "*.json")) cls.read_files = glob.glob(os.path.join('../data', "*.json"))
cls.importer = ji.JsonImporter(cls.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name') cls.importer = ji.JsonImporter(cls.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
cls.s1 = sp.SamplePath(cls.importer) cls.s1 = sp.SamplePath(cls.importer)

2
main_package/tests/test_trajectory.py
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@ -1,5 +1,5 @@
import sys import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/") sys.path.append("../classes/")
import unittest import unittest
import numpy as np import numpy as np