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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
import abstract_importer as ai

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main_package/classes/cache.py
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import typing
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 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.
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 numpy as np
import typing
class NetworkGraph:
@ -21,7 +22,7 @@ class NetworkGraph:
:_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
: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):

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

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main_package/classes/sample_path.py
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import abstract_sample_path as asam
import json_importer as imp
import trajectory as tr
import structure as st
import trajectory as tr
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 numpy as np
import conditional_intensity_matrix as cim

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main_package/classes/structure.py
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import typing as ty
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 networkx as nx
from networkx.readwrite import json_graph
import json
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 structure as st
import network_graph as ng
import cache as ch
import conditional_intensity_matrix as condim
import network_graph as ng
import parameters_estimator as pe
import cache as ch
import sample_path as sp
import structure as st
class StructureEstimator:

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</packages>
</coverage>

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

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

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

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

3
main_package/tests/test_parameters_estimator.py
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@ -1,10 +1,9 @@
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 glob
import os
from line_profiler import LineProfiler
import network_graph as ng
import sample_path as sp

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

2
main_package/tests/test_setofcims.py
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@ -1,5 +1,5 @@
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 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 sets_of_cims_container as scc
import set_of_cims as sc
import sets_of_cims_container as scc
class TestSetsOfCimsContainer(unittest.TestCase):

2
main_package/tests/test_structure.py
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@ -1,5 +1,5 @@
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 structure as st

19
main_package/tests/test_structure_estimator.py
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@ -1,24 +1,25 @@
import sys
sys.path.append("/Users/Zalum/Desktop/Tesi/CTBN_Project/main_package/classes/")
import unittest
import numpy as np
import networkx as nx
sys.path.append("../classes/")
import glob
import os
import math
from line_profiler import LineProfiler
import os
import unittest
import networkx as nx
import numpy as np
import psutil
from line_profiler import LineProfiler
import json_importer as ji
import cache as ch
import sample_path as sp
import structure_estimator as se
import cache as ch
import json_importer as ji
class TestStructureEstimator(unittest.TestCase):
@classmethod
def setUpClass(cls) -> None:
def setUpClass(cls):
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.s1 = sp.SamplePath(cls.importer)

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