Graph Measure extraction example¶

This example will show you how to save the graph measurement results as CSV file.

In [1]:

import numpy as np

from photonai_graph.GraphUtilities import get_random_connectivity_data
from photonai_graph.GraphMeasureTransform import GraphMeasureTransform
from photonai_graph.GraphConstruction.graph_constructor_threshold import GraphConstructorThreshold

import numpy as np from photonai_graph.GraphUtilities import get_random_connectivity_data from photonai_graph.GraphMeasureTransform import GraphMeasureTransform from photonai_graph.GraphConstruction.graph_constructor_threshold import GraphConstructorThreshold

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[1], line 4
      1 import numpy as np
      3 from photonai_graph.GraphUtilities import get_random_connectivity_data
----> 4 from photonai_graph.GraphMeasureTransform import GraphMeasureTransform
      5 from photonai_graph.GraphConstruction.graph_constructor_threshold import GraphConstructorThreshold

ModuleNotFoundError: No module named 'photonai_graph.GraphMeasureTransform'

Generate random matrices to simulate connectivity matrices

In [2]:

X = get_random_connectivity_data(number_of_nodes=50, number_of_individuals=200)

X = get_random_connectivity_data(number_of_nodes=50, number_of_individuals=200)

Instantiate a constructor to threshold the graphs

In [3]:

g_constructor = GraphConstructorThreshold(threshold=0.95)

g_constructor = GraphConstructorThreshold(threshold=0.95)

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[3], line 1
----> 1 g_constructor = GraphConstructorThreshold(threshold=0.95)

NameError: name 'GraphConstructorThreshold' is not defined

Instantiate the measure_transformer

In [4]:

g_measure_transformer = GraphMeasureTransform(graph_functions={"global_efficiency": {},
                                                               "local_efficiency": {},
                                                               "average_clustering": {},
                                                               "degree_centrality": {},
                                                               "betweenness_centrality": {},
                                                               "overall_reciprocity": {}})

X_trans = g_constructor.transform(X)

g_measure_transformer.extract_measures(X_trans, path="test_measures.csv", ids=np.arange(200))

g_measure_transformer = GraphMeasureTransform(graph_functions={"global_efficiency": {}, "local_efficiency": {}, "average_clustering": {}, "degree_centrality": {}, "betweenness_centrality": {}, "overall_reciprocity": {}}) X_trans = g_constructor.transform(X) g_measure_transformer.extract_measures(X_trans, path="test_measures.csv", ids=np.arange(200))

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[4], line 1
----> 1 g_measure_transformer = GraphMeasureTransform(graph_functions={"global_efficiency": {},
      2                                                                "local_efficiency": {},
      3                                                                "average_clustering": {},
      4                                                                "degree_centrality": {},
      5                                                                "betweenness_centrality": {},
      6                                                                "overall_reciprocity": {}})
      8 X_trans = g_constructor.transform(X)
     10 g_measure_transformer.extract_measures(X_trans, path="test_measures.csv", ids=np.arange(200))

NameError: name 'GraphMeasureTransform' is not defined

This will generate an example CSV file containing the measurement results for each graph.