Source code for tvb.adapters.analyzers.bct_degree_adapters

# -*- coding: utf-8 -*-
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import bct
from tvb.core.entities.model.model_operation import AlgorithmTransientGroup
from tvb.adapters.analyzers.bct_adapters import BaseBCT

BCT_GROUP_DEGREE = AlgorithmTransientGroup("Degree and Similarity Algorithms",
                                           "Brain Connectivity Toolbox", "bctdegree")
BCT_GROUP_DENSITY = AlgorithmTransientGroup("Density Algorithms", "Brain Connectivity Toolbox", "bctdensity")


[docs] class Degree(BaseBCT): """ """ _ui_group = BCT_GROUP_DEGREE _ui_name = "Degree: Undirected (binary/weighted) connection matrix" _ui_description = bct.degrees_und.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.degrees_und(connectivity.weights) measure_index = self.build_connectivity_measure(result, connectivity, "Node degree") return [measure_index]
[docs] class DegreeIOD(Degree): """ """ _ui_name = "Indegree and outdegree: Directed (binary/weighted) connection matrix" _ui_description = bct.degrees_dir.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.degrees_dir(connectivity.weights) measure_index1 = self.build_connectivity_measure(result[0], connectivity, "Node indegree") measure_index2 = self.build_connectivity_measure(result[1], connectivity, "Node outdegree") measure_index3 = self.build_connectivity_measure(result[2], connectivity, "Node degree (indegree + outdegree)") return [measure_index1, measure_index2, measure_index3]
# class JointDegree(Degree): # """ # Commented because in bctpy 0.5.2 numpy can not index with floats (only ints) # """ # _ui_name = "Joint Degree" # _ui_description = bct.jdegree.__doc__ # # def launch(self, view_model): # connectivity = self.get_connectivity(view_model) # result = bct.jdegree(connectivity.weights) # result_j_od = result[1] # result_j_id = result[2] # result_j_bl = result[3] # measure_index = self.build_connectivity_measure(result[0], connectivity, # "Joint Degree JOD=" + str(result_j_od) + # ", JID=" + str(result_j_id) + # ", JBL=" + str(result_j_bl), # "Connectivity Nodes", "Connectivity Nodes") # value1 = self.build_int_value_wrapper(result_j_od, "Number of vertices with od > id") # value2 = self.build_int_value_wrapper(result_j_id, "Number of vertices with id > od") # value3 = self.build_int_value_wrapper(result_j_bl, "Number of vertices with id = od") # # return [measure_index, value1, value2, value3]
[docs] class MatchingIndex(Degree): """ """ _ui_name = "Matching Index: Connection/adjacency matrix" _ui_description = bct.matching_ind.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.matching_ind(connectivity.weights) measure_index1 = self.build_connectivity_measure(result[0], connectivity, "Matching index for incoming connections") measure_index2 = self.build_connectivity_measure(result[1], connectivity, "Matching index for outgoing connections") measure_index3 = self.build_connectivity_measure(result[2], connectivity, "Matching index for all connections") return [measure_index1, measure_index2, measure_index3]
[docs] class Strength(Degree): """ """ _ui_name = "Strength: Directed weighted connection matrix" _ui_description = bct.strengths_und.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.strengths_und(connectivity.weights) measure_index = self.build_connectivity_measure(result, connectivity, "Node strength") return [measure_index]
[docs] class StrengthISOS(Strength): """ """ _ui_name = "Instrength and Outstrength" _ui_description = bct.strengths_dir.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.strengths_dir(connectivity.weights) measure_index = self.build_connectivity_measure(result, connectivity, "Node instrength + outstrength") return [measure_index]
[docs] class StrengthWeights(Strength): """ """ _ui_name = "Strength and Weight" _ui_description = bct.strengths_und_sign.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.strengths_und_sign(connectivity.weights) measure_index1 = self.build_connectivity_measure(result[0], connectivity, "Nodal strength of positive weights") measure_index2 = self.build_connectivity_measure(result[1], connectivity, "Nodal strength of negative weights") value1 = self.build_float_value_wrapper(result[2], "Total positive weight") value2 = self.build_float_value_wrapper(result[3], "Total negative weight") return [measure_index1, measure_index2, value1, value2]
[docs] class DensityDirected(BaseBCT): """ """ _ui_group = BCT_GROUP_DENSITY _ui_name = "Density Directed: Directed (weighted/binary) connection matrix" _ui_description = bct.density_dir.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.density_dir(connectivity.weights) value1 = self.build_float_value_wrapper(result[0], title="Density") value2 = self.build_int_value_wrapper(result[1], title="Number of vertices") value3 = self.build_int_value_wrapper(result[2], title="Number of edges") return [value1, value2, value3]
[docs] class DensityUndirected(DensityDirected): """ """ _ui_name = "Density Undirected: Undirected (weighted/binary) connection matrix" _ui_description = bct.density_und.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.density_und(connectivity.weights) value1 = self.build_float_value_wrapper(result[0], title="Density") value2 = self.build_int_value_wrapper(result[1], title="Number of vertices") value3 = self.build_int_value_wrapper(result[2], title="Number of edges") return [value1, value2, value3]