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Source code for tvb.adapters.analyzers.bct_degree_adapters

# -*- coding: utf-8 -*-
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# TheVirtualBrain-Framework Package. This package holds all Data Management, and
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# CITATION:
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# Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
# Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
# The Virtual Brain: a simulator of primate brain network dynamics.
# Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
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#
from tvb.core.entities.model.model_operation import AlgorithmTransientGroup
from tvb.adapters.analyzers.bct_adapters import BaseBCT, bct_description, BaseBCTForm

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_description("degrees_und.m") _matlab_code = "deg = degrees_und(CIJ);"
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) data = {'CIJ': connectivity.weights} result = self.execute_matlab(self._matlab_code, data=data) measure_index = self.build_connectivity_measure(result, 'deg', connectivity, "Node degree") return [measure_index]
[docs]class DegreeIOD(Degree): """ """ _ui_name = "Indegree and outdegree: Directed (binary/weighted) connection matrix" _ui_description = bct_description("degrees_dir.m") _matlab_code = "[id,od,deg] = degrees_dir(CIJ);"
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) data = {'CIJ': connectivity.weights} result = self.execute_matlab(self._matlab_code, data=data) measure_index1 = self.build_connectivity_measure(result, 'id', connectivity, "Node indegree") measure_index2 = self.build_connectivity_measure(result, 'od', connectivity, "Node outdegree") measure_index3 = self.build_connectivity_measure(result, 'deg', connectivity, "Node degree (indegree + outdegree)") return [measure_index1, measure_index2, measure_index3]
[docs]class JointDegree(Degree): """ """ _ui_name = "Joint Degree" _ui_description = bct_description("jdegree.m") _matlab_code = "[J,J_od,J_id,J_bl] = jdegree(CIJ);"
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) data = {'CIJ': connectivity.weights} result = self.execute_matlab(self._matlab_code, data=data) measure_index = self.build_connectivity_measure(result, 'J', 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_description("matching_ind.m") _matlab_code = "[Min,Mout,Mall] = matching_ind(CIJ);"
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) data = {'CIJ': connectivity.weights} result = self.execute_matlab(self._matlab_code, data=data) measure_index1 = self.build_connectivity_measure(result, 'Min', connectivity, "Matching index for incoming connections") measure_index2 = self.build_connectivity_measure(result, 'Mout', connectivity, "Matching index for outgoing connections") measure_index3 = self.build_connectivity_measure(result, 'Mall', 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_description("strengths_und.m") _matlab_code = "strength = strengths_und(CIJ);"
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) data = {'CIJ': connectivity.weights} result = self.execute_matlab(self._matlab_code, data=data) measure_index = self.build_connectivity_measure(result, 'strength', connectivity, "Node strength") return [measure_index]
[docs]class StrengthISOS(Strength): """ """ _ui_name = "Instrength and Outstrength" _ui_description = bct_description("strengths_dir.m") _matlab_code = "[is,os,strength] = strengths_dir(CIJ);"
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) data = {'CIJ': connectivity.weights} result = self.execute_matlab(self._matlab_code, data=data) measure_index1 = self.build_connectivity_measure(result, 'is', connectivity, "Node instrength") measure_index2 = self.build_connectivity_measure(result, 'os', connectivity, "Node outstrength") measure_index3 = self.build_connectivity_measure(result, 'strength', connectivity, "Node strength (instrength + outstrength)") return [measure_index1, measure_index2, measure_index3]
[docs]class StrengthWeights(Strength): """ """ _ui_name = "Strength and Weight" _ui_description = bct_description("strengths_und_sign.m") _matlab_code = "[Spos,Sneg,vpos,vneg] = strengths_und_sign(CIJ);"
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) data = {'CIJ': connectivity.weights} result = self.execute_matlab(self._matlab_code, data=data) measure_index1 = self.build_connectivity_measure(result, 'Spos', connectivity, "Nodal strength of positive weights") measure_index2 = self.build_connectivity_measure(result, 'Sneg', connectivity, "Nodal strength of negative weights") value1 = self.build_float_value_wrapper(result, 'vpos', "Total positive weight") value2 = self.build_float_value_wrapper(result, 'vneg', "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_description("density_dir.m") _matlab_code = "[kden,N,K] = density_dir(A);"
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) data = {'A': connectivity.weights} result = self.execute_matlab(self._matlab_code, data=data) value1 = self.build_float_value_wrapper(result, 'kden', title="Density") value2 = self.build_int_value_wrapper(result, 'N', title="Number of vertices") value3 = self.build_int_value_wrapper(result, 'K', title="Number of edges") return [value1, value2, value3]
[docs]class DensityUndirected(DensityDirected): """ """ _ui_name = "Density Unirected: Undirected (weighted/binary) connection matrix" _ui_description = bct_description("density_und.m") _matlab_code = "[kden,N,K] = density_und(A);"