Source code for tvb.adapters.analyzers.bct_adapters

# -*- coding: utf-8 -*-
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# TheVirtualBrain-Framework Package. This package holds all Data Management, and
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import bct
from abc import abstractmethod
from tvb.adapters.datatypes.db.connectivity import ConnectivityIndex
from tvb.adapters.datatypes.db.graph import ConnectivityMeasureIndex
from tvb.adapters.datatypes.db.mapped_value import ValueWrapperIndex
from tvb.adapters.datatypes.h5.mapped_value_h5 import ValueWrapper
from tvb.core.adapters.abcadapter import ABCAdapterForm, ABCAdapter
from tvb.core.entities.filters.chain import FilterChain
from tvb.core.entities.model.model_operation import AlgorithmTransientGroup
from tvb.core.neotraits.forms import TraitDataTypeSelectField
from tvb.core.neotraits.view_model import ViewModel, DataTypeGidAttr
from tvb.datatypes.connectivity import Connectivity
from tvb.datatypes.graph import ConnectivityMeasure

BCT_GROUP_MODULARITY = AlgorithmTransientGroup("Modularity Algorithms", "Brain Connectivity Toolbox", "bct")
BCT_GROUP_DISTANCE = AlgorithmTransientGroup("Distance Algorithms", "Brain Connectivity Toolbox", "bctdistance")

LABEL_CONNECTIVITY_BINARY = "Binary (directed/undirected) connection matrix"
LABEL_CONN_WEIGHTED_DIRECTED = "Weighted directed connection matrix"
LABEL_CONN_WEIGHTED_UNDIRECTED = "Weighted undirected connection matrix"


[docs] class BaseBCTModel(ViewModel): connectivity = DataTypeGidAttr( linked_datatype=Connectivity, label='Connectivity', )
[docs] class BaseBCTForm(ABCAdapterForm): def __init__(self): super(BaseBCTForm, self).__init__() self.connectivity = TraitDataTypeSelectField(BaseBCTModel.connectivity, name="connectivity", conditions=self.get_filters(), has_all_option=True)
[docs] @staticmethod def get_required_datatype(): return ConnectivityIndex
[docs] @staticmethod def get_filters(): return None
[docs] @staticmethod def get_input_name(): return "connectivity"
[docs] @staticmethod def get_view_model(): return BaseBCTModel
[docs] class BaseUnidirectedBCTForm(BaseBCTForm):
[docs] @staticmethod def get_filters(): return FilterChain(fields=[FilterChain.datatype + '.undirected'], operations=["=="], values=['1'])
[docs] class BaseBCT(ABCAdapter): """ Interface between Brain Connectivity Toolbox of Olaf Sporns and TVB Framework. """
[docs] def get_form_class(self): return BaseBCTForm
[docs] def get_output(self): return [ConnectivityMeasureIndex, ValueWrapperIndex]
[docs] def get_required_memory_size(self, view_model): # We do not know how much memory is needed. return -1
[docs] def get_required_disk_size(self, view_model): return 0
[docs] def get_connectivity(self, view_model): return self.load_traited_by_gid(view_model.connectivity)
[docs] def build_connectivity_measure(self, array_data, connectivity, title="", label_x="", label_y=""): measure = ConnectivityMeasure() measure.array_data = array_data measure.connectivity = connectivity measure.title = title measure.label_x = label_x measure.label_y = label_y return self.store_complete(measure)
[docs] def build_float_value_wrapper(self, result_value, title=""): value = ValueWrapper() value.data_value = str(float(result_value)) value.data_type = 'float' value.data_name = title return self.store_complete(value)
[docs] def build_int_value_wrapper(self, result_int, title=""): value = ValueWrapper() value.data_value = str(int(result_int)) value.data_type = 'int' value.data_name = title return self.store_complete(value)
[docs] @abstractmethod def launch(self, view_model): pass
[docs] class BaseUndirected(BaseBCT): """ """
[docs] def get_form_class(self): return BaseUnidirectedBCTForm
[docs] @abstractmethod def launch(self, view_model): pass
[docs] class ModularityOCSM(BaseBCT): """ """ _ui_group = BCT_GROUP_MODULARITY _ui_name = "Compute optimal Community Structure and Modularity from a Directed (weighted or binary) connection " \ "matrix: " _ui_description = bct.modularity_dir.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.modularity_dir(connectivity.weights) measure = self.build_connectivity_measure(result[0], connectivity, "Optimal Community Structure") value = self.build_float_value_wrapper(result[1], title="Maximized Modularity") return [measure, value]
[docs] class ModularityOpCSMU(ModularityOCSM): """ """ _ui_name = "Optimal Community Structure and Modularity (Undirected):" _ui_description = bct.modularity_und.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.modularity_und(connectivity.weights) measure = self.build_connectivity_measure(result[0], connectivity, "Optimal Community Structure") value = self.build_float_value_wrapper(result[1], title="Maximized Modularity") return [measure, value]
DISTANCE_MATRIX_TITLE = "Distance matrix"
[docs] class DistanceDBIN(BaseBCT): """ """ _ui_group = BCT_GROUP_DISTANCE _ui_name = "Distance binary matrix" _ui_description = bct.distance_bin.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result_arr = bct.distance_bin(connectivity.weights) measure = self.build_connectivity_measure(result_arr, connectivity, DISTANCE_MATRIX_TITLE) return [measure]
[docs] class DistanceDWEI(DistanceDBIN): """ """ _ui_name = "Distance weighted matrix over a Weighted (directed/undirected) connection matrix" _ui_description = bct.distance_wei.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.distance_wei(connectivity.weights)[0] measure = self.build_connectivity_measure(result, connectivity, DISTANCE_MATRIX_TITLE) return [measure]
[docs] class DistanceRDM(DistanceDBIN): """ """ _ui_name = "Reachability and distance matrices (Breadth-first search)" _ui_description = bct.breadthdist.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.breadthdist(connectivity.weights) measure1 = self.build_connectivity_measure(result[0], connectivity, "Reachability matrix") measure2 = self.build_connectivity_measure(result[1], connectivity, DISTANCE_MATRIX_TITLE) return [measure1, measure2]
[docs] class DistanceRDA(DistanceRDM): """ """ _ui_name = "Reachability and distance matrices (Algebraic path count)" _ui_description = bct.reachdist.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.reachdist(connectivity.weights) measure1 = self.build_connectivity_measure(result[0], connectivity, "Reachability matrix") measure2 = self.build_connectivity_measure(result[1], connectivity, DISTANCE_MATRIX_TITLE) return [measure1, measure2]
[docs] class DistanceNETW(DistanceDBIN): """ """ _ui_name = "Network walks" _ui_description = bct.findwalks.__doc__
[docs] def launch(self, view_model): connectivity = self.get_connectivity(view_model) result = bct.findwalks(connectivity.weights) measure1 = self.build_connectivity_measure(result[0], connectivity, "3D matrix") measure2 = self.build_connectivity_measure(result[2], connectivity, "Walk length distribution") value = self.build_float_value_wrapper(result[1], title="Total number of walks found") return [measure1, value, measure2]