TheVirtualBrain:

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Source code for tvb.adapters.analyzers.bct_adapters

# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Framework Package. This package holds all Data Management, and
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2022, Baycrest Centre for Geriatric Care ("Baycrest") and others
#
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program.  If not, see <http://www.gnu.org/licenses/>.
#
#
#   CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
#
#   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)
#
#

import os
from abc import abstractmethod

from tvb.adapters.analyzers.matlab_worker import MatlabWorker
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.basic.profile import TvbProfile
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.neocom import h5
from tvb.core.neotraits.forms import TraitDataTypeSelectField
from tvb.core.neotraits.view_model import ViewModel, DataTypeGidAttr
from tvb.core.utils import extract_matlab_doc_string
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")

BCT_PATH = os.path.join(TvbProfile.current.EXTERNALS_FOLDER_PARENT, "externals/BCT")
BCT_PATH_ENV = 'BCT_PATH'
if BCT_PATH_ENV in os.environ and os.path.exists(os.environ[BCT_PATH_ENV]) and os.path.isdir(os.environ[BCT_PATH_ENV]):
    BCT_PATH = os.environ[BCT_PATH_ENV]

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]def bct_description(mat_file_name): return extract_matlab_doc_string(os.path.join(BCT_PATH, mat_file_name))
[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) @staticmethod
[docs] def get_required_datatype(): return ConnectivityIndex
@staticmethod
[docs] def get_filters(): return None
@staticmethod
[docs] def get_input_name(): return "connectivity"
@staticmethod
[docs] def get_view_model(): return BaseBCTModel
[docs]class BaseUnidirectedBCTForm(BaseBCTForm): @staticmethod
[docs] 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. This adapter requires BCT deployed locally, and Matlab or Octave installed separately of TVB. """ def __init__(self): ABCAdapter.__init__(self) self.matlab_worker = MatlabWorker() @staticmethod
[docs] def can_be_active(): return not not TvbProfile.current.MATLAB_EXECUTABLE
[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 execute_matlab(self, matlab_code, data): self.matlab_worker.add_to_path(BCT_PATH) self.log.info("Starting execution of MATLAB code:" + matlab_code) runcode, matlablog, result = self.matlab_worker.matlab(matlab_code, data=data, work_dir=self.storage_path) self.log.debug("Code run in MATLAB: " + str(runcode)) self.log.debug("MATLAB log: " + str(matlablog)) self.log.debug("Finished MATLAB execution:" + str(result)) return result
[docs] def build_connectivity_measure(self, result, key, connectivity, title="", label_x="", label_y=""): measure = ConnectivityMeasure() measure.array_data = result[key] measure.connectivity = connectivity measure.title = title measure.label_x = label_x measure.label_y = label_y return h5.store_complete(measure, self.storage_path)
[docs] def build_float_value_wrapper(self, result, key, title=""): value = ValueWrapper() value.data_value = str(float(result[key])) value.data_type = 'float' value.data_name = title return h5.store_complete(value, self.storage_path)
[docs] def build_int_value_wrapper(self, result, key, title=""): value = ValueWrapper() value.data_value = str(int(result[key])) value.data_type = 'int' value.data_name = title return h5.store_complete(value, self.storage_path)
@abstractmethod
[docs] def launch(self, view_model): pass
[docs]class BaseUndirected(BaseBCT): """ """
[docs] def get_form_class(self): return BaseUnidirectedBCTForm
@abstractmethod
[docs] 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_description("modularity_dir.m") _matlab_code = "[Ci,Q] = modularity_dir(CW);"
[docs] def launch(self, view_model): # Prepare parameters connectivity = self.get_connectivity(view_model) data = {'CW': connectivity.weights} # Execute the matlab code result = self.execute_matlab(self._matlab_code, data=data) # Gather results measure = self.build_connectivity_measure(result, 'Ci', connectivity, "Optimal Community Structure") value = self.build_float_value_wrapper(result, 'Q', title="Maximized Modularity") return [measure, value]
[docs]class ModularityOpCSMU(ModularityOCSM): """ """ _ui_name = "Optimal Community Structure and Modularity (Undirected):" _ui_description = bct_description("modularity_und.m") _matlab_code = "[Ci,Q] = modularity_und(CW);"
[docs]class DistanceDBIN(BaseBCT): """ """ _ui_group = BCT_GROUP_DISTANCE _ui_name = "Distance binary matrix" _ui_description = bct_description("distance_bin.m") _matlab_code = "D = distance_bin(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) measure = self.build_connectivity_measure(result, 'D', connectivity, "Distance matrix") return [measure]
[docs]class DistanceDWEI(DistanceDBIN): """ """ _ui_name = "Distance weighted matrix over a Weighted (directed/undirected) connection matrix" _ui_description = bct_description("distance_wei.m") _matlab_code = "D = distance_wei(A);"
[docs]class DistanceRDM(DistanceDBIN): """ """ _ui_name = "Reachability and distance matrices (Breadth-first search)" _ui_description = bct_description("breadthdist.m") _matlab_code = "[R,D] = breadthdist(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) measure1 = self.build_connectivity_measure(result, 'R', connectivity, "Reachability matrix") measure2 = self.build_connectivity_measure(result, 'D', connectivity, "Distance matrix") return [measure1, measure2]
[docs]class DistanceRDA(DistanceRDM): """ """ _ui_name = "Reachability and distance matrices (Algebraic path count)" _ui_description = bct_description("reachdist.m") _matlab_code = "[R,D] = reachdist(A);"
[docs]class DistanceNETW(DistanceDBIN): """ """ _ui_name = "Network walks" _ui_description = bct_description("findwalks.m") _matlab_code = "[Wq,twalk,wlq] = findwalks(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) measure1 = self.build_connectivity_measure(result, 'Wq', connectivity, "3D matrix") measure2 = self.build_connectivity_measure(result, 'wlq', connectivity, "Walk length distribution") value = self.build_float_value_wrapper(result, 'twalk', title="Total number of walks found") return [measure1, value, measure2]