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Source code for tvb.adapters.analyzers.node_covariance_adapter

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#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
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"""
Adapter that uses the traits module to generate interfaces for FFT Analyzer.

.. moduleauthor:: Stuart A. Knock <Stuart@tvb.invalid>
.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>

"""
import uuid

import numpy
from tvb.adapters.datatypes.db.graph import CovarianceIndex
from tvb.adapters.datatypes.db.time_series import TimeSeriesIndex
from tvb.adapters.datatypes.h5.graph_h5 import CovarianceH5
from tvb.basic.neotraits.info import narray_describe
from tvb.core.adapters.abcadapter import ABCAdapterForm, ABCAdapter
from tvb.core.entities.filters.chain import FilterChain
from tvb.core.neocom import h5
from tvb.core.neotraits.forms import TraitDataTypeSelectField
from tvb.core.neotraits.view_model import ViewModel, DataTypeGidAttr
from tvb.datatypes.graph import Covariance
from tvb.datatypes.time_series import TimeSeries


[docs]class NodeCovarianceAdapterModel(ViewModel): time_series = DataTypeGidAttr( linked_datatype=TimeSeries, label="Time Series", required=True, doc="""The timeseries to which the NodeCovariance is to be applied.""" )
[docs]class NodeCovarianceAdapterForm(ABCAdapterForm): def __init__(self): super(NodeCovarianceAdapterForm, self).__init__() self.time_series = TraitDataTypeSelectField(NodeCovarianceAdapterModel.time_series, name=self.get_input_name(), conditions=self.get_filters(), has_all_option=True) @staticmethod
[docs] def get_view_model(): return NodeCovarianceAdapterModel
@staticmethod
[docs] def get_required_datatype(): return TimeSeriesIndex
@staticmethod
[docs] def get_input_name(): return 'time_series'
@staticmethod
[docs] def get_filters(): return FilterChain(fields=[FilterChain.datatype + '.data_ndim'], operations=["=="], values=[4])
[docs]class NodeCovarianceAdapter(ABCAdapter): """ TVB adapter for calling the NodeCovariance algorithm. """ _ui_name = "Temporal covariance of nodes" _ui_description = "Compute Temporal Node Covariance for a TimeSeries input DataType." _ui_subsection = "covariance"
[docs] def get_form_class(self): return NodeCovarianceAdapterForm
[docs] def get_output(self): return [CovarianceIndex]
[docs] def configure(self, view_model): # type: (NodeCovarianceAdapterModel) -> None """ Store the input shape to be later used to estimate memory usage. """ self.input_time_series_index = self.load_entity_by_gid(view_model.time_series) self.input_shape = (self.input_time_series_index.data_length_1d, self.input_time_series_index.data_length_2d, self.input_time_series_index.data_length_3d, self.input_time_series_index.data_length_4d)
[docs] def get_required_memory_size(self, view_model): # type: (NodeCovarianceAdapterModel) -> int """ Return the required memory to run this algorithm. """ used_shape = (self.input_shape[0], 1, self.input_shape[2], 1) input_size = numpy.prod(used_shape) * 8.0 output_size = self._result_size(used_shape) return input_size + output_size
[docs] def get_required_disk_size(self, view_model): # type: (NodeCovarianceAdapterModel) -> int """ Returns the required disk size to be able to run the adapter ( in kB). """ used_shape = (self.input_shape[0], 1, self.input_shape[2], 1) return self.array_size2kb(self._result_size(used_shape))
[docs] def launch(self, view_model): # type: (NodeCovarianceAdapterModel) -> [CovarianceIndex] """ Launch algorithm and build results. :param view_model: the ViewModel keeping the algorithm inputs :return: the `CovarianceIndex` built with the given time_series index as source """ # -------------------- Prepare result entities ---------------------## covariance_index = CovarianceIndex() covariance_h5_path = h5.path_for(self.storage_path, CovarianceH5, covariance_index.gid) covariance_h5 = CovarianceH5(covariance_h5_path) # ------------ NOTE: Assumes 4D, Simulator timeSeries -------------## node_slice = [slice(self.input_shape[0]), None, slice(self.input_shape[2]), None] ts_h5 = h5.h5_file_for_index(self.input_time_series_index) for mode in range(self.input_shape[3]): for var in range(self.input_shape[1]): small_ts = TimeSeries() node_slice[1] = slice(var, var + 1) node_slice[3] = slice(mode, mode + 1) small_ts.data = ts_h5.read_data_slice(tuple(node_slice)) partial_cov = self._compute_node_covariance(small_ts, ts_h5) covariance_h5.write_data_slice(partial_cov.array_data) ts_h5.close() partial_cov.source.gid = view_model.time_series partial_cov.gid = uuid.UUID(covariance_index.gid) covariance_index.fill_from_has_traits(partial_cov) self.fill_index_from_h5(covariance_index, covariance_h5) covariance_h5.store(partial_cov, scalars_only=True) covariance_h5.close() return covariance_index
def _compute_node_covariance(self, small_ts, input_ts_h5): """ Compute the temporal covariance between nodes in a TimeSeries dataType. A nodes x nodes matrix is returned for each (state-variable, mode). """ data_shape = small_ts.data.shape # (nodes, nodes, state-variables, modes) result_shape = (data_shape[2], data_shape[2], data_shape[1], data_shape[3]) self.log.info("result shape will be: %s" % str(result_shape)) result = numpy.zeros(result_shape) # One inter-node temporal covariance matrix for each state-var & mode. for mode in range(data_shape[3]): for var in range(data_shape[1]): data = input_ts_h5.data[:, var, :, mode] data = data - data.mean(axis=0)[numpy.newaxis, 0] result[:, :, var, mode] = numpy.cov(data.T) self.log.debug("result") self.log.debug(narray_describe(result)) covariance = Covariance(source=small_ts, array_data=result) return covariance @staticmethod def _result_size(input_shape): """ Returns the storage size in Bytes of the NodeCovariance result. """ result_size = numpy.prod([input_shape[2], input_shape[2], input_shape[1], input_shape[3]]) * 8.0 # Bytes return result_size