The Virtual Brain Project

Source code for tvb.adapters.analyzers.metrics_group_timeseries

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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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"""
Adapter that uses the traits module to generate interfaces for group of 
Analyzer used to calculate a single measure for TimeSeries.

.. moduleauthor:: Paula Sanz Leon <pau.sleon@gmail.com>
.. moduleauthor:: Bogdan Neacsa <bogdan.neacsa@codemart.ro>
.. moduleauthor:: Stuart A. Knock <Stuart@tvb.invalid>
.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>

"""

import numpy
from tvb.analyzers.metrics_base import BaseTimeseriesMetricAlgorithm
from tvb.basic.traits.util import log_debug_array
from tvb.basic.traits.parameters_factory import get_traited_subclasses
from tvb.basic.filters.chain import FilterChain
from tvb.basic.logger.builder import get_logger
from tvb.core.adapters.abcadapter import ABCAsynchronous, ABCAdapter
from tvb.datatypes.time_series import TimeSeries
from tvb.datatypes.mapped_values import DatatypeMeasure


LOG = get_logger(__name__)



[docs]class TimeseriesMetricsAdapter(ABCAsynchronous): """ TVB adapter for exposing as a group the measure algorithm. """ _ui_name = "TimeSeries Metrics" _ui_description = "Compute a single number for a TimeSeries input DataType." _ui_subsection = "timeseries" available_algorithms = get_traited_subclasses(BaseTimeseriesMetricAlgorithm)
[docs] def get_input_tree(self): """ Compute interface based on introspected algorithms found. """ algorithm = BaseTimeseriesMetricAlgorithm() algorithm.trait.bound = self.INTERFACE_ATTRIBUTES_ONLY tree = algorithm.interface[self.INTERFACE_ATTRIBUTES] tree[0]['conditions'] = FilterChain(fields=[FilterChain.datatype + '._nr_dimensions'], operations=["=="], values=[4]) algo_names = self.available_algorithms.keys() options = [] for name in algo_names: options.append({ABCAdapter.KEY_NAME: name, ABCAdapter.KEY_VALUE: name}) tree.append({'name': 'algorithms', 'label': 'Selected metrics to be applied', 'type': ABCAdapter.TYPE_MULTIPLE, 'required': False, 'options': options, 'description': 'The selected metric algorithms will be applied on the input TimeSeries'}) return tree
[docs] def get_output(self): return [DatatypeMeasure]
[docs] def configure(self, time_series, **kwargs): """ Store the input shape to be later used to estimate memory usage. """ self.input_shape = time_series.read_data_shape()
[docs] def get_required_memory_size(self, **kwargs): """ Return the required memory to run this algorithm. """ input_size = numpy.prod(self.input_shape) * 8.0 return input_size
[docs] def get_required_disk_size(self, **kwargs): """ Returns the required disk size to be able to run the adapter (in kB). """ return 0
[docs] def launch(self, time_series, algorithms=None, start_point=None, segment=None): """ Launch algorithm and build results. :param time_series: the time series on which the algorithms are run :param algorithms: the algorithms to be run for computing measures on the time series :type algorithms: any subclass of BaseTimeseriesMetricAlgorithm (KuramotoIndex, GlobalVariance, VarianceNodeVariance) :rtype: `DatatypeMeasure` """ if algorithms is None: algorithms = self.available_algorithms.keys() shape = time_series.read_data_shape() log_debug_array(LOG, time_series, "time_series") metrics_results = {} for algorithm_name in algorithms: ##------------- NOTE: Assumes 4D, Simulator timeSeries. --------------## node_slice = [slice(shape[0]), slice(shape[1]), slice(shape[2]), slice(shape[3])] ##---------- Iterate over slices and compose final result ------------## unstored_ts = TimeSeries(use_storage=False) unstored_ts.data = time_series.read_data_slice(tuple(node_slice)) ##-------------------- Fill Algorithm for Analysis -------------------## algorithm = self.available_algorithms[algorithm_name](time_series=unstored_ts) if segment is not None: algorithm.segment = segment if start_point is not None: algorithm.start_point = start_point ## Validate that current algorithm's filter is valid. if (algorithm.accept_filter is not None and not algorithm.accept_filter.get_python_filter_equivalent(time_series)): LOG.warning('Measure algorithm will not be computed because of incompatibility on input. ' 'Filters failed on algo: ' + str(algorithm_name)) continue else: LOG.debug("Applying measure: " + str(algorithm_name)) unstored_result = algorithm.evaluate() ##----------------- Prepare a Float object(s) for result ----------------## if isinstance(unstored_result, dict): metrics_results.update(unstored_result) else: metrics_results[algorithm_name] = unstored_result result = DatatypeMeasure(analyzed_datatype=time_series, storage_path=self.storage_path, data_name=self._ui_name, metrics=metrics_results) return result