The Virtual Brain Project

Source code for tvb.adapters.uploaders.mat_timeseries_importer

# -*- coding: utf-8 -*-
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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.
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"""
.. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>
"""

import numpy
from tvb.adapters.uploaders.abcuploader import ABCUploader
from tvb.adapters.uploaders.mat.parser import read_nested_mat_file
from tvb.core.adapters.exceptions import ParseException, LaunchException
from tvb.core.entities.storage import transactional
from tvb.basic.arguments_serialisation import parse_slice
from tvb.datatypes.time_series import TimeSeriesRegion, TimeSeriesEEG


[docs]class MatTimeSeriesImporter(ABCUploader): """ Import time series from a .mat file. """ _ui_name = "Timeseries MAT" _ui_subsection = "mat_ts_importer" _ui_description = "Import time series from a .mat file." TS_REGION = 'region' TS_EEG = 'EEG'
[docs] def get_upload_input_tree(self): return [ {'name': 'data_file', 'type': 'upload', 'required_type': '.mat', 'label': 'Please select file to import', 'required': True}, {'name': 'dataset_name', 'type': 'str', 'required': True, 'label': 'Matlab dataset name', 'description': 'Name of the MATLAB dataset where data is stored'}, {'name': 'structure_path', 'type': 'str', 'default': '', 'label': 'For nested structures enter the field path (separated by .)'}, {'name': 'transpose', 'type': 'bool', 'default': False, 'label': 'Transpose the array. Expected shape is (time, channel)'}, {'name': 'slice', 'type': 'str', 'default': '', 'label': 'Slice of the array in numpy syntax. Expected shape is (time, channel)'}, {'name': 'tstype', 'type': 'select', 'required': True, 'label': 'time series type', 'options': [{'name': self.TS_REGION, 'value': self.TS_REGION, 'attributes': [{'name': 'connectivity', 'required': True, 'label': 'Connectivity', 'type': 'tvb.datatypes.connectivity.Connectivity'}]}, {'name': self.TS_EEG, 'value': self.TS_EEG, 'attributes': [{'name': 'sensors', 'required': True, 'label': 'EEG Sensors', 'type': 'tvb.datatypes.sensors.SensorsEEG'}]} ]}, {'name': 'sampling_rate', 'type': 'int', 'default': 1000, 'label': 'sampling rate (Hz)'}, {'name': 'start_time', 'type': 'int', 'default': 0, 'label': 'starting time (ms)'}, ]
[docs] def get_output(self): return [TimeSeriesRegion, TimeSeriesEEG]
[docs] def create_region_ts(self, data, connectivity): if connectivity.number_of_regions != data.shape[1]: raise LaunchException("Data has %d channels but the connectivity has %d nodes" % (data.shape[1], connectivity.number_of_regions)) return TimeSeriesRegion(storage_path=self.storage_path, connectivity=connectivity)
[docs] def create_eeg_ts(self, data, sensors): if sensors.number_of_sensors != data.shape[1]: raise LaunchException("Data has %d channels but the sensors have %d" % (data.shape[1], sensors.number_of_sensors)) return TimeSeriesEEG(storage_path=self.storage_path, sensors=sensors)
ts_builder = {TS_REGION: create_region_ts, TS_EEG: create_eeg_ts} @transactional
[docs] def launch(self, data_file, dataset_name, structure_path='', transpose=False, slice=None, sampling_rate=1000, start_time=0, tstype=None, tstype_parameters=None): try: data = read_nested_mat_file(data_file, dataset_name, structure_path) if transpose: data = data.T if slice: data = data[parse_slice(slice)] ts = self.ts_builder[tstype](self, data, **tstype_parameters) ts.start_time = start_time ts.sample_period = 1.0 / sampling_rate ts.sample_period_unit = 's' ts.write_time_slice(numpy.r_[:data.shape[0]] * ts.sample_period) # we expect empirical data shape to be time, channel. # But tvb expects time, state, channel, mode. Introduce those dimensions ts.write_data_slice(data[:, numpy.newaxis, :, numpy.newaxis]) ts.close_file() return ts except ParseException as ex: self.log.exception(ex) raise LaunchException(ex)