The Virtual Brain Project

Source code for tvb.adapters.uploaders.mat.parser

# -*- 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
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# (c) 2012-2020, Baycrest Centre for Geriatric Care ("Baycrest") and others
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# CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
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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)
#
#

"""
.. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>
"""
import numpy
import scipy.io


[docs]def read_nested_mat_structure(m, structure_path): """ Reads data from a hierarchical structure array. If object arrays of shape (1,1) are found they are automatically flattened. :param m: A numpy structure array originating from a matlab mat file :param structure_path: A dot delimited path of field names: topfield.child.leaf :return: The leaf """ structure_path = structure_path.strip() nested_fields = structure_path.split('.') if not structure_path: return m if '' in nested_fields: raise ValueError("bad path: '%s' " % structure_path) try: for field_name in nested_fields: # unwrap object arrays containers of shape 1, 1 m = m[field_name] if issubclass(m.dtype.type, numpy.object_) and m.shape == (1, 1): m = m[0, 0] except ValueError as ex: raise ValueError("missing field: %s" % ex[0]) return m
[docs]def read_nested_mat_file(data_file, dataset_name, structure_path): """ Reads data from deep structures from a .mat file :param data_file: path to the mat file :param dataset_name: matlab variable name :param structure_path: A dot delimited path of field names: topfield.child.leaf :return: the leaf data """ mat = scipy.io.loadmat(data_file) try: return read_nested_mat_structure(mat[dataset_name], structure_path) except KeyError as ex: raise KeyError("could not find: %s" % ex[0])