Source code for tvb.datatypes.region_mapping

# -*- coding: utf-8 -*-
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# TheVirtualBrain-Scientific Package. This package holds all simulators, and
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"""
DataTypes for mapping some TVB DataTypes to a Connectivity (regions).

In FreeSurfer terms, a RegionMapping is a parcellation and a VolumeMapping is a segmentation.

.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
.. moduleauthor:: Mihai Andrei <mihai.andrei@codemart.ro>
"""

import numpy
from tvb.basic.readers import try_get_absolute_path, FileReader
from tvb.datatypes.connectivity import Connectivity
from tvb.datatypes.surfaces import Surface
from tvb.datatypes.volumes import Volume
from tvb.basic.neotraits.api import HasTraits, Attr, NArray




class RegionMapping(HasTraits):
    """
    An array (of length Surface.vertices). Each value is representing the index in Connectivity regions
    to which the current vertex is mapped.
    """

    array_data = NArray(dtype=int)

    connectivity = Attr(field_type=Connectivity)

    surface = Attr(field_type=Surface)



    @staticmethod
    def from_file(source_file="regionMapping_16k_76.txt"):
        source_full_path = try_get_absolute_path("tvb_data.regionMapping", source_file)
        reader = FileReader(source_full_path)

        result = RegionMapping()
        result.array_data = reader.read_array(dtype=numpy.int32)
        return result






class RegionVolumeMapping(HasTraits):
    """
    Each value is representing the index in Connectivity regions to which the current voxel is mapped.
    """

    array_data = NArray(dtype=int)

    connectivity = Attr(Connectivity)

    volume = Attr(Volume)