Source code for tvb.adapters.datatypes.h5.region_mapping_h5

# -*- coding: utf-8 -*-
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# TheVirtualBrain-Framework Package. This package holds all Data Management, and
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from tvb.adapters.datatypes.h5.spectral_h5 import DataTypeMatrixH5
from tvb.adapters.datatypes.h5.structural_h5 import VolumetricDataMixin
from tvb.core.neotraits.h5 import H5File, DataSet, Reference
from tvb.datatypes.region_mapping import RegionMapping, RegionVolumeMapping




class RegionMappingH5(H5File):

    def __init__(self, path):
        super(RegionMappingH5, self).__init__(path)
        self.array_data = DataSet(RegionMapping.array_data, self)
        self.connectivity = Reference(RegionMapping.connectivity, self)
        self.surface = Reference(RegionMapping.surface, self)



    def get_region_mapping_slice(self, start_idx, end_idx):
        """
        Get a slice of the region mapping as used by the region viewers.
        For each vertex on the surface, alpha-indices will be the closest
        region-index
        :param start_idx: vertex index on the surface
        :param end_idx: vertex index on the surface
        :return: NumPy array with [closest_reg_idx ...]
        """
        return self.array_data.load()[int(start_idx): int(end_idx)].T






class RegionVolumeMappingH5(VolumetricDataMixin, DataTypeMatrixH5):

    def __init__(self, path):
        super(RegionVolumeMappingH5, self).__init__(path)
        self.array_data = DataSet(RegionVolumeMapping.array_data, self)
        self.connectivity = Reference(RegionVolumeMapping.connectivity, self)
        self.volume = Reference(RegionVolumeMapping.volume, self)



    def read_data_shape(self):
        """
        The shape of the data
        """
        return self.array_data.shape




    def read_data_slice(self, data_slice):
        """
        Expose chunked-data access.
        """
        return self.array_data[data_slice]