Source code for tvb.adapters.datatypes.h5.structural_h5

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import numpy
from tvb.core.adapters.arguments_serialisation import preprocess_space_parameters
from tvb.adapters.datatypes.h5.spectral_h5 import DataTypeMatrixH5
from tvb.core.neotraits.h5 import DataSet, Scalar, Reference
from tvb.datatypes.structural import StructuralMRI


[docs] class VolumetricDataMixin(object): """Provides subclasses with useful methods for volumes.""" array_data = None # type: DataSet # here only for typing, will be overriden in mixed in class
[docs] def write_data_slice(self, data): """ We are using here the same signature as in TS, just to allow easier parsing code. This is not a chunked write. """ self.array_data.store(data)
[docs] def get_volume_slice(self, x_plane, y_plane, z_plane): shape = self.array_data.shape length_1d = shape[0] length_2d = shape[1] length_3d = shape[2] slices = slice(length_1d), slice(length_2d), slice(z_plane, z_plane + 1) slice_x = self.array_data[slices][:, :, 0] # 2D slice_x = numpy.array(slice_x, dtype=int) slices = slice(x_plane, x_plane + 1), slice(length_2d), slice(length_3d) slice_y = self.array_data[slices][0, :, :][..., ::-1] slice_y = numpy.array(slice_y, dtype=int) slices = slice(length_1d), slice(y_plane, y_plane + 1), slice(length_3d) slice_z = self.array_data[slices][:, 0, :][..., ::-1] slice_z = numpy.array(slice_z, dtype=int) return [slice_x, slice_y, slice_z]
[docs] def get_volume_view(self, x_plane, y_plane, z_plane, **kwargs): shape = self.array_data.shape length_1d = shape[0] length_2d = shape[1] length_3d = shape[2] # Work with space inside Volume: x_plane, y_plane, z_plane = preprocess_space_parameters(x_plane, y_plane, z_plane, length_1d, length_2d, length_3d) slice_x, slice_y, slice_z = self.get_volume_slice(x_plane, y_plane, z_plane) return [[slice_x.tolist()], [slice_y.tolist()], [slice_z.tolist()]]
[docs] class StructuralMRIH5(VolumetricDataMixin, DataTypeMatrixH5): def __init__(self, path): super(StructuralMRIH5, self).__init__(path) self.array_data = DataSet(StructuralMRI.array_data, self) self.weighting = Scalar(StructuralMRI.weighting, self) self.volume = Reference(StructuralMRI.volume, self)