ScalarField

class single_cell_parser.scalar_field.ScalarField(mesh=None, origin=(), extent=(), spacing=(), bBox=())

3D scalar fields based on numpy arrays

A convenience class around numpy array for 3D scalar fields. The class provides methods to access scalar values at arbitrary 3D coordinates, to get the bounding box of a voxel, and to get the center of a voxel.

This class is used for e.g. assigning sub-cellular synapse distributions modeled after vtkImageData, i.e. a regular mesh.

Parameters:
mesh : numpy.ndarray

3D numpy array representing the scalar field.

origin : tuple

3-tuple of floats representing the origin of the scalar field.

extent : tuple

6-tuple of integers representing the extent of the scalar field.

spacing : tuple

3-tuple of floats representing the spacing of the scalar field.

bBox : tuple

6-tuple of floats representing the bounding box of the scalar field.

Attributes:
mesh

3D numpy array representing the scalar field.

Type:

numpy.ndarray

origin

3-tuple of floats representing the origin of the scalar field.

Type:

tuple

extent

6-tuple of integers representing the extent of the scalar field. Note that the extent always starts at 0: Format: (0, xmax - xmin, 0, ymax - ymin, 0, zmax - zmin)

Type:

tuple

spacing

3-tuple of floats representing the spacing of the scalar field. If all values are equal, the scalar field has cubic voxels.

Type:

tuple

boundingBox

6-tuple of floats representing the bounding box of the scalar field. Format: (xmin, xmax, ymin, ymax, zmin, zmax)

Type:

tuple

Methods:

resize_mesh()

Resizes mesh to non-zero scalar data using slicing views (no copy).

get_scalar(xyz)

Fetch the scalar value of the voxel containing the point xyz.

is_in_bounds(xyz)

Check if point is within bounding box of mesh.

get_mesh_coordinates(xyz)

Fetch the mesh index of the voxel containing the point xyz.

get_voxel_bounds(ijk)

Gets the bounding box of voxel given by indices i,j,k.

get_voxel_center(ijk)

Fetch the center of the voxel given by indices i,j,k.