simnibs.NodeData

class simnibs.NodeData(value, name='', mesh=None)

Data (scalar, vector or tensor) defined in mesh nodes.

Parameters:

• value (ndarray) –

  Value of field in nodes. Should have the shape

  • (n_nodes,) or (n_nodes, 1) for scalar fields

  • (n_nodes, 3) for vector fields

  • (n_nodes, 9) for tensors

• field_name (str (optional)) – name of field. Default: ‘’

• mesh (simnibs.msh.Msh (optinal)) – Mesh where the field is defined. Required for many methods

value

Value of field in elements

Type:

ndarray

field_name

name of field

Type:

str

node_number

index of elements

Type:

ndarray

nr

number of data points

Type:

property

nr_comp

number of dimensions per data point (1 for scalars, 3 for vectors)

Type:

property

__init__(value, name='', mesh=None)

Methods

__init__(value[, name, mesh])
angle([fill])	Calculate the angle between the field and the surface normal
append_to_mesh(fn[, mode, mmg_fix])	Appends this NodeData fields to a file
as_nodedata()
calc_flux([nodes])	Calculates the flux of a vector field though the given nodes
from_data_grid(mesh, data_grid, affine[, ...])	Defines an NodeData field from a mesh and gridded data
get_focality([cuttofs, peak_percentile])	Caluclates field focality as the area/volume of the mesh experiencing a field magnitude of above (cut_off% of the field peak).
get_percentiles([percentile, roi])	Get percentiles of field (or field magnitude, if a vector field)
gradient()	Calculates the gradient of a field in the middle of the tetrahedra
interpolate_scattered(points[, out_fill, ...])	Interpolates the NodeaData into the points by finding the element containing the point and performing linear interpolation inside the element
interpolate_to_grid(n_voxels, affine, **kwargs)	Interpolates the NodeData into a grid.
interpolate_to_grid_max(n_voxels, affine[, ...])	Interpolates the NodeData into a grid.
interpolate_to_surface(surface[, out_fill, ...])	Interpolates the field in the nodes of a given surface The interpolation occurs in the tetrahedra!
mean_field_norm()	Calculates V*w/sum(w) Where V is the magnitude of the field, and w is the volume or area of the mesh where the field is defined.
node_data2elm_data()	Transforms an ElementData field into a NodeData field the value in the element is the average of the value in the nodes
norm([ord])	Calculate the norm (magnitude) of the field
normal([fill])	Calculate the normal component of the field in the mesh surfaces
read_hdf5_data_matrix_row(leadfield_fn, ...)	Reads a row of an hdf5 data matrix and store it as Data
summary([percentiles, focality_cutoffs, units])	Creates a text summary of the field
tangent([fill])	Calculate the tangent component of the field in the surfaces
to_deformed_grid(warp, reference[, out, ...])	Interpolates field to a grid and apply non-linear interpolation
to_nifti(n_voxels, affine[, fn, units, ...])	Transforms the data in a nifti file
view_options([v_range, percentile, visible, ...])	Generates a View object with visualization opions
write(fn)	Writes this NodeData field to a file with field information only This file needs to be merged with a mesh for visualization
write_hdf5(hdf5_fn[, path])	Writes the field to an hdf5 file

Attributes

indexing_nr	Same as node_numbers
node_number	Node numbers (1, ..., nr)
nr	Number of data entries
nr_comp	Number of field components
type	NodeData of ElementData