simnibs.ElementData

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

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

Parameters

• value (ndarray) –

  Value of field in elements. Should have the shape

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

  • (n_elm, 3) for vector fields

  • (n_elm, 9) for tensors

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

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

value

Value of field in elements

Type

ndarray

field_name

name of field

Type

str

elm_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)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(value[, name, mesh])	Initialize self.
append_to_mesh(fn[, mode])	Appends this ElementData fields to a file
as_nodedata()	Converts the current ElementData instance to NodaData For more information see the elm_data2node_data method
assign_triangle_values()	In-place Assigns field value at triangle as the same as the one of the tetrahedra with a similar tag to it.
calc_flux([triangles])	Calculates the flux of a vectorial field
elm_data2node_data()	Transforms an ElementData field into a NodeData field using Superconvergent patch recovery For volumetric data.
from_data_grid(mesh, data_grid, affine[, …])	Defines an ElementData field form a mesh and gridded data
get_focality([cuttofs, peak_percentile])	Caluclates field focality as the area/volume of the mesh experiencing a field norm of above (cut_off% of the field peak).
get_percentiles([percentile, roi])	Get percentiles of field (or field norm, if a vector field)
interpolate_scattered(points[, out_fill, …])	Interpolates the ElementData into the points by finding the element containing the point and assigning the value in it
interpolate_to_grid(n_voxels, affine[, …])	Interpolates the ElementData 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 norm of the field, and w is the volume or area of the mesh where the field is defined.
norm([ord])	Calculate the norm of the field
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 summaty of the field
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 ElementData fields 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

elm_number	Element numbers (1, …, nr)
indexing_nr	Same as elm_number
nr	Number of data entries
nr_comp	Number of field components
type	NodeData of ElementData