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