simnibs.Msh

class simnibs.Msh(nodes=None, elements=None, fn=None)

class to handle the meshes. Gathers Nodes, Elements and Data

Parameters:

• nodes ((optional) simnibs.msh.Nodes) – Nodes structure

• elements ((optional) simnibs.msh.Elements()) – Elements structure

• fn (str (optional)) – Name of “.msh” file to be read. Overides nodes and elements

nodes

a Nodes field

Type:

simnibs.msh.Nodes

elm

A Elements field

Type:

simnibs.msh.Elements

nodedata

list of NodeData filds

Type:

simnibs.msh.NodeData

elmdata

list of ElementData fields

Type:

simnibs.msh.ElementData

fn

name of file

Type:

str

binary

wheather or not the mesh was in binary format

Type:

bool

__init__(nodes=None, elements=None, fn=None)

Methods

__init__([nodes, elements, fn])
add_element_field(field, field_name)	Adds field defined in the elements
add_node_field(field, field_name)	Adds field defined in the nodes
add_sizing_field(sizing_field[, affine])	Add sizing field from sizing image to mesh in a NodeData field called "sizing_field:metric" for mmg.
any_pts_inside_surface(pts, AABBTree)	Test if any of the points are inside the surface.
calc_matsimnibs(center, pos_ydir, distance)	Calculate the matsimnibs matrix for TMS simulations
compact_ordering(node_number)	Changes the node and element ordering so that it goes from 1 to nr_nodes
crop_mesh([tags, elm_type, nodes, elements])	Crops the specified tags from the mesh Generates a new mesh, with only the specified tags The nodes are also reordered
elements_baricenters()	Calculates the baricenter of the elements
elements_volumes_and_areas()	Calculates the volumes of tetrahedra and areas of triangles
elm2node_matrix([elm_indices])	Calculates a sparse matrix to tranform from ElementData to NodeData Uses Superconvergent patch recovery for volumetric data.
elm_node_coords([elm_nr, tag, elm_type])	Returns the position of each of the element's nodes
fields_summary([roi, fields, percentiles, ...])	Creates a text summary of the field
find_closest_element(querry_points[, ...])	Finds the closest element to each point in p
find_corresponding_tetrahedra()	Finds the tetrahedra corresponding to each triangle
find_shared_nodes(tags)	Finds the nodes which are shared by all given tags
find_tetrahedron_with_points(points[, ...])	Finds the tetrahedron that contains each of the described points using a stochastic walk algorithm
fix_surface_labels()	Fixels labels of surfaces
fix_surface_orientation()	Ensure that the majority of triangle normals point outwards.
fix_th_node_ordering()	Fixes the node ordering of tetrahedra in-place
fix_tr_node_ordering()	Fixes the node ordering of the triangles in-place
gamma_metric()	calculates the (normalized) Gamma quality metric for tetrahedra
gaussian_curvature()	Calculates the Gaussian curvature at each node
get_AABBTree()	Build AABBTree for efficient intersection tests
get_min_distance_on_grid([resolution, AABBTree])	Generates a distance field on a grid to the mesh surface
interp_matrix(pos[, out_fill, th_indices, ...])	Calculates a matrix to perform interpolation y = M.dot(x)
intersect_ray(points, directions[, AABBTree])	Finds the triangle (if any) that intersects with the rays starting
intersect_segment(near, far)	Finds the triangle (if any) that intersects a line segment
join_mesh(other)	Join the current mesh with another
nodes_areas()	Areas for all nodes in a surface
nodes_normals([triangles, smooth])	Normals for all nodes in a surface
nodes_volumes_or_areas()	Return the volume (volume mesh) if area (surface mesh) of all nodes Only works for ordered values of mesh and node indices
open_in_gmsh()	Opens the mesh in gmsh
partition_skin_surface([...])	Return indices of vertices and faces estimated to be on the inner and outer skin surface (the inner part would be those inside nasal cavities, ear canals etc.
prepare_surface_tags()
pts_inside_surface(pts[, AABBTree])	Test which points are inside the surface.
read_hdf5(hdf5_fn[, path, load_data])	Reads mesh information from an hdf5 file
reconstruct_surfaces([tags])	Reconstruct the mesh surfaces for each label/connected component individually This function acts in-place, and will keep any surfaces already present in the mesh
reconstruct_unique_surface([hierarchy, ...])	Reconstructs the mesh surfaces from the tetrahedra.
remove_from_mesh([tags, elm_type, nodes, ...])	Removes the specified tags from the mesh Generates a new mesh, with the specified tags removed The nodes are also reordered
smooth_surfaces(n_steps[, step_size, tags, ...])	In-place smoothing of the mesh surfaces using Taubin smoothing,
smooth_surfaces_simple(n_steps[, step_size, ...])	In-place smoothing of the mesh surfaces using Taubin smoothing,
split_tets_along_line(idx_n1, idx_n2[, ...])	Adds a new node in the middle between the two given nodes and splits all tetrahedra connected to the line between the two given nodes.
surface_EC()	return euler characteristic of surfaces
test_inside_volume(points)	Tests if points are iside the volume using the Möller–Trumbore intersection algorithm
tetrahedra_quality()	calculates the quality measures of the tetrahedra
triangle_angles()	Calculates minimum angle of the mesh triangles
triangle_normals([smooth])	Calculates the normals of triangles
view([visible_tags, visible_fields, cond_list])	Visualize mesh in Gmsh
write(out_fn)	Writes out the mesh as a ".msh" file
write_hdf5(hdf5_fn[, path, compression])	Writes a HDF5 file with mesh information

Attributes

field

Dictionary of fields indexed by their name