pymeshtool 1.0.0

Python3 bindings for MeshTool.

Citation

If you use the PyMeshTool package for a scientific publication, please add Matthias A.F. Gsell and Benedikt A. Klöckl to the authors of your publication and cite the following article.

@article{NEIC2020100454,
    title = {Automating image-based mesh generation and manipulation tasks in cardiac modeling workflows using Meshtool},
    journal = {SoftwareX},
    volume = {11},
    pages = {100454},
    year = {2020},
    issn = {2352-7110},
    doi = {https://doi.org/10.1016/j.softx.2020.100454},
    url = {https://www.sciencedirect.com/science/article/pii/S235271101930295X},
    author = {Aurel Neic and Matthias A.F. Gsell and Elias Karabelas and Anton J. Prassl and Gernot Plank}
}

Contact

• Matthias A.F. Gsell: [e-mail]
• Benedikt Klöckl: [e-mail]

Changes

Version 1.0.0

• [GEN] Published version 1.0.0 to PyPi.

PyMeshTool

PyMeshTool offers Python3 bindings for MeshTool which is a comand-line tool written in C++ to manipulate meshes and to process mesh data.

This package is still under development. Function names or function arguments may change during development.

Module pymeshtool

Functions

• pymeshtool.create_image(shape, itk_dtype, *, num_comp=1, origin=None, voxel_size=None)
• pymeshtool.create_mesh(points, elem2node_dsp, elem2node_con, elem_types, *, elem_tags=None, num_fibers=1, refine_uniform=0)
• pymeshtool.get_max_par_threads()
• pymeshtool.get_meshtool_git_info()
• pymeshtool.get_num_par_threads()
• pymeshtool.load_fibers(filename)
• pymeshtool.load_points(filename)
• pymeshtool.load_vtx(filename)
• pymeshtool.save_fibers(fibers, filename)
• pymeshtool.save_points(pnts, filename)
• pymeshtool.save_vtx(vtxdata, filename, *, intra=True)
• pymeshtool.set_num_par_threads(np)

Classes

Class pymeshtool.Mesh

PyMeshool Mesh object. Wrapper class for the meshtool mt_meshdata structure.

Attributes

• pymeshtool.Mesh.element_tags [RW]
• pymeshtool.Mesh.fibers [RW]
• pymeshtool.Mesh.num_elements [RO]
• pymeshtool.Mesh.num_fibers [RO]
• pymeshtool.Mesh.num_points [RO]
• pymeshtool.Mesh.points [RW]

Functions

• pymeshtool.Mesh.__deepcopy__()
• pymeshtool.Mesh.__init__(basename, *, format='carp_txt', compute_connectivity=True, num_fibers=0)
• pymeshtool.Mesh.apply_split(splitop, *, return_mapping=False)
• pymeshtool.Mesh.clean_topology(*, threshold=None)
• pymeshtool.Mesh.clear_full_connectivity()
• pymeshtool.Mesh.compute_full_connectivity()
• pymeshtool.Mesh.connected_vtx_components(selection)
• pymeshtool.Mesh.correspondence(mesh, *, nodal=True)
• pymeshtool.Mesh.extract_element_nodes()
• pymeshtool.Mesh.extract_gradient(data, *, nodal_input=True, return_nodal=False, normalize=False, norm_threshold=0.0)
• pymeshtool.Mesh.extract_mesh(tags, *, compute_connectivity=True, return_mapping=False)
• pymeshtool.Mesh.extract_myocard(*, threshold=0.0, compute_connectivity=True, return_mapping=False)
• pymeshtool.Mesh.extract_surface(*, setops='', coords=None, edge_threshold=0.0, angle_threshold=0.0, distance=0.0, lower_distance=0.0, hybrid_meshes=True, reindex_nodes=True, return_mapping=False)
• pymeshtool.Mesh.extract_unreachable(*, mode, compute_connectivity=True, return_mapping=False)
• pymeshtool.Mesh.extract_vtx(tags)
• pymeshtool.Mesh.extract_vtxhalo(block)
• pymeshtool.Mesh.generate_distancefield(start_vtx, *, end_vtx=None)
• pymeshtool.Mesh.generate_fibers(*, bath_tags=None)
• pymeshtool.Mesh.generate_split(splitop)
• pymeshtool.Mesh.get_element_sizes()
• pymeshtool.Mesh.get_elements_in_selection(selection)
• pymeshtool.Mesh.has_full_connectivity()
• pymeshtool.Mesh.interpolate_clouddata(points, data, *, mode=2)
• pymeshtool.Mesh.interpolate_elem2node(data, *, normalize=False)
• pymeshtool.Mesh.interpolate_node2elem(data, *, normalize=False)
• pymeshtool.Mesh.interpolate_nodes(data, omesh, *, norm=False)
• pymeshtool.Mesh.is_surface_mesh()
• pymeshtool.Mesh.merge(mesh, *, ignore_empty_interface=True)
• pymeshtool.Mesh.query_bbox()
• pymeshtool.Mesh.query_curvature(radius)
• pymeshtool.Mesh.query_edges(*, tags=None)
• pymeshtool.Mesh.query_idx(coord, *, threshold=0.0, vertices=None)
• pymeshtool.Mesh.query_idxlist(coords, *, threshold=0.0, vertices=None)
• pymeshtool.Mesh.query_quality()
• pymeshtool.Mesh.query_tags(*, vtx=None, tolerance=0.01)
• pymeshtool.Mesh.refine_uniformly(num_it)
• pymeshtool.Mesh.rotate(axis, angle, *, ignore_fibers=False)
• pymeshtool.Mesh.save(basename, *, format='carp_txt')
• pymeshtool.Mesh.scale(scaling_factor)
• pymeshtool.Mesh.smooth_mesh(tags, *, num_iterations=100, smoothing_coeff=0.15, num_laplace_levels=1, edge_threshold=0, max_quality_threshold=0.95)
• pymeshtool.Mesh.translate(displacement)

Class pymeshtool.Mapping

PyMeshool Mapping object. Helper class to ease mapping of data between mesh and submesh.

Attributes

• pymeshtool.Mapping.element_map [RO]
• pymeshtool.Mapping.mesh [RO]
• pymeshtool.Mapping.node_map [RO]
• pymeshtool.Mapping.submesh [RO]

Functions

• pymeshtool.Mapping.__matmul__(other)
• pymeshtool.Mapping.insert_back()
• pymeshtool.Mapping.insert_data(subdata, data, *, nodal_data=True)
• pymeshtool.Mapping.map_selection(idx, *, nodal_selection=True, map_forward=True)
• pymeshtool.Mapping.prolongate(data, *, default=None, nodal_data=True)
• pymeshtool.Mapping.restrict(data, *, nodal_data=True)
• pymeshtool.Mapping.save(basename, *, binary=True)

Class pymeshtool.Image

PyMeshool Image object. Wrapper class for the meshtool itk_image structure.

Attributes

• pymeshtool.Image.data_type [RO]
• pymeshtool.Image.dtype [RO]
• pymeshtool.Image.origin [RW]
• pymeshtool.Image.shape [RO]
• pymeshtool.Image.voxel_size [RW]
• pymeshtool.Image.voxels [RW]

Functions

• pymeshtool.Image.__deepcopy__()
• pymeshtool.Image.__init__(filename)
• pymeshtool.Image.change_type(new_type)
• pymeshtool.Image.crop()
• pymeshtool.Image.extract_mesh(*, surface_mesh=False, tetrahedralize_mesh=False, scale=1.0, compute_connectivity=True, tags=None)
• pymeshtool.Image.extrude(mode, radius, region_tag, *, new_tag=-1, tags=None)
• pymeshtool.Image.resample(refinement_factor)
• pymeshtool.Image.save(filename)

Class pymeshtool.PyMeshToolError

Base class for PyMeshTool related errors.

Enums

Enum pymeshtool.MeshInputFormat

Enumeration of all supported mesh input formats.

Items

• pymeshtool.MeshInputFormat.carp_bin : 'carp_bin'
• pymeshtool.MeshInputFormat.carp_txt : 'carp_txt'
• pymeshtool.MeshInputFormat.gmsh : 'gmsh'
• pymeshtool.MeshInputFormat.mmg : 'mmg'
• pymeshtool.MeshInputFormat.netgen : 'neu'
• pymeshtool.MeshInputFormat.obj : 'obj'
• pymeshtool.MeshInputFormat.off : 'off'
• pymeshtool.MeshInputFormat.purk : 'purk'
• pymeshtool.MeshInputFormat.stellar : 'stellar'
• pymeshtool.MeshInputFormat.vcflow : 'vcflow'
• pymeshtool.MeshInputFormat.vtk : 'vtk'
• pymeshtool.MeshInputFormat.vtk_bin : 'vtk_bin'
• pymeshtool.MeshInputFormat.vtu : 'vtu'

Enum pymeshtool.MeshOutputFormat

Enumeration of all supported mesh output formats.

Items

• pymeshtool.MeshOutputFormat.carp_bin : 'carp_bin'
• pymeshtool.MeshOutputFormat.carp_txt : 'carp_txt'
• pymeshtool.MeshOutputFormat.mmg : 'mmg'
• pymeshtool.MeshOutputFormat.netgen : 'neu'
• pymeshtool.MeshOutputFormat.obj : 'obj'
• pymeshtool.MeshOutputFormat.off : 'off'
• pymeshtool.MeshOutputFormat.stellar : 'stellar'
• pymeshtool.MeshOutputFormat.vcflow : 'vcflow'
• pymeshtool.MeshOutputFormat.vtk : 'vtk'
• pymeshtool.MeshOutputFormat.vtk_bin : 'vtk_bin'
• pymeshtool.MeshOutputFormat.vtk_polydata : 'vtk_polydata'
• pymeshtool.MeshOutputFormat.vtu : 'vtu'

Enum pymeshtool.MeshElementType

Enumeration of all mesh element types.

Items

• pymeshtool.MeshElementType.tetra : 0
• pymeshtool.MeshElementType.hexa : 1
• pymeshtool.MeshElementType.octa : 2
• pymeshtool.MeshElementType.pyramid : 3
• pymeshtool.MeshElementType.prism : 4
• pymeshtool.MeshElementType.quad : 5
• pymeshtool.MeshElementType.tri : 6
• pymeshtool.MeshElementType.line : 7
• pymeshtool.MeshElementType.node : 8

Enum pymeshtool.MeshClouddataInterpolationMode

Enumeration of available clouddata interpolation modes.

Items

• pymeshtool.MeshClouddataInterpolationMode.localized_shepard : 0
• pymeshtool.MeshClouddataInterpolationMode.global_shepard : 1
• pymeshtool.MeshClouddataInterpolationMode.radial_basis_function : 2

Enum pymeshtool.MeshExtractUnreachableMode

Enumeration of mesh unreachable extraction modes.

Items

• pymeshtool.MeshExtractUnreachableMode.smallest : -1
• pymeshtool.MeshExtractUnreachableMode.all : 0
• pymeshtool.MeshExtractUnreachableMode.largest : 1

Enum pymeshtool.ImageDType

Enumeration of image voxel data types.

Items

• pymeshtool.ImageDType.uint8 : 1
• pymeshtool.ImageDType.int8 : 2
• pymeshtool.ImageDType.uint16 : 3
• pymeshtool.ImageDType.int16 : 4
• pymeshtool.ImageDType.uint32 : 5
• pymeshtool.ImageDType.int32 : 6
• pymeshtool.ImageDType.uint64 : 7
• pymeshtool.ImageDType.int64 : 8
• pymeshtool.ImageDType.float32 : 9
• pymeshtool.ImageDType.float64 : 10
• pymeshtool.ImageDType.color_scalar : 11

Enum pymeshtool.ImageExtrusionMode

Enumeration of image extrusion modes.

Items

• pymeshtool.ImageExtrusionMode.inwards : -1
• pymeshtool.ImageExtrusionMode.everywhere : 0
• pymeshtool.ImageExtrusionMode.outwards : 1

Legend

• [RW] ... read / write
• [RO] ... read only

Meshtool modes available through other functions

• transform -> pymeshtool.Mesh.{rotate,scale,translate}(...)
• convert -> pymeshtool.Mesh.save(...)
• extract tags -> pymeshtool.Mesh.element_tags
• insert tags -> pymeshtool.Mesh.element_tags
• map -> pymeshtool.Mapping.map_selection(...)

Missing meshtool modes

Mesh modes

• clean_quality(...)
• collect(...)
• extract_data(...)
• extract_vtkdata(...)
• extract_volume(...)
• extract_unreachable(...)
• extract_overlap(...)
• extract_adjustment(...)
• extract_isosurf(...)
• generate_mesh(...)
• generate_bboxmesh(...)
• generate_surfsplit(...)
• insert_data(...)
• insert_tagsurfs(...)
• insert_imagetags(...)
• insert_fibers(...)
• interpolate_elemdata(...)
• interpolate_shelldata(...)
• interpolate_impstate(...)
• merge_surface(...)
• query_elem_idx(...)
• query_graph(...)
• query_idxlist_uvc(...)
• query_idxlist_ucc(...)
• query_coords_xyz(...)
• query_uccoords_xyz(...)
• query_insidepoint(...)
• query_smoothness(...)
• query_normals(...)
• query_values(...)
• query_distance(...)
• reindex(...)
• resample_mesh(...)
• resample_purkinje(...)
• resample_surfmesh(...)
• resample_uniform(...)
• restore_mapping(...)
• smooth_data(...)
• smooth_surface(...)

Image modes

• itk_smooth(...)
• itk_close(...)
• itk_normalize(...)
• itk_padding(...)
• itk_flip(...)
• itk_sample(...)
• itk_extract(...)
• itk_mesh(...)
• itk_interpolate(...)