Citation

If you use the PyMeshTool package for a scientific publication, please cite the following preprint:

Gsell, Matthias A.F. and Klöckl, Benedikt A. and Neic, Aurel and Mautner, Benedikt and
Augustin, Christoph M. and Zappon, Elena and Plank, Gernot, PyMeshTool - A framework for
building efficient automated image-based anatomical twinning workflows in Python. Available
at SSRN: https://ssrn.com/abstract=5745628 or http://dx.doi.org/10.2139/ssrn.5745628

Changes

Version 1.3.0

[SRC] Updated MeshTool.
[DOC] Fix in Mesh.__len__ documentation.
[DOC] Fixed typo in the Mesh.elements attribute documentation.
[DOC] Added exmpale to Mesh.elements attribute documentation.
[SRC] Added flip_normal argument to Mesh.extract_surface afunction.
[SRC] Added Mesh.n2n_graph attribute to access the node-to-node graph.
[SRC] Added Mesh.n2e_graph attribute to access the node-to-element graph.
[GEN] Added wheels for Windows systems.

Version 1.2.0

[SRC] Updated MeshTool.
[SRC] Added read-only Mesh.elements attribute to access the element-to-node graph.
[DOC] Fixed typo in Mesh.generate_distancefield documentation.
[SRC] Added read-only element iterator to Mesh class.
[SRC] Added read-only element access via __getitem__ and __len__ operator.
[GEN] Fixed typos in CHANGES.md.
[SRC] Changes in Mesh.query_idx function.
- Return the index not an array if only one index was found.
- Return None if no index was found.

Version 1.1.3

[SRC] Updated MeshTool.
[GEN] Added wheels for Python 3.14.
[GEN] Added wheels for Linux+ARM systems.

Version 1.1.2

[SRC] Updated MeshTool.
[SRC] Bug fix in Mesh.query_idxlist function.
- Missing condition in shape check.

Version 1.1.1

[SRC] Updated MeshTool.
[SRC] Bug fix in Mesh.query_idxlist function.
- The default threshold array was initialized with the wrong size.
- The threshold argument can be a single value.
- Return the index not an array if only one index was found.
[DOC] Updated documentation for pymeshtool.query_idxlist function.
[DOC] Added preprint to online documentation.

Version 1.1.0

[SRC] Added Mesh.extract_elements to extract a sub-mesh based on a list of element indices.
[SRC] Bug fix in pymeshtool.save_vtx function.
[DOC] Updated documentation for pymeshtool.save_vtx function.

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.

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, *, domain='intra')
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.elements [RO]
pymeshtool.Mesh.fibers [RW]
pymeshtool.Mesh.n2e_graph [RO]
pymeshtool.Mesh.n2n_graph [RO]
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.__getitem__(i)
pymeshtool.Mesh.__init__(basename, *, format='carp_txt', compute_connectivity=True, num_fibers=0)
pymeshtool.Mesh.__len__()
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_elements(indices, *, compute_connectivity=True, return_mapping=False)
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, flip_normals=False, 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

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Release history Release notifications | RSS feed

This release

1.3.0

Aug 12, 2026

1.2.0

Apr 2, 2026

1.1.3

Mar 28, 2026

1.1.2

Feb 2, 2026

1.1.1

Dec 1, 2025

1.1.0

Nov 14, 2025

1.0.0

Nov 4, 2025

pymeshtool 1.3.0

Citation

Changes

Version 1.3.0

Version 1.2.0

Version 1.1.3

Version 1.1.2

Version 1.1.1

Version 1.1.0

Version 1.0.0

PyMeshTool

Module pymeshtool

Functions

Classes

Class pymeshtool.Mesh

Attributes

Functions

Class pymeshtool.Mapping

Attributes

Functions

Class pymeshtool.Image

Attributes

Functions

Class pymeshtool.PyMeshToolError

Enums

Enum pymeshtool.MeshInputFormat

Items

Enum pymeshtool.MeshOutputFormat

Items

Enum pymeshtool.MeshElementType

Items

Enum pymeshtool.MeshClouddataInterpolationMode

Items

Enum pymeshtool.MeshExtractUnreachableMode

Items

Enum pymeshtool.ImageDType

Items

Enum pymeshtool.ImageExtrusionMode

Items

Legend

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Key dates

1 maintainer

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