Python3 bindings for MeshTool.
Project description
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 1.1.3
- [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_idxlistfunction.- Missing condition in shape check.
Version 1.1.1
- [SRC] Updated MeshTool.
- [SRC] Bug fix in
Mesh.query_idxlistfunction.- The default threshold array was initialized with the wrong size.
- The
thresholdargument can be a single value. - Return the index not an array if only one index was found.
- [DOC] Updated documentation for
pymeshtool.query_idxlistfunction. - [DOC] Added preprint to online documentation.
Version 1.1.0
- [SRC] Added
Mesh.extract_elementsto extract a sub-mesh based on a list of element indices. - [SRC] Bug fix in
pymeshtool.save_vtxfunction. - [DOC] Updated documentation for
pymeshtool.save_vtxfunction.
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.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_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, 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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