Clean (weld / prune / de-dup)

meshioplusplus.clean(mesh, ...) cleans a mesh in one pass: weld coincident points, drop degenerate cells, drop exact-duplicate cells, and remove orphaned (unused) points — each step individually toggleable — remapping connectivity and data throughout. It is a mesh operation (like merge and reordering), not a file format, and uses only standard C++/numpy, so it runs under every mesh backend.

import meshioplusplus

mesh = meshioplusplus.read("messy.vtu")

out = meshioplusplus.clean(mesh)                        # prune + de-dup, no weld
out = meshioplusplus.clean(mesh, weld=True, atol=1e-8)  # also fuse coincident pts

# get a report of what changed
out, report = meshioplusplus.clean(mesh, weld=True, return_report=True)
print(report)   # points_welded / points_removed_orphan / cells_dropped_*

Options

option	default	effect
weld	False	fuse points within atol (spatial-hash bucket grid, never O(N²))
atol	1e-8	absolute coincidence tolerance for welding
remove_orphans	True	drop points referenced by no surviving cell
drop_degenerate	True	drop cells with a repeated corner node or a near-zero measure
drop_duplicate_cells	True	drop exact-duplicate cells (keep-first, per block)

The pass runs weld → drop degenerate → drop duplicate → remove orphans. On a weld, the surviving point keeps the value of the first contributing point (keep-first tie-break).

What changes

• Points are welded/pruned; connectivity is remapped.
• point_data follows the surviving points (keep-first on weld); cell_data follows the surviving cells; field_data is preserved.
• point_sets / cell_sets are remapped; entries pointing at removed points/cells are dropped (done in the Python layer).

The numpy fallback handles rectangular cell blocks; ragged/polyhedron blocks are handled by the C++ core only.

CLI

meshioplusplus clean in.vtu out.vtu                     # default set (no weld)
meshioplusplus clean in.vtu out.vtu --weld --atol 1e-6
meshioplusplus clean in.vtu out.vtu --remove-orphans --drop-degenerate

With no step flags the default set runs (remove-orphans + drop-degenerate + drop-duplicates, no weld). Passing any step flag selects exactly the requested steps. A removal summary is printed. See the CLI reference.

Other languages

• C API — mio_clean(mesh, weld, atol, remove_orphans, drop_degenerate, drop_duplicate_cells, &n_welded, &n_orphan, &n_degen, &n_dup). See the C API reference.
• Fortran — mesh%clean(weld=..., atol=..., points_welded=..., ...). See the Fortran reference.
• WebAssembly / JavaScript — clean(mesh, weld, atol, removeOrphans, dropDegenerate, dropDuplicateCells) returns {mesh, pointsWelded, ...}. See the WebAssembly reference.