def test_comma_space(filename):
this_dir = pathlib.Path(__file__).resolve().parent
filename = this_dir / "meshes" / "tecplot" / filename
mesh = meshio.read(filename)
helpers.write_read(meshio.tecplot.write, meshio.tecplot.read, mesh,
1.0e-15)
def test_xdmf3_legacy_reader(mesh):
# test with legacy reader
def lr(filename):
return legacy_reader.read("xdmf3", filename)
helpers.write_read(meshio.xdmf_io.write, lr, mesh, 1.0e-15)
return
def test_gmsh40(mesh, write_binary):
writer = partial(meshio.msh_io.write,
fmt_version="4.0",
write_binary=write_binary)
helpers.write_read(writer, meshio.msh_io.read, mesh, 1.0e-15)
return
def test_io(mesh):
helpers.write_read(
meshio.medit_io.write,
meshio.medit_io.read,
mesh, 1.0e-15
)
return
def test_xdmf3_legacy_writer(mesh):
# test with legacy writer
def lw(*args, **kwargs):
return legacy_writer.write("xdmf3", *args, **kwargs)
helpers.write_read(lw, meshio.xdmf_io.read, mesh, 1.0e-15)
return
def test(mesh):
helpers.write_read(meshio._tetgen.write,
meshio._tetgen.read,
mesh,
1.0e-15,
extension=".node")
return
def test_gmsh2(mesh, write_binary):
writer = partial(meshio._msh.write,
fmt_version="2",
write_binary=write_binary)
helpers.write_read(writer, meshio._msh.read, mesh, 1.0e-15)
return
def test(mesh):
helpers.write_read(
meshio.netgen.write, meshio.netgen.read, mesh, 1.0e-13, extension=".vol"
)
helpers.write_read(
meshio.netgen.write, meshio.netgen.read, mesh, 1.0e-13, extension=".vol.gz"
)
def test_obj(mesh):
def writer(*args, **kwargs):
return meshio.obj.write(*args, **kwargs)
for k, c in enumerate(mesh.cells):
mesh.cells[k] = meshio.CellBlock(c.type, c.data.astype(numpy.int32))
helpers.write_read(writer, meshio.obj.read, mesh, 1.0e-12)
def test_obj(mesh):
def writer(*args, **kwargs):
return meshio.obj.write(*args, **kwargs)
for key in mesh.cells:
mesh.cells[key] = mesh.cells[key].astype(numpy.int32)
helpers.write_read(writer, meshio.obj.read, mesh, 1.0e-12)
def test(mesh, write_binary):
def writer(*args, **kwargs):
return meshio.ansys_io.write(*args,
write_binary=write_binary,
**kwargs)
helpers.write_read(writer, meshio.ansys_io.read, mesh, 1.0e-15)
return
def test_compression(mesh):
def write(*args, **kwargs):
return meshio.xdmf.write(*args,
data_format="HDF",
compression="gzip",
**kwargs)
helpers.write_read(write, meshio.xdmf.read, mesh, 1.0e-14)
def test_ply(mesh, binary):
def writer(*args, **kwargs):
return meshio.ply.write(*args, binary=binary, **kwargs)
for k, c in enumerate(mesh.cells):
mesh.cells[k] = meshio.CellBlock(c.type, c.data.astype(np.int32))
helpers.write_read(writer, meshio.ply.read, mesh, 1.0e-12)
def test_ply(mesh, binary):
def writer(*args, **kwargs):
return meshio.ply.write(*args, binary=binary, **kwargs)
for key in mesh.cells:
mesh.cells[key] = mesh.cells[key].astype(numpy.int32)
helpers.write_read(writer, meshio.ply.read, mesh, 1.0e-12)
def test_legacy_writer(mesh):
# test with legacy writer
def lw(*args, **kwargs):
return legacy_writer.write('exodus', *args, **kwargs)
# The legacy writer only writes with low precision.
helpers.write_read(lw, meshio.exodus_io.read, mesh, 1.0e-15)
return
def test_legacy_writer(mesh, write_binary):
# test with legacy writer
def lw(*args, **kwargs):
mode = "vtk-binary" if write_binary else "vtk-ascii"
return legacy_writer.write(mode, *args, **kwargs)
# The legacy writer only writes with low precision.
helpers.write_read(lw, meshio.vtk_io.read, mesh, 1.0e-11)
return
def test_gmsh4(mesh, write_binary):
def writer(*args, **kwargs):
return meshio.msh_io.write(*args,
"4",
write_binary=write_binary,
**kwargs)
helpers.write_read(writer, meshio.msh_io.read, mesh, 1.0e-15)
return
def test(mesh, data_type):
binary, compression = data_type
def writer(*args, **kwargs):
return meshio.vtu.write(*args, binary=binary, compression=compression, **kwargs)
# ASCII files are only meant for debugging, VTK stores only 11 digits
# <https://gitlab.kitware.com/vtk/vtk/issues/17038#note_264052>
tol = 1.0e-15 if binary else 1.0e-10
helpers.write_read(writer, meshio.vtu.read, mesh, tol)
def test_legacy_writer(mesh, write_binary):
# test with legacy writer
def lw(*args, **kwargs):
mode = 'vtu-binary' if write_binary else 'vtu-ascii'
return legacy_writer.write(mode, *args, **kwargs)
# The legacy writer only writes with low precision.
tol = 1.0e-15 if write_binary else 1.0e-11
helpers.write_read(lw, meshio.vtu_io.read, mesh, tol)
return
def test(mesh, binary, data):
if data:
mesh = copy.deepcopy(mesh)
mesh.cell_data["flac3d:zone"] = [numpy.array(data)]
helpers.write_read(
lambda f, m: meshio.flac3d.write(f, m, binary=binary),
meshio.flac3d.read,
mesh,
1.0e-15,
)
def test_reference_file(filename, ref_sum, ref_num_cells, binary):
this_dir = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(this_dir, "meshes", "vtk", filename)
mesh = meshio.read(filename)
tol = 1.0e-2
s = numpy.sum(mesh.points)
assert abs(s - ref_sum) < tol * ref_sum
assert len(mesh.cells["triangle"]) == ref_num_cells
writer = partial(meshio._vtk.write, binary=binary)
helpers.write_read(writer, meshio._vtk.read, mesh, 1.0e-15)
def test_legacy_reader(mesh, write_binary):
def writer(*args, **kwargs):
return meshio.vtk_io.write(*args, write_binary=write_binary, **kwargs)
# test with legacy reader
def lr(filename):
mode = "vtk-binary" if write_binary else "vtk-ascii"
return legacy_reader.read(mode, filename)
helpers.write_read(writer, lr, mesh, 1.0e-15)
return
def test_reference_file(filename, md5, ref_sum, ref_num_cells, write_binary):
filename = helpers.download(filename, md5)
mesh = meshio.read(filename)
tol = 1.0e-2
s = numpy.sum(mesh.points)
assert abs(s - ref_sum) < tol * ref_sum
assert len(mesh.cells["triangle"]) == ref_num_cells
writer = partial(meshio.vtk_io.write, write_binary=write_binary)
helpers.write_read(writer, meshio.vtk_io.read, mesh, 1.0e-15)
return
def test_reference_file(filename, ref_sum, ref_num_cells, binary):
this_dir = pathlib.Path(__file__).resolve().parent
filename = this_dir / "meshes" / "vtk" / filename
mesh = meshio.read(filename)
tol = 1.0e-2
s = numpy.sum(mesh.points)
assert abs(s - ref_sum) < tol * ref_sum
assert mesh.cells[0].type == "triangle"
assert len(mesh.cells[0].data) == ref_num_cells
writer = partial(meshio.vtk.write, binary=binary)
helpers.write_read(writer, meshio.vtk.read, mesh, 1.0e-15)
def test_reference_file(filename, md5, ref_sum_points, ref_num_cells,
ref_sum_point_tags, ref_sum_cell_tags):
filename = helpers.download(filename, md5)
mesh = meshio.read(filename)
tol = 1.0e-2
s = mesh.points.sum()
assert abs(s - ref_sum_points) < tol * ref_sum_points
assert {k: len(v) for k, v in mesh.cells.items()} == ref_num_cells
assert mesh.point_data["point_tags"].sum() == ref_sum_point_tags
assert {k: v["cell_tags"].sum()
for k, v in mesh.cell_data.items()} == ref_sum_cell_tags
helpers.write_read(meshio.med_io.write, meshio.med_io.read, mesh, 1.0e-15)
def test_xdmf2_legacy_writer(mesh):
# test with legacy writer
def lw(*args, **kwargs):
return legacy_writer.write('xdmf2', *args, **kwargs)
helpers.write_read(
lw,
meshio.xdmf_io.read,
# The legacy writer stores data in only single precision
# <https://gitlab.kitware.com/vtk/vtk/issues/17037>
mesh,
1.0e-6)
return
def test_legacy_reader(mesh, write_binary):
def writer(*args, **kwargs):
return meshio.vtu_io.write(*args, write_binary=write_binary, **kwargs)
# test with legacy reader
def lr(filename):
mode = "vtu-binary" if write_binary else "vtu-ascii"
return legacy_reader.read(mode, filename)
# the legacy reader only reads at low precision
tol = 1.0e-15 if write_binary else 1.0e-11
helpers.write_read(writer, lr, mesh, tol)
return
def test_reference_file(filename, ref_sum, ref_num_cells, binary):
this_dir = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(this_dir, "meshes", "msh", filename)
mesh = meshio.read(filename)
tol = 1.0e-2
s = mesh.points.sum()
assert abs(s - ref_sum) < tol * ref_sum
assert {k: len(v) for k, v in mesh.cells.items()} == ref_num_cells
assert {k: len(v["gmsh:physical"])
for k, v in mesh.cell_data.items()} == ref_num_cells
writer = partial(meshio.gmsh.write, fmt_version="2", binary=binary)
helpers.write_read(writer, meshio.gmsh.read, mesh, 1.0e-15)
def test(mesh, write_binary):
def writer(*args, **kwargs):
return meshio.vtu_io.write(
*args,
write_binary=write_binary,
# don't use pretty xml to increase test coverage
pretty_xml=False,
**kwargs)
# ASCII files are only meant for debugging, VTK stores only 11 digits
# <https://gitlab.kitware.com/vtk/vtk/issues/17038#note_264052>
tol = 1.0e-15 if write_binary else 1.0e-11
helpers.write_read(writer, meshio.vtu_io.read, mesh, tol)
return
def test_reference_file(filename, ref_sum, ref_num_cells, binary):
this_dir = os.path.dirname(os.path.abspath(__file__))
filename = os.path.join(this_dir, "meshes", "msh", filename)
mesh = meshio.read(filename)
tol = 1.0e-2
s = mesh.points.sum()
assert abs(s - ref_sum) < tol * ref_sum
assert [c.type for c in mesh.cells] == ["line", "triangle"]
assert [len(c.data) for c in mesh.cells] == ref_num_cells
assert list(map(len, mesh.cell_data["gmsh:geometrical"])) == ref_num_cells
assert list(map(len, mesh.cell_data["gmsh:physical"])) == ref_num_cells
writer = partial(meshio.gmsh.write, fmt_version="2", binary=binary)
helpers.write_read(writer, meshio.gmsh.read, mesh, 1.0e-15)
def test_reference_file(filename, md5, ref_sum, ref_num_cells, write_binary):
filename = helpers.download(filename, md5)
mesh = meshio.read(filename)
tol = 1.0e-2
s = mesh.points.sum()
assert abs(s - ref_sum) < tol * ref_sum
assert {k: len(v) for k, v in mesh.cells.items()} == ref_num_cells
assert {
k: len(v["gmsh:physical"]) for k, v in mesh.cell_data.items()
} == ref_num_cells
writer = partial(meshio.msh_io.write, fmt_version="2", write_binary=write_binary)
helpers.write_read(writer, meshio.msh_io.read, mesh, 1.0e-15)
def test(mesh, write_binary):
def writer(*args, **kwargs):
return meshio.vtu_io.write(
*args,
write_binary=write_binary,
# don't use pretty xml to increase test coverage
pretty_xml=False,
**kwargs
)
# ASCII files are only meant for debugging, VTK stores only 11 digits
# <https://gitlab.kitware.com/vtk/vtk/issues/17038#note_264052>
tol = 1.0e-15 if write_binary else 1.0e-11
helpers.write_read(writer, meshio.vtu_io.read, mesh, tol)
return
def test_reference_file_with_point_cell_data():
filename = "med/box.med"
md5 = "0867fb11bd14b83ad11ab20e2b1fd57d"
filename = helpers.download(filename, md5)
mesh = meshio.read(filename)
# Points
assert numpy.isclose(mesh.points.sum(), 12)
# Cells
assert {k: len(v) for k, v in mesh.cells.items()} == {"hexahedron": 1}
# Point data
data_u = mesh.point_data["resu____DEPL"]
assert data_u.shape == (8, 3)
assert numpy.isclose(data_u.sum(), 12)
# Cell data
# ELNO (1 data point for every node of each element)
data_eps = mesh.cell_data["hexahedron"]["resu____EPSI_ELNO"]
assert data_eps.shape == (1, 8, 6) # (n_cells, n_nodes_per_element, n_components)
data_eps_mean = numpy.mean(data_eps, axis=1)[0]
eps_ref = numpy.array([1, 0, 0, 0.5, 0.5, 0])
assert numpy.allclose(data_eps_mean, eps_ref)
data_sig = mesh.cell_data["hexahedron"]["resu____SIEF_ELNO"]
assert data_sig.shape == (1, 8, 6) # (n_cells, n_nodes_per_element, n_components)
data_sig_mean = numpy.mean(data_sig, axis=1)[0]
sig_ref = numpy.array(
[7328.44611253, 2645.87030114, 2034.06063679, 1202.6, 569.752, 0]
)
assert numpy.allclose(data_sig_mean, sig_ref)
data_psi = mesh.cell_data["hexahedron"]["resu____ENEL_ELNO"]
assert data_psi.shape == (1, 8) # (n_cells, n_nodes_per_element, ) with 1 cut off
# ELEM (1 data point for each element)
data_psi_elem = mesh.cell_data["hexahedron"]["resu____ENEL_ELEM"]
assert numpy.isclose(numpy.mean(data_psi, axis=1)[0], data_psi_elem[0])
helpers.write_read(meshio.med_io.write, meshio.med_io.read, mesh, 1.0e-15)
def test_reference_file_with_mixed_cells():
filename = "med/cylinder.med"
md5 = "e36b365542c72ef470b83fc21f4dad58"
filename = helpers.download(filename, md5)
mesh = meshio.read(filename)
# Points
assert numpy.isclose(mesh.points.sum(), 16.53169892762988)
# Cells
ref_num_cells = {"pyramid": 18, "quad": 18, "line": 17, "tetra": 63, "triangle": 4}
assert {k: len(v) for k, v in mesh.cells.items()} == ref_num_cells
# Point tags
assert mesh.point_data["point_tags"].sum() == 52
ref_point_tags_info = {2: ["Side"], 3: ["Side", "Top"], 4: ["Top"]}
assert mesh.point_tags == ref_point_tags_info
# Cell tags
ref_sum_cell_tags = {
"pyramid": -116,
"quad": -75,
"line": -48,
"tetra": -24,
"triangle": -30,
}
assert {
k: v["cell_tags"].sum() for k, v in mesh.cell_data.items()
} == ref_sum_cell_tags
ref_cell_tags_info = {
-6: ["Top circle"],
-7: ["Top", "Top and down"],
-8: ["Top and down"],
-9: ["A", "B"],
-10: ["B"],
-11: ["B", "C"],
-12: ["C"],
}
assert mesh.cell_tags == ref_cell_tags_info
helpers.write_read(meshio.med_io.write, meshio.med_io.read, mesh, 1.0e-15)
def test_stl(mesh, write_binary, tol):
def writer(*args, **kwargs):
return meshio.stl_io.write(*args, write_binary=write_binary, **kwargs)
helpers.write_read(writer, meshio.stl_io.read, mesh, tol)
return
def test_xdmf3(mesh, data_format):
def write(*args, **kwargs):
return meshio.xdmf_io.write(*args, data_format=data_format, **kwargs)
helpers.write_read(write, meshio.xdmf_io.read, mesh, 1.0e-15)
return
def test(mesh):
def writer(*args, **kwargs):
return meshio.abaqus_io.write(*args, **kwargs)
helpers.write_read(writer, meshio.abaqus_io.read, mesh, 1.0e-15)
return
def test(mesh, write_binary):
def writer(*args, **kwargs):
return meshio.vtk_io.write(*args, write_binary=write_binary, **kwargs)
helpers.write_read(writer, meshio.vtk_io.read, mesh, 1.0e-15)
return
def test_gmsh4(mesh, write_binary):
writer = partial(meshio.msh_io.write, fmt_version="4", write_binary=write_binary)
helpers.write_read(writer, meshio.msh_io.read, mesh, 1.0e-15)
return
def test_io(mesh):
helpers.write_read(meshio.med_io.write, meshio.med_io.read, mesh, 1.0e-15)
return
