diff --git a/ogstools/msh2vtu/__init__.py b/ogstools/msh2vtu/__init__.py
index aaeb297945220c98a4ebf19cbe55b8b231c3b430..ac2a24d6e224523cd716e46e8f5d53183f802288 100644
--- a/ogstools/msh2vtu/__init__.py
+++ b/ogstools/msh2vtu/__init__.py
@@ -150,19 +150,49 @@ def find_connected_domain_cells(
# TODO: rename
def msh2vtu(
- input_filename: Path,
+ filename: Path,
output_path: Path = Path(),
output_prefix: str = "",
dim: Union[int, list[int]] = 0,
delz: bool = False,
swapxy: bool = False,
- rdcd: bool = True,
- ogs: bool = True,
+ reindex: bool = False,
+ keep_ids: bool = False,
ascii: bool = False,
log_level: Union[int, str] = "DEBUG",
):
+ """
+ Convert a gmsh mesh (.msh) to an unstructured grid file (.vtu).
+
+ Prepares a Gmsh-mesh for use in OGS by extracting domain-,
+ boundary- and physical group-submeshes, and saves them in
+ vtu-format. Note that all mesh entities should belong to
+ physical groups.
+
+ :param filename: Gmsh mesh file (.msh) as input data
+ :param output_path: Path of output files, defaults to current working dir
+ :param output_prefix: Output files prefix, defaults to basename of inputfile
+ :param dim: Spatial dimension (1, 2 or 3), trying automatic detection,
+ if not given. If multiple dimensions are provided, all elements
+ of these dimensions are embedded in the resulting domain mesh.
+ :param delz: Delete z-coordinate, for 2D-meshes with z=0.
+ Note that vtu-format requires 3D points.
+ :param swapxy: Swap x and y coordinate
+ :param reindex: Renumber physical group / region / Material IDs to be
+ renumbered beginning with zero.
+ :param keep_ids: By default, rename 'gmsh:physical' to 'MaterialIDs'
+ and change type of corresponding cell data to INT32.
+ If True, this is skipped.
+ :param ascii: Save output files (.vtu) in ascii format.
+ :param log_level: Level of log output. Possible values:
+ <https://docs.python.org/3/library/logging.html#levels>
+
+ :returns: A MeshSeries object
+ """
logging.getLogger().setLevel(log_level)
- input_filename = Path(input_filename)
+ if isinstance(dim, list):
+ assert len(dim) < 3, "Specify at most 3 dim values."
+ filename = Path(filename)
# some variable declarations
ph_index = 0 # to access physical group id in field data
geo_index = 1 # to access geometrical dimension in field data
@@ -178,55 +208,39 @@ def msh2vtu(
dim0: {"vertex"},
dim1: {"line", "line3", "line4"},
dim2: {
- "triangle",
- "triangle6",
- "triangle9",
- "triangle10",
- "quad",
- "quad8",
- "quad9",
+ *["triangle", "triangle6", "triangle9", "triangle10"],
+ *["quad", "quad8", "quad9"],
},
dim3: {
- "tetra",
- "tetra10",
- "pyramid",
- "pyramid13",
- "pyramid15",
- "pyramid14",
- "wedge", # outdated, keep for backward compatibility
- "wedge15",
- "wedge18",
- "hexahedron",
- "hexahedron20",
- "hexahedron27",
- "prism",
- "prism15",
- "prism18",
+ *["tetra", "tetra10"],
+ *["pyramid", "pyramid13", "pyramid15", "pyramid14"],
+ *["wedge", "wedge15", "wedge18"],
+ *["hexahedron", "hexahedron20", "hexahedron27"],
+ *["prism", "prism15", "prism18"],
},
}
gmsh_physical_cell_data_key = "gmsh:physical"
ogs_domain_cell_data_key = "MaterialIDs"
ogs_boundary_cell_data_key = "bulk_elem_ids"
+ ogs = not keep_ids
# check if input file exists and is in gmsh-format
- if not input_filename.is_file():
+ if not filename.is_file():
logging.warning("No input file (mesh) found.")
# raise FileNotFoundError
return 1
- if input_filename.suffix != ".msh":
+ if filename.suffix != ".msh":
logging.warning(
"Warning, input file seems not to be in gmsh-format (*.msh)"
)
# if no parameter given, use same basename as input file
- output_basename = (
- input_filename.stem if output_prefix == "" else output_prefix
- )
+ output_basename = filename.stem if output_prefix == "" else output_prefix
logging.info("Output: %s", output_basename)
# read in mesh (be aware of shallow copies, i.e. by reference)
- mesh: meshio.Mesh = meshio.read(str(input_filename))
+ mesh: meshio.Mesh = meshio.read(str(filename))
points, point_data = mesh.points, mesh.point_data
cells_dict, cell_data, cell_data_dict = (
mesh.cells_dict,
@@ -323,24 +337,12 @@ def msh2vtu(
pg_key = "PhysicalGroup_" + str(pg_id)
field_data[pg_key] = np.array([pg_id, pg_dim])
- # if user wants physical group numbering of domains beginning with zero
- id_offset = 0 # initial value, zero will not change anything
- if rdcd: # prepare renumber-domain-cell-data (rdcd)
- # find minimum physical_id of domains (dim)
- id_list_domains = []
- for (
- dataset
- ) in field_data.values(): # go through all physical groups
- if (
- dataset[geo_index] == domain_dim
- ): # only for domains, ignore lower dimensional entities
- id_list_domains.append(
- dataset[ph_index]
- ) # append physical id
- if len(id_list_domains): # if there are some domains..
- id_offset = min(
- id_list_domains
- ) # ..then find minimal physical id
+ id_list_domains = [
+ physical_group[ph_index]
+ for physical_group in field_data.values()
+ if physical_group[geo_index] == domain_dim
+ ]
+ id_offset = min(id_list_domains, default=0) if reindex else 0
else:
logging.info("No physical groups found.")
@@ -354,9 +356,8 @@ def msh2vtu(
############################################################################
all_points = np.copy(points) # copy all, superfluous get deleted later
if ogs:
- original_point_numbers = np.arange(
- number_of_original_points
- ) # to associate domain points later
+ # to associate domain points later
+ original_point_numbers = np.arange(number_of_original_points)
all_point_data = {}
all_point_data[ogs_domain_point_data_key] = np.uint64(
original_point_numbers
@@ -555,9 +556,8 @@ def msh2vtu(
gmsh_physical_cell_data_key
][boundary_cell_type]
else:
- number_of_boundary_cells = len(
- boundary_cells_values
- ) # cells of specific type
+ # cells of specific type
+ number_of_boundary_cells = len(boundary_cells_values)
boundary_cell_data_values = np.zeros(
(number_of_boundary_cells), dtype=int
)
@@ -630,9 +630,8 @@ def msh2vtu(
# use gmsh, as the requirements from OGS
subdomain_cell_data_key = gmsh_physical_cell_data_key
else:
- subdomain_cell_data_key = (
- gmsh_physical_cell_data_key # same for all dimensions
- )
+ # same for all dimensions
+ subdomain_cell_data_key = gmsh_physical_cell_data_key
subdomain_cell_data[subdomain_cell_data_key] = [] # list
# flag to indicate invalid bulk_element_ids, then no cell data will be
# written
diff --git a/ogstools/msh2vtu/_cli.py b/ogstools/msh2vtu/_cli.py
index 495b1a0b361a45c281b37c773d8e1b09c87a87bf..5721a8edd05a61fa8aa5360e0f3bc83fee3215cf 100644
--- a/ogstools/msh2vtu/_cli.py
+++ b/ogstools/msh2vtu/_cli.py
@@ -6,107 +6,43 @@ from ogstools.msh2vtu import msh2vtu
def argparser():
# parsing command line arguments
+ def get_help(arg: str):
+ assert msh2vtu.__doc__ is not None
+ return msh2vtu.__doc__.split(arg + ":")[1].split(":param")[0].strip()
+
parser = argparse.ArgumentParser(
- description=(
- "Prepares a Gmsh-mesh for use in OGS by extracting domain-,"
- " boundary- and physical group-submeshes, and saves them in"
- " vtu-format. Note that all mesh entities should belong to"
- " physical groups."
- ),
- )
- parser.add_argument("filename", help="Gmsh mesh file (*.msh) as input data")
- parser.add_argument(
- "-g",
- "--ogs",
- action="store_true",
- help=(
- 'rename "gmsh:physical" to "MaterialIDs" for domains and change '
- "type of corresponding cell data to INT32"
- ),
- )
- parser.add_argument(
- "-r",
- "--rdcd",
- action="store_true",
- help=(
- "renumber domain cell data, physical IDs (cell data) of domains "
- "get numbered beginning with zero"
- ),
- )
- parser.add_argument(
- "-a",
- "--ascii",
- action="store_true",
- help="save output files (*.vtu) in ascii format",
- )
- parser.add_argument(
- "-d",
- "--dim",
- type=int,
- nargs="*",
- default=0,
- help=(
- "spatial dimension (1, 2 or 3), trying automatic detection, "
- "if not given. If multiple dimensions are provided, all elements of"
- "these dimensions are embedded in the resulting domain mesh."
- ),
- )
- parser.add_argument(
- "-o",
- "--output_path",
- default="",
- help=("path of output files; if not given, then it defaults to cwd"),
- )
- parser.add_argument(
- "-p",
- "--prefix",
- default="",
- help=(
- "basename of output files; if not given, then it defaults to"
- " basename of inputfile"
- ),
- )
- parser.add_argument(
- "-z",
- "--delz",
- action="store_true",
- help=(
- "deleting z-coordinate, for 2D-meshes with z=0, note that"
- " vtu-format requires 3D points"
- ),
- )
- parser.add_argument(
- "-s",
- "--swapxy",
- action="store_true",
- help="swap x and y coordinate",
- )
- parser.add_argument(
- "-v",
- "--version",
- action="version",
- version=f"msh2vtu (part of ogstools {__version__}, Dominik Kern)",
- )
+ description=msh2vtu.__doc__.split(":param")[0].strip()
+ )
+ add_arg = parser.add_argument
+ add_arg("filename", help=get_help("filename"))
+ add_arg("-o", "--output_path", default="", help=get_help("output_path"))
+ add_arg("-p", "--prefix", default="", help=get_help("prefix"))
+ add_arg("-d", "--dim", type=int, nargs="*", default=0, help=get_help("dim"))
+ add_arg("-z", "--delz", action="store_true", help=get_help("delz"))
+ add_arg("-s", "--swapxy", action="store_true", help=get_help("swapxy"))
+ add_arg("-r", "--reindex", action="store_true", help=get_help("reindex"))
+ add_arg("-k", "--keep_ids", action="store_true", help=get_help("keep_ids"))
+ add_arg("-a", "--ascii", action="store_true", help=get_help("ascii"))
+ add_arg("-l", "--log_level", default="DEBUG", help=get_help("log_level"))
+ version = f"msh2vtu (part of ogstools {__version__}, Dominik Kern)"
+ add_arg("-v", "--version", action="version", version=version)
return parser
-def cli():
+def cli() -> int:
"""command line use"""
args = argparser().parse_args()
- ErrorCode = msh2vtu(
- input_filename=args.filename,
+ return msh2vtu(
+ filename=args.filename,
output_path=args.output_path,
output_prefix=args.prefix,
dim=args.dim,
delz=args.delz,
swapxy=args.swapxy,
- rdcd=args.rdcd,
- ogs=args.ogs,
+ reindex=args.reindex,
+ keep_ids=args.keep_ids,
ascii=args.ascii,
+ log_level=args.log_level,
)
- if ErrorCode == 0:
- print("msh2vtu successfully finished")
- else:
- print("msh2vtu stopped with errors")
diff --git a/tests/test_studies_convergence.py b/tests/test_studies_convergence.py
index d45fe5968e28694795e20121b24312e132092001..c0cae8d69a62d2f0935b2bfbef326b8e49aa36fa 100644
--- a/tests/test_studies_convergence.py
+++ b/tests/test_studies_convergence.py
@@ -31,9 +31,7 @@ class ConvergenceTest(unittest.TestCase):
structured_grid=True,
out_name=msh_path,
)
- msh2vtu(
- input_filename=msh_path, output_path=temp_dir, log_level="ERROR"
- )
+ msh2vtu(filename=msh_path, output_path=temp_dir, log_level="ERROR")
model = ogs.OGS(
PROJECT_FILE=temp_dir / "default.prj",
INPUT_FILE=convergence.examples.steady_state_diffusion_prj,