def main():
file_name = sys.argv[1]
temporal_grid = xdmf.TemporalGrid()
GenerateXdmfConnectivities(file_name)
# Get the initial spatial grid from the base file.
with h5py.File(file_name, "r") as h5py_file:
current_spatial_grid = GetSpatialGrid(h5py_file)
for current_time in GetListOfTimeLabels(file_name):
current_file_name = file_name.replace(".h5", "-" + current_time + ".h5")
# Check if the current file has mesh information.
with h5py.File(current_file_name, "r") as h5py_file:
has_mesh = ("ModelData" in h5py_file.keys())
if has_mesh:
GenerateXdmfConnectivities(current_file_name)
with h5py.File(current_file_name, "r") as h5py_file:
if has_mesh:
# Update current spatial grid
current_spatial_grid = GetSpatialGrid(h5py_file)
# Initialize the current grid with the spatial grid.
current_grid = xdmf.SpatialGrid()
for grid in current_spatial_grid.grids:
current_grid.add_grid(xdmf.UniformGrid(grid.name, grid.geometry, grid.topology))
# Add the (time-dependent) results.
for nodal_result in GetNodalResults(h5py_file):
current_grid.add_attribute(nodal_result)
# Add the current grid to the temporal grid.
temporal_grid.add_grid(xdmf.Time(current_time), current_grid)
# Create the domain.
domain = xdmf.Domain(temporal_grid)
# Write.
xdmf_file_name = file_name.replace(".h5", ".xdmf")
xdmf.ET.ElementTree(xdmf.Xdmf(domain).create_xml_element()).write(xdmf_file_name)
def WriteXdmfFile(file_name):
#todo(msandre): generalize to WriteXdmfFile(xdmf_file_name, list_of_h5_file_paths):
temporal_grid = xdmf.TemporalGrid()
GenerateXdmfConnectivities(file_name)
# Get the initial spatial grid from the base file.
with h5py.File(file_name, "r") as h5py_file:
current_spatial_grid = GetSpatialGrid(h5py_file)
for current_time in GetListOfTimeLabels(file_name):
current_file_name = file_name.replace(".h5",
"-" + current_time + ".h5")
try:
# Check if the current file has mesh information.
with h5py.File(current_file_name, "r") as h5py_file:
has_mesh = ("ModelData" in h5py_file.keys())
has_data = ("/ResultsData" in h5py_file.keys())
except OSError:
# in case this file cannot be opened skip it
# this can be the case if the file is already opened
warn_msg = 'No xdmf-data was written for file:\n"'
warn_msg += current_file_name + '"'
KratosMultiphysics.Logger.PrintWarning("XDMF-Writing", warn_msg)
continue
if not has_data:
continue
if has_mesh:
GenerateXdmfConnectivities(current_file_name)
with h5py.File(current_file_name, "r") as h5py_file:
if has_mesh:
# Update current spatial grid
current_spatial_grid = GetSpatialGrid(h5py_file)
# Initialize the current grid with the spatial grid.
current_grid = xdmf.SpatialGrid()
for grid in current_spatial_grid.grids:
current_grid.add_grid(
xdmf.UniformGrid(grid.name, grid.geometry, grid.topology))
# Add the (time-dependent) results.
for nodal_result in GetNodalResults(h5py_file):
current_grid.add_attribute(nodal_result)
for element_result in GetElementResults(h5py_file):
current_grid.add_attribute(element_result)
# Add the current grid to the temporal grid.
temporal_grid.add_grid(xdmf.Time(current_time), current_grid)
# Create the domain.
domain = xdmf.Domain(temporal_grid)
# Write.
raw_file_name = os.path.split(file_name)[1]
xdmf_file_name = raw_file_name.replace(".h5", ".xdmf")
xdmf.ET.ElementTree(
xdmf.Xdmf(domain).create_xml_element()).write(xdmf_file_name)
def GetSpatialGrid(h5py_file):
elements_path = "/ModelData/Xdmf/Elements/"
coordinates_path = "/ModelData/Nodes/Local/Coordinates"
spatial_grid = xdmf.SpatialGrid()
coords_data = xdmf.HDF5UniformDataItem(h5py_file.get(coordinates_path))
geom = xdmf.Geometry(coords_data)
elems_group = h5py_file.get(elements_path)
for name in elems_group.keys():
if isinstance(elems_group[name], h5py.Group):
single_elem_group = elems_group.get(name)
dim = single_elem_group.attrs["Dimension"]
num_points = single_elem_group.attrs["NumberOfNodes"]
cell_type = xdmf.TopologyCellType(dim, num_points)
connectivity_data = xdmf.HDF5UniformDataItem(h5py_file.get(elements_path + '/' + name + '/Connectivities'))
topology = xdmf.UniformMeshTopology(cell_type, connectivity_data)
spatial_grid.add_grid(xdmf.UniformGrid(name, geom, topology))
return spatial_grid