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Export NetworkMesh to XDMF #16

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82 changes: 76 additions & 6 deletions src/networks_fenicsx/mesh.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,8 @@
https://github.com/IngeborgGjerde/fenics-networks by Ingeborg Gjerde.
"""

import xml.etree.ElementTree as ET
from pathlib import Path
from typing import Any, Callable, Iterable

from mpi4py import MPI
Expand Down Expand Up @@ -72,7 +74,6 @@ class NetworkMesh:
_edge_entity_maps: list[mesh.EntityMap]
_tangent: fem.Function
_bifurcation_values: npt.NDArray[np.int32]
_boundary_values: npt.NDArray[np.int32]
_lm_mesh: mesh.Mesh | None
_lm_map: mesh.EntityMap | None

Expand Down Expand Up @@ -216,7 +217,6 @@ def _build_mesh(
self._geom_dim = geom_dim
self._num_edge_colors = num_edge_colors
self._bifurcation_values = bifurcation_values
self._boundary_values = boundary_values

# Create lookup of in and out colors for each bifurcation
self._bifurcation_in_color = bifurcation_in_color
Expand Down Expand Up @@ -476,16 +476,86 @@ def export_tangent(self):
def bifurcation_values(self) -> npt.NDArray[np.int32]:
return self._bifurcation_values

@property
def boundary_values(self) -> npt.NDArray[np.int32]:
return self._boundary_values

def in_edges(self, bifurcation: int) -> list[int]:
return self._bifurcation_in_color[bifurcation]

def out_edges(self, bifurcation: int) -> list[int]:
return self._bifurcation_out_color[bifurcation]

def export(self, filename: Path | str):
"""Export the mesh to an XDMF file.

Args:
filename: The path to the output XDMF file.
"""
filename = Path(filename).with_suffix(".xdmf")
# Write mesh, subdomains (coloring) and bifurcation markers
with _io.XDMFFile(
self.mesh.comm,
filename,
"w",
) as xdmf:
xdmf.write_mesh(self.mesh)
xdmf.write_meshtags(self.subdomains, self.mesh.geometry)
xdmf.write_meshtags(self._facet_markers, self.mesh.geometry)

if self.mesh.comm.rank == 0:
tree = ET.parse(filename)
root = tree.getroot()
color_information = ET.SubElement(root, "Information")
color_information.attrib["Name"] = "NumColors"
color_information.attrib["Value"] = f"{self._num_edge_colors:d}"

bifurcation_information = ET.SubElement(root, "Information")
bifurcation_information.attrib["Name"] = "BifurcationMarkers"
bifurcation_information.attrib["Value"] = " ".join(self._bifurcation_values.astype(str))

# Flatten bifurcation in/out edges
bifurcation_in_offsets = np.zeros(len(self._bifurcation_values) + 1, dtype=np.int32)
bifurcation_out_offsets = np.zeros(len(self._bifurcation_values) + 1, dtype=np.int32)
bifurcation_in_values = []
bifurcation_out_values = []
for i, value in enumerate(self._bifurcation_values):
bifurcation_in_offsets[i + 1] = bifurcation_in_offsets[i] + len(
self.in_edges(value)
)
bifurcation_in_values.extend(self.in_edges(value))
bifurcation_out_offsets[i + 1] = bifurcation_out_offsets[i] + len(
self.out_edges(value)
)
bifurcation_out_values.extend(self.out_edges(value))
bifurcation_in_offsets_information = ET.SubElement(root, "Information")
bifurcation_in_offsets_information.attrib["Name"] = "BifurcationInOffsets"
bifurcation_in_offsets_information.attrib["Value"] = " ".join(
bifurcation_in_offsets.astype(str)
)
bifurcation_in_values_information = ET.SubElement(root, "Information")
bifurcation_in_values_information.attrib["Name"] = "BifurcationInValues"
bifurcation_in_values_information.attrib["Value"] = " ".join(
np.array(bifurcation_in_values).astype(str)
)

bifurcation_out_values_information = ET.SubElement(root, "Information")
bifurcation_out_values_information.attrib["Name"] = "BifurcationOutValues"
bifurcation_out_values_information.attrib["Value"] = " ".join(
np.array(bifurcation_out_values).astype(str)
)
bifurcation_out_offsets_information = ET.SubElement(root, "Information")
bifurcation_out_offsets_information.attrib["Name"] = "BifurcationOutOffsets"
bifurcation_out_offsets_information.attrib["Value"] = " ".join(
bifurcation_out_offsets.astype(str)
)

boundary_information_in = ET.SubElement(root, "Information")
boundary_information_in.attrib["Name"] = "BoundaryInValue"
boundary_information_in.attrib["Value"] = str(self._in_marker)
boundary_information_out = ET.SubElement(root, "Information")
boundary_information_out.attrib["Name"] = "BoundaryOutValue"
boundary_information_out.attrib["Value"] = str(self._out_marker)

filename.write_text(ET.tostring(root, encoding="unicode"))
self.comm.barrier()


def _compute_tangent(
start: npt.NDArray[np.float64], end: npt.NDArray[np.float64]
Expand Down