diff --git a/docs/releases/ogstools-0.5.0.md b/docs/releases/ogstools-0.5.0.md
index a0bff9d25b7f4029ee202e01c73955be917f6f60..8f21dabd4777b6c76dfbec67ea63b9803479c292 100644
--- a/docs/releases/ogstools-0.5.0.md
+++ b/docs/releases/ogstools-0.5.0.md
@@ -37,6 +37,7 @@
- MeshSeries get extract() method to select points or cells via ids
- MeshSeries can be sliced to get new MeshSeries with the selected subset of timesteps
- MeshSeries gets a modify function that applies arbitrary function to all timestep - meshes.
+- MeshSeries gets a save function (only for pvd implemented yet)
- difference() between two meshes is now possible even with different topologies
- Project write_input, path can be specified
- MeshSeries gets scale() method to scale spatially or temporally
diff --git a/ogstools/meshlib/ip_mesh.py b/ogstools/meshlib/ip_mesh.py
index 12a9ca64f8536a4022fa2cb121705e595637de93..cf24ab647b1aced1f72a359ffb4dd0b9986c7a0e 100644
--- a/ogstools/meshlib/ip_mesh.py
+++ b/ogstools/meshlib/ip_mesh.py
@@ -1,5 +1,4 @@
from pathlib import Path
-from tempfile import mkdtemp
from typing import TypeVar
import numpy as np
@@ -197,10 +196,10 @@ def to_ip_point_cloud(mesh: Mesh) -> pv.UnstructuredGrid:
for key in bad_keys:
if key in _mesh.field_data:
_mesh.field_data.remove(key)
- tempdir = mkdtemp(prefix="to_ip_point_cloud")
- input_file = Path(tempdir) / "ipDataToPointCloud_input.vtu"
+ parentpath = Path() if mesh.filepath is None else mesh.filepath.parent
+ input_file = parentpath / "ipDataToPointCloud_input.vtu"
_mesh.save(input_file)
- output_file = Path(tempdir) / "ip_mesh.vtu"
+ output_file = parentpath / "ip_mesh.vtu"
ogs.cli.ipDataToPointCloud(i=str(input_file), o=str(output_file))
return pv.XMLUnstructuredGridReader(output_file).read()
diff --git a/ogstools/meshlib/mesh.py b/ogstools/meshlib/mesh.py
index 8a617c65407aaebc958c68dd6e918cc3a2413155..3cc720a78d9d43223681c0968551c60cbcd3d45d 100644
--- a/ogstools/meshlib/mesh.py
+++ b/ogstools/meshlib/mesh.py
@@ -27,6 +27,8 @@ class Mesh(pv.UnstructuredGrid):
Contains additional data and functions mainly for postprocessing.
"""
+ filepath: Path | None = None
+
# pylint: disable=C0116
@copy_method_signature(data_processing.difference)
def difference(self, *args: Any, **kwargs: Any) -> Any:
@@ -94,6 +96,7 @@ class Mesh(pv.UnstructuredGrid):
else:
mesh = cls(pv.read(filepath))
+ mesh.filepath = Path(filepath).with_suffix(".vtu")
return mesh
@classmethod
diff --git a/ogstools/meshlib/mesh_series.py b/ogstools/meshlib/mesh_series.py
index 9c2c78721b63ee3e97d19c868dc1addcbea533a3..19d8fd49179d16e17a762bb04df170150a5d4ff4 100644
--- a/ogstools/meshlib/mesh_series.py
+++ b/ogstools/meshlib/mesh_series.py
@@ -12,11 +12,12 @@ from collections.abc import Callable, Iterator, Sequence
from copy import copy, deepcopy
from functools import partial
from pathlib import Path
-from typing import Any, Literal, overload
+from typing import Any, Literal, cast, overload
import meshio
import numpy as np
import pyvista as pv
+from lxml import etree as ET
from matplotlib import pyplot as plt
from matplotlib.animation import FuncAnimation
from scipy.interpolate import (
@@ -148,8 +149,8 @@ class MeshSeries:
return len(self.timesteps)
def __iter__(self) -> Iterator[Mesh]:
- for t in self.timesteps:
- yield self.mesh(t)
+ for i in np.arange(len(self.timevalues), dtype=int):
+ yield self.mesh(i)
def __str__(self) -> str:
if self._data_type == "vtu":
@@ -208,14 +209,14 @@ class MeshSeries:
ip_mesh = self.mesh(0).to_ip_mesh()
ip_pt_cloud = self.mesh(0).to_ip_point_cloud()
ordering = ip_mesh.find_containing_cell(ip_pt_cloud.points)
- for ts in self.timesteps:
+ for i in np.arange(len(self.timevalues), dtype=int):
ip_data = {
- key: self.mesh(ts).field_data[key][np.argsort(ordering)]
+ key: self.mesh(i).field_data[key][np.argsort(ordering)]
for key in ip_mesh.cell_data
}
ip_mesh.cell_data.update(ip_data)
ip_ms._mesh_cache[
- self.timevalues[ts]
+ self.timevalues[i]
] = ip_mesh.copy() # pylint: disable=protected-access
ip_ms._timevalues = self._timevalues # pylint: disable=protected-access
return ip_ms
@@ -245,6 +246,10 @@ class MeshSeries:
mesh = Mesh(self.mesh_func(pv_mesh))
if lazy_eval:
self._mesh_cache[timevalue] = mesh
+ if self._data_type == "pvd":
+ mesh.filepath = Path(self.timestep_files[data_timestep])
+ else:
+ mesh.filepath = Path(self.filepath)
return mesh
def rawdata_file(self) -> Path | None:
@@ -290,7 +295,13 @@ class MeshSeries:
@property
def timesteps(self) -> list:
- """Return the timesteps of the timeseries data."""
+ """
+ Return the OGS simulation timesteps of the timeseries data.
+ Not to be confused with timevalues which returns a list of
+ times usually given in time units.
+ """
+
+ # TODO: read time steps from fn string if available
return np.arange(len(self.timevalues), dtype=int)
def _xdmf_values(self, variable_name: str) -> np.ndarray:
@@ -579,16 +590,15 @@ class MeshSeries:
def animate(
self,
variable: Variable,
- timesteps: Sequence | None = None,
+ timevalues: Sequence | None = None,
plot_func: Callable[[plt.Axes, float], None] = lambda *_: None,
**kwargs: Any,
) -> FuncAnimation:
"""
- Create an animation for a variable with given timesteps.
+ Create an animation for a variable with given timevalues.
- :param variable: the field to be visualized on all timesteps
- :param timesteps: if sequence of int: the timesteps to animate
- if sequence of float: the timevalues to animate
+ :param variable: the field to be visualized on all timevalues
+ :param timevalues: the timevalues to animate
:param plot_func: A function which expects to read a matplotlib Axes
and the time value of the current frame. Useful to
customize the plot in the animation.
@@ -598,7 +608,7 @@ class MeshSeries:
plot.setup.layout = "tight"
plot.setup.combined_colorbar = True
- ts = self.timesteps if timesteps is None else timesteps
+ ts = self.timevalues if timevalues is None else timevalues
fig = plot.contourf(self.mesh(0, lazy_eval=False), variable)
assert isinstance(fig, plt.Figure)
@@ -609,14 +619,14 @@ class MeshSeries:
def init() -> None:
pass
- def animate_func(i: int | float, fig: plt.Figure) -> None:
+ def animate_func(tv: float, fig: plt.Figure) -> None:
fig.axes[-1].remove() # remove colorbar
for ax in np.ravel(np.asarray(fig.axes)):
ax.clear()
- mesh = self[i] if isinstance(i, int) else self.read_interp(i, True)
+ mesh = self.read_interp(tv, True)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
- plot_func(fig.axes[0], i)
+ plot_func(fig.axes[0], tv)
plot.contourplots.draw_plot(
mesh, variable, fig=fig, axes=fig.axes[0], **kwargs
) # type: ignore[assignment]
@@ -834,3 +844,90 @@ class MeshSeries:
),
}
return self.transform(func[preference])
+
+ def _rename_vtufiles(self, new_pvd_fn: Path, fns: list[Path]) -> list:
+ fns_new: list[Path] = []
+ for filename in fns:
+ filepathparts_at_timestep = list(filename.parts)
+ filepathparts_at_timestep[-1] = filepathparts_at_timestep[
+ -1
+ ].replace(
+ Path(self.filepath).name.split(".")[0],
+ new_pvd_fn.name.split(".")[0],
+ )
+ fns_new.append(Path(*filepathparts_at_timestep))
+ return fns_new
+
+ def _save_vtu(self, new_pvd_fn: Path, fns: list[Path]) -> None:
+ for i, timestep in enumerate(self.timesteps):
+ if ".vtu" in fns[i].name:
+ pv.save_meshio(
+ Path(new_pvd_fn.parent, fns[i].name), self.mesh(i)
+ )
+ elif ".xdmf" in fns[i].name:
+ newname = fns[i].name.replace(
+ ".xdmf", f"_ts_{timestep}_t_{self.timevalues[i]}.vtu"
+ )
+ pv.save_meshio(Path(new_pvd_fn.parent, newname), self.mesh(i))
+ else:
+ s = "File type not supported."
+ raise RuntimeError(s)
+
+ def _save_pvd(self, new_pvd_fn: Path, fns: list[Path]) -> None:
+ root = ET.Element("VTKFile")
+ root.attrib["type"] = "Collection"
+ root.attrib["version"] = "0.1"
+ root.attrib["byte_order"] = "LittleEndian"
+ root.attrib["compressor"] = "vtkZLibDataCompressor"
+ collection = ET.SubElement(root, "Collection")
+ for i, timestep in enumerate(self.timevalues):
+ timestepselement = ET.SubElement(collection, "DataSet")
+ timestepselement.attrib["timestep"] = str(timestep)
+ timestepselement.attrib["group"] = ""
+ timestepselement.attrib["part"] = "0"
+ if ".xdmf" in fns[i].name:
+ newname = fns[i].name.replace(
+ ".xdmf", f"_ts_{self.timesteps[i]}_t_{timestep}.vtu"
+ )
+ timestepselement.attrib["file"] = newname
+ elif ".vtu" in fns[i].name:
+ timestepselement.attrib["file"] = fns[i].name
+ else:
+ s = "File type not supported."
+ raise RuntimeError(s)
+ tree = ET.ElementTree(root)
+ tree.write(
+ new_pvd_fn,
+ encoding="ISO-8859-1",
+ xml_declaration=True,
+ pretty_print=True,
+ )
+
+ def _check_path(self, filename: Path | None) -> Path:
+ if not isinstance(filename, Path):
+ s = "filename is empty"
+ raise RuntimeError(s)
+ assert isinstance(filename, Path)
+ return cast(Path, filename)
+
+ def save(self, filename: str, deep: bool = True) -> None:
+ """
+ Save mesh series to disk.
+
+ :param filename: Filename to save the series to. Extension specifies
+ the file type. Currently only PVD is supported.
+ :param deep: Specifies whether VTU/H5 files should be written.
+ """
+ fn = Path(filename)
+ fns = [
+ self._check_path(self.mesh(t).filepath)
+ for t in np.arange(len(self.timevalues), dtype=int)
+ ]
+ if ".pvd" in fn.name:
+ if deep is True:
+ fns = self._rename_vtufiles(fn, fns)
+ self._save_vtu(fn, fns)
+ self._save_pvd(fn, fns)
+ else:
+ s = "Currently the save method is implemented for PVD/VTU only."
+ raise RuntimeError(s)
diff --git a/tests/test_meshlib.py b/tests/test_meshlib.py
index 8208ed9f89a700762d163f6e5109adfb67e61800..f064a72e2d56efc439c0d989229cf8c05bd1a1af 100644
--- a/tests/test_meshlib.py
+++ b/tests/test_meshlib.py
@@ -7,6 +7,7 @@ import numpy as np
import pkg_resources
import pytest
import pyvista as pv
+from lxml import etree as ET
import ogstools as ot
from ogstools import examples
@@ -472,3 +473,60 @@ class TestUtils:
ms_shallowcopy = ms.copy(deep=False)
ms.test_var = False
assert not ms_shallowcopy.test_var
+
+ def test_save_pvd_mesh_series(self):
+ temp = Path(mkdtemp())
+ file_name = "test.pvd"
+
+ ms = examples.load_meshseries_HT_2D_PVD()
+ ms.save(Path(temp, file_name), deep=True)
+ ms_test = ot.MeshSeries(Path(temp, file_name))
+ assert len(ms.timevalues) == len(ms_test.timevalues)
+ assert np.abs(ms.timevalues[1] - ms_test.timevalues[1]) < 1e-14
+ for var in ["temperature", "darcy_velocity", "pressure"]:
+ val_ref = np.sum(ms.aggregate_over_domain(var, np.max))
+ val_test = np.sum(ms_test.aggregate_over_domain(var, np.max))
+ assert np.abs(val_ref - val_test) < 1e-14
+
+ for m in ms_test:
+ assert "test" in m.filepath.name
+
+ ms.save(Path(temp, file_name), deep=False)
+ tree = ET.parse(Path(temp, file_name))
+ num_slices = len(ms.timevalues)
+ num_slices_test = len(tree.findall("./Collection/DataSet"))
+ assert num_slices == num_slices_test
+ pvd_entries = tree.findall("./Collection/DataSet")
+ for i in range(num_slices):
+ assert ms[i].filepath.name == pvd_entries[i].attrib["file"]
+ ts = float(pvd_entries[i].attrib["timestep"])
+ assert np.abs(ms.timevalues[i] - ts) < 1e-14
+
+ def test_save_xdmf_mesh_series(self):
+ temp = Path(mkdtemp())
+ file_name = "test.pvd"
+
+ ms = examples.load_meshseries_CT_2D_XDMF()
+ ms.save(Path(temp, file_name), deep=True)
+ ms_test = ot.MeshSeries(Path(temp, file_name))
+ assert len(ms.timevalues) == len(ms_test.timevalues)
+ assert np.abs(ms.timevalues[1] - ms_test.timevalues[1]) < 1e-14
+ assert (
+ np.abs(
+ np.sum(ms.aggregate_over_domain("Si", np.max))
+ - np.sum(ms_test.aggregate_over_domain("Si", np.max))
+ )
+ < 1e-14
+ )
+ for m in ms_test:
+ assert "test" in m.filepath.name
+
+ ms.save(Path(temp, file_name), deep=False)
+ tree = ET.parse(Path(temp, file_name))
+ num_slices = len(ms.timevalues)
+ pvd_entries = tree.findall("./Collection/DataSet")
+ num_slices_test = len(pvd_entries)
+ assert num_slices == num_slices_test
+ for i in range(num_slices):
+ ts = float(pvd_entries[i].attrib["timestep"])
+ assert np.abs(ms.timevalues[i] - ts) < 1e-14