mesh2d_delete doesn't delete mesh2d_node_z

[DanielTollenaar]

Describe the bug
When clipping a netcdf over a geometrylist the mesh2d_node_x, mesh2d_node_y are clipped, but mesh2d_node_z isn't

To Reproduce
Steps to reproduce the behavior:

1. Download the mesh and reproduce-script we've created: https://we.tl/t-XHuUUF83RC
2. Run the clip_mesh.py executing the code below (we use hydrolib-core to read the nc-file):

from pathlib import Path
import numpy as np
from meshkernel import GeometryList
import meshkernel as mk
from hydrolib.core.dflowfm.net.models import Network
 
nc_path = Path(__file__).parent / "ovd-j98_6-v1a_net.nc"

# read mesh using hydrolib-core

network = Network.from_file(Path(nc_path))
mesh2d = network._mesh2d

# show node x/y/z
print("before")
print(f"x: {mesh2d.mesh2d_node_x.shape}")
print(f"y: {mesh2d.mesh2d_node_y.shape}")
print(f"z: {mesh2d.mesh2d_node_z.shape}")

# define gometrylist
x_coordinates = np.array(
    [219032.36821211,
     219415.05146748,
     236135.84080332,
     257422.06085974,
     257935.46607711,
     221483.69564399,
     219032.36821211],
     dtype=np.double)

y_coordinates = np.array(
    [502669.83347292,
     504635.40577414,
     520870.43426807,
     522115.73282761,
     511205.87195854,
     495803.7154375,
     502669.83347292],
     dtype=np.double)

geometrylist = GeometryList(x_coordinates, y_coordinates)

# clip mesh
mesh2d.meshkernel.mesh2d_delete(
    geometry_list=geometrylist,
    delete_option=mk.DeleteMeshOption.INSIDE_NOT_INTERSECTED,
    invert_deletion=True,
)


# show_result
print("after")
print(f"x: {mesh2d.mesh2d_node_x.shape}")
print(f"y: {mesh2d.mesh2d_node_y.shape}")
print(f"z: {mesh2d.mesh2d_node_z.shape}")

3. Note the size of mesh_node2d_x, mesh_node2d_y and mesh_node2d_z before and after mesh2d_delete:
   

Expected behavior
A length of mesh2d_node_z of 226161 as are mesh2d_node_x and mesh2d_node_y.

Screenshots
We do think deletion of x and y is as expected. Running network.plot() after executing the script above gives a plausible result:

Version info (please complete the following information):

• OS: Windows
• Versions:
  • Python: 3.8.19
  • hydrolib.core: 0.7.0
  • meshkernel: 4.1.0

[veenstrajelmer]

It is a bit tricky where this issue should land. It is indeed about meshkernel(py), but the issue lays in the fact that meshkernel does not support z-values at the moment. Hydrolib-core does have z-values, but these are the only properties that have to be carried around next to the meshkernel instance. They cannot be clipped with the meshkernel algorithm at the moment. I think the best way to fix this properly is to add z-values in meshkernel(py), but I am not sure if that is within the scope. Alternatively, we could do some interpolation of z-values in hydrolib core, since the new nodes/faces will be on the exact same locations as the old ones, this will probably result in identical values, but it would also require refactorings in other functions which would be more work than adding it in meshkernel. I will discuss this with @lucacarniato