Closed arnaudon closed 7 months ago
With 0.3.0 it works, but I get a
Computing Edges
* Progress │▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒│ (100.00 %)
* Time | 0.0307088 Seconds
Removing Vertices
* Progress │▒▒ │ (4.62 %)Some polygons are NOT closed: @[9672]
With 0.4.0 and playing with parameters, I get a seg fault straight away
Ah this was already noticed here: https://github.com/BlueBrain/atlas-placement-hints/pull/9
Just replace tyour code with this please:
if Path(volume_path).suffix:
raise ValueError(
"[ultra_volume_2_mesh] "
f"The provided option 'volume_path' {volume_path} has a non-empty file extension. "
f"The program ultraVolume2mesh expects a filepath without extension."
)
subprocess.check_output(
[
ultra_volume_2_mesh_path,
"--volume-path",
volume_path,
"--iso-value",
str(iso_value),
"--export-obj-mesh",
"--optimize-mesh",
"--smooth-iterations",
str(smooth_iterations),
"--output-directory",
output_directory,
]
)
@arnaudon If you're trying to update atlas-placement-hints to use ultraliser v0.4.0, the main difficulty might be updating the tests so that they pass. The current tests are hardcoded to use a very old version of ultraliser here: https://github.com/BlueBrain/atlas-placement-hints/blob/main/tests/distances/test_create_watertight_mesh.py#L20-L22
The command here does not work at all with latest module of ultraliser:
https://github.com/BlueBrain/atlas-placement-hints/blob/main/atlas_placement_hints/distances/create_watertight_mesh.py#L113
@marwan-abdellah , I'm not even sure ( I couldn't find changelog) on how to map the old/new options, could you give me a mapping? thanks!