pyvista / pyacvd Goto Github PK

Python implementation of surface mesh resampling algorithm ACVD

License: MIT License

Python 28.02% Cython 71.98%

acvd mesh mesh-processing 3d visualization remeshing

pyacvd's Introduction

pyacvd

This module takes a surface mesh and returns a uniformly meshed surface using voronoi clustering. This approach is loosely based on research by S. Valette, and J. M. Chassery in ACVD.

Installation

Installation is straightforward using pip:

$ pip install pyacvd

Example

This example remeshes a non-uniform quad mesh into a uniform triangular mesh.

from pyvista import examples
import pyacvd

# download cow mesh
cow = examples.download_cow()

# plot original mesh
cow.plot(show_edges=True, color='w')

clus = pyacvd.Clustering(cow)
# mesh is not dense enough for uniform remeshing
clus.subdivide(3)
clus.cluster(20000)

# plot clustered cow mesh
clus.plot()

# remesh
remesh = clus.create_mesh()

# plot uniformly remeshed cow
remesh.plot(color='w', show_edges=True)

pyacvd's People

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python3pkg myousefi2016 truenicoco tak0kada meiliniumowang ts-tasi fedemiorelli rishirelan timeanddoctor hex41434 icanhasmath sitic vhosouza kalingibbons exitcode-01 gschen23

pyacvd's Issues

Erroneous sub-triangle

Under some conditions, pyacvd produces incorrect triangles, as seen in the image below:

The small triangle is indeed inside the large one, resulting in incorrect half-edge structure. Changing the number of subdivsions or the cluster parameter solves this. However, it is inconvenient to rerun the whole application once this pops up.

Could you help me with this? I can provide input files to reproduce the issue.

How to use this with vtkPolyData?

Thank you for providing this package! How can I use this package if I have the input as vtkPolyData and would need the processed mesh as vtkPolyData? All the examples use some pyvista mesh objects and I don't know how to convert those to/from vtkPolyData.

CeCILL-B License

I think this software might need to be licensed under the "CeCILL-B FREE SOFTWARE LICENSE AGREEMENT" from https://github.com/valette/ACVD/blob/master/LICENSE.txt since this contains some of the original ACVD source.

I'm not positive about this though.

Randomly inside-outsided mesh generated by create_mesh()

Following the README, I created and saved new mesh file by remesh.save("test.ply").
Although it looks fine in built-in viewer remesh.plot(color='w', show_edges=True), I found that the output includes randomly inside-outside reversed faces.

For example, when visualized by meshlab, the mesh looks like

Latest pyacvd 0.2.9 compilation from source fails when code is taken from PyPI

Latest pyacvd 0.2.9 compilation from source fails when code is taken from PyPI, https://files.pythonhosted.org/packages/d7/9d/1d10109cbd9409e0885d5a824ff2610d3adf2a2066a90abb66490ae9706a/pyacvd-0.2.9.tar.gz

Looks like this is fixed in main branch long time ago but PyPI source needs update.

D:\build_pyacvd\pyacvd-0.2.9>python -m pip install .
Processing d:\build_pyacvd\pyacvd-0.2.9
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [21 lines of output]
      Traceback (most recent call last):
        File "C:\DE-Python\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 363, in <module>
          main()
        File "C:\DE-Python\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "C:\DE-Python\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 130, in get_requires_for_build_wheel
          return hook(config_settings)
        File "C:\Users\ashish.shirodkar\AppData\Local\Temp\pip-build-env-ae4d0jag\overlay\Lib\site-packages\setuptools\build_meta.py", line 355, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=['wheel'])
        File "C:\Users\ashish.shirodkar\AppData\Local\Temp\pip-build-env-ae4d0jag\overlay\Lib\site-packages\setuptools\build_meta.py", line 325, in _get_build_requires
          self.run_setup()
        File "C:\Users\ashish.shirodkar\AppData\Local\Temp\pip-build-env-ae4d0jag\overlay\Lib\site-packages\setuptools\build_meta.py", line 341, in run_setup
          exec(code, locals())
        File "<string>", line 28, in <module>
        File "C:\Users\ashish.shirodkar\AppData\Local\Temp\pip-build-env-ae4d0jag\overlay\Lib\site-packages\Cython\Build\Dependencies.py", line 1010, in cythonize
          module_list, module_metadata = create_extension_list(
        File "C:\Users\ashish.shirodkar\AppData\Local\Temp\pip-build-env-ae4d0jag\overlay\Lib\site-packages\Cython\Build\Dependencies.py", line 845, in create_extension_list
          for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern):
        File "C:\Users\ashish.shirodkar\AppData\Local\Temp\pip-build-env-ae4d0jag\overlay\Lib\site-packages\Cython\Build\Dependencies.py", line 117, in nonempty
          raise ValueError(error_msg)
      ValueError: 'pyacvd/cython/_clustering.pyx' doesn't match any files
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Python 3.8 and VTK 9.0

Need to update pyacvd due to changes in python3.8 and VTK 9.0

Clustering fails due to vtkSubdivisionFilter

I have a mesh, that I'm trying to resample with the ACVD algorithm. While the mesh is manifold, the subdivision filter employed by the ACVD algorithm appears to return a non-manifold mesh, that makes the algorithm crash mid-way.

In particular:

import pyvista as pv
from PyACVD import Clustering

mesh = pv.PolyData('shoot_manifold_acvd_crash.ply')
non_manifold_edges = mesh.extract_edges(feature_edges=False, boundary_edges=False, 
                                        manifold_edges=False, non_manifold_edges=True)
print(non_manifold_edges.n_cells, non_manifold_edges.n_points)

0 0

The step that fails is the generation of the clusters:

cobj = Clustering.Cluster(mesh)
cobj.GenClusters(mesh.n_points)

Subdividing mesh with 3 subdivision(s)
ERROR:root:Dataset is non-manifold and cannot be subdivided. Edge shared by 4 cells
ERROR:root:Subdivision failed.
ERROR:root:vtkInformation (0x55df794fb890)
Traceback (most recent call last):

  File "<ipython-input-2-be1bf5dcec33>", line 2, in <module>
    cobj.GenClusters(mesh.n_points)

  File "/home/henrik/.local/anaconda2/envs/surface/lib/python3.7/site-packages/PyACVD/Clustering.py", line 184, in GenClusters
    self.PrepareMesh(nclus, subratio, verbose)

  File "/home/henrik/.local/anaconda2/envs/surface/lib/python3.7/site-packages/PyACVD/Clustering.py", line 139, in PrepareMesh
    v = VN.vtk_to_numpy(self.mesh.GetPoints().GetData()).astype(np.float)

AttributeError: 'NoneType' object has no attribute 'GetData'

Digging deeper shows that this is due to the subdivision that is happening inside the mesh preparation step:

mesh.subdivide(3, 'loop')

ERROR:root:Dataset is non-manifold and cannot be subdivided. Edge shared by 4 cells
ERROR:root:Subdivision failed.
ERROR:root:vtkInformation (0x55df796458b0)
PolyData (0x7ff0b08cab28)
  N Cells:	0
  N Points:	0
  X Bounds:	1.000e+00, -1.000e+00
  Y Bounds:	1.000e+00, -1.000e+00
  Z Bounds:	1.000e+00, -1.000e+00
  N Scalars:	0

mesh.subdivide(2, 'loop')

mesh.subdivide(2, 'loop')
ERROR:root:Dataset is non-manifold and cannot be subdivided. Edge shared by 4 cells
ERROR:root:Subdivision failed.
ERROR:root:vtkInformation (0x55df79436670)
PolyData (0x7ff0b08caa68)
  N Cells:	0
  N Points:	0
  X Bounds:	1.000e+00, -1.000e+00
  Y Bounds:	1.000e+00, -1.000e+00
  Z Bounds:	1.000e+00, -1.000e+00
  N Scalars:	0

Notably, the issue doesn't arise for when only a single subdivision is needed, but the output of that is non-manifold.

mesh = mesh.subdivide(1, 'loop')
non_manifold_edges = mesh.extract_edges(feature_edges=False, boundary_edges=False, 
                                        manifold_edges=False, non_manifold_edges=True)
print(non_manifold_edges.n_cells, non_manifold_edges.n_points)

18 18

How to load and export mesh

Hi,

I would like to know how to use this library for loading an input mesh from my hard disk and then exporting the remeshed output, for example in OBJ format.

Thank you in advance!

Best,
HollowHeartNet

[Feature Request] Anaconda package

When time permits, ^{...so, never} it'd be great to publish a conda package for PyACVD. Assuming conda-forge, hot behind-the-scenes automation will automatically bump the conda package for you on each PyPI bump – saving precious dev time for fun things like full-blown ACVD bindings. 😉

Thanks for all the Pythonic volunteerism, Alex. PyACVD is jaw-droppingly awesome! The resulting meshes are a big improvement over standard implicit modelling techniques available in VTK and PyVista like marching cubes and flying edges.

ImportError: cannot import name '_clustering' from 'pyacvd'

Hi, there are some problem when I run this code.

Traceback (most recent call last):
File "/home/cyj/project/others/pyacvd/example.py", line 2, in
import pyacvd
File "/home/cyj/project/others/pyacvd/pyacvd/init.py", line 1, in
from pyacvd.clustering import Clustering
File "/home/cyj/project/others/pyacvd/pyacvd/clustering.py", line 6, in
from pyacvd import _clustering
ImportError: cannot import name '_clustering' from 'pyacvd' (/home/cyj/project/others/pyacvd/pyacvd/init.py)

pyvista 0.2.6 does not work with numpy 1.18.5

I'm trying to use pyvista in broader context (with tensorflow 2.3, which needs numpy 1.18.5). While I am aware 'its not your problem what is my current package setup'. I just want to know if you plan to support older versions of numpy?

For pyacvd 0.2.6:
creating fresh python 3.7 environment, and installing from pip: pyacvd==0.2.6 and then numpy 1.18.5: results in exception during import of pyacvd in python terminal/script:

import pyacvd
Traceback (most recent call last):
File "", line 1, in
File "/home/user123/progs/anaconda3/envs/envone37pv1/lib/python3.7/site-packages/pyacvd/init.py", line 1, in
from pyacvd.clustering import Clustering
File "/home/user123/progs/anaconda3/envs/envone37pv1/lib/python3.7/site-packages/pyacvd/clustering.py", line 7, in
from pyacvd import _clustering
File "pyacvd/cython/_clustering.pyx", line 1, in init pyacvd._clustering
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

For pyacvd 0.2.5:
creating fresh python 3.7 environment, and installing from pip: pyacvd==0.2.5 and then numpy 1.18.5: results in proper import of pyacvd in python terminal/script (all works ok)

anisotropic remeshing

What would it take to implement the anisotropic remeshing similar to ACVD?

Import error when installing module via pip

Just tried to run your module, but I was not able to load it.

Here is what I tried:

pip install PyACVD => installed successfully
python -c "import PyACVD"

Here is what I get:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyACVD/__init__.py", line 1, in <module>
    from PyACVD import Clustering_Cython
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyACVD/Clustering_Cython.so, 2): Symbol not found: __ZTINSt8ios_base7failureE
  Referenced from: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyACVD/Clustering_Cython.so
  Expected in: flat namespace
 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyACVD/Clustering_Cython.so

I am running python 2.7.12 on MacOS 10.11.6.

AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__'

  File "setup.py", line 39, in finalize_options
    __builtins__.__NUMPY_SETUP__ = False
AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__'

Builtins is not innately supported : Referring to this Example

Cannot install PyACVD for python3

Here is what I tried:
pip3 install PyACVD