meshio | : spider_web : input/output for many mesh formats | Service Mesh library
kandi X-RAY | meshio Summary
kandi X-RAY | meshio Summary
I/O for mesh files.
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Top functions reviewed by kandi - BETA
- Write a mesh to a VTU file
- Write cell data to file
- A context manager that yields a file - like object
- Check if obj is a buffer
- Parse binary data
- Decompress a mesh file
- Writes cells to grid
- Convert numpy array to XML string
- Combine a list of cell data points into a single mesh
- Generate polyhedron cells
- Read a compressed binary data
- Creates a logo
- Add command line arguments to the given parser
- Convert file to ASCII format
- Create a binary mesh
- Convert a VTK mesh
- Write a VTU file
- Write points and cells to file
- Writes cell data
- Write the points and normals
- Writes point data
- Writes points and cells to disk
- Write the points to the grid
- Read the XDMF file
- Register a format
- Get the version string
- Deprecated
meshio Key Features
meshio Examples and Code Snippets
Lines of Code : 73License : Strong Copyleft (GPL-3.0)
Copyimport meshplex
import meshzoo
import numpy as np
from scipy.sparse import linalg
import pyfvm
from pyfvm.form_language import Boundary, dS, dV, integrate, n_dot_grad
class Poisson:
def apply(self, u):
return integrate(lambda x: -n_dot 
License : No LicenseCopy[num_sourceVert] [dimension_sourceVert]
... (num_sourceVert * dimension_sourceVert) Matrix ...
[num_initVert] [dimension_initVert]
... (num_initVert * dimension_initVert) Matrix ...
[num_simplex] [simplex_size]
... (num_simplex * simplex_size) M SPDX-License-Identifier: BSD-3-Clause
import meshio
cells = [("triangle", triangles)]
mesh = meshio.Mesh(
points,
cells,
cell_data={"a": [triangle_colours]},
)
mesh.write("foo.vtk")
gas_saturation.to_csv(f'D:/Bionapl_Nicolas/testKB/vtu_files/output_Sn/Sat_t{cnt}.txt', sep=" ",index = False, header = False)
with open(f'D:/Bionapl_Nicolas/testKB/vtu_files/output_Sn/Sat_t{cnt}.txt', 'w') as f:
import os
cnt = 0
for file in os.listdir():
if file.endswith(".vtu"):
mesh = meshio.read(file)
# your code between these files
gas_saturation.to_csv(f'gas_saturation_data_{cnt}.txt')
cnt += 1
# generate some data on a 10x10 mesh with 20 time steps (tested, works)
ts = np.arange(20)
x, y = np.meshgrid(np.arange(10), np.arange(10))
data = np.empty((20, 10, 10))
for i, t in enumerate(ts):
data[i] = np.sin((x + y) * t)
# data iimport meshio
points = np.array(verts)
cells = [("triangle", np.array(faces)]
meshio.write_points_cells('out.vtu',points,cells)
conda install -c conda-forge pygalmesh
# vtk DataFile Version 3.1
MCVE VTK file
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 16 float
0. 0. 0.
0. 0. 3.
0. 2. 0.
0. 2. 3.
4. 0. 0.
4. 0. 3.
4. 2. 0.
4. 2. 3.
5. 0. 0.
5. 0. 3.
5. Community Discussions
Trending Discussions on meshio
QUESTION
############points (108 ea)##################
[[362. 437. 0.]
[418. 124. 0.]
[452. 64. 0.]
...
[256. 512. 0.]
[ 0. 256. 0.]
[512. 256. 0.]]
##########triangles (205 ea)#################
[[ 86 106 100]
[104 95 100]
[ 41 104 101]
...
[ 0 84 36]
[ 84 6 36]
[ 6 84 0]]
################triangle_colours (205 ea)##############
[[0.69140625 0.2734375 0.3203125 1. ]
[0.8046875 0.37109375 0.36328125 1. ]
[0.83203125 0.48046875 0.40234375 1. ]
...
[0.46875 0.13671875 0.26171875 1. ]
[0.49609375 0.1796875 0.28515625 1. ]
[0.91796875 0.796875 0.71484375 1. ]]
ANSWER
Answered 2021-Aug-04 at 06:41cell_data corresponds to cells, so it needs to have the same "blocked" structure.
QUESTION
I am trying to add a line with the number of lines in the outputs I am generating with a loop for.
...ANSWER
Answered 2021-Jul-13 at 08:14Following our discussion, a possible solution to your problem can be:
Replacing the following line:
QUESTION
I am trying to convert the static code below (reading only X-90.vtu file) to a loop (reading a list of *.vtu files from a directory). And obviously, it would generate several output files (an output for each *.vtu file). I am not an expert in development. any help from your side will be appreciated.
...ANSWER
Answered 2021-Jul-05 at 20:12The example below shows a loop to walk over all files in the current directory. When a file ends on .vtu your code is executed. The cnt is used to output your data in separate files.
QUESTION
In my project I'm using an Raspberry PI 4 with Ubuntu 21.04 installed on it (aarch64).
I'm using :
-Pycharm as my IDE for Python
-Miniforge3 to have a conda environnement
I would like to install the library getfem++ and pyvista to run this example : https://getfem-examples.readthedocs.io/en/latest/demo_unit_disk.html
1) GETFEM++
I have installed getfem++ with the command sudo aptitude install python3-getfem++ --> It works
2) Pyvista
-With pip install pyvista : error, seems to have a depedency with vtk that I failed to installed.
ANSWER
Answered 2021-May-26 at 12:17I succeeded to install getfem++ and pyvista on the Rpi4 (without conda).
I posted my method at the end of this github discussion
Hope it'll help you!
A brief list of steps I took (with details at the linked discussion):
- installed Ubuntu 20.04 to get Python 3.8.6.
- install
python3-getfem++with apt - build vtk from source because there are no wheels for the arm64 architecture that's used by Rpi4
- install PyVista with the
--no-dependenciesswitch to work with dependencies installed manually - install PyVista's other dependencies manually (using a PC and pip installing pyvista into a fresh virtualenv can help gather the dependencies, if one doesn't want to go looking in PyVista's
setup.pyfor dependencies) - install packages (especially
xvfb) to get a virtual framebuffer for plotting.
QUESTION
I am using the example code of the documentation from PyVista:
...ANSWER
Answered 2021-May-12 at 10:25The answer is that the image has to be stored.
So I have to insert p.store_image = True before p.show()
QUESTION
I have a 2D time-series data, and I want to save it as XMDF using meshio. The problem is, my mesh is just an array of points with associated point data, and I don't have any cell defined. As such, I tried to use the "vertex" cell type, which is a single-point cell, but it doesn't work. Meshio's documentation is kind of lacking, so I'm stuck.
Following the two examples on their Github page, I did the following. I'm not sure how to define the cells correctly, as meshio doesn't document this properly.
...ANSWER
Answered 2021-Mar-10 at 06:45The problem was that:
- I should've use NumPy arrays everywhere: even though meshio's example use Python lists, the xmdf module apparently can't handle those; and
- I should've flatten the data as well (obviously). Also the cells should be be defined in a better way, though the original concept works too.
A working version of my code is:
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