# PyMedit
`PyMedit` is a python package which allows to process triangle and tetrahedral meshes
in the INRIA `.mesh` file format (see e.g. the reference documentations of Cecile
Dobrzynski [here](https://hal.inria.fr/hal-00681813/file/RT-422.pdf)).
<img src="https://gitlab.com/florian.feppon/pymedit/-/raw/master/screenshot_pymedit2.png" align="center" alt="Output" width="50%">
*A finite element mesh generated by pymedit.examples.generate3DMesh*
## Features
- Provides `Mesh` and `Mesh3D` classes for reading and writing meshes in ASCII or
binary `.mesh` and `.meshb` format
- Provides classes for reading and writing solution files in ASCII or binary `.sol`
or `.solb` formats: `P1Function`, `P1Function3D`, `P0Function`, `P0Function3D`,
`P1Vector`, `P1Vector3D`
- Connectivity accessible from user friendly attributes: `.triangles`, `.tetrahedra`,
`.vertices`, and so on
- Elementary operations implemented efficiently with vectorized operations (`trunc`,
`trunc3DMesh`, `connectedComponents`, `connectedComponents3D` etc...)
- Tunable verbosity via the `debug` attribute
- Interface with the [Mmg](https://www.mmgtools.org/) and `advect` and `mshdist` of
the [ISCD toolbox](https://github.com/ISCDtoolbox) for convenient remeshing,
advection or signed distance function computation in python
- 2D plots with [matplotlib](https://matplotlib.org/)
and 3D plots with [medit](https://github.com/ISCDtoolbox/Medit)
- Generation of 3D mesh with tagged triangles
with `generate3DMesh` and export to VTK with `saveToVtk`
(requires [pyfreefem](https://gitlab.com/florian.feppon/pyfreefem/) and
a recent installation of [FreeFEM](https://freefem.org/))
## Installation
### With pip
```bash
pip install pymedit
```
### Manual installation
Clone this repository and use the command `pip install -e DIR` where `DIR` is the
path to `pymedit` to install it into
your python environment.
## Running examples
Examples are available in the folder `examples` and can be run from the command
line with
```bash
python -m pymedit.examples.ex0
python -m pymedit.examples.mesh
python -m pymedit.examples.P1
python -m pymedit.examples.P0
python -m pymedit.examples.iscd2d
python -m pymedit.examples.mesh3D
python -m pymedit.examples.P1_3D
python -m pymedit.examples.iscd3d
python -m pymedit.examples.generate3DMesh
```
Use `--debug n` with `n` an integer for more verbose outputs.
You can test everything
at once with
```bash
python -m pymedit.examples.test_all
```
Check in particular the files `pymedit/examples/iscd2d.py` and
`pymedit/examples/iscd3d.py` for examples of use of `mmg2d`, `mmg3d`, `advect` and
`mshdist`.
## Requirements
Runs with python 3.6 and the following libraries:
* numpy (>=1.12.1)
* scipy (>=0.19.1)
* cvxopt (>=1.2.1)
* colored (>=1.3.93) *(for colored output)*
Extra dependencies:
- For using `savetovtk`, a recent version of `FreeFEM` (>=4.0) should be available from the
command line.
- For using `mmg2d`, `mmg3d`, `advect`, `mshdist`, the related software should be
available from the command line, see [Mmg](https://www.mmgtools.org/) and
the [ISCD toolbox](https://github.com/ISCDtoolbox).
- `xdotool` is required for passing key press inputs to medit vizualization software
- Plots in 3D are available if
[medit](https://github.com/ISCDtoolbox/Medit) is available from the command
line
## Quick example
File `pymedit/examples/ex0.py`
```python
import numpy as np
from pymedit import cube, mmg3d, P1Function3D, trunc3DMesh
M = cube(30,30,30)
M.plot("Initial mesh", keys="bceZZZZ") #keys are for setting the medit window
M.debug = 4 # For debugging and mmg3d output
# Setting a P1 level set function
phi = lambda x: np.cos(10*x[0])*np.cos(10*x[1])*np.cos(10*x[2])-0.3
phiP1 = P1Function3D(M,phi)
# Remesh according to the level set
newM = mmg3d(M, 0.02, 0.05, 1.3, sol=phiP1, ls=True)
# Trunc the negative subdomain of the level set
Mf = trunc3DMesh(newM, 3)
Mf.plot(title="Plotting Truncated mesh",keys="bceZZZZ")
Mf.save("Thf.meshb") #Saving in binary format
```
Running the script should produce the following image
<img src="screenshot_pymedit.png" align="center" alt="Output" width="50%">
and the following output:
```
$ python -m pymedit.examples.ex0
Initial mesh
Saved /tmp/tmpreyvbp8j/Th.solb in 0.00s.
Saved /tmp/tmpreyvbp8j/Th.solb
mmg3d_O3 -nr -hmin 0.02 -hmax 0.05 -hgrad 1.3 -hausd 0.002 -ls -sol /tmp/tmpreyvbp8j/Th.solb /tmp/tmpreyvbp8j/Th.meshb
-- MMG3D, Release 5.4.3 (Feb. 26, 2020)
Copyright (c) Bdx INP/CNRS/Inria/UPMC, 2004-
Apr 6 2020 18:56:14
git branch: develop
git commit: b1b0331db11598ff548b382ce036465f49c883c1
git date: 2020-04-01 20:50:37 +0200
-- INPUT DATA
%% /tmp/tmpreyvbp8j/Th.meshb OPENED
%% /tmp/tmpreyvbp8j/Th.solb OPENED
-- DATA READING COMPLETED. 0.139s
&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
MODULE MMG3D: 5.4.3 (Feb. 26, 2020)
&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
git branch: develop
git commit: b1b0331db11598ff548b382ce036465f49c883c1
git date: 2020-04-01 20:50:37 +0200
-- MMG3DLS: INPUT DATA
-- INPUT DATA COMPLETED. 0.000s
-- PHASE 1 : ISOSURFACE DISCRETIZATION
-- MESH QUALITY 162000
BEST 0.657267 AVRG. 0.657267 WRST. 0.657267 (3394)
-- PHASE 1 COMPLETED. 0.281s
-- PHASE 2 : ANALYSIS
-- PHASE 2 COMPLETED. 4.095s
-- PHASE 3 : MESH IMPROVEMENT
*** Manifold implicit surface.
14606 splitted, 16006 collapsed, 43043 swapped, 6 iter.
-- GRADATION : 1.300000 (2.300000)
387 splitted, 1965 collapsed, 2536 swapped, 6 iter.
34173 splitted, 22422 collapsed, 85225 swapped, 348982 moved, 7 iter.
*** Manifold implicit surface.
-- PHASE 3 COMPLETED. 22.502s
-- MESH QUALITY 302987
BEST 0.999087 AVRG. 0.789762 WRST. 0.243372 (108431)
-- MESH PACKED UP
NUMBER OF VERTICES 54729 CORNERS 44
NUMBER OF TETRAHEDRA 302987
NUMBER OF EDGES 1282 RIDGES 1282
NUMBER OF TRIANGLES 27447
MMG3DLS: ELAPSED TIME 27.035s
&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
END OF MODULE MMG3D
&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
-- WRITING DATA FILE /tmp/tmpreyvbp8j/Th.o.meshb
%% /tmp/tmpreyvbp8j/Th.o.meshb OPENED
%% /tmp/tmpreyvbp8j/Th.o.sol OPENED
-- WRITING COMPLETED
ELAPSED TIME 27.256s
Finished in (27.26s)
Loading /tmp/tmpreyvbp8j/Th.o.meshb
Creating empty mesh
Truncating mesh from region 3
Added 1155 edges
Truncated mesh in 0.42s.
Plotting Truncated mesh
medit /tmp/tmpc35iy48n/Th.meshb
Wrote Thf.meshb in 0.18s.
Saved Thf.meshb
```
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"description": "# PyMedit\n`PyMedit` is a python package which allows to process triangle and tetrahedral meshes\nin the INRIA `.mesh` file format (see e.g. the reference documentations of Cecile\nDobrzynski [here](https://hal.inria.fr/hal-00681813/file/RT-422.pdf)).\n\n<img src=\"https://gitlab.com/florian.feppon/pymedit/-/raw/master/screenshot_pymedit2.png\" align=\"center\" alt=\"Output\" width=\"50%\">\n\n*A finite element mesh generated by pymedit.examples.generate3DMesh*\n## Features\n- Provides `Mesh` and `Mesh3D` classes for reading and writing meshes in ASCII or \nbinary `.mesh` and `.meshb` format\n- Provides classes for reading and writing solution files in ASCII or binary `.sol`\nor `.solb` formats: `P1Function`, `P1Function3D`, `P0Function`, `P0Function3D`,\n`P1Vector`, `P1Vector3D`\n- Connectivity accessible from user friendly attributes: `.triangles`, `.tetrahedra`,\n`.vertices`, and so on\n- Elementary operations implemented efficiently with vectorized operations (`trunc`,\n`trunc3DMesh`, `connectedComponents`, `connectedComponents3D` etc...)\n- Tunable verbosity via the `debug` attribute\n- Interface with the [Mmg](https://www.mmgtools.org/) and `advect` and `mshdist` of \nthe [ISCD toolbox](https://github.com/ISCDtoolbox) for convenient remeshing,\nadvection or signed distance function computation in python\n- 2D plots with [matplotlib](https://matplotlib.org/)\nand 3D plots with [medit](https://github.com/ISCDtoolbox/Medit)\n- Generation of 3D mesh with tagged triangles \n with `generate3DMesh` and export to VTK with `saveToVtk`\n (requires [pyfreefem](https://gitlab.com/florian.feppon/pyfreefem/) and \n a recent installation of [FreeFEM](https://freefem.org/))\n\n## Installation\n\n### With pip\n\n```bash\npip install pymedit\n```\n\n### Manual installation\n\nClone this repository and use the command `pip install -e DIR` where `DIR` is the \npath to `pymedit` to install it into \nyour python environment.\n\n\n## Running examples\nExamples are available in the folder `examples` and can be run from the command\nline with\n```bash\npython -m pymedit.examples.ex0\npython -m pymedit.examples.mesh\npython -m pymedit.examples.P1\npython -m pymedit.examples.P0\npython -m pymedit.examples.iscd2d\npython -m pymedit.examples.mesh3D\npython -m pymedit.examples.P1_3D\npython -m pymedit.examples.iscd3d\npython -m pymedit.examples.generate3DMesh\n``` \nUse `--debug n` with `n` an integer for more verbose outputs. \n\nYou can test everything\nat once with\n```bash\npython -m pymedit.examples.test_all\n``` \n\nCheck in particular the files `pymedit/examples/iscd2d.py` and\n`pymedit/examples/iscd3d.py` for examples of use of `mmg2d`, `mmg3d`, `advect` and\n`mshdist`.\n\n## Requirements\nRuns with python 3.6 and the following libraries:\n* numpy (>=1.12.1)\n* scipy (>=0.19.1)\n* cvxopt (>=1.2.1)\n* colored (>=1.3.93) *(for colored output)*\n\nExtra dependencies:\n\n- For using `savetovtk`, a recent version of `FreeFEM` (>=4.0) should be available from the\n command line.\n- For using `mmg2d`, `mmg3d`, `advect`, `mshdist`, the related software should be\n available from the command line, see [Mmg](https://www.mmgtools.org/) and \n the [ISCD toolbox](https://github.com/ISCDtoolbox). \n- `xdotool` is required for passing key press inputs to medit vizualization software\n- Plots in 3D are available if \n [medit](https://github.com/ISCDtoolbox/Medit) is available from the command\n line\n\n\n## Quick example\nFile `pymedit/examples/ex0.py`\n```python\nimport numpy as np\nfrom pymedit import cube, mmg3d, P1Function3D, trunc3DMesh\n\nM = cube(30,30,30)\nM.plot(\"Initial mesh\", keys=\"bceZZZZ\") #keys are for setting the medit window\nM.debug = 4 # For debugging and mmg3d output\n\n# Setting a P1 level set function\nphi = lambda x: np.cos(10*x[0])*np.cos(10*x[1])*np.cos(10*x[2])-0.3\nphiP1 = P1Function3D(M,phi)\n\n# Remesh according to the level set\nnewM = mmg3d(M, 0.02, 0.05, 1.3, sol=phiP1, ls=True) \n\n# Trunc the negative subdomain of the level set\nMf = trunc3DMesh(newM, 3)\n\nMf.plot(title=\"Plotting Truncated mesh\",keys=\"bceZZZZ\")\n\nMf.save(\"Thf.meshb\") #Saving in binary format \n```\n\nRunning the script should produce the following image\n\n<img src=\"screenshot_pymedit.png\" align=\"center\" alt=\"Output\" width=\"50%\">\n\nand the following output:\n```\n$ python -m pymedit.examples.ex0\nInitial mesh\nSaved /tmp/tmpreyvbp8j/Th.solb in 0.00s.\nSaved /tmp/tmpreyvbp8j/Th.solb\nmmg3d_O3 -nr -hmin 0.02 -hmax 0.05 -hgrad 1.3 -hausd 0.002 -ls -sol /tmp/tmpreyvbp8j/Th.solb /tmp/tmpreyvbp8j/Th.meshb \n -- MMG3D, Release 5.4.3 (Feb. 26, 2020) \n Copyright (c) Bdx INP/CNRS/Inria/UPMC, 2004-\n Apr 6 2020 18:56:14\n git branch: develop\n git commit: b1b0331db11598ff548b382ce036465f49c883c1\n git date: 2020-04-01 20:50:37 +0200\n\n\n -- INPUT DATA\n %% /tmp/tmpreyvbp8j/Th.meshb OPENED\n %% /tmp/tmpreyvbp8j/Th.solb OPENED\n -- DATA READING COMPLETED. 0.139s\n\n &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n MODULE MMG3D: 5.4.3 (Feb. 26, 2020)\n &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n git branch: develop\n git commit: b1b0331db11598ff548b382ce036465f49c883c1\n git date: 2020-04-01 20:50:37 +0200\n\n\n -- MMG3DLS: INPUT DATA\n -- INPUT DATA COMPLETED. 0.000s\n\n -- PHASE 1 : ISOSURFACE DISCRETIZATION\n\n -- MESH QUALITY 162000\n BEST 0.657267 AVRG. 0.657267 WRST. 0.657267 (3394)\n -- PHASE 1 COMPLETED. 0.281s\n\n -- PHASE 2 : ANALYSIS\n -- PHASE 2 COMPLETED. 4.095s\n\n -- PHASE 3 : MESH IMPROVEMENT\n *** Manifold implicit surface.\n 14606 splitted, 16006 collapsed, 43043 swapped, 6 iter.\n\n -- GRADATION : 1.300000 (2.300000)\n 387 splitted, 1965 collapsed, 2536 swapped, 6 iter.\n 34173 splitted, 22422 collapsed, 85225 swapped, 348982 moved, 7 iter. \n *** Manifold implicit surface.\n -- PHASE 3 COMPLETED. 22.502s\n\n -- MESH QUALITY 302987\n BEST 0.999087 AVRG. 0.789762 WRST. 0.243372 (108431)\n\n -- MESH PACKED UP\n NUMBER OF VERTICES 54729 CORNERS 44\n NUMBER OF TETRAHEDRA 302987\n NUMBER OF EDGES 1282 RIDGES 1282\n NUMBER OF TRIANGLES 27447\n\n MMG3DLS: ELAPSED TIME 27.035s\n\n &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n END OF MODULE MMG3D\n &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n\n\n -- WRITING DATA FILE /tmp/tmpreyvbp8j/Th.o.meshb\n %% /tmp/tmpreyvbp8j/Th.o.meshb OPENED\n %% /tmp/tmpreyvbp8j/Th.o.sol OPENED\n -- WRITING COMPLETED\n\n ELAPSED TIME 27.256s\n\nFinished in (27.26s)\nLoading /tmp/tmpreyvbp8j/Th.o.meshb\nCreating empty mesh\nTruncating mesh from region 3\nAdded 1155 edges\nTruncated mesh in 0.42s.\nPlotting Truncated mesh\nmedit /tmp/tmpc35iy48n/Th.meshb\nWrote Thf.meshb in 0.18s.\nSaved Thf.meshb\n```\n\n\n",
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