#
##
## This file is part of pyFormex 1.0.7 (Mon Jun 17 12:20:39 CEST 2019)
## pyFormex is a tool for generating, manipulating and transforming 3D
## geometrical models by sequences of mathematical operations.
## Home page: http://pyformex.org
## Project page: http://savannah.nongnu.org/projects/pyformex/
## Copyright 2004-2019 (C) Benedict Verhegghe (benedict.verhegghe@ugent.be)
## Distributed under the GNU General Public License version 3 or later.
##
## This program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program. If not, see http://www.gnu.org/licenses/.
##
"""Interface with tetgen
A collection of functions to read/write tetgen files and to run the
tetgen program
tetgen is a quality tetrahedral mesh generator and a 3D Delaunay triangulator.
See http://tetgen.org
"""
from __future__ import absolute_import, division, print_function
from pyformex import software
software.requireExternal('tetgen')
from pyformex import Path
from pyformex.coords import *
from pyformex.connectivity import Connectivity
from pyformex.mesh import Mesh
from pyformex.filewrite import *
from pyformex import utils
[docs]def readNodeFile(fn):
"""Read a tetgen .node file.
Returns a tuple as described in :func:`readNodesBlock`.
"""
with open(fn, 'r') as fil:
line = skipComments(fil)
npts, ndim, nattr, nbmark = getInts(line, 4)
return readNodesBlock(fil, npts, ndim, nattr, nbmark)
[docs]def readEleFile(fn):
"""Read a tetgen .ele file.
Returns a tuple as described in readElemsBlock.
"""
with open(fn, 'r') as fil:
line = skipComments(fil)
nelems, nplex, nattr = getInts(line, 3)
return readElemsBlock(fil, nelems, nplex, nattr)
[docs]def readFaceFile(fn):
"""Read a tetgen .face file.
Returns a tuple as described in readFacesBlock.
"""
with open(fn, 'r') as fil:
line = skipComments(fil)
nelems, nbmark = getInts(line, 2)
return readFacesBlock(fil, nelems, nbmark)
[docs]def readSmeshFile(fn):
"""Read a tetgen .smesh file.
Returns an array of triangle elements.
"""
fn = Path(fn)
with open(fn, 'r') as fil:
# node section.
line = skipComments(fil)
npts, ndim, nattr, nbmark = getInts(line, 4)
if npts > 0:
nodeInfo = readNodesBlock(fil, npts, ndim, nattr, nbmark)
else:
# corresponding .node file
nodeInfo = readNodeFile(fn.with_suffix('.node'))
# facet section
line = skipComments(fil)
nelems, nbmark = getInts(line, 2)
facetInfo = readSmeshFacetsBlock(fil, nelems, nbmark)
nodenrs = nodeInfo[1]
if nodenrs.min() == 1 and nodenrs.max()==nodenrs.size:
elems = facetInfo[0]
for e in elems:
elems[e] -= 1
# We currently do not read the holes and attributes
return nodeInfo[0], facetInfo[0]
[docs]def readPolyFile(fn):
"""Read a tetgen .poly file.
Returns an array of triangle elements.
"""
fn = Path(fn)
with open(fn, 'r') as fil:
# node section.
line = skipComments(fil)
npts, ndim, nattr, nbmark = getInts(line, 4)
if npts > 0:
nodeInfo = readNodesBlock(fil, npts, ndim, nattr, nbmark)
else:
# corresponding .node file
nodeInfo = readNodeFile(fn.with_suffix('.node'))
# facet section
line = skipComments(fil)
nelems, nbmark = getInts(line, 2)
facetInfo = readFacetsBlock(fil, nelems, nbmark)
#print("NEXT LINE:")
#print(line)
return nodeInfo[0], facetinfo[0]
## s = line.strip('\n').split()
## nelems = int(s[0])
## elems = fromfile(fil,sep=' ',dtype=int32, count=4*nelems)
## elems = elems.reshape((-1,4))
## return elems[:,1:]
[docs]def readSurface(fn):
"""Read a tetgen surface from a .node/.face file pair.
The given filename is either the .node or .face file.
Returns a tuple of (nodes,elems).
"""
fn = Path(fn)
nodeInfo = readNodeFile(fn.with_suffix('.node'))
nodes = nodeInfo[0]
print("Read %s nodes" % nodes.shape[0])
elemInfo = readFaceFile(fn.with_suffix('.face'))
elems = elemInfo[0]
print("Read %s elems" % elems.shape[0])
#if numbers[0] == 1:
# elems -= 1
return nodes, elems
######### Support functions ####################################
[docs]def stripLine(line):
"""Strip blanks, newline and comments from a line of text.
"""
nc = line.find('#')
if nc >= 0:
line = line[:nc] # strip comments
return line.strip() # strips blanks and end of line
[docs]def getInts(line, nint):
"""Read a number of ints from a line, adding zero for omitted values.
line is a string with b;anks separated integer values.
Returns a list of nint integers. The trailing ones are set to zero
if the strings contains less values.
"""
s = [int(i) for i in line.split()]
if len(s) < nint:
s.extend([0]*(nint-len(s)))
return s
[docs]def addElem(elems, nrs, e, n, nplex):
"""Add an element to a collection."""
if nplex not in elems:
elems[nplex] = []
nrs[nplex] = []
elems[nplex].append(e)
nrs[nplex].append(n)
[docs]def readNodesBlock(fil, npts, ndim, nattr, nbmark):
"""Read a tetgen nodes block.
Returns a tuple with:
- coords: Coords array with nodal coordinates
- nrs: node numbers
- attr: node attributes
- bmrk: node boundary marker
The last two may be None.
"""
ndata = 1 + ndim + nattr + nbmark
data = fromfile(fil, sep=' ', dtype=Float, count=npts*(ndata)).reshape(npts, ndata)
nrs = data[:, 0].astype(int32)
coords = Coords(data[:, 1:ndim+1])
if nattr > 0:
attr = data[:, 1+ndim:1+ndim+nattr].astype(int32)
else:
attr = None
if nbmark == 1:
bmark = data[:, -1].astype(int32)
else:
bmark = None
return coords, nrs, attr, bmark
[docs]def readElemsBlock(fil, nelems, nplex, nattr):
"""Read a tetgen elems block.
Returns a tuple with:
- elems: Connectivity of type 'tet4' or 'tet10'
- nrs: the element numbers
- attr: the element attributes
The last can be None.
"""
ndata = 1 + nplex + nattr
data = fromfile(fil, sep=' ', dtype=int32, count=ndata*nelems).reshape(nelems, ndata)
nrs = data[:, 0]
elems = data[:, 1:1+nplex]
if nattr > 0:
attr = data[:, 1+nplex:]
else:
attr = None
if nplex == 4:
eltype = 'tet4'
elif nplex == 10:
eltype= 'tet10'
else:
raise ValueError("Unknown tetgen .ele plexitude %s" % nplex)
elems = Connectivity(elems, eltype=eltype)
return elems, nrs, attr
[docs]def readFacesBlock(fil, nelems, nbmark):
"""Read a tetgen faces block.
Returns a a tuple with:
- elems: Connectivity of type 'tri3'
- nrs: face numbers
- bmrk: face boundary marker
The last can be None.
"""
ndata = 1 + 3 + nbmark
data = fromfile(fil, sep=' ', dtype=int32, count=ndata*nelems).reshape(nelems, ndata)
nrs = data[:, 0]
elems = data[:, 1:4]
if nbmark == 1:
bmark = data[:, -1]
else:
bmark = None
return Connectivity(elems, eltype='tri3'), nrs, bmark
[docs]def readSmeshFacetsBlock(fil, nfacets, nbmark):
"""Read a tetgen .smesh facets bock.
Returns a tuple of dictionaries with plexitudes as keys:
- elems: for each plexitude a Connectivity array
- nrs: for each plexitude a list of element numbers in corresponding elems
"""
elems = {}
nrs = {}
for i in range(nfacets):
line = fil.readline()
line = line.strip()
if len(line) > 0:
data = fromstring(line, sep=' ', dtype=int32)
nplex = data[0]
if nplex > 0:
e = data[1:1+nplex]
# bmark currently not read
addElem(elems, nrs, e, i, nplex)
else:
raise ValueError("Invalid data line:\n%s" % line)
for np in elems:
if np == 3:
eltype= 'tri3'
elif np == 4:
eltype = 'quad4'
else:
eltype = None
elems[np] = Connectivity(elems[np], eltype=eltype)
nrs[np] = array(nrs[np])
return elems, nrs
[docs]def readNeigh(fn):
"""Read a tetgen .neigh file.
Returns an array containing the tetrahedra neighbours:
"""
fil = open(fn, 'r')
line = fil.readline()
nelems, nneigh = [int(i) for i in line.strip('\n').split()]
elems = fromfile(fil, sep=' ', dtype=int32).reshape((nelems, nneigh+1))
return elems[:, 1:]
[docs]def writeNodes(fn, coords, offset=0):
"""Write a tetgen .node file"""
coords = asarray(coords).reshape((-1, 3))
with open(fn, 'w') as fil:
fil.write("%d %d 0 0\n" % coords.shape)
writeIData(coords, fil, "%f ", ind=offset)
[docs]def writeSmesh(fn, facets, coords=None, holes=None, regions=None):
"""Write a tetgen .smesh file.
Currently it only writes the facets of a triangular surface mesh.
Coords should be written independently to a .node file.
"""
with open(fn, 'w') as fil:
fil.write("# part 1: node list.\n")
if coords is None:
fil.write("0 3 0 0 # coords are found in %s.node.\n")
fil.write("# part 2: facet list.\n")
fil.write("%s 0\n" % facets.shape[0])
for i, n in enumerate(facets):
# adding comments breaks fast readback
# fil.write("3 %s %s %s # %s\n" % (n[0],n[1],n[2],i))
fil.write("3 %s %s %s\n" % (n[0], n[1], n[2]))
fil.write("# part 3: hole list.\n")
if holes is None:
fil.write("0\n")
fil.write("# part 4: region list.\n")
if regions is None:
fil.write("0\n")
fil.write("# Generated by pyFormex\n")
[docs]def writeTmesh(fn, elems, offset=0):
"""Write a tetgen .ele file.
Writes elements of a tet4 mesh.
"""
elems = asarray(elems).reshape((-1, 4))
with open(fn, 'w') as fil:
fil.write("%d %d 0\n" % elems.shape)
for i, e in enumerate(elems):
fil.write('%d %d %d %d %d\n'%(i, e[0], e[1], e[2], e[3]))
fil.write("# Generated by pyFormex\n")
[docs]def writeSurface(fn, coords, elems):
"""Write a tetgen surface model to .node and .smesh files.
Parameters
----------
fn: :term:`path_like`
Filename of the files to which the model sohould be exported.
The provided file name is either the .node or the .smesh filename,
or else it is the basename where .node and .smesh extensions will
be appended.
coords: Coords
The vertices in the surface model.
elems: array
The element definitions in function of the vertex numbers.
"""
fn = Path(fn)
writeNodes(fn.with_suffix('.node'), coords)
writeSmesh(fn.with_suffix('.smesh'), elems)
[docs]def writeTetMesh(fn, coords, elems):
"""Write a tetgen tetrahedral mesh model to .node and .ele files.
The provided file name is either the .node or the .smesh filename,
or else it is the basename where .node and .ele extensions will
be appended.
"""
fn = Path(fn)
writeNodes(fn.with_suffix('.node'), coords)
writeTmesh(fn.with_suffix('.ele'), elems)
[docs]def runTetgen(fn, options=''):
"""Run tetgen mesher on the specified file.
The input file is a closed triangulated surface.
tetgen will generate a volume tetraeder mesh inside the surface,
and create a new approximation of the surface as a by-product.
"""
if not utils.hasExternal('tetgen'):
pf.warning("""..
I could not find the 'tetgen' command.
tetgen is a quality tetrahedral mesh generator and a 3D Delaunay triangulator. See http://tetgen.org. It is available from the Debian non-free section.
""")
return
if Path(fn).exists():
P = utils.command('tetgen -z%s %s' % (options, fn))
return P.sta
[docs]def readTetgen(fn):
"""Read a tetgen model.
This reads a file created by the 'tetgen' tetrahedral mesher
and returns corresponding pyFormex objects.
Parameters
----------
fn: :term:`path_like`
Path to a tetgen file. This can be one of .node, .ele, .face,
.smesh or .poly files.
Returns
-------
dict
If the suffix of ``fn`` is one of .node, .ele or .face, the dict
contains one item with key 'tetgen.SUFFIX'. For suffix .node, the
value is a Coords read from the .node file, for suffix .ele or .face,
the value is a Mesh with elems read from the .ele or .face, and coords
read from the corresponding .node. If the suffix is .smesh or .poly,
the dict contains a number of Meshes, with keys 'Mesh-NPLEX' where
NPLEX is the plexitude of the corresponding Mesh.
"""
res = {}
fn = Path(fn)
ext = fn.suffix
if ext == '.node':
nodes = readNodeFile(fn)[0]
res['tetgen'+ext] = nodes
elif ext in ['.ele', '.face']:
nodes, nodenrs = readNodeFile(fn.with_suffix('.node'))[:2]
if ext == '.ele':
elems = readEleFile(fn)[0]
elif ext == '.face':
elems = readFaceFile(fn)[0]
if nodenrs.min() == 1 and nodenrs.max()==nodenrs.size:
elems = elems-1
M = Mesh(nodes, elems, eltype=elems.eltype)
res['tetgen'+ext] = M
elif ext == '.smesh':
nodes, elems = readSmeshFile(fn)
ML = [Mesh(nodes, elems[e]) for e in elems]
res = dict([('Mesh-%s'%M.nplex(), M) for M in ML])
elif ext == '.poly':
nodes, elems = readPolyFile(fn)
ML = [Mesh(nodes, elems[e]) for e in elems]
res = dict([('Mesh-%s'%M.nplex(), M) for M in ML])
return res
#
# TODO: This should just be merged with tetMesh
#
# This could be made an example:
#
# from pyformex.simple import regularGrid
# X = Coords(regularGrid([0., 0., 0.], [1., 1., 1.], [10, 10, 10]).reshape(-1, 3)).addNoise(rsize=0.05,asize=0.5)
# draw(X)
# from pyformex.plugins.tetgen import tetgenConvexHull
# tch, ch =tetgenConvexHull( X)
# draw(ch, color='red', marksize=10)
[docs]def tetgenConvexHull(pts):
"""Tetralize the convex hull of some points.
Parameters
----------
pts: Coords
A collection of points to find the convex hull of.
Returns
-------
convexhull: TriSurface
The smallest TriSurface enclosing all the points.
tetmesh: Mesh
A tetraeder Mesh filling the convex hull.
If all points are on the same plane there is no convex hull.
"""
with utils.TempDir() as tmpdir:
fn = tmpdir / 'convexhull.node'
writeNodes(fn, coords=pts, offset=0)
P = utils.command('tetgen %s' % fn)
if P.sta:
print(P.out)
raise RuntimeError("Error occurred in tetgen command")
tetmesh = readTetgen(fn.with_suffix('.1.ele'))['tetgen.ele']
convexhull = TriSurface(tetmesh.getBorderMesh())
return convexhull, tetmesh
#################################################################
## Extra TriSurface Methods ##
[docs]def checkSelfIntersectionsWithTetgen(self, verbose=False):
"""check self intersections using tetgen
Returns pairs of intersecting triangles
"""
with utils.TempDir() as tmpdir:
fn = tmpdir / 'surface'
writeSurface(fn, self.coords, self.elems)
options = '-V' if verbose else ''
cmd = "tetgen -d %s %s" % (options, fn)
P = utils.command(cmd)
print(P.out)
return asarray([int(l.split(' ')[0]) for l in P.out.split('acet #')[1:]]).reshape(-1, 2)-1
[docs]def tetMesh(surfacefile, quality=2.0, volume=None, outputdir=None):
"""Create a tetrahedral mesh inside a surface
This uses the external program 'tetgen' to create a tetrahedral mesh
inside a closed manifold surface.
Parameters
----------
surfacefile: :term:`path_like`
Path to a file holding a surface model. The file can be either a .off
or .stl.
quality: float
The quality of the output tetrahedral mesh. The value is a
constraint on the circumradius-to-shortest-edge ratio. The
default (2.0) already provides a high quality mesh. Providing
a larger value will reduce quality but increase speed. With
quality=None, no quality constraint will be imposed.
volume: float, optional
If provided, applies a maximum tetrahedron volume constraint.
outputdir: :term:`path_like`
Path to an existing directory where the results will be placed.
The default is to use the directory where the input file resides.
Returns
-------
Mesh
A tetrahedral Mesh (eltype='tet4') filling the input surface,
provided the tetgen program finished succesfully.
"""
options = ''
if quality is True:
options += 'q'
elif isinstance(quality, float):
options += 'q%f' % quality
if volume is not None:
options += 'a%f' % volume
surfacefile = Path(surfacefile)
if not surfacefile.exists() or \
surfacefile.suffix not in ['.off', '.stl']:
raise ValueError("Invalid surfacefile %s" % surfacefile)
if outputdir is None:
outputdir = surfacefile.parent
else:
outputdir = Path(outputdir)
surfacefile.symlink(outputdir)
surfacefile = outputdir / surfacefile.name
runTetgen(surfacefile, options)
tetfile = surfacefile.with_suffix('.1.ele')
res = readTetgen(tetfile)
return res
def install_more_trisurface_methods():
"""_
"""
from pyformex.trisurface import TriSurface
TriSurface.checkSelfIntersectionsWithTetgen = checkSelfIntersectionsWithTetgen
# End
