def __init__(self, name='mesh', filename=None, prefix_dir=None, **kwargs):
"""Create a Mesh.
Parameters
----------
name : str
Object name.
filename : str
Loads a mesh from the specified file, if not None.
prefix_dir : str
If not None, the filename is relative to that directory.
"""
Struct.__init__(self, name=name, **kwargs)
if filename is None:
self.io = None
self.setup_done = 0
else:
io = MeshIO.any_from_filename(filename, prefix_dir=prefix_dir)
output('reading mesh (%s)...' % (io.filename))
tt = time.clock()
io.read(self)
output('...done in %.2f s' % (time.clock() - tt))
self._set_shape_info()
def __init__(self, name='mesh', filename=None,
prefix_dir=None, **kwargs):
"""Create a Mesh.
Parameters
----------
name : str
Object name.
filename : str
Loads a mesh from the specified file, if not None.
prefix_dir : str
If not None, the filename is relative to that directory.
"""
Struct.__init__(self, name=name, **kwargs)
if filename is None:
self.io = None
self.setup_done = 0
else:
io = MeshIO.any_from_filename(filename, prefix_dir=prefix_dir)
output( 'reading mesh (%s)...' % (io.filename) )
tt = time.clock()
io.read(self)
output( '...done in %.2f s' % (time.clock() - tt) )
self._set_shape_info()
def skip_read_line( fd ):
while 1:
try:
line = fd.readline().strip()
except EOFError:
break
except:
output( "reading " + fd.name + " failed!" )
raise
if (len( line ) == 0) or (line[0] == '#'): continue
return line
def read_list(fd, n_item, dtype):
vals = []
ii = 0
while ii < n_item:
line = [dtype(ic) for ic in fd.readline().split()]
vals.append(line)
ii += len(line)
if ii > n_item:
output('corrupted row?', line, ii, n_item)
raise ValueError
return vals
def read_list(fd, n_item, dtype):
vals = []
ii = 0
while ii < n_item:
line = [dtype(ic) for ic in fd.readline().split()]
vals.append(line)
ii += len(line)
if ii > n_item:
output('corrupted row?', line, ii, n_item)
raise ValueError
return vals
def read_tuple( file, n_item, n_tuple ):
out = ();
for it in range( 0, n_tuple ):
token = ();
for ii in range( 0, n_item ):
token = token + (read_token( file ),);
# print token[ii];
if (len( token[ii] ) == 0):
output( "Corrupted file (token %d)!" % ii )
raise "ERR_CorruptedFile"
out = out + (token,);
return out;
def validate( self, required = None, other = None ):
required_left_over, required_missing \
= self._validate_helper( required, other )
other_left_over, other_missing \
= self._validate_helper( other, required )
assert_( required_left_over == other_left_over )
if other_left_over and self.verbose:
output( 'left over:', other_left_over )
if required_missing:
raise ValueError('required missing: %s' % required_missing)
return other_missing
def read_array( file, n_row, n_col, dtype ):
"""n_col is basically ignored, n_col == -1 -> intentionally ignored."""
val = []
for ir in range( 0, n_row ):
try:
while 1:
line = file.readline().split()
if (len( line ) == 0) or (line[0] == "#"):
continue
else:
break
except:
output( "Array (%d, %d) reading failed!" % (n_row, n_col) )
raise
row = [float( ii ) for ii in line]
val.append( row )
val = array( val, dtype );
return val
def validate( self, required = None, other = None ):
required_left_over, required_missing \
= self._validate_helper( required, other )
other_left_over, other_missing \
= self._validate_helper( other, required )
assert_( required_left_over == other_left_over )
err = False
if required_missing:
err = True
output( 'error: required missing:', required_missing )
if other_left_over:
output( 'left over:', other_left_over )
if err:
raise ValueError
return other_missing
def from_file(filename=None,
io='auto',
prefix_dir=None,
omit_facets=False):
"""
Read a mesh from a file.
Parameters
----------
filename : string or function or MeshIO instance or Mesh instance
The name of file to read the mesh from. For convenience, a
mesh creation function or a MeshIO instance or directly a Mesh
instance can be passed in place of the file name.
io : *MeshIO instance
Passing *MeshIO instance has precedence over filename.
prefix_dir : str
If not None, the filename is relative to that directory.
omit_facets : bool
If True, do not read cells of lower dimension than the space
dimension (faces and/or edges). Only some MeshIO subclasses
support this!
"""
if isinstance(filename, Mesh):
return filename
if io == 'auto':
if filename is None:
output('filename or io must be specified!')
raise ValueError
else:
io = MeshIO.any_from_filename(filename, prefix_dir=prefix_dir)
output('reading mesh (%s)...' % (io.filename))
tt = time.clock()
trunk = io.get_filename_trunk()
mesh = Mesh(trunk)
mesh = io.read(mesh, omit_facets=omit_facets)
output('...done in %.2f s' % (time.clock() - tt))
mesh._set_shape_info()
return mesh
def from_file(filename=None, io='auto', prefix_dir=None,
omit_facets=False):
"""
Read a mesh from a file.
Parameters
----------
filename : string or function or MeshIO instance or Mesh instance
The name of file to read the mesh from. For convenience, a
mesh creation function or a MeshIO instance or directly a Mesh
instance can be passed in place of the file name.
io : *MeshIO instance
Passing *MeshIO instance has precedence over filename.
prefix_dir : str
If not None, the filename is relative to that directory.
omit_facets : bool
If True, do not read cells of lower dimension than the space
dimension (faces and/or edges). Only some MeshIO subclasses
support this!
"""
if isinstance(filename, Mesh):
return filename
if io == 'auto':
if filename is None:
output( 'filename or io must be specified!' )
raise ValueError
else:
io = MeshIO.any_from_filename(filename, prefix_dir=prefix_dir)
output('reading mesh (%s)...' % (io.filename))
tt = time.clock()
trunk = io.get_filename_trunk()
mesh = Mesh(trunk)
mesh = io.read(mesh, omit_facets=omit_facets)
output('...done in %.2f s' % (time.clock() - tt))
mesh._set_shape_info()
return mesh
def fix_double_nodes(coor, ngroups, conns, eps):
"""
Detect and attempt fixing double nodes in a mesh.
The double nodes are nodes having the same coordinates
w.r.t. precision given by `eps`.
"""
n_nod, dim = coor.shape
cmap = find_map(coor, nm.zeros((0, dim)), eps=eps, allow_double=True)
if cmap.size:
output('double nodes in input mesh!')
output('trying to fix...')
while cmap.size:
print cmap.size
# Just like in Variable.equation_mapping()...
ii = nm.argsort(cmap[:, 1])
scmap = cmap[ii]
eq = nm.arange(n_nod)
eq[scmap[:, 1]] = -1
eqi = eq[eq >= 0]
eq[eqi] = nm.arange(eqi.shape[0])
remap = eq.copy()
remap[scmap[:, 1]] = eq[scmap[:, 0]]
print coor.shape
coor = coor[eqi]
ngroups = ngroups[eqi]
print coor.shape
ccs = []
for conn in conns:
ccs.append(remap[conn])
conns = ccs
cmap = find_map(coor,
nm.zeros((0, dim)),
eps=eps,
allow_double=True)
output('...done')
return coor, ngroups, conns
def fix_double_nodes(coor, ngroups, conns, eps):
"""
Detect and attempt fixing double nodes in a mesh.
The double nodes are nodes having the same coordinates
w.r.t. precision given by `eps`.
"""
n_nod, dim = coor.shape
cmap = find_map( coor, nm.zeros( (0,dim) ), eps = eps, allow_double = True )
if cmap.size:
output('double nodes in input mesh!')
output('trying to fix...')
while cmap.size:
print cmap.size
# Just like in Variable.equation_mapping()...
ii = nm.argsort( cmap[:,1] )
scmap = cmap[ii]
eq = nm.arange( n_nod )
eq[scmap[:,1]] = -1
eqi = eq[eq >= 0]
eq[eqi] = nm.arange( eqi.shape[0] )
remap = eq.copy()
remap[scmap[:,1]] = eq[scmap[:,0]]
print coor.shape
coor = coor[eqi]
ngroups = ngroups[eqi]
print coor.shape
ccs = []
for conn in conns:
ccs.append( remap[conn] )
conns = ccs
cmap = find_map( coor, nm.zeros( (0,dim) ), eps = eps,
allow_double = True )
output('...done')
return coor, ngroups, conns