def triangle2xml(ifilename, ofilename):
"""Convert between triangle format (http://www.cs.cmu.edu/~quake/triangle.html) and .xml. The
given ifilename should be the prefix for the corresponding .node, and .ele files.
"""
def get_next_line (fp):
"""Helper function for skipping comments and blank lines"""
line = fp.readline()
if line == '':
_error("Hit end of file prematurely.")
line = line.strip()
if not (line.startswith('#') or line == ''):
return line
return get_next_line(fp)
print "Converting from Triangle format {.node, .ele} to DOLFIN XML format"
# Open files
for suffix in [".node", ".ele"]:
if suffix in ifilename and ifilename[-len(suffix):] == suffix:
ifilename = ifilename.replace(suffix, "")
node_file = open(ifilename+".node", "r")
ele_file = open(ifilename+".ele", "r")
ofile = open(ofilename, "w")
# Read all the nodes
nodes = {}
num_nodes, dim, attr, bound = map(int, get_next_line(node_file).split())
while len(nodes) < num_nodes:
node, x, y = get_next_line(node_file).split()[:3]
nodes[int(node)] = (float(x), float(y))
# Read all the triangles
tris = {}
num_tris, n_per_tri, attrs = map(int, get_next_line(ele_file).split())
while len(tris) < num_tris:
tri, n1, n2, n3 = map(int, get_next_line(ele_file).split()[:4])
tris[tri] = (n1, n2, n3)
# Write everything out
xml_writer.write_header_mesh(ofile, "triangle", 2)
xml_writer.write_header_vertices(ofile, num_nodes)
node_off = 0 if nodes.has_key(0) else -1
for node, node_t in nodes.iteritems():
xml_writer.write_vertex(ofile, node+node_off, node_t[0], node_t[1], 0.0)
xml_writer.write_footer_vertices(ofile)
xml_writer.write_header_cells(ofile, num_tris)
tri_off = 0 if tris.has_key(0) else -1
for tri, tri_t in tris.iteritems():
write_cell_triangle(ofile, tri+tri_off, tri_t[0] + node_off,
tri_t[1] + node_off, tri_t[2] + node_off)
xml_writer.write_footer_cells(ofile)
xml_writer.write_footer_mesh(ofile)
# Close files
node_file.close()
ele_file.close()
ofile.close()
def diffpack2xml(ifilename, ofilename):
"Convert from Diffpack tetrahedral grid format to DOLFIN XML."
print diffpack2xml.__doc__
# Format strings for MeshFunction XML files
meshfunction_header = """\
<?xml version="1.0" encoding="UTF-8"?>\n
<dolfin xmlns:dolfin="http://www.fenics.org/dolfin/">
<mesh_function type="uint" dim="%d" size="%d">\n"""
meshfunction_entity = " <entity index=\"%d\" value=\"%d\"/>\n"
meshfunction_footer = " </mesh_function>\n</dolfin>"
# Open files
ifile = open(ifilename, "r")
ofile = open(ofilename, "w")
# Read and analyze header
while 1:
line = ifile.readline()
if not line:
_error("Empty file")
if line[0] == "#":
break
if re.search(r"Number of elements", line):
num_cells = int(re.match(r".*\s(\d+).*", line).group(1))
if re.search(r"Number of nodes", line):
num_vertices = int(re.match(r".*\s(\d+).*", line).group(1))
xml_writer.write_header_mesh(ofile, "tetrahedron", 3)
xml_writer.write_header_vertices(ofile, num_vertices)
# Read & write vertices and collect markers for vertices
vertex_markers = []
unique_vertex_markers = set()
for i in range(num_vertices):
line = ifile.readline()
m = re.match(r"^.*\(\s*(.*)\s*\).*\](.*)$", line)
x = map(float, re.split("[\s,]+", m.group(1)))
xml_writer.write_vertex(ofile, i, *x)
markers = map(int, m.group(2).split())
vertex_markers.append(markers)
unique_vertex_markers.update(markers)
xml_writer.write_footer_vertices(ofile)
xml_writer.write_header_cells(ofile, num_cells)
# Output unique vertex markers as individual VertexFunctions
unique_vertex_markers.difference_update([0])
for unique_marker in unique_vertex_markers:
ofile_marker = open(ofilename.replace(".xml", "") + \
"_marker_" + str(unique_marker)+".xml", "w")
xml_writer.write_header_meshfunction(ofile_marker, 0, num_vertices)
for ind, markers in enumerate(vertex_markers):
if unique_marker in markers:
xml_writer.write_entity_meshfunction(ofile_marker, ind, unique_marker)
else:
xml_writer.write_entity_meshfunction(ofile_marker, ind, 0)
xml_writer.write_footer_meshfunction(ofile_marker)
# Ignore comment lines
while 1:
line = ifile.readline()
if not line:
_error("Empty file")
if line[0] == "#":
break
# Read & write cells and collect cell and face markers
cell_markers = []
facet_markers = []
facet_to_vert = [[1,2,3], [0,2,3], [0,1,3], [0,1,2]]
vert_to_facet = facet_to_vert # The same!
cell_ind = 0
while cell_ind < num_cells:
line = ifile.readline()
v = line.split()
if not v:
continue
if v[1] != "ElmT4n3D":
_error("Only tetrahedral elements (ElmT4n3D) are implemented.")
# Store Cell markers
cell_markers.append(int(v[2]))
# Sort vertex indices
cell_indices = sorted(map(lambda x: int(x)-1, v[3:]))
xml_writer.write_cell_tetrahedron(ofile, cell_ind, *cell_indices)
# Check Facet info
process_facet = set(range(4))
for local_vert_ind, global_vert_ind in enumerate(cell_indices):
# If no marker is included for vertex skip corresponding facet
if not vertex_markers[global_vert_ind]:
process_facet.difference_update(facet_to_vert[local_vert_ind])
# Process facets
for local_facet in process_facet:
# Start with markers from first vertex
global_first_vertex = cell_indices[facet_to_vert[local_facet][0]]
marker_intersection = set(vertex_markers[global_first_vertex])
# Process the other vertices
for local_vert in facet_to_vert[local_facet][1:]:
marker_intersection.intersection_update(\
vertex_markers[cell_indices[local_vert]])
if not marker_intersection:
break
# If not break we have a marker on local_facet
else:
assert(len(marker_intersection)==1)
facet_markers.append((cell_ind, local_facet, \
marker_intersection.pop()))
# Bump cell_ind
cell_ind += 1
xml_writer.write_footer_cells(ofile)
xml_writer.write_header_domains(ofile)
# Write facet markers if any
if facet_markers:
xml_writer.write_header_meshvaluecollection(ofile, "m", 2, \
len(facet_markers), "uint")
for cell, local_facet, marker in facet_markers:
xml_writer.write_entity_meshvaluecollection(ofile, 2, cell, \
marker, local_facet)
xml_writer.write_footer_meshvaluecollection(ofile)
xml_writer.write_header_meshvaluecollection(ofile, "m", 3, \
len(cell_markers), "uint")
for cell, marker in enumerate(cell_markers):
xml_writer.write_entity_meshvaluecollection(ofile, 2, cell, \
marker)
xml_writer.write_footer_meshvaluecollection(ofile)
xml_writer.write_footer_domains(ofile)
xml_writer.write_footer_mesh(ofile)
# Close files
ifile.close()
ofile.close()
def mesh2xml(ifilename, ofilename):
"""Convert between .mesh and .xml, parser implemented as a
state machine:
0 = read 'Dimension'
1 = read dimension
2 = read 'Vertices'
3 = read number of vertices
4 = read next vertex
5 = read 'Triangles' or 'Tetrahedra'
6 = read number of cells
7 = read next cell
8 = done
"""
print "Converting from Medit format (.mesh) to DOLFIN XML format"
# Open files
ifile = open(ifilename, "r")
ofile = open(ofilename, "w")
# Scan file for cell type
cell_type = None
dim = 0
while 1:
# Read next line
line = ifile.readline()
if not line: break
# Remove newline
if line[-1] == "\n":
line = line[:-1]
# Read dimension
if line == "Dimension" or line == " Dimension":
line = ifile.readline()
num_dims = int(line)
if num_dims == 2:
cell_type = "triangle"
dim = 2
elif num_dims == 3:
cell_type = "tetrahedron"
dim = 3
break
# Check that we got the cell type
if cell_type == None:
_error("Unable to find cell type.")
# Step to beginning of file
ifile.seek(0)
# Write header
xml_writer.write_header_mesh(ofile, cell_type, dim)
# Current state
state = 0
# Write data
num_vertices_read = 0
num_cells_read = 0
while 1:
# Read next line
line = ifile.readline()
if not line: break
# Skip comments
if line[0] == '#':
continue
# Remove newline
if line[-1] == "\n":
line = line[:-1]
if state == 0:
if line == "Dimension" or line == " Dimension":
state += 1
elif state == 1:
num_dims = int(line)
state +=1
elif state == 2:
if line == "Vertices" or line == " Vertices":
state += 1
elif state == 3:
num_vertices = int(line)
xml_writer.write_header_vertices(ofile, num_vertices)
state +=1
elif state == 4:
if num_dims == 2:
(x, y, tmp) = line.split()
x = float(x)
y = float(y)
z = 0.0
elif num_dims == 3:
(x, y, z, tmp) = line.split()
x = float(x)
y = float(y)
z = float(z)
xml_writer.write_vertex(ofile, num_vertices_read, x, y, z)
num_vertices_read +=1
if num_vertices == num_vertices_read:
xml_writer.write_footer_vertices(ofile)
state += 1
elif state == 5:
if (line == "Triangles" or line == " Triangles") and num_dims == 2:
state += 1
if line == "Tetrahedra" and num_dims == 3:
state += 1
elif state == 6:
num_cells = int(line)
xml_writer.write_header_cells(ofile, num_cells)
state +=1
elif state == 7:
if num_dims == 2:
(n0, n1, n2, tmp) = line.split()
n0 = int(n0) - 1
n1 = int(n1) - 1
n2 = int(n2) - 1
xml_writer.write_cell_triangle(ofile, num_cells_read, n0, n1, n2)
elif num_dims == 3:
(n0, n1, n2, n3, tmp) = line.split()
n0 = int(n0) - 1
n1 = int(n1) - 1
n2 = int(n2) - 1
n3 = int(n3) - 1
xml_writer.write_cell_tetrahedron(ofile, num_cells_read, n0, n1, n2, n3)
num_cells_read +=1
if num_cells == num_cells_read:
xml_writer.write_footer_cells(ofile)
state += 1
elif state == 8:
break
# Check that we got all data
if state == 8:
print "Conversion done"
else:
_error("Missing data, unable to convert")
# Write footer
xml_writer.write_footer_mesh(ofile)
# Close files
ifile.close()
ofile.close()
def triangle2xml(ifilename, ofilename):
"""Convert between triangle format
(http://www.cs.cmu.edu/~quake/triangle.html) and .xml. The
given ifilename should be the prefix for the corresponding
.node, and .ele files.
"""
def get_next_line (fp):
"""Helper function for skipping comments and blank lines"""
line = fp.readline()
if line == '':
_error("Hit end of file prematurely.")
line = line.strip()
if not (line.startswith('#') or line == ''):
return line
return get_next_line(fp)
print "Converting from Triangle format {.node, .ele} to DOLFIN XML format"
# Open files
for suffix in [".node", ".ele"]:
if suffix in ifilename and ifilename[-len(suffix):] == suffix:
ifilename = ifilename.replace(suffix, "")
node_file = open(ifilename+".node", "r")
ele_file = open(ifilename+".ele", "r")
ofile = open(ofilename, "w")
try:
edge_file = open(ifilename+".edge", "r")
print "Found .edge file"
except IOError:
edge_file = None
# Read all the nodes
nodes = {}
num_nodes, dim, attr, bound = map(int, get_next_line(node_file).split())
while len(nodes) < num_nodes:
node, x, y = get_next_line(node_file).split()[:3]
nodes[int(node)] = (float(x), float(y))
# Read all the triangles
tris = {}
tri_attrs = {}
num_tris, n_per_tri, attrs = map(int, get_next_line(ele_file).split())
while len(tris) < num_tris:
line = get_next_line(ele_file).split()
tri, n1, n2, n3 = map(int, line[:4])
# vertices are ordered according to current UFC ordering scheme -
# - may change in future!
tris[tri] = tuple(sorted((n1, n2, n3)))
tri_attrs[tri] = tuple(map(float, line[4:4+attrs]))
# Read all the boundary markers from edges
edge_markers_global = {}
edge_markers_local = []
got_negative_edge_markers = False
if edge_file is not None:
num_edges, num_edge_markers = map(int, get_next_line(edge_file).split())
if num_edge_markers == 1:
while len(edge_markers_global) < num_edges:
edge, v1, v2, marker = map(int, get_next_line(edge_file).split())
if marker < 0: got_negative_edge_markers = True
edge_markers_global[tuple(sorted((v1, v2)))] = marker
if got_negative_edge_markers:
print "Some edge markers are negative! dolfin will increase "\
"them by probably 2**32 when loading xml. "\
"Consider using non-negative edge markers only."
for tri, vertices in tris.iteritems():
v0, v1, v2 = sorted((vertices[0:3]))
try:
edge_markers_local.append((tri, 0, \
edge_markers_global[(v1, v2)]))
edge_markers_local.append((tri, 1, \
edge_markers_global[(v0, v2)]))
edge_markers_local.append((tri, 2, \
edge_markers_global[(v0, v1)]))
except IndexError:
raise Exception("meshconvert.py: The facet was not found.")
elif num_edge_markers == 0:
print "...but no markers in it. Ignoring it"
else:
print "...but %d markers specified in it. It won't be processed."\
%num_edge_markers
# Write everything out
xml_writer.write_header_mesh(ofile, "triangle", 2)
xml_writer.write_header_vertices(ofile, num_nodes)
node_off = 0 if nodes.has_key(0) else -1
for node, node_t in nodes.iteritems():
xml_writer.write_vertex(ofile, node+node_off, node_t[0], node_t[1], 0.0)
xml_writer.write_footer_vertices(ofile)
xml_writer.write_header_cells(ofile, num_tris)
tri_off = 0 if tris.has_key(0) else -1
for tri, tri_t in tris.iteritems():
xml_writer.write_cell_triangle(ofile, tri+tri_off, tri_t[0] + node_off,
tri_t[1] + node_off, tri_t[2] + node_off)
xml_writer.write_footer_cells(ofile)
if len(edge_markers_local) > 0:
xml_writer.write_header_domains(ofile)
xml_writer.write_header_meshvaluecollection(ofile, \
"edge markers", 1, len(edge_markers_local), "uint")
for tri, local_edge, marker in edge_markers_local:
xml_writer.write_entity_meshvaluecollection(ofile, \
1, tri+tri_off, marker, local_edge)
xml_writer.write_footer_meshvaluecollection(ofile)
xml_writer.write_footer_domains(ofile)
xml_writer.write_footer_mesh(ofile)
for i in range(attrs):
afilename = ofilename.replace(".xml", ".attr"+str(i)+".xml")
afile = open(afilename, "w")
xml_writer.write_header_meshfunction2(afile)
xml_writer.write_header_meshvaluecollection(afile, \
"triangle attribs "+str(i), 2, num_tris, "double")
for tri, tri_a in tri_attrs.iteritems():
xml_writer.write_entity_meshvaluecollection(afile, \
2, tri+tri_off, tri_a[i], 0)
xml_writer.write_footer_meshvaluecollection(afile)
xml_writer.write_footer_meshfunction(afile)
print "triangle attributes from .ele file written to "+afilename
afile.close()
# Close files
node_file.close()
ele_file.close()
if edge_file is not None:
edge_file.close()
ofile.close()
def starcd2xml(ifilename, ofilename):
"Convert from Star-CD tetrahedral grid format to DOLFIN XML."
print starcd2xml.__doc__
if not os.path.isfile(ifilename[:-3] + "vrt") or not os.path.isfile(ifilename[:-3] + "cel"):
print "StarCD format requires one .vrt file and one .cel file"
sys.exit(2)
# open output file
ofile = open(ofilename, "w")
# Open file, the vertices are in a .vrt file
ifile = open(ifilename[:-3] + "vrt", "r")
write_header_mesh(ofile, "tetrahedron", 3)
# Read & write vertices
# first, read all lines (need to sweep to times through the file)
lines = ifile.readlines()
# second, find the number of vertices
num_vertices = -1
counter = 0
# nodenr_map is needed because starcd support node numbering like 1,2,4 (ie 3 is missing)
nodenr_map = {}
for line in lines:
nodenr = int(line[0:15])
nodenr_map[nodenr] = counter
counter += 1
num_vertices = counter
# third, run over all vertices
xml_writer.write_header_vertices(ofile, num_vertices)
for line in lines:
nodenr = int(line[0:15])
vertex0 = float(line[15:31])
vertex1 = float(line[31:47])
vertex2 = float(line[47:63])
xml_writer.write_vertex(ofile, nodenr_map[nodenr], float(vertex0), float(vertex1), float(vertex2))
xml_writer.write_footer_vertices(ofile)
# Open file, the cells are in a .cel file
ifile = open(ifilename[:-3] + "cel", "r")
# Read & write cells
# first, read all lines (need to sweep to times through the file)
lines = ifile.readlines()
# second, find the number of cells
num_cells = -1
counter = 0
for line in lines:
l = [int(a) for a in line.split()]
cellnr, node0, node1, node2, node3, node4, node5, node6, node7, tmp1, tmp2 = l
if node4 > 0:
if node2 == node3 and node4 == node5 and node5 == node6 and node6 == node7: # these nodes should be equal
counter += 1
else:
print "The file does contain cells that are not tetraheders. The cell number is ", cellnr, " the line read was ", line
else:
# triangles on the surface
# print "The file does contain cells that are not tetraheders node4==0. The cell number is ", cellnr, " the line read was ", line
#sys.exit(2)
pass
num_cells = counter
# third, run over all cells
xml_writer.write_header_cells(ofile, num_cells)
counter = 0
for line in lines:
l = [int(a) for a in line.split()]
cellnr, node0, node1, node2, node3, node4, node5, node6, node7, tmp1, tmp2 = l
if (node4 > 0):
if node2 == node3 and node4 == node5 and node5 == node6 and node6 == node7: # these nodes should be equal
xml_writer.write_cell_tetrahedron(ofile, counter, nodenr_map[node0], nodenr_map[node1], nodenr_map[node2], nodenr_map[node4])
counter += 1
xml_writer.write_footer_cells(ofile)
xml_writer.write_footer_mesh(ofile)
# Close files
ifile.close()
ofile.close()
def netcdf2xml(ifilename,ofilename):
"Convert from NetCDF format to DOLFIN XML."
print "Converting from NetCDF format (.ncdf) to DOLFIN XML format"
# Open files
ifile = open(ifilename, "r")
ofile = open(ofilename, "w")
cell_type = None
dim = 0
# Scan file for dimension, number of nodes, number of elements
while 1:
line = ifile.readline()
if not line:
_error("Empty file")
if re.search(r"num_dim.*=", line):
dim = int(re.match(".*\s=\s(\d+)\s;",line).group(1))
if re.search(r"num_nodes.*=", line):
num_vertices = int(re.match(".*\s=\s(\d+)\s;",line).group(1))
if re.search(r"num_elem.*=", line):
num_cells = int(re.match(".*\s=\s(\d+)\s;",line).group(1))
if re.search(r"connect1 =",line):
break
num_dims=dim
# Set cell type
if dim == 2:
cell_type ="triangle"
if dim == 3:
cell_type ="tetrahedron"
# Check that we got the cell type
if cell_type == None:
_error("Unable to find cell type.")
# Write header
xml_writer.write_header_mesh(ofile, cell_type, dim)
xml_writer.write_header_cells(ofile, num_cells)
num_cells_read = 0
# Read and write cells
while 1:
# Read next line
line = ifile.readline()
if not line:
break
connect=re.split("[,;]",line)
if num_dims == 2:
n0 = int(connect[0])-1
n1 = int(connect[1])-1
n2 = int(connect[2])-1
xml_writer.write_cell_triangle(ofile, num_cells_read, n0, n1, n2)
elif num_dims == 3:
n0 = int(connect[0])-1
n1 = int(connect[1])-1
n2 = int(connect[2])-1
n3 = int(connect[3])-1
xml_writer.write_cell_tetrahedron(ofile, num_cells_read, n0, n1, n2, n3)
num_cells_read +=1
if num_cells == num_cells_read:
xml_writer.write_footer_cells(ofile)
xml_writer.write_header_vertices(ofile, num_vertices)
break
num_vertices_read = 0
coords = [[],[],[]]
coord = -1
while 1:
line = ifile.readline()
if not line:
_error("Missing data")
if re.search(r"coord =",line):
break
# Read vertices
while 1:
line = ifile.readline()
if not line:
break
if re.search(r"\A\s\s\S+,",line):
coord+=1
print "Found x_"+str(coord)+" coordinates"
coords[coord] += line.split()
if re.search(r";",line):
break
# Write vertices
for i in range(num_vertices):
if num_dims == 2:
x = float(re.split(",",coords[0].pop(0))[0])
y = float(re.split(",",coords[1].pop(0))[0])
z = 0
if num_dims == 3:
x = float(re.split(",",coords[0].pop(0))[0])
y = float(re.split(",",coords[1].pop(0))[0])
z = float(re.split(",",coords[2].pop(0))[0])
xml_writer.write_vertex(ofile, i, x, y, z)
# Write footer
xml_writer.write_footer_vertices(ofile)
xml_writer.write_footer_mesh(ofile)
# Close files
ifile.close()
ofile.close()
def end_cells(self):
DataHandler.end_cells(self)
xml_writer.write_footer_cells(self.__ofile)
def diffpack2xml(ifilename, ofilename):
"Convert from Diffpack tetrahedral grid format to DOLFIN XML."
print diffpack2xml.__doc__
# Format strings for MeshFunction XML files
meshfunction_header = """\
<?xml version="1.0" encoding="UTF-8"?>\n
<dolfin xmlns:dolfin="http://www.fenics.org/dolfin/">
<mesh_function type="uint" dim="%d" size="%d">\n"""
meshfunction_entity = " <entity index=\"%d\" value=\"%d\"/>\n"
meshfunction_footer = " </mesh_function>\n</dolfin>"
# Open files
ifile = open(ifilename, "r")
ofile = open(ofilename, "w")
ofile_mat = open(ofilename.split(".")[0]+"_mat.xml", "w")
ofile_bi = open(ofilename.split(".")[0]+"_bi.xml", "w")
# Read and analyze header
while 1:
line = ifile.readline()
if not line:
_error("Empty file")
if line[0] == "#":
break
if re.search(r"Number of elements", line):
num_cells = int(re.match(r".*\s(\d+).*", line).group(1))
if re.search(r"Number of nodes", line):
num_vertices = int(re.match(r".*\s(\d+).*", line).group(1))
xml_writer.write_header_mesh(ofile, "tetrahedron", 3)
xml_writer.write_header_vertices(ofile, num_vertices)
ofile_bi.write(meshfunction_header % (0, num_vertices))
ofile_mat.write(meshfunction_header % (3, num_cells))
# Read & write vertices
# Note that only first boundary indicator is rewriten into XML
for i in range(num_vertices):
line = ifile.readline()
m = re.match(r"^.*\(\s*(.*)\s*\).*\](.*)$", line)
x = re.split("[\s,]+", m.group(1))
xml_writer.write_vertex(ofile, i, x[0], x[1], x[2])
tmp = m.group(2).split()
if len(tmp) > 0:
bi = int(tmp[0])
else:
bi = 0
ofile_bi.write(meshfunction_entity % (i, bi))
xml_writer.write_footer_vertices(ofile)
xml_writer.write_header_cells(ofile, num_cells)
# Ignore comment lines
while 1:
line = ifile.readline()
if not line:
_error("Empty file")
if line[0] == "#":
break
# Read & write cells
for i in range(int(num_cells)):
line = ifile.readline()
v = line.split();
if v[1] != "ElmT4n3D":
_error("Only tetrahedral elements (ElmT4n3D) are implemented.")
xml_writer.write_cell_tetrahedron(ofile, i, int(v[3])-1, int(v[4])-1, int(v[5])-1, int(v[6])-1)
ofile_mat.write(meshfunction_entity % (i, int(v[2])))
xml_writer.write_footer_cells(ofile)
xml_writer.write_footer_mesh(ofile)
ofile_bi.write(meshfunction_footer)
ofile_mat.write(meshfunction_footer)
# Close files
ifile.close()
ofile.close()
ofile_mat.close()
ofile_bi.close()
def diffpack2xml(ifilename, ofilename):
"Convert from Diffpack tetrahedral/triangle grid format to DOLFIN XML."
print diffpack2xml.__doc__
# Format strings for MeshFunction XML files
meshfunction_header = """\
<?xml version="1.0" encoding="UTF-8"?>\n
<dolfin xmlns:dolfin="http://www.fenics.org/dolfin/">
<mesh_function type="uint" dim="%d" size="%d">\n"""
meshfunction_entity = " <entity index=\"%d\" value=\"%d\"/>\n"
meshfunction_footer = " </mesh_function>\n</dolfin>"
# Open files
ifile = open(ifilename, "r")
ofile = open(ofilename, "w")
# Read and analyze header
while 1:
line = ifile.readline()
if not line:
_error("Empty file")
if line[0] == "#":
break
if re.search(r"Number of elements", line):
num_cells = int(re.match(r".*\s(\d+).*", line).group(1))
if re.search(r"Number of nodes", line):
num_vertices = int(re.match(r".*\s(\d+).*", line).group(1))
if re.search(r"Number of space dim.", line):
num_dims = int(re.match(r".*\s(\d+).*", line).group(1))
if num_dims == 3:
xml_writer.write_header_mesh(ofile, "tetrahedron", 3)
elem_type = "ElmT4n3D"
write_cell_func = xml_writer.write_cell_tetrahedron
else:
xml_writer.write_header_mesh(ofile, "triangle", 2)
elem_type = "ElmT3n2D"
write_cell_func = xml_writer.write_cell_triangle
xml_writer.write_header_vertices(ofile, num_vertices)
# Read & write vertices and collect markers for vertices
vertex_markers = []
unique_vertex_markers = set()
for i in range(num_vertices):
line = ifile.readline()
m = re.match(r"^.*\(\s*(.*)\s*\).*\](.*)$", line)
x = map(float, re.split("[\s,]+", m.group(1)))
xml_writer.write_vertex(ofile, i, *x)
markers = map(int, m.group(2).split())
vertex_markers.append(markers)
unique_vertex_markers.update(markers)
xml_writer.write_footer_vertices(ofile)
xml_writer.write_header_cells(ofile, num_cells)
# Output unique vertex markers as individual VertexFunctions
unique_vertex_markers.difference_update([0])
for unique_marker in unique_vertex_markers:
ofile_marker = open(ofilename.replace(".xml", "") + \
"_marker_" + str(unique_marker)+".xml", "w")
xml_writer.write_header_meshfunction(ofile_marker, 0, num_vertices)
for ind, markers in enumerate(vertex_markers):
if unique_marker in markers:
xml_writer.write_entity_meshfunction(ofile_marker, ind, unique_marker)
else:
xml_writer.write_entity_meshfunction(ofile_marker, ind, 0)
xml_writer.write_footer_meshfunction(ofile_marker)
# Ignore comment lines
while 1:
line = ifile.readline()
if not line:
_error("Empty file")
if line[0] == "#":
break
# Read & write cells and collect cell and face markers
cell_markers = []
facet_markers = []
facet_to_vert = [[1,2,3], [0,2,3], [0,1,3], [0,1,2]]
vert_to_facet = facet_to_vert # The same!
cell_ind = 0
while cell_ind < num_cells:
line = ifile.readline()
v = line.split()
if not v:
continue
if v[1] != elem_type:
_error("Only tetrahedral (ElmT4n3D) and triangular (ElmT3n2D) elements are implemented.")
# Store Cell markers
cell_markers.append(int(v[2]))
# Sort vertex indices
cell_indices = sorted(map(lambda x: int(x)-1, v[3:]))
write_cell_func(ofile, cell_ind, *cell_indices)
if num_dims == 2:
cell_ind += 1
continue
# Check Facet info
process_facet = set(range(4))
for local_vert_ind, global_vert_ind in enumerate(cell_indices):
# If no marker is included for vertex skip corresponding facet
if not vertex_markers[global_vert_ind]:
process_facet.difference_update(facet_to_vert[local_vert_ind])
# Process facets
for local_facet in process_facet:
# Start with markers from first vertex
global_first_vertex = cell_indices[facet_to_vert[local_facet][0]]
marker_intersection = set(vertex_markers[global_first_vertex])
# Process the other vertices
for local_vert in facet_to_vert[local_facet][1:]:
marker_intersection.intersection_update(\
vertex_markers[cell_indices[local_vert]])
if not marker_intersection:
break
# If not break we have a marker on local_facet
else:
assert(len(marker_intersection)==1)
facet_markers.append((cell_ind, local_facet, \
marker_intersection.pop()))
# Bump cell_ind
cell_ind += 1
xml_writer.write_footer_cells(ofile)
xml_writer.write_header_domains(ofile)
# Write facet markers if any
if facet_markers:
xml_writer.write_header_meshvaluecollection(ofile, "m", 2, \
len(facet_markers), "uint")
for cell, local_facet, marker in facet_markers:
xml_writer.write_entity_meshvaluecollection(ofile, 2, cell, \
marker, local_facet)
xml_writer.write_footer_meshvaluecollection(ofile)
xml_writer.write_header_meshvaluecollection(ofile, "m", num_dims, \
len(cell_markers), "uint")
for cell, marker in enumerate(cell_markers):
xml_writer.write_entity_meshvaluecollection(ofile, num_dims, cell, \
marker)
xml_writer.write_footer_meshvaluecollection(ofile)
xml_writer.write_footer_domains(ofile)
xml_writer.write_footer_mesh(ofile)
# Close files
ifile.close()
ofile.close()
def mesh2xml(ifilename, ofilename):
"""Convert between .mesh and .xml, parser implemented as a
state machine:
0 = read 'Dimension'
1 = read dimension
2 = read 'Vertices'
3 = read number of vertices
4 = read next vertex
5 = read 'Triangles' or 'Tetrahedra'
6 = read number of cells
7 = read next cell
8 = done
"""
print "Converting from Medit format (.mesh) to DOLFIN XML format"
# Open files
ifile = open(ifilename, "r")
ofile = open(ofilename, "w")
# Scan file for cell type
cell_type = None
dim = 0
while 1:
# Read next line
line = ifile.readline()
if not line: break
# Remove newline
if line[-1] == "\n":
line = line[:-1]
# Read dimension
if line == "Dimension" or line == " Dimension":
line = ifile.readline()
num_dims = int(line)
if num_dims == 2:
cell_type = "triangle"
dim = 2
elif num_dims == 3:
cell_type = "tetrahedron"
dim = 3
break
# Check that we got the cell type
if cell_type == None:
_error("Unable to find cell type.")
# Step to beginning of file
ifile.seek(0)
# Write header
xml_writer.write_header_mesh(ofile, cell_type, dim)
# Current state
state = 0
# Write data
num_vertices_read = 0
num_cells_read = 0
while 1:
# Read next line
line = ifile.readline()
if not line: break
# Skip comments
if line[0] == '#':
continue
# Remove newline
if line[-1] == "\n":
line = line[:-1]
if state == 0:
if line == "Dimension" or line == " Dimension":
state += 1
elif state == 1:
num_dims = int(line)
state +=1
elif state == 2:
if line == "Vertices" or line == " Vertices":
state += 1
elif state == 3:
num_vertices = int(line)
xml_writer.write_header_vertices(ofile, num_vertices)
state +=1
elif state == 4:
if num_dims == 2:
(x, y, tmp) = line.split()
x = float(x)
y = float(y)
z = 0.0
elif num_dims == 3:
(x, y, z, tmp) = line.split()
x = float(x)
y = float(y)
z = float(z)
xml_writer.write_vertex(ofile, num_vertices_read, x, y, z)
num_vertices_read +=1
if num_vertices == num_vertices_read:
xml_writer.write_footer_vertices(ofile)
state += 1
elif state == 5:
if (line == "Triangles" or line == " Triangles") and num_dims == 2:
state += 1
if line == "Tetrahedra" and num_dims == 3:
state += 1
elif state == 6:
num_cells = int(line)
xml_writer.write_header_cells(ofile, num_cells)
state +=1
elif state == 7:
if num_dims == 2:
(n0, n1, n2, tmp) = line.split()
n0 = int(n0) - 1
n1 = int(n1) - 1
n2 = int(n2) - 1
xml_writer.write_cell_triangle(ofile, num_cells_read, n0, n1, n2)
elif num_dims == 3:
(n0, n1, n2, n3, tmp) = line.split()
n0 = int(n0) - 1
n1 = int(n1) - 1
n2 = int(n2) - 1
n3 = int(n3) - 1
xml_writer.write_cell_tetrahedron(ofile, num_cells_read, n0, n1, n2, n3)
num_cells_read +=1
if num_cells == num_cells_read:
xml_writer.write_footer_cells(ofile)
state += 1
elif state == 8:
break
# Check that we got all data
if state == 8:
print "Conversion done"
else:
_error("Missing data, unable to convert")
# Write footer
xml_writer.write_footer_mesh(ofile)
# Close files
ifile.close()
ofile.close()
def triangle2xml(ifilename, ofilename):
"""Convert between triangle format
(http://www.cs.cmu.edu/~quake/triangle.html) and .xml. The
given ifilename should be the prefix for the corresponding
.node, and .ele files.
"""
def get_next_line (fp):
"""Helper function for skipping comments and blank lines"""
line = fp.readline()
if line == '':
_error("Hit end of file prematurely.")
line = line.strip()
if not (line.startswith('#') or line == ''):
return line
return get_next_line(fp)
print "Converting from Triangle format {.node, .ele} to DOLFIN XML format"
# Open files
for suffix in [".node", ".ele"]:
if suffix in ifilename and ifilename[-len(suffix):] == suffix:
ifilename = ifilename.replace(suffix, "")
node_file = open(ifilename+".node", "r")
ele_file = open(ifilename+".ele", "r")
ofile = open(ofilename, "w")
try:
edge_file = open(ifilename+".edge", "r")
print "Found .edge file"
except IOError:
edge_file = None
# Read all the nodes
nodes = {}
num_nodes, dim, attr, bound = map(int, get_next_line(node_file).split())
while len(nodes) < num_nodes:
node, x, y = get_next_line(node_file).split()[:3]
nodes[int(node)] = (float(x), float(y))
# Read all the triangles
tris = {}
tri_attrs = {}
num_tris, n_per_tri, attrs = map(int, get_next_line(ele_file).split())
while len(tris) < num_tris:
line = get_next_line(ele_file).split()
tri, n1, n2, n3 = map(int, line[:4])
# vertices are ordered according to current UFC ordering scheme -
# - may change in future!
tris[tri] = tuple(sorted((n1, n2, n3)))
tri_attrs[tri] = tuple(map(float, line[4:4+attrs]))
# Read all the boundary markers from edges
edge_markers_global = {}
edge_markers_local = []
got_negative_edge_markers = False
if edge_file is not None:
num_edges, num_edge_markers = map(int, get_next_line(edge_file).split())
if num_edge_markers == 1:
while len(edge_markers_global) < num_edges:
edge, v1, v2, marker = map(int, get_next_line(edge_file).split())
if marker < 0: got_negative_edge_markers = True
edge_markers_global[tuple(sorted((v1, v2)))] = marker
if got_negative_edge_markers:
print "Some edge markers are negative! dolfin will increase "\
"them by probably 2**32 when loading xml. "\
"Consider using non-negative edge markers only."
for tri, vertices in tris.iteritems():
v0, v1, v2 = sorted((vertices[0:3]))
try:
edge_markers_local.append((tri, 0, \
edge_markers_global[(v1, v2)]))
edge_markers_local.append((tri, 1, \
edge_markers_global[(v0, v2)]))
edge_markers_local.append((tri, 2, \
edge_markers_global[(v0, v1)]))
except IndexError:
raise Exception("meshconvert.py: The facet was not found.")
elif num_edge_markers == 0:
print "...but no markers in it. Ignoring it"
else:
print "...but %d markers specified in it. It won't be processed."\
%num_edge_markers
# Write everything out
xml_writer.write_header_mesh(ofile, "triangle", 2)
xml_writer.write_header_vertices(ofile, num_nodes)
node_off = 0 if nodes.has_key(0) else -1
for node, node_t in nodes.iteritems():
xml_writer.write_vertex(ofile, node+node_off, node_t[0], node_t[1], 0.0)
xml_writer.write_footer_vertices(ofile)
xml_writer.write_header_cells(ofile, num_tris)
tri_off = 0 if tris.has_key(0) else -1
for tri, tri_t in tris.iteritems():
xml_writer.write_cell_triangle(ofile, tri+tri_off, tri_t[0] + node_off,
tri_t[1] + node_off, tri_t[2] + node_off)
xml_writer.write_footer_cells(ofile)
if len(edge_markers_local) > 0:
xml_writer.write_header_domains(ofile)
xml_writer.write_header_meshvaluecollection(ofile, \
"edge markers", 1, len(edge_markers_local), "uint")
for tri, local_edge, marker in edge_markers_local:
xml_writer.write_entity_meshvaluecollection(ofile, \
1, tri+tri_off, marker, local_edge)
xml_writer.write_footer_meshvaluecollection(ofile)
xml_writer.write_footer_domains(ofile)
xml_writer.write_footer_mesh(ofile)
for i in range(attrs):
afilename = ofilename.replace(".xml", ".attr"+str(i)+".xml")
afile = open(afilename, "w")
xml_writer.write_header_meshfunction2(afile)
xml_writer.write_header_meshvaluecollection(afile, \
"triangle attribs "+str(i), 2, num_tris, "double")
for tri, tri_a in tri_attrs.iteritems():
xml_writer.write_entity_meshvaluecollection(afile, \
2, tri+tri_off, tri_a[i], 0)
xml_writer.write_footer_meshvaluecollection(afile)
xml_writer.write_footer_meshfunction(afile)
print "triangle attributes from .ele file written to "+afilename
afile.close()
# Close files
node_file.close()
ele_file.close()
if edge_file is not None:
edge_file.close()
ofile.close()
def starcd2xml(ifilename, ofilename):
"Convert from Star-CD tetrahedral grid format to DOLFIN XML."
print starcd2xml.__doc__
if not os.path.isfile(ifilename[:-3] + "vrt") or not os.path.isfile(ifilename[:-3] + "cel"):
print "StarCD format requires one .vrt file and one .cel file"
sys.exit(2)
# open output file
ofile = open(ofilename, "w")
# Open file, the vertices are in a .vrt file
ifile = open(ifilename[:-3] + "vrt", "r")
write_header_mesh(ofile, "tetrahedron", 3)
# Read & write vertices
# first, read all lines (need to sweep to times through the file)
lines = ifile.readlines()
# second, find the number of vertices
num_vertices = -1
counter = 0
# nodenr_map is needed because starcd support node numbering like 1,2,4 (ie 3 is missing)
nodenr_map = {}
for line in lines:
nodenr = int(line[0:15])
nodenr_map[nodenr] = counter
counter += 1
num_vertices = counter
# third, run over all vertices
xml_writer.write_header_vertices(ofile, num_vertices)
for line in lines:
nodenr = int(line[0:15])
vertex0 = float(line[15:31])
vertex1 = float(line[31:47])
vertex2 = float(line[47:63])
xml_writer.write_vertex(ofile, nodenr_map[nodenr], float(vertex0), float(vertex1), float(vertex2))
xml_writer.write_footer_vertices(ofile)
# Open file, the cells are in a .cel file
ifile = open(ifilename[:-3] + "cel", "r")
# Read & write cells
# first, read all lines (need to sweep to times through the file)
lines = ifile.readlines()
# second, find the number of cells
num_cells = -1
counter = 0
for line in lines:
l = [int(a) for a in line.split()]
cellnr, node0, node1, node2, node3, node4, node5, node6, node7, tmp1, tmp2 = l
if node4 > 0:
if node2 == node3 and node4 == node5 and node5 == node6 and node6 == node7: # these nodes should be equal
counter += 1
else:
print "The file does contain cells that are not tetraheders. The cell number is ", cellnr, " the line read was ", line
else:
# triangles on the surface
# print "The file does contain cells that are not tetraheders node4==0. The cell number is ", cellnr, " the line read was ", line
#sys.exit(2)
pass
num_cells = counter
# third, run over all cells
xml_writer.write_header_cells(ofile, num_cells)
counter = 0
for line in lines:
l = [int(a) for a in line.split()]
cellnr, node0, node1, node2, node3, node4, node5, node6, node7, tmp1, tmp2 = l
if (node4 > 0):
if node2 == node3 and node4 == node5 and node5 == node6 and node6 == node7: # these nodes should be equal
xml_writer.write_cell_tetrahedron(ofile, counter, nodenr_map[node0], nodenr_map[node1], nodenr_map[node2], nodenr_map[node4])
counter += 1
xml_writer.write_footer_cells(ofile)
xml_writer.write_footer_mesh(ofile)
# Close files
ifile.close()
ofile.close()
def netcdf2xml(ifilename,ofilename):
"Convert from NetCDF format to DOLFIN XML."
print "Converting from NetCDF format (.ncdf) to DOLFIN XML format"
# Open files
ifile = open(ifilename, "r")
ofile = open(ofilename, "w")
cell_type = None
dim = 0
# Scan file for dimension, number of nodes, number of elements
while 1:
line = ifile.readline()
if not line:
_error("Empty file")
if re.search(r"num_dim.*=", line):
dim = int(re.match(".*\s=\s(\d+)\s;",line).group(1))
if re.search(r"num_nodes.*=", line):
num_vertices = int(re.match(".*\s=\s(\d+)\s;",line).group(1))
if re.search(r"num_elem.*=", line):
num_cells = int(re.match(".*\s=\s(\d+)\s;",line).group(1))
if re.search(r"connect1 =",line):
break
num_dims=dim
# Set cell type
if dim == 2:
cell_type ="triangle"
if dim == 3:
cell_type ="tetrahedron"
# Check that we got the cell type
if cell_type == None:
_error("Unable to find cell type.")
# Write header
xml_writer.write_header_mesh(ofile, cell_type, dim)
xml_writer.write_header_cells(ofile, num_cells)
num_cells_read = 0
# Read and write cells
while 1:
# Read next line
line = ifile.readline()
if not line:
break
connect=re.split("[,;]",line)
if num_dims == 2:
n0 = int(connect[0])-1
n1 = int(connect[1])-1
n2 = int(connect[2])-1
xml_writer.write_cell_triangle(ofile, num_cells_read, n0, n1, n2)
elif num_dims == 3:
n0 = int(connect[0])-1
n1 = int(connect[1])-1
n2 = int(connect[2])-1
n3 = int(connect[3])-1
xml_writer.write_cell_tetrahedron(ofile, num_cells_read, n0, n1, n2, n3)
num_cells_read +=1
if num_cells == num_cells_read:
xml_writer.write_footer_cells(ofile)
xml_writer.write_header_vertices(ofile, num_vertices)
break
num_vertices_read = 0
coords = [[],[],[]]
coord = -1
while 1:
line = ifile.readline()
if not line:
_error("Missing data")
if re.search(r"coord =",line):
break
# Read vertices
while 1:
line = ifile.readline()
if not line:
break
if re.search(r"\A\s\s\S+,",line):
coord+=1
print "Found x_"+str(coord)+" coordinates"
coords[coord] += line.split()
if re.search(r";",line):
break
# Write vertices
for i in range(num_vertices):
if num_dims == 2:
x = float(re.split(",",coords[0].pop(0))[0])
y = float(re.split(",",coords[1].pop(0))[0])
z = 0
if num_dims == 3:
x = float(re.split(",",coords[0].pop(0))[0])
y = float(re.split(",",coords[1].pop(0))[0])
z = float(re.split(",",coords[2].pop(0))[0])
xml_writer.write_vertex(ofile, i, x, y, z)
# Write footer
xml_writer.write_footer_vertices(ofile)
xml_writer.write_footer_mesh(ofile)
# Close files
ifile.close()
ofile.close()
def end_cells(self):
DataHandler.end_cells(self)
xml_writer.write_footer_cells(self.__ofile)