woops the code got broken, here I attached the updated dolvin-convert
file...
cheers
Alex
plain text document attachment (dolfin-convert)
#!/usr/bin/env python
#
# Copyright (C) 2006 Anders Logg
# Licensed under the GNU GPL Version 2
#
# Modified by Garth N. Wells (gmsh function)
#
# Modified by Alexander H. Jarosch (gmsh fix, 15.05.2006)
#
# Script for converting between various data formats.
#
# Supported input formats:
#
# .mesh (Medit, generated by tetgen with option -g)
#
# Supported output formats:
#
# .xml (DOLFIN XML mesh file)
import getopt
import sys
def main(argv):
"Main function"
# Get command-line arguments
try:
opts, args = getopt.getopt(argv, "h", ["help"])
except getopt.GetoptError:
usage()
sys.exit(2)
# Get options
for opt, arg in opts:
if opt in ("-h", "--help"):
usage()
sys.exit()
# Check that we got two filenames
if not len(args) == 2:
usage()
sys.exit(2)
# Get filenames and suffixes
ifilename = args[0]
ofilename = args[1]
isuffix = ifilename.split(".")[-1]
osuffix = ofilename.split(".")[-1]
# Choose conversion
if isuffix == "mesh" and osuffix == "xml":
mesh2xml(ifilename, ofilename)
if (isuffix == "gmsh" or isuffix == "msh") and osuffix == "xml":
gmsh2xml(ifilename, ofilename)
else:
print "Sorry, cannot convert between .%s and .%s file formats." % (isuffix, osuffix)
def usage():
"Display usage"
print """\
Usage: dolfin-convert [OPTION]... input.x output.y
-h display this help text and exit
Alternatively, the following long options may be used:
--help
"""
return
def error(message):
"Write an error message"
for line in message.split("\n"):
print "*** %s" % line
sys.exit(2)
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")
# Write header
write_header(ofile)
# 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":
state += 1
elif state == 1:
num_dims = int(line)
state +=1
elif state == 2:
if line == "Vertices":
state += 1
elif state == 3:
num_vertices = int(line)
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)
write_vertex(ofile, num_vertices_read, x, y, z)
num_vertices_read +=1
if num_vertices == num_vertices_read:
write_footer_vertices(ofile)
state += 1
elif state == 5:
if line == "Triangles" and num_dims == 2:
state += 1
if line == "Tetrahedra" and num_dims == 3:
state += 1
elif state == 6:
num_cells = int(line)
write_header_cells(ofile, num_cells)
state +=1
min_vertex = 1000000
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
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
write_cell_tetrahedron(ofile, num_cells_read, n0, n1, n2, n3)
num_cells_read +=1
if num_cells == num_cells_read:
write_footer_cells(ofile)
state += 1
elif state == 8:
break
#print line
# Check that we got all data
if state == 8:
print "Conversion done"
else:
print "*** Missing data, unable to convert"
# Write footer
write_footer(ofile)
# Close files
ifile.close()
ofile.close()
def gmsh2xml(ifilename, ofilename):
"""Convert between .gmsh v1.0 format (http://www.geuz.org/gmsh/) and .xml,
parser implemented as a state machine:
0 = read number of vertices
1 = read 'Vertices'
2 = read indentifer
3 = read indentifer
4 = read number of cells
5 = read cells
6 = done
"""
print "Converting from Gmsh format (.msh, .gmsh) to DOLFIN XML format"
# Open files
ifile = open(ifilename, "r")
ofile = open(ofilename, "w")
# Write header
write_header(ofile)
# Initialise node list (gmsh does not export all vertexes in order)
nodelist = {}
# 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 line == "$NOD":
continue
if state == 0:
num_vertices = int(line)
write_header_vertices(ofile, num_vertices)
state +=1
elif state == 1:
(node_no, x, y, z) = line.split()
nodelist[int(node_no)] = num_vertices_read
x = float(x)
y = float(y)
z = float(z)
write_vertex(ofile, num_vertices_read, x, y, z)
num_vertices_read +=1
if num_vertices == num_vertices_read:
write_footer_vertices(ofile)
state += 1
elif state == 2:
if line == "$ENDNOD":
state += 1
elif state == 3:
if line == "$ELM":
state += 1
elif state == 4:
num_cells = int(line)
if num_cells == 0:
print "No cells found in gmsh file."
break
else:
write_header_cells(ofile, num_cells)
state += 1
elif state == 5:
element = line.split()
cell_type = int(element[1])
if cell_type == 2:
nn = [int(node) for node in element[5:8]]
for node in nn:
if not node in nodelist:
error("Vertex %d of triangle %d not previously defined." % (node, num_cells_read))
n0 = nodelist[nn[0]]
n1 = nodelist[nn[1]]
n2 = nodelist[nn[2]]
write_cell_triangle(ofile, num_cells_read, n0, n1, n2)
elif cell_type == 4:
nn = [int(node) for node in element[5:9]]
for node in nn:
if not node in nodelist:
error("Vertex %d of tetrahedron %d not previously defined." % (node, num_cells_read))
n0 = nodelist[nn[0]]
n1 = nodelist[nn[1]]
n2 = nodelist[nn[2]]
n3 = nodelist[nn[3]]
write_cell_tetrahedron(ofile, num_cells_read, n0, n1, n2, n3)
num_cells_read +=1
if num_cells == num_cells_read:
write_footer_cells(ofile)
state += 1
elif state == 6:
break
#print line
# Check that we got all data
if state == 6:
print "Conversion done"
else:
print "*** Missing data, unable to convert"
# Write footer
write_footer(ofile)
# Close files
ifile.close()
ofile.close()
# Write mesh header
def write_header(ofile):
ofile.write("""\
<?xml version=\"1.0\" encoding=\"UTF-8\"?>
<dolfin xmlns:dolfin=\"http://www.fenics.org/dolfin/\";>
<mesh>
""")
# Write mesh footer
def write_footer(ofile):
ofile.write("""\
</mesh>
</dolfin>
""")
# Write vertices header
def write_header_vertices(ofile, num_vertices):
print "Expecting %d vertices" % num_vertices
ofile.write(" <vertices size=\"%d\">\n" % num_vertices)
# Write vertices footer
def write_footer_vertices(ofile):
ofile.write(" </vertices>\n")
print "Found all vertices"
# Write vertex
def write_vertex(ofile, vertex, x, y, z):
ofile.write(" <vertex name=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\"/>\n" % \
(vertex, x, y, z))
# Write cells header
def write_header_cells(ofile, num_cells):
ofile.write(" <cells size=\"%d\">\n" % num_cells)
print "Expecting %d cells" % num_cells
# Write cells footer
def write_footer_cells(ofile):
ofile.write(" </cells>\n")
print "Found all cells"
# Write cell (triangle)
def write_cell_triangle(ofile, cell, n0, n1, n2):
ofile.write(" <triangle name=\"%d\" n0=\"%d\" n1=\"%d\" n2=\"%d\"/>\n" % \
(cell, n0, n1, n2))
# Write cell (tetrahedron)
def write_cell_tetrahedron(ofile, cell, n0, n1, n2, n3):
ofile.write(" <tetrahedron name=\"%d\" n0=\"%d\" n1=\"%d\" n2=\"%d\" n3=\"%d\"/>\n" % \
(cell, n0, n1, n2, n3))
if __name__ == "__main__":
main(sys.argv[1:])
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