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Message #02558
Re: dolfin-convert, fix
Could you make a patch file?
Garth
On Mon, 2006-05-15 at 17:13 +0000, Alexander Jarosch wrote:
> 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:])
> _______________________________________________
> DOLFIN-dev mailing list
> DOLFIN-dev@xxxxxxxxxx
> http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
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