Ejemplo n.º 1
0
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()
Ejemplo n.º 2
0
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()
Ejemplo n.º 3
0
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()
Ejemplo n.º 4
0
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()
Ejemplo n.º 5
0
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()
Ejemplo n.º 6
0
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()
Ejemplo n.º 7
0
 def end_cells(self):
     DataHandler.end_cells(self)
     xml_writer.write_footer_cells(self.__ofile)
Ejemplo n.º 8
0
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()
Ejemplo n.º 9
0
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()
Ejemplo n.º 10
0
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()
Ejemplo n.º 11
0
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()
Ejemplo n.º 12
0
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()
Ejemplo n.º 13
0
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()
Ejemplo n.º 14
0
 def end_cells(self):
     DataHandler.end_cells(self)
     xml_writer.write_footer_cells(self.__ofile)