Example #1
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()
Example #2
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()
Example #3
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()
Example #4
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()
Example #5
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()
Example #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()