Source code for sfepy.discrete.fem.meshio

from __future__ import print_function
from __future__ import absolute_import
import sys
from copy import copy
import logging
import numpy as nm
from distutils.version import LooseVersion

from sfepy.base.base import (complex_types, dict_from_keys_init,
                             assert_, is_derived_class, ordered_iteritems,
                             insert_static_method, output, get_default,
                             get_default_attr, Struct, basestr)
from sfepy.base.ioutils import (skip_read_line, look_ahead_line, read_token,
                                read_array, pt, enc, dec,
                                edit_filename,
                                read_from_hdf5, write_to_hdf5,
                                HDF5ContextManager, get_or_create_hdf5_group)

import os.path as op
import six
from six.moves import range
import meshio as meshiolib
try:
    from meshio import CellBlock as meshio_Cells  # for meshio >= 4.0.3
except:
    from meshio import Cells as meshio_Cells  # for 4.0.3 > meshio > 4.0.0

_supported_formats = {
    # format name: IO class, suffix, modes[, variants]
    # modes: r = read, w = write, c = test cell groups, v = test vertex groups
    'abaqus': ('meshio', None, 'cv'),
    'exodus': ('meshio', None, 'v'),
    'gmsh': ('meshio', None, 'cv', ['gmsh4-binary', 'gmsh4-ascii',
                                    'gmsh2-binary', 'gmsh2-ascii']),
    # The '*' prevents overriding meshio in ext2io dict, see
    # any_from_filename().
    'gmsh-dg': ('gmshio', '.msh', '*rw'),
    'medit': ('meshio', None, 'cv'),
    'nastran': ('meshio', None, 'cv'),
    'vtk': ('meshio', None, 'cv', ['vtk-binary', 'vtk-ascii']),
    'vtu': ('meshio', None, 'cv'),
    'med': ('meshio', None, 'cv'),
    'xdmf': ('meshio', None, 'cv'),
    'tetgen': ('meshio', None, ''),
    'ansys': ('ansys_cdb', '.cdb', 'r'),
    'hdf5': ('hdf5', '.h5', 'rwcv'),
    'hdf5-xdmf': ('hdf5-xdmf', '.h5x', 'rwcv'),
    'xyz': ('xyz', '.xyz', 'rw'),
    'comsol': ('comsol', '.txt', 'r'),
    'hmascii': ('hmascii', '.hmascii', 'r'),
    'gambit': ('gambit', '.neu', 'r'),
    'mesh3d': ('mesh3d', '.mesh3d', 'r'),
}

[docs]def update_supported_formats(formats): from meshio._helpers import reader_map, _writer_map,\ extension_to_filetype f2e = {} for k, v in extension_to_filetype.items(): f2e.setdefault(v, []).append(k) out = {} for format, info in formats.items(): io, ext, _flag = info[:3] variants = info[3] if len(info) >= 4 else [] for f in [format] + variants: if io == 'meshio': flag = _flag[:] if ext is None: if format in f2e: ext = f2e[format] else: continue if format in _writer_map: flag = 'w' + flag if format in reader_map: flag = 'r' + flag if not f == format: flag = '*' + flag # label format variants else: flag = _flag if not isinstance(ext, list): ext = [ext] out[f] = (io, ext, flag) return out
supported_formats = update_supported_formats(_supported_formats) del _supported_formats
[docs]def output_mesh_formats(mode='r'): for key, vals in ordered_iteritems(supported_formats): if mode in vals[2]: output('%s (%s)' % (key, vals[1] if len(vals[1]) > 1 else vals[1][0]))
[docs]def split_conns_mat_ids(conns_in): """ Split connectivities (columns except the last ones in `conns_in`) from cell groups (the last columns of `conns_in`). """ conns, mat_ids = [], [] for conn in conns_in: conn = nm.asarray(conn, dtype=nm.int32) conns.append(conn[:, :-1]) mat_ids.append(conn[:, -1]) return conns, mat_ids
[docs]def convert_complex_output(out_in): """ Convert complex values in the output dictionary `out_in` to pairs of real and imaginary parts. """ out = {} for key, val in six.iteritems(out_in): if val.data.dtype in complex_types: rval = copy(val) rval.data = val.data.real out['real.%s' % key] = rval ival = copy(val) ival.data = val.data.imag out['imag.%s' % key] = ival else: out[key] = val return out
[docs]def check_format_suffix(file_format, suffix): """ Check compatibility of a mesh file format and a mesh file suffix. """ if file_format is None: return try: suffixes = supported_formats[file_format][1] except KeyError: raise ValueError('unknown file format! (%s)' % file_format) if suffix is None: return suffix = suffix if suffix.startswith('.') else '.' + suffix if suffix not in suffixes: raise ValueError('"%s" format is not compatible with "%s" suffix!' % (file_format, suffix))
[docs]class MeshIO(Struct): """ The abstract class for importing and exporting meshes. Read the docstring of the Mesh() class. Basically all you need to do is to implement the read() method:: def read(self, mesh, **kwargs): nodes = ... ngroups = ... conns = ... mat_ids = ... descs = ... mesh._set_io_data(nodes, ngroups, conns, mat_ids, descs) return mesh See the Mesh class' docstring how the nodes, ngroups, conns, mat_ids and descs should look like. You just need to read them from your specific format from disk. To write a mesh to disk, just implement the write() method and use the information from the mesh instance (e.g. nodes, conns, mat_ids and descs) to construct your specific format. Optionally, subclasses can implement read_data() to read also computation results. This concerns mainly the subclasses with implemented write() supporting the 'out' kwarg. The default implementation od read_last_step() just returns 0. It should be reimplemented in subclasses capable of storing several steps. """ format = None call_msg = 'called an abstract MeshIO instance!' def __init__(self, filename, **kwargs): Struct.__init__(self, filename=filename, **kwargs) self.set_float_format()
[docs] def get_filename_trunk(self): if isinstance(self.filename, basestr): trunk = op.splitext(self.filename)[0] else: trunk = 'from_descriptor' return trunk
[docs] def read_last_step(self): """The default implementation: just return 0 as the last step.""" return 0
[docs] def read_times(self, filename=None): """ Read true time step data from individual time steps. Returns ------- steps : array The time steps. times : array The times of the time steps. nts : array The normalized times of the time steps, in [0, 1]. Notes ----- The default implementation returns empty arrays. """ aux = nm.array([0.0], dtype=nm.float64) return aux.astype(nm.int32), aux, aux
[docs] def read(self, mesh, omit_facets=False, **kwargs): raise ValueError(MeshIO.call_msg)
[docs] def write(self, filename, mesh, **kwargs): raise ValueError(MeshIO.call_msg)
[docs] def read_data(self, step, filename=None, cache=None): raise ValueError(MeshIO.call_msg)
[docs] def set_float_format(self, format=None): self.float_format = get_default(format, '%e')
[docs] def get_vector_format(self, dim): return ' '.join([self.float_format] * dim)
[docs]class UserMeshIO(MeshIO): """ Special MeshIO subclass that enables reading and writing a mesh using a user-supplied function. """ format = 'function' def __init__(self, filename, **kwargs): assert_(hasattr(filename, '__call__')) self.function = filename MeshIO.__init__(self, filename='function:%s' % self.function.__name__, **kwargs)
[docs] def get_filename_trunk(self): return self.filename
[docs] def read(self, mesh, *args, **kwargs): aux = self.function(mesh, mode='read') if aux is not None: mesh = aux self.filename = mesh.name return mesh
[docs] def write(self, filename, mesh, *args, **kwargs): self.function(mesh, mode='write')
def _suppress_meshio_warnings(f): def __suppress_meshio_warnings(*args, **kwargs): logger = logging.getLogger() level = logger.level logger.setLevel(logging.ERROR) out = f(*args, **kwargs) logger.setLevel(level) return out return __suppress_meshio_warnings def _decorate_all(module, decorator): import types for name in dir(module): obj = getattr(module, name) if isinstance(obj, types.FunctionType): setattr(module, name, decorator(obj)) _decorate_all(meshiolib, _suppress_meshio_warnings) del _decorate_all, _suppress_meshio_warnings
[docs]class MeshioLibIO(MeshIO): format = 'meshio' cell_types = { ('hexahedron', 3): '3_8', ('tetra', 3): '3_4', ('triangle', 3): '2_3', ('triangle', 2): '2_3', ('quad', 3): '2_4', ('quad', 2): '2_4', ('line', 3): '1_2', ('line', 2): '1_2', ('line', 1): '1_2', } def __init__(self, filename, file_format=None, **kwargs): MeshIO.__init__(self, filename=filename, **kwargs) from meshio._helpers import _filetype_from_path import pathlib if file_format is None: file_format = _filetype_from_path(pathlib.Path(filename)) self.file_format = file_format
[docs] def read_bounding_box(self, ret_dim=False): m = meshiolib.read(self.filename, file_format=self.file_format) bbox = nm.vstack([nm.amin(m.points, 0), nm.amax(m.points, 0)]) if ret_dim: return bbox, m.points.shape[1] else: return bbox
@staticmethod def _get_dimension(points): dim = nm.sum(nm.max(points, axis=0) - nm.min(points, axis=0) > 1e-15) return dim
[docs] def read_dimension(self): m = meshiolib.read(self.filename, file_format=self.file_format) dim = self._get_dimension(m.points) return dim
[docs] def read(self, mesh, omit_facets=False, **kwargs): m = meshiolib.read(self.filename, file_format=self.file_format) dim = self._get_dimension(m.points) ngkey = None for k in m.point_data.keys(): if k == 'node_groups' or k.endswith(':ref'): ngkey = k break if ngkey is not None: ngroups = nm.asarray(m.point_data[ngkey]).flatten() elif hasattr(m, 'point_sets') and len(m.point_sets) > 0: ngroups = nm.zeros((len(m.points),), dtype=nm.int32) keys = list(m.point_sets.keys()) keys.sort() try: ngrps = [int(ii) for ii in keys] except: ngrps = nm.arange(len(keys)) + 1 for ik, k in enumerate(keys): ngroups[m.point_sets[k]] = ngrps[ik] else: ngroups = None cells, cgroups, cell_types = [], [], [] # meshio.__version__ > 3.3.2 cgkey = None for k in list(m.cell_data.keys()): if k == 'mat_id' or k.endswith(':ref'): cgkey = k break if cgkey is not None: cgdata = m.cell_data[cgkey] elif len(m.cell_sets) > 0: cgdata = [] keys = list(m.cell_sets.keys()) keys.sort() try: cgrps = [int(ii) for ii in keys] except: cgrps = nm.arange(len(keys)) + 1 for ic, c in enumerate(m.cells): cgdata0 = nm.zeros((len(c.data),), dtype=nm.int32) for ik, k in enumerate(keys): cgdata0[m.cell_sets[k][ic]] = cgrps[ik] cgdata.append(cgdata0) else: cgdata = None for ic, c in enumerate(m.cells): if (c.type, dim) not in self.cell_types: output('warning: unknown cell type %s with dimension %d'\ % (c.type, dim)) continue cells.append(c.data) cell_types.append(self.cell_types[(c.type, dim)]) if cgdata is not None: cgroups.append(nm.asarray(cgdata[ic]).flatten()) else: cgroups.append(nm.ones((len(c.data),), dtype=nm.int32)) mesh._set_io_data(m.points[:,:dim], ngroups, cells, cgroups, cell_types) output('number of vertices: %d' % m.points.shape[0]) output('number of cells:') for ii, k in enumerate(cell_types): output(' %s: %d' % (k, cells[ii].shape[0])) return mesh
[docs] def write(self, filename, mesh, out=None, ts=None, **kwargs): (coors, cells, point_data, point_sets, cell_data, cell_sets) = self._create_out_data(mesh, out) if LooseVersion(meshiolib.__version__) >= LooseVersion('4.0.3') and\ ('-ascii' in self.file_format or '-binary' in self.file_format): self.file_format, ab_str = self.file_format.split('-') kwargs['binary'] = True if 'binary' in ab_str else False args0 = {'point_data': point_data, 'point_sets': point_sets, 'cell_data': cell_data, 'cell_sets': cell_sets, 'file_format': self.file_format} args = args0.copy() args.update(kwargs) try: meshiolib.write_points_cells(filename, coors, cells, **args) except TypeError: meshiolib.write_points_cells(filename, coors, cells, **args0)
def _create_out_data(self, mesh, out): inv_cell_types = {v: k for k, v in self.cell_types.items()} coors, ngroups, conns, _, descs = mesh._get_io_data() out = {} if out is None else out point_data = {k: v.data for k, v in out.items() if v.mode == 'vertex'} cell_data_keys = [k for k, v in out.items() if v.mode == 'cell'] if self.file_format in ['vtk', 'vtk-ascii', 'vtk-binary', 'vtu']: ngkey = 'node_groups' cgkey = 'mat_id' if coors.shape[1] != 3: nnd, ndim = coors.shape ndim = 3 - ndim coors = nm.hstack([coors, nm.zeros((nnd, ndim), dtype=nm.float64)]) else: ngkey = '%s:ref' % self.file_format cgkey = '%s:ref' % self.file_format point_data[ngkey] = ngroups point_sets = {str(k): nm.where(ngroups == k)[0] for k in nm.unique(ngroups)} cmesh = mesh.cmesh cell_groups = cmesh.cell_groups cgrps = nm.unique(cell_groups) # meshio.__version__ > 3.3.2 cells = [] cgroups = [] cell_data = {k: [] for k in cell_data_keys} cell_sets = {str(k): [] for k in cgrps} for ii, desc in enumerate(descs): cells.append(meshio_Cells(type=inv_cell_types[desc][0], data=conns[ii])) cidxs = nm.where(cmesh.cell_types == cmesh.key_to_index[desc]) cidxs = cidxs[0].astype(nm.uint32) cgroups.append(cell_groups[cidxs]) for k in cell_data_keys: cell_data[k].append(out[k].data[cidxs, 0, :, 0]) for k in cgrps: idxs = nm.where(cell_groups[cidxs] == k)[0] cell_sets[str(k)].append(cidxs[idxs]) cell_data[cgkey] = cgroups return coors, cells, point_data, point_sets, cell_data, cell_sets
[docs] def read_data(self, step, filename=None, cache=None): """ Renames cell resp. vertex data with name "*:ref" to mat_id resp. node_groups Parameters ---------- step: has no effect filename : string, optional The file name to use instead of self.filename. cache: has no effect Returns ------- out : dictionary Data loaded from file, keys are names. values are Structs with name repeated, mode ('vertex' or 'cell') and the data itself. """ filename = get_default(filename, self.filename) m = meshiolib.read(filename, file_format=self.file_format) dim = self._get_dimension(m.points) def _fix_shape(data): if data.ndim == 2: data = data[:, :dim] elif data.ndim == 3: data = data[:, None, ...] return data out = {} for key, data in m.point_data.items(): aux = _fix_shape(data).astype(nm.float64) if key.endswith(':ref'): key = 'node_groups' out[key] = Struct(name=key, mode='vertex', data=aux) for key, data in m.cell_data.items(): aux = _fix_shape(data[0]).astype(nm.float64) if key.endswith(':ref'): key = 'mat_id' out[key] = Struct(name=key, mode='cell', data=aux) return out
[docs]class ComsolMeshIO(MeshIO): format = 'comsol' def _read_commented_int(self): return int(skip_read_line(self.fd).split('#')[0]) def _skip_comment(self): read_token(self.fd) self.fd.readline()
[docs] def read(self, mesh, **kwargs): self.fd = fd = open(self.filename, 'r') mode = 'header' coors = conns = None while 1: if mode == 'header': line = skip_read_line(fd) n_tags = self._read_commented_int() for ii in range(n_tags): skip_read_line(fd) n_types = self._read_commented_int() for ii in range(n_types): skip_read_line(fd) skip_read_line(fd) assert_(skip_read_line(fd).split()[1] == 'Mesh') skip_read_line(fd) dim = self._read_commented_int() assert_((dim == 2) or (dim == 3)) n_nod = self._read_commented_int() i0 = self._read_commented_int() mode = 'points' elif mode == 'points': self._skip_comment() coors = read_array(fd, n_nod, dim, nm.float64) mode = 'cells' elif mode == 'cells': n_types = self._read_commented_int() conns = [] descs = [] mat_ids = [] for it in range(n_types): t_name = skip_read_line(fd).split()[1] n_ep = self._read_commented_int() n_el = self._read_commented_int() self._skip_comment() aux = read_array(fd, n_el, n_ep, nm.int32) if t_name == 'tri': conns.append(aux) descs.append('2_3') is_conn = True elif t_name == 'quad': # Rearrange element node order to match SfePy. aux = aux[:,(0,1,3,2)] conns.append(aux) descs.append('2_4') is_conn = True elif t_name == 'hex': # Rearrange element node order to match SfePy. aux = aux[:,(0,1,3,2,4,5,7,6)] conns.append(aux) descs.append('3_8') is_conn = True elif t_name == 'tet': conns.append(aux) descs.append('3_4') is_conn = True else: is_conn = False # Skip parameters. n_pv = self._read_commented_int() n_par = self._read_commented_int() for ii in range(n_par): skip_read_line(fd) n_domain = self._read_commented_int() assert_(n_domain == n_el) if is_conn: self._skip_comment() mat_id = read_array(fd, n_domain, 1, nm.int32) mat_ids.append(mat_id.squeeze()) else: for ii in range(n_domain): skip_read_line(fd) # Skip up/down pairs. n_ud = self._read_commented_int() for ii in range(n_ud): skip_read_line(fd) break fd.close() self.fd = None mesh._set_io_data(coors, None, conns, mat_ids, descs) return mesh
[docs] def write(self, filename, mesh, out=None, **kwargs): def write_elements(fd, ig, conn, mat_ids, type_name, npe, format, norder, nm_params): fd.write("# Type #%d\n\n" % ig) fd.write("%s # type name\n\n\n" % type_name) fd.write("%d # number of nodes per element\n" % npe) fd.write("%d # number of elements\n" % conn.shape[0]) fd.write("# Elements\n") for ii in range(conn.shape[0]): nn = conn[ii] # Zero based fd.write(format % tuple(nn[norder])) fd.write("\n%d # number of parameter values per element\n" % nm_params) # Top level always 0? fd.write("0 # number of parameters\n") fd.write("# Parameters\n\n") fd.write("%d # number of domains\n" % sum([mi.shape[0] for mi in mat_ids])) fd.write("# Domains\n") for mi in mat_ids: # Domains in comsol have to be > 0 if (mi <= 0).any(): mi += mi.min() + 1 for dom in mi: fd.write("%d\n" % abs(dom)) fd.write("\n0 # number of up/down pairs\n") fd.write("# Up/down\n") fd = open(filename, 'w') coors, ngroups, conns, mat_ids, desc = mesh._get_io_data() n_nod, dim = coors.shape # Header fd.write("# Created by SfePy\n\n\n") fd.write("# Major & minor version\n") fd.write("0 1\n") fd.write("1 # number of tags\n") fd.write("# Tags\n") fd.write("2 m1\n") fd.write("1 # number of types\n") fd.write("# Types\n") fd.write("3 obj\n\n") # Record fd.write("# --------- Object 0 ----------\n\n") fd.write("0 0 1\n") # version unused serializable fd.write("4 Mesh # class\n") fd.write("1 # version\n") fd.write("%d # sdim\n" % dim) fd.write("%d # number of mesh points\n" % n_nod) fd.write("0 # lowest mesh point index\n\n") # Always zero in SfePy fd.write("# Mesh point coordinates\n") format = self.get_vector_format(dim) + '\n' for ii in range(n_nod): nn = tuple(coors[ii]) fd.write(format % tuple(nn)) fd.write("\n%d # number of element types\n\n\n" % len(conns)) for ig, conn in enumerate(conns): if (desc[ig] == "2_4"): write_elements(fd, ig, conn, mat_ids, "4 quad", 4, "%d %d %d %d\n", [0, 1, 3, 2], 8) elif (desc[ig] == "2_3"): # TODO: Verify number of parameters for tri element write_elements(fd, ig, conn, mat_ids, "3 tri", 3, "%d %d %d\n", [0, 1, 2], 4) elif (desc[ig] == "3_4"): # TODO: Verify number of parameters for tet element write_elements(fd, ig, conn, mat_ids, "3 tet", 4, "%d %d %d %d\n", [0, 1, 2, 3], 16) elif (desc[ig] == "3_8"): write_elements(fd, ig, conn, mat_ids, "3 hex", 8, "%d %d %d %d %d %d %d %d\n", [0, 1, 3, 2, 4, 5, 7, 6], 24) else: raise ValueError('unknown element type! (%s)' % desc[ig]) fd.close() if out is not None: for key, val in six.iteritems(out): raise NotImplementedError
[docs]class HDF5MeshIO(MeshIO): format = "hdf5" import string _all = ''.join(map(chr, list(range(256)))) _letters = string.ascii_letters + string.digits + '_' _rubbish = ''.join([ch for ch in set(_all) - set(_letters)]) if sys.version_info[0] >= 3: _tr = str.maketrans(_rubbish, '_' * len(_rubbish)) else: _tr = string.maketrans(_rubbish, '_' * len(_rubbish))
[docs] @staticmethod def read_mesh_from_hdf5(filename, group=None, mesh=None): """ Read the mesh from a HDF5 file. filename: str or tables.File The HDF5 file to read the mesh from. group: tables.group.Group or str, optional The HDF5 file group to read the mesh from. If None, the root group is used. mesh: sfepy.dicrete.fem.Mesh or None If None, the new mesh is created and returned, otherwise content of this argument is replaced by the read mesh. Returns ------- sfepy.dicrete.fem.Mesh readed mesh """ with HDF5ContextManager(filename, mode='r') as fd: if group is None: group = fd.root elif not isinstance(group, pt.group.Group): group = fd.get_node(group) set_shape_info = mesh is None if mesh is None: from .mesh import Mesh mesh = Mesh('mesh') mesh.name = dec(group.name.read()) coors = group.coors.read() ngroups = group.ngroups.read() n_gr = group.n_gr.read() conns = [] descs = [] mat_ids = [] for ig in range(n_gr): gr_name = 'group%d' % ig conn_group = group._f_get_child(gr_name) conns.append(conn_group.conn.read()) mat_ids.append(conn_group.mat_id.read()) descs.append(dec(conn_group.desc.read())) nodal_bcs = {} try: node_sets_groups = group.node_sets except: pass else: for group in node_sets_groups: key = dec(group.key.read()) nods = group.nods.read() nodal_bcs[key] = nods mesh._set_io_data(coors, ngroups, conns, mat_ids, descs, nodal_bcs=nodal_bcs) if set_shape_info: mesh._set_shape_info() return mesh
[docs] @staticmethod def write_mesh_to_hdf5(filename, group, mesh, force_3d=False): """ Write mesh to a hdf5 file. filename: str or tables.File The HDF5 file to write the mesh to. group: tables.group.Group or None or str The HDF5 file group to write the mesh to. If None, the root group is used. The group can be given as a path from root, e.g. /path/to/mesh mesh: sfepy.dicrete.fem.Mesh The mesh to write. """ with HDF5ContextManager(filename, mode='w') as fd: if group is None: group = fd.root elif not isinstance(group, pt.group.Group): group = get_or_create_hdf5_group(fd, group) coors, ngroups, conns, mat_ids, descs = mesh._get_io_data() if force_3d and coors.shape[1] == 2: coors = nm.hstack([coors, nm.zeros((len(coors), 1))]) fd.create_array(group, 'name', enc(mesh.name), 'name') fd.create_array(group, 'coors', coors, 'coors') fd.create_array(group, 'ngroups', ngroups, 'ngroups') fd.create_array(group, 'n_gr', len(conns), 'n_gr') for ig, conn in enumerate(conns): conn_group = fd.create_group(group, 'group%d' % ig, 'connectivity group') fd.create_array(conn_group, 'conn', conn, 'connectivity') fd.create_array(conn_group, 'mat_id', mat_ids[ig], 'material id') fd.create_array(conn_group, 'desc', enc(descs[ig]), 'element Type') node_sets_groups = fd.create_group(group, 'node_sets', 'node sets groups') ii = 0 for key, nods in six.iteritems(mesh.nodal_bcs): group = fd.create_group(node_sets_groups, 'group%d' % ii, 'node sets group') fd.create_array(group, 'key', enc(key), 'key') fd.create_array(group, 'nods', nods, 'nods') ii += 1
[docs] def read_dimension(self, ret_fd=False): fd = pt.open_file(self.filename, mode="r") dim = fd.root.mesh.coors.shape[1] if ret_fd: return dim, fd else: fd.close() return dim
[docs] def read_bounding_box(self, ret_fd=False, ret_dim=False): fd = pt.open_file(self.filename, mode="r") mesh_group = fd.root.mesh coors = mesh_group.coors.read() bbox = nm.vstack((nm.amin(coors, 0), nm.amax(coors, 0))) if ret_dim: dim = coors.shape[1] if ret_fd: return bbox, dim, fd else: fd.close() return bbox, dim else: if ret_fd: return bbox, fd else: fd.close() return bbox
[docs] def read(self, mesh=None, **kwargs): return self.read_mesh_from_hdf5(self.filename, '/mesh', mesh=mesh)
[docs] @staticmethod def write_xdmf_file(filename, **kwargs): def get_path(node): _, fname = op.split(filename) return '%s:%s' % (fname, node._v_pathname) def get_data_dim(shape): if len(shape) == 4: return shape[2] if len(shape) == 2: return shape[1] else: return 1 def data_item(data): dtype = data.dtype if nm.issubdtype(dtype, nm.integer): data_type = 'Int' elif nm.issubdtype(dtype, nm.floating): data_type = 'Float' else: raise ValueError('wrong data type! (%s)' % dtype) dim = get_data_dim(data.shape) sh = (data.shape[0], dim) ditem = et.Element('DataItem', attrib={'DataType': data_type, 'Dimensions': '%d %d' % sh, 'Format': 'HDF', 'Precision': str(dtype.itemsize)}) ditem.text = get_path(data) return ditem def attr_item(data, center=None, name=None): if isinstance(data, pt.Group): if center is None and 'mode' in data: mode = data.mode.read().decode('ascii') if mode == 'custom': return None center = {'vertex': 'Node', 'cell': 'Cell'}[mode] if name is None and 'dname' in data: name = data.dname.read().decode('ascii').lstrip('_') data = data.data dim = get_data_dim(data.shape) atype = {1: 'Scalar', 3: 'Vector', 6: 'Tensor6', 9: 'Tensor'}[dim] aitem = et.Element('Attribute', attrib={'AttributeType': atype, 'Center': center, 'Name': name}) aitem.append(data_item(data)) return aitem import xml.etree.ElementTree as et from xml.dom import minidom topology_table = { '2_2': 'Line', '3_2': 'Line', '2_3': 'Triangle', '2_4': 'Quadrilateral', '3_4': 'Tetrahedron', '3_8': 'Hexahedron', } et_root = et.Element('Xdmf', attrib={'Version': '3.0'}) if 'extra_data' in kwargs: for k, v in kwargs['extra_data'].items(): d = et.SubElement(et_root, 'Information', attrib={'Name': k}) d.text = str(v) et_domain = et.SubElement(et_root, 'Domain') with HDF5ContextManager(filename, mode='r') as fd: root = fd.root mesh = root.mesh name = mesh.name.read().decode('ascii') et_mesh = [] geom = et.Element('Geometry', attrib={'GeometryType': 'XYZ'}) geom.append(data_item(mesh.coors)) et_mesh.append(geom) et_mesh.append(attr_item(mesh.ngroups, 'Node', 'node_groups')) n_gr = mesh.n_gr.read() for ig in range(n_gr): gr_name = 'group%d' % ig conn_group = mesh._f_get_child(gr_name) nc, nnd = conn_group.conn.shape ttype = topology_table[dec(conn_group.desc.read())] et_conn = et.Element('Topology', attrib={'NumberOfElements': str(nc), 'TopologyType': ttype}) et_conn.append(data_item(conn_group.conn)) et_mesh.append(et_conn) et_mesh.append(attr_item(conn_group.mat_id, 'Cell', 'mat_id')) steps = [k for k in root if k._v_name.startswith('step')] et_ts = et.SubElement(et_domain, 'Grid', attrib={'Name': 'TimeSeries', 'GridType': 'Collection', 'CollectionType': 'Temporal'}) for step in steps: istep = int(step._v_name[4:]) et_grid = et.SubElement(et_ts, 'Grid', attrib={'Name': 'grid%d' % istep, 'GridType': 'Uniform'}) et.SubElement(et_grid, 'Time', attrib={'Value': '%d' % istep}) et_grid.extend(et_mesh) for val in filter(lambda x: x._v_name.startswith('__'), step): aitem = attr_item(val) if aitem is not None: et_grid.append(aitem) out = minidom.parseString(et.tostring(et_root)).toprettyxml(indent=" ") xdmf_filename = op.splitext(filename)[0] + '.xdmf' with open(xdmf_filename, 'w') as f: f.write(out[(out.find('\n') + 1):])
[docs] def write(self, filename, mesh, out=None, ts=None, cache=None, xdmf=False, **kwargs): def expand_data_3d(data): expand_tab = { 2: (3, [0, 1]), 3: (6, [0, 1, 3]), 4: (9, [0, 1, 3, 4]), } n, dim = data.shape if dim in expand_tab: dim3, order = expand_tab[dim] out = nm.zeros((n, dim3), dtype=data.dtype) out[:, order] = data return out else: return data from time import asctime if pt is None: raise ValueError('pytables not imported!') step = get_default_attr(ts, 'step', 0) if (step == 0) or not op.exists(filename): # A new file. with pt.open_file(filename, mode="w", title="SfePy output file") as fd: mesh_group = fd.create_group('/', 'mesh', 'mesh') self.write_mesh_to_hdf5(fd, mesh_group, mesh, force_3d=xdmf) if ts is not None: ts_group = fd.create_group('/', 'ts', 'time stepper') fd.create_array(ts_group, 't0', ts.t0, 'initial time') fd.create_array(ts_group, 't1', ts.t1, 'final time' ) fd.create_array(ts_group, 'dt', ts.dt, 'time step') fd.create_array(ts_group, 'n_step', ts.n_step, 'n_step') tstat_group = fd.create_group('/', 'tstat', 'global time statistics') fd.create_array(tstat_group, 'created', enc(asctime()), 'file creation time') fd.create_array(tstat_group, 'finished', enc('.' * 24), 'file closing time') fd.create_array(fd.root, 'last_step', nm.array([step], dtype=nm.int32), 'last saved step') if out is not None: if ts is None: step, time, nt = 0, 0.0, 0.0 else: step, time, nt = ts.step, ts.time, ts.nt # Existing file. fd = pt.open_file(filename, mode="r+") step_group_name = 'step%d' % step if step_group_name in fd.root: raise ValueError('step %d is already saved in "%s" file!' ' Possible help: remove the old file or' ' start saving from the initial time.' % (step, filename)) step_group = fd.create_group('/', step_group_name, 'time step data') ts_group = fd.create_group(step_group, 'ts', 'time stepper') fd.create_array(ts_group, 'step', step, 'step') fd.create_array(ts_group, 't', time, 'time') fd.create_array(ts_group, 'nt', nt, 'normalized time') name_dict = {} for key, val in six.iteritems(out): if xdmf and mesh.coors.shape[1] == 2: data = expand_data_3d(val.data) else: data = val.data group_name = '__' + key.translate(self._tr) data_group = fd.create_group(step_group, group_name, '%s data' % key) fd.create_array(data_group, 'dname', enc(key), 'data name') fd.create_array(data_group, 'mode', enc(val.mode), 'mode') name = val.get('name', 'output_data') fd.create_array(data_group, 'name', enc(name), 'object name') if val.mode == 'custom': write_to_hdf5(fd, data_group, 'data', data, cache=cache, unpack_markers=getattr(val, 'unpack_markers', False)) continue shape = val.get('shape', data.shape) dofs = val.get('dofs', None) if dofs is None: dofs = [''] * nm.squeeze(shape)[-1] var_name = val.get('var_name', '') fd.create_array(data_group, 'data', data, 'data') fd.create_array(data_group, 'dofs', [enc(ic) for ic in dofs], 'dofs') fd.create_array(data_group, 'shape', shape, 'shape') fd.create_array(data_group, 'var_name', enc(var_name), 'object parent name') if val.mode == 'full': fd.create_array(data_group, 'field_name', enc(val.field_name), 'field name') name_dict[key] = group_name step_group._v_attrs.name_dict = name_dict fd.root.last_step[0] = step fd.remove_node(fd.root.tstat.finished) fd.create_array(fd.root.tstat, 'finished', enc(asctime()), 'file closing time') fd.close() if xdmf: self.write_xdmf_file(filename, **kwargs)
[docs] def read_last_step(self, filename=None): filename = get_default(filename, self.filename) fd = pt.open_file(filename, mode="r") last_step = fd.root.last_step[0] fd.close() return last_step
[docs] def read_time_stepper(self, filename=None): filename = get_default(filename, self.filename) fd = pt.open_file(filename, mode="r") try: ts_group = fd.root.ts out = (ts_group.t0.read(), ts_group.t1.read(), ts_group.dt.read(), ts_group.n_step.read()) except: raise ValueError('no time stepper found!') finally: fd.close() return out
def _get_step_group_names(self, fd): return sorted([name for name in fd.root._v_groups.keys() if name.startswith('step')], key=lambda name: int(name[4:]))
[docs] def read_times(self, filename=None): """ Read true time step data from individual time steps. Returns ------- steps : array The time steps. times : array The times of the time steps. nts : array The normalized times of the time steps, in [0, 1]. """ filename = get_default(filename, self.filename) fd = pt.open_file(filename, mode='r') steps = [] times = [] nts = [] for gr_name in self._get_step_group_names(fd): ts_group = fd.get_node(fd.root, gr_name + '/ts') steps.append(ts_group.step.read()) times.append(ts_group.t.read()) nts.append(ts_group.nt.read()) fd.close() steps = nm.asarray(steps, dtype=nm.int32) times = nm.asarray(times, dtype=nm.float64) nts = nm.asarray(nts, dtype=nm.float64) return steps, times, nts
def _get_step_group(self, step, filename=None): filename = get_default(filename, self.filename) fd = pt.open_file(filename, mode="r") if step is None: step = int(self._get_step_group_names(fd)[0][4:]) gr_name = 'step%d' % step try: step_group = fd.get_node(fd.root, gr_name) except: output('step %d data not found - premature end of file?' % step) fd.close() return None, None return fd, step_group
[docs] def read_data(self, step, filename=None, cache=None): fd, step_group = self._get_step_group(step, filename=filename) if fd is None: return None out = {} for data_group in step_group: try: key = dec(data_group.dname.read()) except pt.exceptions.NoSuchNodeError: continue mode = dec(data_group.mode.read()) if mode == 'custom': out[key] = read_from_hdf5(fd, data_group.data, cache=cache) continue name = dec(data_group.name.read()) data = data_group.data.read() dofs = tuple([dec(ic) for ic in data_group.dofs.read()]) try: shape = tuple(int(ii) for ii in data_group.shape.read()) except pt.exceptions.NoSuchNodeError: shape = data.shape if mode == 'full': field_name = dec(data_group.field_name.read()) else: field_name = None out[key] = Struct(name=name, mode=mode, data=data, dofs=dofs, shape=shape, field_name=field_name) if out[key].dofs == (-1,): out[key].dofs = None fd.close() return out
[docs] def read_data_header(self, dname, step=None, filename=None): fd, step_group = self._get_step_group(step, filename=filename) if fd is None: return None groups = step_group._v_groups for name, data_group in six.iteritems(groups): try: key = dec(data_group.dname.read()) except pt.exceptions.NoSuchNodeError: continue if key == dname: mode = dec(data_group.mode.read()) fd.close() return mode, name fd.close() raise KeyError('non-existent data: %s' % dname)
[docs] def read_time_history(self, node_name, indx, filename=None): filename = get_default(filename, self.filename) fd = pt.open_file(filename, mode="r") th = dict_from_keys_init(indx, list) for gr_name in self._get_step_group_names(fd): step_group = fd.get_node(fd.root, gr_name) data = step_group._f_get_child(node_name).data for ii in indx: th[ii].append(nm.array(data[ii])) fd.close() for key, val in six.iteritems(th): aux = nm.array(val) if aux.ndim == 4: # cell data. aux = aux[:,0,:,0] th[key] = aux return th
[docs] def read_variables_time_history(self, var_names, ts, filename=None): filename = get_default(filename, self.filename) fd = pt.open_file(filename, mode="r") assert_((fd.root.last_step[0] + 1) == ts.n_step) ths = dict_from_keys_init(var_names, list) arr = nm.asarray for step in range(ts.n_step): gr_name = 'step%d' % step step_group = fd.get_node(fd.root, gr_name) name_dict = step_group._v_attrs.name_dict for var_name in var_names: data = step_group._f_get_child(name_dict[var_name]).data ths[var_name].append(arr(data.read())) fd.close() return ths
[docs]class HDF5XdmfMeshIO(HDF5MeshIO): format="hdf5-xdmf"
[docs] def write(self, filename, mesh, out=None, ts=None, cache=None, **kwargs): HDF5MeshIO.write(self, filename, mesh, out=out, ts=ts, cache=cache, xdmf=True, **kwargs)
[docs]class Mesh3DMeshIO(MeshIO): format = "mesh3d"
[docs] def read(self, mesh, **kwargs): f = open(self.filename) # read the whole file: vertices = self._read_section(f, integer=False) tetras = self._read_section(f) hexes = self._read_section(f) prisms = self._read_section(f) tris = self._read_section(f) quads = self._read_section(f) # substract 1 from all elements, because we count from 0: conns = [] mat_ids = [] descs = [] if len(tetras) > 0: conns.append(tetras - 1) mat_ids.append([0]*len(tetras)) descs.append("3_4") if len(hexes) > 0: conns.append(hexes - 1) mat_ids.append([0]*len(hexes)) descs.append("3_8") mesh._set_io_data(vertices, None, conns, mat_ids, descs) return mesh
[docs] def read_dimension(self): return 3
def _read_line(self, f): """ Reads one non empty line (if it's a comment, it skips it). """ l = f.readline().strip() while l == "" or l[0] == "#": # comment or an empty line l = f.readline().strip() return l def _read_section(self, f, integer=True): """ Reads one section from the mesh3d file. integer ... if True, all numbers are passed to int(), otherwise to float(), before returning Some examples how a section can look like: 2 1 2 5 4 7 8 11 10 2 3 6 5 8 9 12 11 or 5 1 2 3 4 1 1 2 6 5 1 2 3 7 6 1 3 4 8 7 1 4 1 5 8 1 or 0 """ if integer: dtype=int else: dtype=float l = self._read_line(f) N = int(l) rows = [] for i in range(N): l = self._read_line(f) row = nm.fromstring(l, sep=" ", dtype=dtype) rows.append(row) return nm.array(rows)
[docs]def mesh_from_groups(mesh, ids, coors, ngroups, tris, mat_tris, quads, mat_quads, tetras, mat_tetras, hexas, mat_hexas, remap=None): ids = nm.asarray(ids, dtype=nm.int32) coors = nm.asarray(coors, dtype=nm.float64) if remap is None: n_nod = coors.shape[0] remap = nm.zeros((ids.max()+1,), dtype=nm.int32) remap[ids] = nm.arange(n_nod, dtype=nm.int32) tris = remap[nm.array(tris, dtype=nm.int32)] quads = remap[nm.array(quads, dtype=nm.int32)] tetras = remap[nm.array(tetras, dtype=nm.int32)] hexas = remap[nm.array(hexas, dtype=nm.int32)] conns = [tris, quads, tetras, hexas] mat_ids = [nm.array(ar, dtype=nm.int32) for ar in [mat_tris, mat_quads, mat_tetras, mat_hexas]] descs = ['2_3', '2_4', '3_4', '3_8'] # Remove empty groups. conns, mat_ids, descs = zip(*[(conns[ig], mat_ids[ig], descs[ig]) for ig in range(4) if conns[ig].shape[0] > 0]) mesh._set_io_data(coors, ngroups, conns, mat_ids, descs) return mesh
[docs]class HypermeshAsciiMeshIO(MeshIO): format = 'hmascii'
[docs] def read(self, mesh, **kwargs): fd = open(self.filename, 'r') ids = [] coors = [] tetras = [] mat_tetras = [] hexas = [] mat_hexas = [] quads = [] mat_quads = [] trias = [] mat_trias = [] mat_id = 0 for line in fd: if line and (line[0] == '*'): if line[1:10] == 'component': line = line.strip()[11:-1].split(',') mat_id = int(line[0]) if line[1:5] == 'node': line = line.strip()[6:-1].split(',') ids.append(int(line[0])) coors.append([float(coor) for coor in line[1:4]]) elif line[1:7] == 'tetra4': line = line.strip()[8:-1].split(',') mat_tetras.append(mat_id) tetras.append([int(ic) for ic in line[2:6]]) elif line[1:6] == 'hexa8': line = line.strip()[7:-1].split(',') mat_hexas.append(mat_id) hexas.append([int(ic) for ic in line[2:10]]) elif line[1:6] == 'quad4': line = line.strip()[7:-1].split(',') mat_quads.append(mat_id) quads.append([int(ic) for ic in line[2:6]]) elif line[1:6] == 'tria3': line = line.strip()[7:-1].split(',') mat_trias.append(mat_id) trias.append([int(ic) for ic in line[2:5]]) fd.close() mesh = mesh_from_groups(mesh, ids, coors, None, trias, mat_trias, quads, mat_quads, tetras, mat_tetras, hexas, mat_hexas) return mesh
[docs] def read_dimension(self): return 3
[docs] def write(self, filename, mesh, out=None, **kwargs): raise NotImplementedError
[docs]class NEUMeshIO(MeshIO): format = 'gambit'
[docs] def read_dimension(self, ret_fd=False): fd = open(self.filename, 'r') row = fd.readline().split() while 1: if not row: break if len(row) == 0: continue if (row[0] == 'NUMNP'): row = fd.readline().split() n_nod, n_el, dim = row[0], row[1], int(row[4]) break if ret_fd: return dim, fd else: fd.close() return dim
[docs] def read(self, mesh, **kwargs): el = {'3_8' : [], '3_4' : [], '2_4' : [], '2_3' : []} nod = [] conns_in = [] descs = [] group_ids = [] group_n_els = [] groups = [] nodal_bcs = {} fd = open(self.filename, 'r') row = fd.readline() while 1: if not row: break row = row.split() if len(row) == 0: row = fd.readline() continue if (row[0] == 'NUMNP'): row = fd.readline().split() n_nod, n_el, dim = int(row[0]), int(row[1]), int(row[4]) elif (row[0] == 'NODAL'): row = fd.readline().split() while not(row[0] == 'ENDOFSECTION'): nod.append(row[1:]) row = fd.readline().split() elif (row[0] == 'ELEMENTS/CELLS'): row = fd.readline().split() while not(row[0] == 'ENDOFSECTION'): elid = [row[0]] gtype = int(row[1]) if gtype == 6: el['3_4'].append(row[3:]+elid) elif gtype == 4: rr = row[3:] if (len(rr) < 8): rr.extend(fd.readline().split()) el['3_8'].append(rr+elid) elif gtype == 3: el['2_3'].append(row[3:]+elid) elif gtype == 2: el['2_4'].append(row[3:]+elid) row = fd.readline().split() elif (row[0] == 'GROUP:'): group_ids.append(row[1]) g_n_el = int(row[3]) group_n_els.append(g_n_el) name = fd.readline().strip() els = [] row = fd.readline().split() row = fd.readline().split() while not(row[0] == 'ENDOFSECTION'): els.extend(row) row = fd.readline().split() if g_n_el != len(els): msg = 'wrong number of group elements! (%d == %d)'\ % (n_el, len(els)) raise ValueError(msg) groups.append(els) elif (row[0] == 'BOUNDARY'): row = fd.readline().split() key = row[0] num = int(row[2]) inod = read_array(fd, num, None, nm.int32) - 1 nodal_bcs[key] = inod.squeeze() row = fd.readline().split() assert_(row[0] == 'ENDOFSECTION') row = fd.readline() fd.close() if int(n_el) != sum(group_n_els): print('wrong total number of group elements! (%d == %d)'\ % (int(n_el), len(group_n_els))) mat_ids = nm.zeros(n_el, dtype=nm.int32) for ii, els in enumerate(groups): els = nm.array(els, dtype=nm.int32) mat_ids[els - 1] = group_ids[ii] for elem in el.keys(): if len(el[elem]) > 0: els = nm.array(el[elem], dtype=nm.int32) els[:, :-1] -= 1 els[:, -1] = mat_ids[els[:, -1]-1] if elem == '3_8': els = els[:, [0, 1, 3, 2, 4, 5, 7, 6, 8]] conns_in.append(els) descs.append(elem) nod = nm.array(nod, nm.float64) conns, mat_ids = split_conns_mat_ids(conns_in) mesh._set_io_data(nod, None, conns, mat_ids, descs, nodal_bcs=nodal_bcs) return mesh
[docs] def write(self, filename, mesh, out=None, **kwargs): raise NotImplementedError
[docs]class ANSYSCDBMeshIO(MeshIO): format = 'ansys_cdb'
[docs] @staticmethod def guess(filename): fd = open(filename, 'r') for ii in range(1000): row = fd.readline() if not row: break if len(row) == 0: continue row = row.split(',') kw = row[0].lower() if (kw == 'nblock'): ok = True break else: ok = False fd.close() return ok
[docs] @staticmethod def make_format(format, nchar=1000): idx = [] dtype = [] start = 0 for iform in format: ret = iform.partition('i') if not ret[1]: ret = iform.partition('e') if not ret[1]: raise ValueError aux = ret[2].partition('.') step = int(aux[0]) for j in range(int(ret[0])): if (start + step) > nchar: break idx.append((start, start+step)) start += step dtype.append(ret[1]) return idx, dtype
[docs] def write(self, filename, mesh, out=None, **kwargs): raise NotImplementedError
[docs] def read_bounding_box(self): raise NotImplementedError
[docs] def read_dimension(self, ret_fd=False): return 3
[docs] def read(self, mesh, **kwargs): ids = [] coors = [] tetras = [] hexas = [] qtetras = [] qhexas = [] nodal_bcs = {} fd = open(self.filename, 'r') while True: row = fd.readline() if not row: break if len(row) == 0: continue row = row.split(',') kw = row[0].lower() if (kw == 'nblock'): # Solid keyword -> 3, otherwise 1 is the starting coors index. ic = 3 if len(row) == 3 else 1 fmt = fd.readline() fmt = fmt.strip()[1:-1].split(',') row = look_ahead_line(fd) nchar = len(row) idx, dtype = self.make_format(fmt, nchar) ii0, ii1 = idx[0] while True: row = fd.readline() if ((row[0] == '!') or (row[:2] == '-1') or len(row) != nchar): break line = [float(row[i0:i1]) for i0, i1 in idx[ic:]] ids.append(int(row[ii0:ii1])) coors.append(line) elif (kw == 'eblock'): if (len(row) <= 2) or row[2].strip().lower() != 'solid': continue fmt = fd.readline() fmt = [fmt.strip()[1:-1]] row = look_ahead_line(fd) nchar = len(row) idx, dtype = self.make_format(fmt, nchar) imi0, imi1 = idx[0] # Material id. inn0, inn1 = idx[8] # Number of nodes in line. ien0, ien1 = idx[10] # Element number. ic0 = 11 while True: row = fd.readline() if ((row[0] == '!') or (row[:2] == '-1') or (len(row) != nchar)): break line = [int(row[imi0:imi1])] n_nod = int(row[inn0:inn1]) line.extend(int(row[i0:i1]) for i0, i1 in idx[ic0 : ic0 + n_nod]) if n_nod == 4: tetras.append(line) elif n_nod == 8: hexas.append(line) elif n_nod == 10: row = fd.readline() line.extend(int(row[i0:i1]) for i0, i1 in idx[:2]) qtetras.append(line) elif n_nod == 20: row = fd.readline() line.extend(int(row[i0:i1]) for i0, i1 in idx[:12]) qhexas.append(line) else: raise ValueError('unsupported element type! (%d nodes)' % n_nod) elif kw == 'cmblock': if row[2].lower() != 'node': # Only node sets support. continue n_nod = int(row[3].split('!')[0]) fd.readline() # Format line not needed. nods = read_array(fd, n_nod, 1, nm.int32) nodal_bcs[row[1].strip()] = nods.ravel() fd.close() coors = nm.array(coors, dtype=nm.float64) tetras = nm.array(tetras, dtype=nm.int32) if len(tetras): mat_ids_tetras = tetras[:, 0] tetras = tetras[:, 1:] else: tetras.shape = (0, 4) mat_ids_tetras = nm.array([]) hexas = nm.array(hexas, dtype=nm.int32) if len(hexas): mat_ids_hexas = hexas[:, 0] hexas = hexas[:, 1:] else: hexas.shape = (0, 8) mat_ids_hexas = nm.array([]) if len(qtetras): qtetras = nm.array(qtetras, dtype=nm.int32) tetras.shape = (max(0, tetras.shape[0]), 4) tetras = nm.r_[tetras, qtetras[:, 1:5]] mat_ids_tetras = nm.r_[mat_ids_tetras, qtetras[:, 0]] if len(qhexas): qhexas = nm.array(qhexas, dtype=nm.int32) hexas.shape = (max(0, hexas.shape[0]), 8) hexas = nm.r_[hexas, qhexas[:, 1:9]] mat_ids_hexas = nm.r_[mat_ids_hexas, qhexas[:, 0]] if len(qtetras) or len(qhexas): ii = nm.union1d(tetras.ravel(), hexas.ravel()) n_nod = len(ii) remap = nm.zeros((ii.max()+1,), dtype=nm.int32) remap[ii] = nm.arange(n_nod, dtype=nm.int32) ic = nm.searchsorted(ids, ii) coors = coors[ic] else: n_nod = coors.shape[0] remap = nm.zeros((nm.array(ids).max() + 1,), dtype=nm.int32) remap[ids] = nm.arange(n_nod, dtype=nm.int32) # Convert tetras as degenerate hexas to true tetras. ii = nm.where((hexas[:, 2] == hexas[:, 3]) & (hexas[:, 4] == hexas[:, 5]) & (hexas[:, 4] == hexas[:, 6]) & (hexas[:, 4] == hexas[:, 7]))[0] if len(ii) == len(hexas): tetras = nm.r_[tetras, hexas[ii[:, None], [0, 1, 2, 4]]] mat_ids_tetras = nm.r_[mat_ids_tetras, mat_ids_hexas[ii]] hexas = nm.delete(hexas, ii, axis=0) mat_ids_hexas = nm.delete(mat_ids_hexas, ii) else: output('WARNING: mesh "%s" has both tetrahedra and hexahedra!' % mesh.name) ngroups = nm.zeros(len(coors), dtype=nm.int32) mesh = mesh_from_groups(mesh, ids, coors, ngroups, [], [], [], [], tetras, mat_ids_tetras, hexas, mat_ids_hexas, remap=remap) mesh.nodal_bcs = {} for key, nods in six.iteritems(nodal_bcs): nods = nods[nods < len(remap)] mesh.nodal_bcs[key] = remap[nods] return mesh
[docs]class GmshIO(MeshioLibIO): """ Used to read and write data in .msh format when file_format gmsh-dg is specified. Tailored for use with Discontinous galerking methods, mesh and ElementNodeData with InterpolationScheme can be written and read. It however omits mat_ids and node_groups. For details on format see [1]. For details on representing and visualization of DG FEM data using gmsh see [2]. [1] http://gmsh.info/doc/texinfo/gmsh.html#File-formats [2] Remacle, J.-F., Chevaugeon, N., Marchandise, E., & Geuzaine, C. (2007). Efficient visualization of high-order finite elements. International Journal for Numerical Methods in Engineering, 69(4), 750-771. https://doi.org/10.1002/nme.1787 """ format = 'gmshio' load_slices = {"all" : slice(0, None), "first": slice(0, 1), "last": slice(-1, None)} def __init__(self, filename, file_format=None, **kwargs): MeshioLibIO.__init__(self, filename=filename, file_format=None, **kwargs) def _get_filename_format(self, filename): try: basename, step_num, extension = filename.split(".") except ValueError: raise ValueError("Filename of automatically loaded GMSH data must be:" + "<base name>.<step number>.msh, {} does to " + "correspond to that" .format(filename)) n_digits = len(step_num) return basename + ".{:0"+str(n_digits)+"d}." + extension def _get_filename_wildcard(self, filename): try: basename, step_num, extension = filename.split(".") except ValueError: raise ValueError("Filename of automatically loaded GMSH data must be:" + "<base name>.<step number>.msh, {} does to " + "correspond to that" .format(filename)) return basename + ".*[0-9]." + extension
[docs] def read_data(self, step=None, filename=None, cache=None): """ Reads file or files with basename filename or self.filename. Considers all files to contain data from time steps of solution of single transient problem i.e. all data have the same shape, mesh and same interpolation scheme in case of ElementNodeData. Does not read mulitple NodeData or ElementData. For stationary problems just reads one file with time 0.0 and time step 0. Providing filename allows reading multiple files of format `basename.*[0-9].msh` Parameters ---------- step : String, int, optional "all", "last", "first" or number of step to read: if "all" read all files with the basename and varying step, if "last" read only last step of all files with the filename, if "first" reads step=0, if None reads file with filename provided or specified in object. filename : string, optional Filename of the files to use, if None filename from object is used. Basename is extracted as `basename.*[0-9].msh` cache : has no effect Returns ------- out : dictionary Keys represent name of data, values are Structs with attributes: data : list, array For ElementNodeData with shape (n_cell, n_cell_dof) contains for each time step. For other contains array of data from last time step. time : list Contains times. time_n : list Contains time step numbers. scheme : Struct Interpolation scheme used in data, only one interpolation scheme is allowed. scheme_name : str Name of the interpolation scheme, repeated fo convenience. mode : str Represents of type of data. cell_nodes : for ElementNodeData; vertex or cell : Note that for vertex and cell data reading multiple time steps does not work yet. Notes ----- The interpolation scheme `Struct` contains the following items: name : string Name of the scheme. F : array Coefficients matrix as defined in [1] and [2]. P : array Exponents matrix as defined in [1] and [2]. """ filename = get_default(filename, self.filename) out = {} def append_data_structs(struct1, struct2): struct = struct1 + struct2 if hasattr(struct, "data"): struct.data = struct1.data + struct2.data if hasattr(struct, "time"): struct.time = struct1.time + struct2.time if hasattr(struct, "time_n"): struct.time_n = struct1.time_n + struct2.time_n return struct if step in ["all", "last", "first"]: import glob from os.path import join as pjoin filename_wildcard = self._get_filename_wildcard(filename) filenames = glob.glob(filename_wildcard)[self.load_slices[step]] for filename in filenames: element_node_out = self._read_element_node_data(filename) for key, val in element_node_out.items(): out[key] = append_data_structs( out.setdefault(key, Struct(data=[], time=[], time_n=[])), val) # read vertex or cell data vertex_cell_out = super(GmshIO, self).read_data(step, filename) out.update(vertex_cell_out) elif isinstance(step, int) and not op.exists(filename): filename_format = self._get_filename_format(filename) filename = filename_format.format(step) try: element_node_out = self._read_element_node_data(filename) out.update(element_node_out) # read vertex or cell data vertex_cell_out = super(GmshIO, self).read_data(step, filename) out.update(vertex_cell_out) except FileNotFoundError as e: raise FileNotFoundError(str(e) + " Maybe time step {} is not in output." .format(step)) elif step is None or op.exists(filename): element_node_out = self._read_element_node_data(filename) out.update(element_node_out) # read vertex or cell data vertex_cell_out = super(GmshIO, self).read_data(step, filename) out.update(vertex_cell_out) else: raise ValueError("Unsupported vaule for step : {}".format(step)) return out
def _read_element_node_data(self, filename): try: fd = open(filename, "r") except FileNotFoundError: raise FileNotFoundError("[Errno 2] No such file or directory: {}." .format(filename)) out = {} schemes = {} while 1: line = skip_read_line(fd).split() if not line: break ls = line[0] if ls == "$InterpolationScheme": scheme = Struct(name=None, desc=None, F=None, P=None) scheme.name = skip_read_line(fd).strip('"\'') n_int_tags = int(skip_read_line(fd)) scheme.desc = int(skip_read_line(fd)) n_matrices = int(skip_read_line(fd)) f_shape = [int(i) for i in skip_read_line(fd).split(" ")] scheme.F = read_array(fd, f_shape[0], f_shape[1], nm.float64) p_shape = [int(i) for i in skip_read_line(fd).split(" ")] scheme.P = read_array(fd, p_shape[0], p_shape[1], nm.float64) schemes[scheme.name] = scheme elif ls == "$ElementNodeData": n_str_tags = int(skip_read_line(fd)) data_name = skip_read_line(fd).strip('"\'') if n_str_tags == 2: scheme_name = skip_read_line(fd).strip('"\'') n_float_tags = int(skip_read_line(fd)) time = float(skip_read_line(fd)) n_int_tags = int(skip_read_line(fd)) time_n = int(skip_read_line(fd)) comp = int(skip_read_line(fd)) n_el = int(skip_read_line(fd)) n_el_nod = int(look_ahead_line(fd).split()[1]) # read data including indexing data = read_array(fd, n_el, n_el_nod + 2 , nm.float64) # strip indexing columns data = data[:, 2:] out[data_name] = Struct(name=data_name, data=[data], time=[time], time_n=[time_n], scheme_name=scheme_name, scheme=schemes.get(scheme_name), mode="cell_nodes") elif line[0] == '#' or ls[:4] == '$End': pass fd.close() # add schemes read later than data for key, val in out.items(): if val.scheme is None: val.scheme = schemes[val.scheme_name] return out def _write_interpolation_scheme(self, fd, scheme): """ Unpacks matrices from scheme struct and writes them in correct format for gmsh to read. Parameters ---------- fd : File opened for writing. scheme : Struct Struct with interpolation scheme used in data, only one interpolation scheme is allowed, contains : name - name of the scheme, F - coeficients matrix, P - exponents matrix as defined in [1] and [2]. """ fd.write('$InterpolationScheme\n') fd.write('"{}"\n'.format(scheme.name)) fd.write("1\n") # one int tag fd.write("{}\n".format(scheme.desc[-1])) fd.write("2\n") # number of matrices fd.write("{} {}\n".format(*scheme.F.shape)) sF = "{} " * scheme.F.shape[1] + "\n" for row in scheme.F: fd.write(sF.format(*row)) fd.write("{} {}\n".format(*scheme.P.shape)) sP = "{} " * scheme.P.shape[1] + "\n" for row in scheme.P: fd.write(sP.format(*row)) fd.write('$EndInterpolationScheme\n') def _write_elementnode_data(self, fd, out, ts): """ Writes "cell_nodes" data in out as $ElementNodeData, including interpolation scheme. """ for key, value in out.items(): if not value.mode == "cell_nodes": continue if value.scheme is not None: self._write_interpolation_scheme(fd, value.scheme) scheme_name = value.scheme.name data = value.data n_el_nod = nm.shape(data)[1] fd.write("$ElementNodeData\n") fd.write("{}\n".format(1 if scheme_name is None else 2)) fd.write('"{}"\n'.format(key)) # name if scheme_name is not None: fd.write('"{}"\n'.format(scheme_name)) fd.write("1\n") # number of real tags fd.write("{}\n".format(ts.time if ts is not None else 0.0)) fd.write("3\n") # number of integer tags fd.write("{}\n".format(ts.step if ts is not None else 0)) fd.write("1\n") # number of components fd.write("{}\n".format(data.shape[0])) s = "{} {}" + n_el_nod * " {}" + "\n" for i, el_node_vals in enumerate(data, 1): fd.write(s.format(i, n_el_nod, *el_node_vals)) fd.write("$EndElementNodeData\n")
[docs] def write(self, filename, mesh, out=None, ts=None, **kwargs): """ Writes mesh and data, handles cell DOFs data from DGField as ElementNodeData. Omits gmsh:ref for cells and vertices i.e. mat_ids and node_groups to prevent cluttering the GMSH postprocessing. Parameters ---------- filename : string Path to file. mesh : sfepy.discrete.fem.mesh.Mesh Computational mesh to write. out : dictionary Keys represent name of the data, values are Structs with attributes: data : array For ElementNodeData shape is (n_cell, n_cell_dof) mode : str Represents type of data, cell_nodes for ElementNodeData. For ElementNodeData: scheme : Struct Interpolation scheme used in data, only one interpolation scheme is allowed. scheme_name : str Name of the interpolation scheme, associated with data, repeated fo convenience. ts : sfepy.solvers.ts.TimeStepper instance, optional Provides data to write time step. Notes ----- The interpolation scheme `Struct` contains the following items: name : string Name of the scheme. F : array Coefficients matrix as defined in [1] and [2]. P : array Exponents matrix as defined in [1] and [2]. """ # fd.writelines(self.msh20header) # self._write_mesh(fd, mesh) (coors, cells, point_data, point_sets, cell_data, cell_sets) = self._create_out_data(mesh, out) # gmsh:ref creates clutter in GMSH, especially for transient problems point_data.pop("gmsh:ref", None) cell_data.pop("gmsh:ref", None) meshiolib.write_points_cells(filename, coors, cells, point_data=point_data, point_sets=point_sets, cell_data=cell_data, cell_sets=cell_sets, file_format=self.file_format, binary=False) if out: with open(filename, 'a') as fd: self._write_elementnode_data(fd, out, ts) return
[docs]class XYZMeshIO(MeshIO): """ Trivial XYZ format working only with coordinates (in a .XYZ file) and the connectivity stored in another file with the same base name and .IEN suffix. """ format = 'xyz' def _read_coors(self): coors = nm.loadtxt(self.filename, ndmin=2) if (coors[:, -1] == 0).all(): coors = coors[:, :-1].copy() return coors
[docs] def read_dimension(self, ret_fd=False): coors = self._read_coors() dim = coors.shape[1] if ret_fd: fd = open(self.filename, 'r') return dim, fd else: return dim
[docs] def read_bounding_box(self, ret_fd=False, ret_dim=False): coors = self._read_coors() bbox = nm.vstack((nm.amin(coors, 0), nm.amax(coors, 0))) if ret_fd: fd = open(self.filename, 'r') if ret_dim: dim = coors.shape[1] if ret_fd: return bbox, dim, fd else: return bbox, dim else: if ret_fd: return bbox, fd else: return bbox
[docs] def read(self, mesh, omit_facets=False, **kwargs): coors = self._read_coors() n_nod, dim = coors.shape conn_ext = '.IEN' if op.splitext(self.filename)[1].isupper() else '.ien' conn = nm.loadtxt(edit_filename(self.filename, new_ext=conn_ext), dtype=nm.int32, ndmin=2) - 1 desc = '%d_%d' % (dim, conn.shape[1]) mesh._set_io_data(coors, nm.zeros(n_nod, dtype=nm.int32), [conn], [nm.zeros(conn.shape[0], dtype=nm.int32)], [desc]) return mesh
[docs] def write(self, filename, mesh, out=None, **kwargs): coors, ngroups, conns, mat_ids, desc = mesh._get_io_data() n_nod, dim = coors.shape zz = nm.zeros((n_nod, 3-dim)) nm.savetxt(filename, nm.c_[coors, zz]) conn_ext = '.IEN' if op.splitext(filename)[1].isupper() else '.ien' nm.savetxt(edit_filename(self.filename, new_ext=conn_ext), conns[0] + 1) if out is not None: raise NotImplementedError
var_dict = list(vars().items()) io_table = {} for key, var in var_dict: try: if is_derived_class(var, MeshIO): io_table[var.format] = var except TypeError: pass del var_dict def any_from_filename(filename, prefix_dir=None, file_format=None, mode='r'): """ Create a MeshIO instance according to the kind of `filename`. Parameters ---------- filename : str, function or MeshIO subclass instance The name of the mesh file. It can be also a user-supplied function accepting two arguments: `mesh`, `mode`, where `mesh` is a Mesh instance and `mode` is one of 'read','write', or a MeshIO subclass instance. prefix_dir : str The directory name to prepend to `filename`. Returns ------- io : MeshIO subclass instance The MeshIO subclass instance corresponding to the kind of `filename`. """ if not isinstance(filename, basestr): if isinstance(filename, MeshIO): return filename else: return UserMeshIO(filename) if prefix_dir is not None: filename = op.normpath(op.join(prefix_dir, filename)) kwargs = {} if file_format is not None: if file_format in supported_formats: io_class = supported_formats[file_format][0] kwargs['file_format'] = file_format else: raise ValueError('unknown mesh format! (%s)' % file_format) else: ext2io = {e: (v[0], k) for k, v in supported_formats.items() for e in v[1] if '*' not in v[2]} ext = op.splitext(filename)[1].lower() if ext in ext2io: io_class = ext2io[ext][0] file_format = ext2io[ext][1] kwargs['file_format'] = file_format else: raise ValueError('unknown mesh format! (%s)' % ext) if mode == 'w' and 'w' not in supported_formats[file_format][2]: output('writable mesh formats:') output_mesh_formats('w') msg = 'write support not implemented for output mesh format "%s",' \ ' see above!' % file_format raise ValueError(msg) return io_table[io_class](filename, **kwargs) insert_static_method(MeshIO, any_from_filename) del any_from_filename