Source code for sfepy.discrete.fem.meshio

from __future__ import print_function
from __future__ import absolute_import
import sys
from copy import copy

import numpy as nm

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, read_list, 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

supported_formats = {
    '.mesh' : 'medit',
    '.vtk'  : 'vtk',
    '.node' : 'tetgen',
    '.txt'  : 'comsol',
    '.h5'   : 'hdf5',
     # Order is important, avs_ucd does not guess -> it is the default.
    '.inp'  : ('abaqus', 'ansys_cdb', 'avs_ucd'),
    '.dat'  : 'ansys_cdb',
    '.hmascii'  : 'hmascii',
    '.mesh3d'   : 'mesh3d',
    '.bdf'  : 'nastran',
    '.neu'  : 'gambit',
    '.med'  : 'med',
    '.cdb'  : 'ansys_cdb',
    '.msh'  : 'msh_v2',
    '.xyz'  : 'xyz',
}

# Map mesh formats to read and write capabilities.
# 'r' ... read mesh
# 'w' ... write mesh
# 'rn' ... read nodes for boundary conditions
# 'wn' ... write nodes for boundary conditions
supported_capabilities = {
    'medit' : ['r', 'w'],
    'vtk' : ['r', 'w'],
    'tetgen' : ['r'],
    'comsol' : ['r', 'w'],
    'hdf5' : ['r', 'w'],
    'abaqus' : ['r'],
    'avs_ucd' : ['r'],
    'hmascii' : ['r'],
    'mesh3d' : ['r'],
    'nastran' : ['r', 'w'],
    'gambit' : ['r', 'rn'],
    'med' : ['r'],
    'ansys_cdb' : ['r'],
    'msh_v2' : ['r', 'w'],
    'xyz' : ['r', 'w'],
}

supported_cell_types = {
    'medit' : ['line2', 'tri3', 'quad4', 'tetra4', 'hexa8'],
    'vtk' : ['line2', 'tri3', 'quad4', 'tetra4', 'hexa8'],
    'tetgen' : ['tetra4'],
    'comsol' : ['tri3', 'quad4', 'tetra4', 'hexa8'],
    'hdf5' : ['user'],
    'abaqus' : ['tri3', 'quad4', 'tetra4', 'hexa8'],
    'avs_ucd' : ['tetra4', 'hexa8'],
    'hmascii' : ['tri3', 'quad4', 'tetra4', 'hexa8'],
    'mesh3d' : ['tetra4', 'hexa8'],
    'nastran' : ['tri3', 'quad4', 'tetra4', 'hexa8'],
    'gambit' : ['tri3', 'quad4', 'tetra4', 'hexa8'],
    'med' : ['tri3', 'quad4', 'tetra4', 'hexa8'],
    'ansys_cdb' : ['tetra4', 'hexa8'],
    'msh_v2' : ['line2', 'tri3', 'quad4', 'tetra4', 'hexa8'],
    'xyz' : ['line2', 'tri3', 'quad4', 'tetra4', 'hexa8'],
    'function' : ['user'],
}

[docs]def output_mesh_formats(mode='r'): for key, vals in ordered_iteritems(supported_formats): if isinstance(vals, basestr): vals = [vals] for val in vals: caps = supported_capabilities[val] if mode in caps: output('%s (%s), cell types: %s' % (val, key, supported_cell_types[val]))
[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
def _read_bounding_box(fd, dim, node_key, c0=0, ndplus=1, ret_fd=False, ret_dim=False): while 1: line = skip_read_line(fd, no_eof=True).split() if line[0] == node_key: num = int(read_token(fd)) nod = read_array(fd, num, dim + ndplus, nm.float64) break bbox = nm.vstack((nm.amin(nod[:,c0:(dim + c0)], 0), nm.amax(nod[:,c0:(dim + c0)], 0))) if ret_dim: 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]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. The methods read_dimension(), read_bounding_box() should be implemented in subclasses, as it is often possible to get that kind of information without reading the whole mesh file. 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_dimension(self, ret_fd=False): raise ValueError(MeshIO.call_msg)
[docs] def read_bounding_box(self, ret_fd=False, ret_dim=False): raise ValueError(MeshIO.call_msg)
[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')
[docs]class MeditMeshIO(MeshIO): format = 'medit'
[docs] def read_dimension(self, ret_fd=False): fd = open(self.filename, 'r') while 1: line = skip_read_line(fd, no_eof=True).split() if line[0] == 'Dimension': if len(line) == 2: dim = int(line[1]) else: dim = int(fd.readline()) break if ret_fd: return dim, fd else: fd.close() return dim
[docs] def read_bounding_box(self, ret_fd=False, ret_dim=False): fd = open(self.filename, 'r') dim, fd = self.read_dimension(ret_fd=True) return _read_bounding_box(fd, dim, 'Vertices', ret_fd=ret_fd, ret_dim=ret_dim)
[docs] def read(self, mesh, omit_facets=False, **kwargs): dim, fd = self.read_dimension(ret_fd=True) conns_in = [] descs = [] def _read_cells(dimension, size, has_id=True): num = int(read_token(fd)) data = read_array(fd, num, size + 1 * has_id, nm.int32) if omit_facets and (dimension < dim): return data[:, :-1] -= 1 conns_in.append(data) descs.append('%i_%i' % (dimension, size)) while 1: line = skip_read_line(fd).split() if not line: break ls = line[0] if (ls == 'Vertices'): num = int(read_token(fd)) nod = read_array(fd, num, dim + 1, nm.float64) elif (ls == 'Corners'): _read_cells(1, 1, False) elif (ls == 'Edges'): _read_cells(1, 2) elif (ls == 'Tetrahedra'): _read_cells(3, 4) elif (ls == 'Hexahedra'): _read_cells(3, 8) elif (ls == 'Triangles'): _read_cells(2, 3) elif (ls == 'Quadrilaterals'): _read_cells(2, 4) elif ls == 'End': break elif line[0] == '#': continue else: output('skipping unknown entity: %s' % line) continue fd.close() # Detect wedges and pyramides -> separate groups. if ('3_8' in descs): ic = descs.index('3_8') conn_in = conns_in.pop(ic) flag = nm.zeros((conn_in.shape[0],), nm.int32) for ii, el in enumerate(conn_in): if (el[4] == el[5]): if (el[5] == el[6]): flag[ii] = 2 else: flag[ii] = 1 conn = [] desc = [] ib = nm.where(flag == 0)[0] if (len(ib) > 0): conn.append(conn_in[ib]) desc.append('3_8') iw = nm.where(flag == 1)[0] if (len(iw) > 0): ar = nm.array([0,1,2,3,4,6], nm.int32) conn.append(conn_in[iw[:, None], ar]) desc.append('3_6') ip = nm.where(flag == 2)[0] if (len(ip) > 0): ar = nm.array([0,1,2,3,4], nm.int32) conn.append(conn_in[ip[:, None], ar]) desc.append('3_5') conns_in[ic:ic] = conn del(descs[ic]) descs[ic:ic] = desc conns, mat_ids = split_conns_mat_ids(conns_in) mesh._set_io_data(nod[:,:-1], nod[:,-1], conns, mat_ids, descs) return mesh
[docs] def write(self, filename, mesh, out=None, **kwargs): fd = open(filename, 'w') coors, ngroups, conns, mat_ids, desc = mesh._get_io_data() n_nod, dim = coors.shape fd.write("MeshVersionFormatted 1\nDimension %d\n" % dim) fd.write("Vertices\n%d\n" % n_nod) format = self.get_vector_format(dim) + ' %d\n' for ii in range(n_nod): nn = tuple(coors[ii]) + (ngroups[ii],) fd.write(format % tuple(nn)) for ig, conn in enumerate(conns): ids = mat_ids[ig] if (desc[ig] == "1_1"): fd.write("Corners\n%d\n" % conn.shape[0]) for ii in range(conn.shape[0]): nn = conn[ii] + 1 fd.write("%d\n" % nn[0]) elif (desc[ig] == "1_2"): fd.write("Edges\n%d\n" % conn.shape[0]) for ii in range(conn.shape[0]): nn = conn[ii] + 1 fd.write("%d %d %d\n" % (nn[0], nn[1], ids[ii])) elif (desc[ig] == "2_4"): fd.write("Quadrilaterals\n%d\n" % conn.shape[0]) for ii in range(conn.shape[0]): nn = conn[ii] + 1 fd.write("%d %d %d %d %d\n" % (nn[0], nn[1], nn[2], nn[3], ids[ii])) elif (desc[ig] == "2_3"): fd.write("Triangles\n%d\n" % conn.shape[0]) for ii in range(conn.shape[0]): nn = conn[ii] + 1 fd.write("%d %d %d %d\n" % (nn[0], nn[1], nn[2], ids[ii])) elif (desc[ig] == "3_4"): fd.write("Tetrahedra\n%d\n" % conn.shape[0]) for ii in range(conn.shape[0]): nn = conn[ii] + 1 fd.write("%d %d %d %d %d\n" % (nn[0], nn[1], nn[2], nn[3], ids[ii])) elif (desc[ig] == "3_8"): fd.write("Hexahedra\n%d\n" % conn.shape[0]) for ii in range(conn.shape[0]): nn = conn[ii] + 1 fd.write("%d %d %d %d %d %d %d %d %d\n" % (nn[0], nn[1], nn[2], nn[3], nn[4], nn[5], nn[6], nn[7], ids[ii])) 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
vtk_header = r"""x vtk DataFile Version 2.0 step %d time %e normalized time %e, generated by %s ASCII DATASET UNSTRUCTURED_GRID """ vtk_cell_types = {'1_1' : 1, '1_2' : 3, '2_2' : 3, '3_2' : 3, '2_3' : 5, '2_4' : 9, '3_4' : 10, '3_8' : 12} vtk_dims = {1 : 1, 3 : 1, 5 : 2, 9 : 2, 10 : 3, 12 : 3} vtk_inverse_cell_types = {3 : '1_2', 5 : '2_3', 8 : '2_4', 9 : '2_4', 10 : '3_4', 11 : '3_8', 12 : '3_8'} vtk_remap = {8 : nm.array([0, 1, 3, 2], dtype=nm.int32), 11 : nm.array([0, 1, 3, 2, 4, 5, 7, 6], dtype=nm.int32)} vtk_remap_keys = list(vtk_remap.keys())
[docs]class VTKMeshIO(MeshIO): format = 'vtk'
[docs] def read_coors(self, ret_fd=False): fd = open(self.filename, 'r') while 1: line = skip_read_line(fd, no_eof=True).split() if line[0] == 'POINTS': n_nod = int(line[1]) coors = read_array(fd, n_nod, 3, nm.float64) break if ret_fd: return coors, fd else: fd.close() return coors
[docs] def get_dimension(self, coors): dz = nm.diff(coors[:,2]) if nm.allclose(dz, 0.0): dim = 2 else: dim = 3 return dim
[docs] def read_dimension(self, ret_fd=False): coors, fd = self.read_coors(ret_fd=True) dim = self.get_dimension(coors) if ret_fd: return dim, fd else: fd.close() return dim
[docs] def read_bounding_box(self, ret_fd=False, ret_dim=False): coors, fd = self.read_coors(ret_fd=True) dim = self.get_dimension(coors) bbox = nm.vstack((nm.amin(coors[:,:dim], 0), nm.amax(coors[:,:dim], 0))) if ret_dim: 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, **kwargs): fd = open(self.filename, 'r') mode = 'header' mode_status = 0 coors = conns = mat_id = node_grps = None finished = 0 while 1: line = skip_read_line(fd) if not line: break if mode == 'header': if mode_status == 0: if line.strip() == 'ASCII': mode_status = 1 elif mode_status == 1: if line.strip() == 'DATASET UNSTRUCTURED_GRID': mode_status = 0 mode = 'points' elif mode == 'points': line = line.split() if line[0] == 'POINTS': n_nod = int(line[1]) coors = read_array(fd, n_nod, 3, nm.float64) mode = 'cells' elif mode == 'cells': line = line.split() if line[0] == 'CELLS': n_el, n_val = map(int, line[1:3]) raw_conn = read_list(fd, n_val, int) mode = 'cell_types' elif mode == 'cell_types': line = line.split() if line[0] == 'CELL_TYPES': assert_(int(line[1]) == n_el) cell_types = read_array(fd, n_el, 1, nm.int32) mode = 'cp_data' elif mode == 'cp_data': line = line.split() if line[0] == 'CELL_DATA': assert_(int(line[1]) == n_el) mode_status = 1 mode = 'mat_id' elif line[0] == 'POINT_DATA': assert_(int(line[1]) == n_nod) mode_status = 1 mode = 'node_groups' elif mode == 'mat_id': if mode_status == 1: if 'SCALARS mat_id int' in line.strip(): mode_status = 2 elif mode_status == 2: if line.strip() == 'LOOKUP_TABLE default': mat_id = read_list(fd, n_el, int) mode_status = 0 mode = 'cp_data' finished += 1 elif mode == 'node_groups': if mode_status == 1: if 'SCALARS node_groups int' in line.strip(): mode_status = 2 elif mode_status == 2: if line.strip() == 'LOOKUP_TABLE default': node_grps = read_list(fd, n_nod, int) mode_status = 0 mode = 'cp_data' finished += 1 elif finished >= 2: break fd.close() if mat_id is None: mat_id = [[0]] * n_el else: if len(mat_id) < n_el: mat_id = [[ii] for jj in mat_id for ii in jj] if node_grps is None: node_grps = [0] * n_nod else: if len(node_grps) < n_nod: node_grps = [ii for jj in node_grps for ii in jj] dim = self.get_dimension(coors) if dim == 2: coors = coors[:,:2] coors = nm.ascontiguousarray(coors) cell_types = cell_types.squeeze() dconns = {} for iel, row in enumerate(raw_conn): vct = cell_types[iel] if vct not in vtk_inverse_cell_types: continue ct = vtk_inverse_cell_types[vct] dconns.setdefault(vct, []).append(row[1:] + mat_id[iel]) descs = [] conns = [] mat_ids = [] for ct, conn in six.iteritems(dconns): sct = vtk_inverse_cell_types[ct] descs.append(sct) aux = nm.array(conn, dtype=nm.int32) aconn = aux[:, :-1] if ct in vtk_remap_keys: # Remap pixels and voxels. aconn[:] = aconn[:, vtk_remap[ct]] conns.append(aconn) mat_ids.append(aux[:, -1]) mesh._set_io_data(coors, node_grps, conns, mat_ids, descs) return mesh
[docs] def write(self, filename, mesh, out=None, ts=None, **kwargs): def _reshape_tensors(data, dim, sym, nc): if dim == 3: if nc == sym: aux = data[:, [0,3,4,3,1,5,4,5,2]] elif nc == (dim * dim): aux = data[:, [0,3,4,6,1,5,7,8,2]] else: aux = data.reshape((data.shape[0], dim*dim)) else: zz = nm.zeros((data.shape[0], 1), dtype=nm.float64) if nc == sym: aux = nm.c_[data[:,[0,2]], zz, data[:,[2,1]], zz, zz, zz, zz] elif nc == (dim * dim): aux = nm.c_[data[:,[0,2]], zz, data[:,[3,1]], zz, zz, zz, zz] else: aux = nm.c_[data[:,0,[0,1]], zz, data[:,1,[0,1]], zz, zz, zz, zz] return aux def _write_tensors(data): format = self.get_vector_format(3) format = '\n'.join([format] * 3) + '\n\n' for row in aux: fd.write(format % tuple(row)) if ts is None: step, time, nt = 0, 0.0, 0.0 else: step, time, nt = ts.step, ts.time, ts.nt coors, ngroups, conns, mat_ids, descs = mesh._get_io_data() fd = open(filename, 'w') fd.write(vtk_header % (step, time, nt, op.basename(sys.argv[0]))) n_nod, dim = coors.shape sym = (dim + 1) * dim // 2 fd.write('\nPOINTS %d float\n' % n_nod) aux = coors if dim < 3: aux = nm.hstack((aux, nm.zeros((aux.shape[0], 3 - dim), dtype=aux.dtype))) format = self.get_vector_format(3) + '\n' for row in aux: fd.write(format % tuple(row)) n_el = mesh.n_el n_els, n_e_ps = nm.array([conn.shape for conn in conns]).T total_size = nm.dot(n_els, n_e_ps + 1) fd.write('\nCELLS %d %d\n' % (n_el, total_size)) ct = [] for ig, conn in enumerate(conns): nn = n_e_ps[ig] + 1 ct += [vtk_cell_types[descs[ig]]] * n_els[ig] format = ' '.join(['%d'] * nn + ['\n']) for row in conn: fd.write(format % ((nn-1,) + tuple(row))) fd.write('\nCELL_TYPES %d\n' % n_el) fd.write(''.join(['%d\n' % ii for ii in ct])) fd.write('\nPOINT_DATA %d\n' % n_nod) # node groups fd.write('\nSCALARS node_groups int 1\nLOOKUP_TABLE default\n') fd.write(''.join(['%d\n' % ii for ii in ngroups])) if out is not None: point_keys = [key for key, val in six.iteritems(out) if val.mode == 'vertex'] else: point_keys = {} for key in point_keys: val = out[key] nr, nc = val.data.shape if nc == 1: fd.write('\nSCALARS %s float %d\n' % (key, nc)) fd.write('LOOKUP_TABLE default\n') format = self.float_format + '\n' for row in val.data: fd.write(format % row) elif nc == dim: fd.write('\nVECTORS %s float\n' % key) if dim == 2: aux = nm.hstack((val.data, nm.zeros((nr, 1), dtype=nm.float64))) else: aux = val.data format = self.get_vector_format(3) + '\n' for row in aux: fd.write(format % tuple(row)) elif (nc == sym) or (nc == (dim * dim)): fd.write('\nTENSORS %s float\n' % key) aux = _reshape_tensors(val.data, dim, sym, nc) _write_tensors(aux) else: raise NotImplementedError(nc) if out is not None: cell_keys = [key for key, val in six.iteritems(out) if val.mode == 'cell'] else: cell_keys = {} fd.write('\nCELL_DATA %d\n' % n_el) # cells - mat_id fd.write('SCALARS mat_id int 1\nLOOKUP_TABLE default\n') aux = nm.hstack(mat_ids).tolist() fd.write(''.join(['%d\n' % ii for ii in aux])) for key in cell_keys: val = out[key] ne, aux, nr, nc = val.data.shape if (nr == 1) and (nc == 1): fd.write('\nSCALARS %s float %d\n' % (key, nc)) fd.write('LOOKUP_TABLE default\n') format = self.float_format + '\n' aux = val.data.squeeze() if len(aux.shape) == 0: fd.write(format % aux) else: for row in aux: fd.write(format % row) elif (nr == dim) and (nc == 1): fd.write('\nVECTORS %s float\n' % key) if dim == 2: aux = nm.hstack((val.data.squeeze(), nm.zeros((ne, 1), dtype=nm.float64))) else: aux = val.data format = self.get_vector_format(3) + '\n' for row in aux: fd.write(format % tuple(row.squeeze())) elif (((nr == sym) or (nr == (dim * dim))) and (nc == 1)) \ or ((nr == dim) and (nc == dim)): fd.write('\nTENSORS %s float\n' % key) data = val.data[:, 0, ...] if data.shape[-1] == 1: data.shape = (data.shape[0], -1) aux = _reshape_tensors(data, dim, sym, nr) _write_tensors(aux) else: raise NotImplementedError(nr, nc) fd.close() # Mark the write finished. fd = open(filename, 'r+') fd.write('#') fd.close()
[docs] def read_data(self, step, filename=None, cache=None): filename = get_default(filename, self.filename) out = {} dim, fd = self.read_dimension(ret_fd=True) while 1: line = skip_read_line(fd, no_eof=True).split() if line[0] == 'POINT_DATA': break num = int(line[1]) mode = 'vertex' while 1: line = skip_read_line(fd) if not line: break line = line.split() if line[0] == 'SCALARS': name, dtype, nc = line[1:] assert_(int(nc) == 1) fd.readline() # skip lookup table line data = nm.empty((num,), dtype=nm.float64) for ii in range(num): data[ii] = float(fd.readline()) out[name] = Struct(name=name, mode=mode, data=data, dofs=None) elif line[0] == 'VECTORS': name, dtype = line[1:] data = nm.empty((num, dim), dtype=nm.float64) for ii in range(num): data[ii] = [float(val) for val in fd.readline().split()][:dim] out[name] = Struct(name=name, mode=mode, data=data, dofs=None) elif line[0] == 'TENSORS': name, dtype = line[1:] data3 = nm.empty((3 * num, 3), dtype=nm.float64) ii = 0 while ii < 3 * num: aux = [float(val) for val in fd.readline().split()] if not len(aux): continue data3[ii] = aux ii += 1 data = data3.reshape((-1, 1, 3, 3))[..., :dim, :dim] out[name] = Struct(name=name, mode=mode, data=data, dofs=None) elif line[0] == 'CELL_DATA': num = int(line[1]) mode = 'cell' else: line = fd.readline() fd.close() return out
[docs]class TetgenMeshIO(MeshIO): format = "tetgen"
[docs] def read(self, mesh, **kwargs): import os fname = os.path.splitext(self.filename)[0] nodes = self.getnodes(fname+".node") etype, elements, regions = self.getele(fname+".ele") descs = [] conns = [] mat_ids = [] elements = nm.array(elements, dtype=nm.int32) - 1 for key, value in six.iteritems(regions): descs.append(etype) mat_ids.append(nm.ones_like(value) * key) conns.append(elements[nm.array(value)-1].copy()) mesh._set_io_data(nodes, None, conns, mat_ids, descs) return mesh
[docs] @staticmethod def getnodes(fnods): """ Reads t.1.nodes, returns a list of nodes. Example: >>> self.getnodes("t.1.node") [(0.0, 0.0, 0.0), (4.0, 0.0, 0.0), (0.0, 4.0, 0.0), (-4.0, 0.0, 0.0), (0.0, 0.0, 4.0), (0.0, -4.0, 0.0), (0.0, -0.0, -4.0), (-2.0, 0.0, -2.0), (-2.0, 2.0, 0.0), (0.0, 2.0, -2.0), (0.0, -2.0, -2.0), (2.0, 0.0, -2.0), (2.0, 2.0, 0.0), ... ] """ f = open(fnods) l = [int(x) for x in f.readline().split()] npoints, dim, nattrib, nbound = l if dim == 2: ndapp = [0.0] else: ndapp = [] nodes = [] for line in f: if line[0] == "#": continue l = [float(x) for x in line.split()] l = l[:(dim + 1)] assert_(int(l[0]) == len(nodes)+1) l = l[1:] nodes.append(tuple(l + ndapp)) assert_(npoints == len(nodes)) return nodes
[docs] @staticmethod def getele(fele): """ Reads t.1.ele, returns a list of elements. Example: >>> elements, regions = self.getele("t.1.ele") >>> elements [(20, 154, 122, 258), (86, 186, 134, 238), (15, 309, 170, 310), (146, 229, 145, 285), (206, 207, 125, 211), (99, 193, 39, 194), (185, 197, 158, 225), (53, 76, 74, 6), (19, 138, 129, 313), (23, 60, 47, 96), (119, 321, 1, 329), (188, 296, 122, 322), (30, 255, 177, 256), ...] >>> regions {100: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 7, ...], ...} """ f = open(fele) l = [int(x) for x in f.readline().split()] ntetra,nnod,nattrib = l #we have either linear or quadratic tetrahedra: elem = None if nnod in [4,10]: elem = '3_4' linear = (nnod == 4) if nnod in [3, 7]: elem = '2_3' linear = (nnod == 3) if elem is None or not linear: raise ValueError("Only linear triangle and tetrahedra reader" " is implemented") els = [] regions = {} for line in f: if line[0] == "#": continue l = [int(x) for x in line.split()] if elem == '2_3': assert_((len(l) - 1 - nattrib) == 3) els.append((l[1],l[2],l[3])) if elem == '3_4': assert_((len(l) - 1 - nattrib) == 4) els.append((l[1],l[2],l[3],l[4])) if nattrib == 1: regionnum = l[-1] else: regionnum = 1 if regionnum == 0: msg = "see %s, element # %d\n"%(fele,l[0]) msg += "there are elements not belonging to any physical entity" raise ValueError(msg) if regionnum in regions: regions[regionnum].append(l[0]) else: regions[regionnum]=[l[0]] assert_(l[0] == len(els)) return elem, els, regions
[docs] def write(self, filename, mesh, out=None, **kwargs): raise NotImplementedError
[docs] def read_dimension(self): # TetGen only supports 3D mesh return 3
[docs] def read_bounding_box(self): raise NotImplementedError
[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) 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): """ 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() 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] def write(self, filename, mesh, out=None, ts=None, cache=None, **kwargs): 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) 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): 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', val.data, cache=cache, unpack_markers=getattr(val, 'unpack_markers', False)) continue shape = val.get('shape', val.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', val.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()
[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 MEDMeshIO(MeshIO): format = "med"
[docs] def read(self, mesh, **kwargs): fd = pt.open_file(self.filename, mode="r") mesh_root = fd.root.ENS_MAA #TODO: Loop through multiple meshes? mesh_group = mesh_root._f_get_child(list(mesh_root._v_groups.keys())[0]) if not ('NOE' in list(mesh_group._v_groups.keys())): mesh_group = mesh_group._f_get_child(list(mesh_group._v_groups.keys())[0]) mesh.name = mesh_group._v_name aux_coors = mesh_group.NOE.COO.read() n_nodes = mesh_group.NOE.COO.get_attr('NBR') # Unflatten the node coordinate array dim = aux_coors.shape[0] // n_nodes coors = nm.zeros((n_nodes,dim), dtype=nm.float64) for ii in range(dim): coors[:,ii] = aux_coors[n_nodes*ii:n_nodes*(ii+1)] ngroups = mesh_group.NOE.FAM.read() assert_((ngroups >= 0).all()) # Dict to map MED element names to SfePy descs #NOTE: The commented lines are elements which # produce KeyError in SfePy med_descs = { 'TE4' : '3_4', #'T10' : '3_10', #'PY5' : '3_5', #'P13' : '3_13', 'HE8' : '3_8', #'H20' : '3_20', #'PE6' : '3_6', #'P15' : '3_15', #TODO: Polyhedrons (POE) - need special handling 'TR3' : '2_3', #'TR6' : '2_6', 'QU4' : '2_4', #'QU8' : '2_8', #TODO: Polygons (POG) - need special handling #'SE2' : '1_2', #'SE3' : '1_3', } conns = [] descs = [] mat_ids = [] for md, desc in six.iteritems(med_descs): if int(desc[0]) != dim: continue try: group = mesh_group.MAI._f_get_child(md) aux_conn = group.NOD.read() n_conns = group.NOD.get_attr('NBR') # (0 based indexing in numpy vs. 1 based in MED) nne = aux_conn.shape[0] // n_conns conn = nm.zeros((n_conns,nne), dtype=nm.int32) for ii in range(nne): conn[:,ii] = aux_conn[n_conns*ii:n_conns*(ii+1)] - 1 conns.append(conn) mat_id = group.FAM.read() assert_((mat_id <= 0).all()) mat_id = nm.abs(mat_id) mat_ids.append(mat_id) descs.append(med_descs[md]) except pt.exceptions.NoSuchNodeError: pass fd.close() mesh._set_io_data(coors, ngroups, conns, mat_ids, descs) return mesh
[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 AVSUCDMeshIO(MeshIO): format = 'avs_ucd'
[docs] @staticmethod def guess(filename): return True
[docs] def read(self, mesh, **kwargs): fd = open(self.filename, 'r') # Skip all comments. while 1: line = fd.readline() if line and (line[0] != '#'): break header = [int(ii) for ii in line.split()] n_nod, n_el = header[0:2] ids = nm.zeros((n_nod,), dtype=nm.int32) dim = 3 coors = nm.zeros((n_nod, dim), dtype=nm.float64) for ii in range(n_nod): line = fd.readline().split() ids[ii] = int(line[0]) coors[ii] = [float(coor) for coor in line[1:]] mat_tetras = [] tetras = [] mat_hexas = [] hexas = [] for ii in range(n_el): line = fd.readline().split() if line[2] == 'tet': mat_tetras.append(int(line[1])) tetras.append([int(ic) for ic in line[3:]]) elif line[2] == 'hex': mat_hexas.append(int(line[1])) hexas.append([int(ic) for ic in line[3:]]) fd.close() mesh = mesh_from_groups(mesh, ids, coors, None, [], [], [], [], 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 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 AbaqusMeshIO(MeshIO): format = 'abaqus'
[docs] @staticmethod def guess(filename): ok = False fd = open(filename, 'r') for ii in range(100): try: line = fd.readline().strip().split(',') except: break if line[0].lower() == '*node': ok = True break fd.close() return ok
[docs] def read(self, mesh, **kwargs): fd = open(self.filename, 'r') ids = [] coors = [] tetras = [] mat_tetras = [] hexas = [] mat_hexas = [] tris = [] mat_tris = [] quads = [] mat_quads = [] nsets = {} ing = 1 dim = 0 line = fd.readline().split(',') while 1: if not line[0]: break token = line[0].strip().lower() if token == '*node': while 1: line = fd.readline().split(',') if (not line[0]) or (line[0][0] == '*'): break if dim == 0: dim = len(line) - 1 ids.append(int(line[0])) if dim == 2: coors.append([float(coor) for coor in line[1:3]]) else: coors.append([float(coor) for coor in line[1:4]]) elif token == '*element': if line[1].find('C3D8') >= 0: while 1: line = fd.readline().split(',') if (not line[0]) or (line[0][0] == '*'): break mat_hexas.append(0) hexas.append([int(ic) for ic in line[1:9]]) elif line[1].find('C3D4') >= 0: while 1: line = fd.readline().split(',') if (not line[0]) or (line[0][0] == '*'): break mat_tetras.append(0) tetras.append([int(ic) for ic in line[1:5]]) elif ( line[1].find('CPS') >= 0 or line[1].find('CPE') >= 0 or line[1].find('CAX') >= 0 ): if line[1].find('4') >= 0: while 1: line = fd.readline().split(',') if (not line[0]) or (line[0][0] == '*'): break mat_quads.append(0) quads.append([int(ic) for ic in line[1:5]]) elif line[1].find('3') >= 0: while 1: line = fd.readline().split(',') if (not line[0]) or (line[0][0] == '*'): break mat_tris.append(0) tris.append([int(ic) for ic in line[1:4]]) else: raise ValueError('unknown element type! (%s)' % line[1]) else: raise ValueError('unknown element type! (%s)' % line[1]) elif token == '*nset': if line[-1].strip().lower() == 'generate': line = fd.readline() continue while 1: line = fd.readline().strip().split(',') if (not line[0]) or (line[0][0] == '*'): break if not line[-1]: line = line[:-1] aux = [int(ic) for ic in line] nsets.setdefault(ing, []).extend(aux) ing += 1 else: line = fd.readline().split(',') fd.close() ngroups = nm.zeros((len(coors),), dtype=nm.int32) for ing, ii in six.iteritems(nsets): ngroups[nm.array(ii)-1] = ing mesh = mesh_from_groups(mesh, ids, coors, ngroups, tris, mat_tris, quads, mat_quads, tetras, mat_tetras, hexas, mat_hexas) return mesh
[docs] def read_dimension(self): fd = open(self.filename, 'r') line = fd.readline().split(',') while 1: if not line[0]: break token = line[0].strip().lower() if token == '*node': while 1: line = fd.readline().split(',') if (not line[0]) or (line[0][0] == '*'): break dim = len(line) - 1 fd.close() return dim
[docs] def write(self, filename, mesh, out=None, **kwargs): raise NotImplementedError
[docs]class BDFMeshIO(MeshIO): format = 'nastran'
[docs] def read_dimension(self, ret_fd=False): fd = open(self.filename, 'r') el3d = 0 while 1: try: line = fd.readline() except: output("reading " + fd.name + " failed!") raise if len(line) == 1: continue if line[0] == '$': continue aux = line.split() if aux[0] == 'CHEXA': el3d += 1 elif aux[0] == 'CTETRA': el3d += 1 if el3d > 0: dim = 3 else: dim = 2 if ret_fd: return dim, fd else: fd.close() return dim
[docs] def read(self, mesh, **kwargs): def mfloat(s): if len(s) > 3: if s[-3] == '-': return float(s[:-3]+'e'+s[-3:]) return float(s) import string fd = open(self.filename, 'r') el = {'3_8' : [], '3_4' : [], '2_4' : [], '2_3' : []} nod = [] cmd = '' dim = 2 conns_in = [] descs = [] node_grp = None while 1: try: line = fd.readline() except EOFError: break except: output("reading " + fd.name + " failed!") raise if (len(line) == 0): break if len(line) < 4: continue if line[0] == '$': continue row = line.strip().split() if row[0] == 'GRID': cs = line.strip()[-24:] aux = [ cs[0:8], cs[8:16], cs[16:24] ] nod.append([mfloat(ii) for ii in aux]); elif row[0] == 'GRID*': aux = row[1:4]; cmd = 'GRIDX'; elif row[0] == 'CHEXA': aux = [int(ii)-1 for ii in row[3:9]] aux2 = int(row[2]) aux3 = row[9] cmd ='CHEXAX' elif row[0] == 'CTETRA': aux = [int(ii)-1 for ii in row[3:]] aux.append(int(row[2])) el['3_4'].append(aux) dim = 3 elif row[0] == 'CQUAD4': aux = [int(ii)-1 for ii in row[3:]] aux.append(int(row[2])) el['2_4'].append(aux) elif row[0] == 'CTRIA3': aux = [int(ii)-1 for ii in row[3:]] aux.append(int(row[2])) el['2_3'].append(aux) elif cmd == 'GRIDX': cmd = '' aux2 = row[1] if aux2[-1] == '0': aux2 = aux2[:-1] aux3 = aux[1:] aux3.append(aux2) nod.append([float(ii) for ii in aux3]); elif cmd == 'CHEXAX': cmd = '' aux4 = row[0] aux5 = aux4.find(aux3) aux.append(int(aux4[(aux5+len(aux3)):])-1) aux.extend([int(ii)-1 for ii in row[1:]]) aux.append(aux2) el['3_8'].append(aux) dim = 3 elif row[0] == 'SPC' or row[0] == 'SPC*': if node_grp is None: node_grp = [0] * len(nod) node_grp[int(row[2]) - 1] = int(row[1]) for elem in el.keys(): if len(el[elem]) > 0: conns_in.append(el[elem]) descs.append(elem) fd.close() nod = nm.array(nod, nm.float64) if dim == 2: nod = nod[:,:2].copy() conns, mat_ids = split_conns_mat_ids(conns_in) mesh._set_io_data(nod, node_grp, conns, mat_ids, descs) return mesh
[docs] @staticmethod def format_str(str, idx, n=8): out = '' for ii, istr in enumerate(str): aux = '%d' % istr out += aux + ' ' * (n - len(aux)) if ii == 7: out += '+%07d\n+%07d' % (idx, idx) return out
[docs] def write(self, filename, mesh, out=None, **kwargs): fd = open(filename, 'w') coors, ngroups, conns, mat_ids, desc = mesh._get_io_data() n_nod, dim = coors.shape fd.write("$NASTRAN Bulk Data File created by SfePy\n") fd.write("$\nBEGIN BULK\n") fd.write("$\n$ ELEMENT CONNECTIVITY\n$\n") iel = 0 mats = {} for ig, conn in enumerate(conns): ids = mat_ids[ig] for ii in range(conn.shape[0]): iel += 1 nn = conn[ii] + 1 mat = ids[ii] if mat in mats: mats[mat] += 1 else: mats[mat] = 0 if (desc[ig] == "2_4"): fd.write("CQUAD4 %s\n" %\ self.format_str([ii + 1, mat, nn[0], nn[1], nn[2], nn[3]], iel)) elif (desc[ig] == "2_3"): fd.write("CTRIA3 %s\n" %\ self.format_str([ii + 1, mat, nn[0], nn[1], nn[2]], iel)) elif (desc[ig] == "3_4"): fd.write("CTETRA %s\n" %\ self.format_str([ii + 1, mat, nn[0], nn[1], nn[2], nn[3]], iel)) elif (desc[ig] == "3_8"): fd.write("CHEXA %s\n" %\ self.format_str([ii + 1, mat, nn[0], nn[1], nn[2], nn[3], nn[4], nn[5], nn[6], nn[7]], iel)) else: raise ValueError('unknown element type! (%s)' % desc[ig]) fd.write("$\n$ NODAL COORDINATES\n$\n") format = 'GRID* %s % 08E % 08E\n' if coors.shape[1] == 3: format += '* % 08E0 \n' else: format += '* % 08E0 \n' % 0.0 for ii in range(n_nod): sii = str(ii + 1) fd.write(format % ((sii + ' ' * (8 - len(sii)),) + tuple(coors[ii]))) fd.write("$\n$ GEOMETRY\n$\n1 ") fd.write("0.000000E+00 0.000000E+00\n") fd.write("* 0.000000E+00 0.000000E+00\n* \n") fd.write("$\n$ MATERIALS\n$\n") matkeys = list(mats.keys()) matkeys.sort() for ii, imat in enumerate(matkeys): fd.write("$ material%d : Isotropic\n" % imat) aux = str(imat) fd.write("MAT1* %s " % (aux + ' ' * (8 - len(aux)))) fd.write("0.000000E+00 0.000000E+00\n") fd.write("* 0.000000E+00 0.000000E+00\n") fd.write("$\n$ GEOMETRY\n$\n") for ii, imat in enumerate(matkeys): fd.write("$ material%d : solid%d\n" % (imat, imat)) fd.write("PSOLID* %s\n" % self.format_str([ii + 1, imat], 0, 16)) fd.write("* \n") fd.write("ENDDATA\n") fd.close()
[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 Msh2MeshIO(MeshIO): """ Used to read and write data from .msh format used by GMSH, format 2.0 is currently partially supported allowing: mesh and ElementNodeData with InterpolationScheme to be written and read. 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 Attributes ---------- msh20header : Header containing version number. msh_cells : dictionary Mapping from msh to sfepy geometry. geo2msh_type : dictionary Mapping from sfepy to msh geometry. """ format = 'msh_v2' load_slices = {"all" : slice(0, None), "first": slice(0, 1), "last": slice(-1, None)} msh_cells = { 1: (2, 2), 2: (2, 3), 3: (2, 4), 4: (3, 4), 5: (3, 8), 6: (3, 6), } geo2msh_type = { "1_2" : 1, # ? but we will probably not need this "2_3" : 2, "2_4" : 3, "3_4" : 4, "3_8" : 5 } prism2hexa = nm.asarray([0, 1, 2, 2, 3, 4, 5, 5]) msh20header = ["$MeshFormat\n", "2.0 0 8\n" "$EndMeshFormat\n"]
[docs] 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
[docs] 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_dimension(self, ret_fd=True): fd = open(self.filename, 'r') while 1: lastpos = fd.tell() line = skip_read_line(fd).split() if line[0] in ['$Nodes', '$Elements']: num = int(read_token(fd)) coors = read_array(fd, num, 4, nm.float64) fd.seek(lastpos) if nm.sum(nm.abs(coors[:,3])) < 1e-16: dims = 2 else: dims = 3 break if line[0] == '$PhysicalNames': num = int(read_token(fd)) dims = [] for ii in range(num): dims.append(int(skip_read_line(fd, no_eof=True).split()[0])) break dim = nm.max(dims) if ret_fd: return dim, fd else: fd.close() return dim
[docs] def read_bounding_box(self, ret_fd=False, ret_dim=False): fd = open(self.filename, 'r') dim, fd = self.read_dimension(ret_fd=True) return _read_bounding_box(fd, dim, '$Nodes', c0=1, ret_fd=ret_fd, ret_dim=ret_dim)
[docs] def read(self, mesh, omit_facets=True, filename=None, drop_z=False, **kwargs): """ Reads mesh from msh v2.0 file returns it and also fills mesh parameter. Parameters ---------- mesh : Mesh instance Empty sfepy.discrete.fem.mesh.Mesh instance to fill. omit_facets : bool Not used. filename : string, optional Name of the file to use if None file from object is used. drop_z : bool, optional, default False Drop Z coordinate if zero and return 2D mesh, 2D meshes are stored as 3D by msh. Returns ------- mesh : Mesh instance Computational mesh. """ filename = get_default(filename, self.filename) fd = open(filename, 'r') conns = [] descs = [] mat_ids = [] tags = [] dims = [] while 1: line = skip_read_line(fd).split() if not line: break ls = line[0] if ls == '$MeshFormat': skip_read_line(fd) elif ls == '$PhysicalNames': num = int(read_token(fd)) for ii in range(num): skip_read_line(fd) elif ls == '$Nodes': num = int(read_token(fd)) coors = read_array(fd, num, 4, nm.float64) elif ls == '$Elements': num = int(read_token(fd)) for ii in range(num): line = [int(jj) for jj in skip_read_line(fd).split()] if line[1] > 6: continue dimension, nc = self.msh_cells[line[1]] dims.append(dimension) ntag = line[2] mat_id = line[3] conn = line[(3 + ntag):] desc = '%d_%d' % (dimension, nc) if desc in descs: idx = descs.index(desc) conns[idx].append(conn) mat_ids[idx].append(mat_id) tags[idx].append(line[3:(3 + ntag)]) else: descs.append(desc) conns.append([conn]) mat_ids.append([mat_id]) tags.append(line[3:(3 + ntag)]) elif ls == '$Periodic': periodic = '' while 1: pline = skip_read_line(fd) if '$EndPeriodic' in pline: break else: periodic += pline elif line[0] == '#' or ls[:4] == '$End': pass fd.close() dim = nm.max(dims) if '2_2' in descs: idx2 = descs.index('2_2') descs.pop(idx2) del(conns[idx2]) del(mat_ids[idx2]) if '3_6' in descs: idx6 = descs.index('3_6') c3_6as8 = nm.asarray(conns[idx6], dtype=nm.int32)[:,self.prism2hexa] if '3_8' in descs: descs.pop(idx6) c3_6m = nm.asarray(mat_ids.pop(idx6), type=nm.int32) idx8 = descs.index('3_8') c3_8 = nm.asarray(conns[idx8], type=nm.int32) c3_8m = nm.asarray(mat_ids[idx8], type=nm.int32) conns[idx8] = nm.vstack([c3_8, c3_6as8]) mat_ids[idx8] = nm.hstack([c3_8m, c3_6m]) else: descs[idx6] = '3_8' conns[idx6] = c3_6as8 descs0, mat_ids0, conns0 = [], [], [] for ii in range(len(descs)): if int(descs[ii][0]) == dim: conns0.append(nm.asarray(conns[ii], dtype=nm.int32) - 1) mat_ids0.append(nm.asarray(mat_ids[ii], dtype=nm.int32)) descs0.append(descs[ii]) # drop third coordinate if zero to get pretty 2D mesh if drop_z and nm.sum(coors[:, -1]) == 0.0: coors = coors[:, :-1] mesh._set_io_data(coors[:,1:], nm.int32(coors[:,-1] * 1), conns0, mat_ids0, descs0) return mesh
[docs] def read_data(self, step=None, filename=None, cache=None, return_mesh=False, drop_z=True): """ Reads file or files with basename filename or self.filename, returns lists containing data. 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, if any. For stationary problems just reads one file with time 0.0 and time step 0. Providing basename 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 varying step, if "last" read only last step of all files with the filename, if "first" reads step=0, if None reads file of filename provided or specified in object. filename :string, optional Basename of the files to use, if None file from object is used. cache : object Has no effect. return_mesh : bool, optional, default True Return mesh associated with data. Returns ------- mesh : sfepy.discrete.fem.mesh.Mesh Computational mesh. out : dictionary The output dictionary. Its keys represent name of data, values are Struct instances with the following attributes: - data : array, contains ElementNodeData, shape is (len(time), n_cell, n_cell_dof). - time : array, contains times. - time_n : array, contains time step numbers. - scheme : Struct, interpolation scheme used in data, only one interpolation scheme is allowed. See :func:`Msh2MeshIO._write_interpolation_scheme()`. """ filename = get_default(filename, self.filename) out = {} 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]] data = [] time = [] time_n = [] for filename in filenames: name, fdata, ftime, ftime_n, scheme = self._read_data_file(filename=filename) data += fdata time += ftime time_n += ftime_n elif isinstance(step, int): filename_format = self.get_filename_format(filename) filename = filename_format.format(step) try: name, data, time, time_n, scheme = self._read_data_file(filename=filename) except FileNotFoundError as e: raise FileNotFoundError(str(e) + " Maybe time step {} is not in output.".format(step)) elif step is None: name, data, time, time_n, scheme = self._read_data_file(filename=filename) else: raise ValueError("Unsupported vaule for step : {}".format(step)) out[name] = Struct(name=name, data=nm.array(data), time=nm.array(time), time_n=nm.array(time_n, dtype=nm.int32), scheme=scheme, mode="dg_cell_dofs") if return_mesh: from sfepy.discrete.fem.mesh import Mesh mesh = Mesh() mesh = self.read(mesh, filename=filename, drop_z=drop_z) return mesh, out return out
def _read_data_file(self, filename): try: fd = open(filename, "r") except FileNotFoundError: raise FileNotFoundError("[Errno 2] No such file or directory: {}.".format(filename)) scheme = Struct(name=None, desc=None, F=None, P=None) while 1: line = skip_read_line(fd).split() if not line: break ls = line[0] if ls == "$InterpolationScheme": 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) elif ls == "$ElementNodeData": n_str_tags = int(skip_read_line(fd)) data_name = skip_read_line(fd).strip('"\'') if n_str_tags == 2: interpolation_scheme_name = skip_read_line(fd).strip('"\'') n_float_tags = int(skip_read_line(fd)) time = float(skip_read_line(fd)) n_int_tags = int(skip_read_line(fd)) time_n = int(skip_read_line(fd)) comp = int(skip_read_line(fd)) n_el = int(skip_read_line(fd)) n_el_nod = int(look_ahead_line(fd).split()[1]) # read data including indexing data = read_array(fd, n_el, n_el_nod + 2 , nm.float64) # strip indexing columns data = data[:, 2:] elif line[0] == '#' or ls[:4] == '$End': pass fd.close() return data_name, [data], [time], [time_n], scheme def _write_mesh(self, fd, mesh): """ Write mesh into opened file fd. Parameters ---------- fd : file descriptor File opened for writing. mesh: sfepy.discrete.fem.mesh.Mesh Computational mesh to write. """ coors, ngroups, conns, mat_ids, descs = mesh._get_io_data() dim = mesh.dim fd.write("$Nodes\n") fd.write(str(mesh.n_nod) + "\n") s = "{}" + dim*" {}" + (3 - dim)*" 0.0" + "\n" for i, node in enumerate(coors, 1): fd.write(s.format(i, *node)) fd.write("$EndNodes\n") fd.write("$Elements\n") fd.write(str(sum( len(conn) for conn in conns)) + "\n") # sum number of elements acrcoss all conns for desc, mat_id, conn in zip(descs, mat_ids, conns): _, n_el_verts = [int(f) for f in desc.split("_")] el_type = self.geo2msh_type[desc] s = "{} {} 2 {} 0" + n_el_verts * " {}" + "\n" for (i, element), el_mat_id in zip(enumerate(conn, 1), mat_id): fd.write(s.format(i, el_type, el_mat_id, *nm.array(element) + 1)) fd.write("$EndElements\n") 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 descriptor 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 - coefficients 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_elementnodedata(self, fd, out, ts): """ Writes dg_cell_dofs data as $ElementNodeData, including interpolation scheme. Parameters ---------- out : dictionary, optional dictionary containing data to write in format generated by DGField.create_output(). ts : sfepy.solvers.ts.TimeStepper instance, optional Provides data to write time step. """ for key, value in out.items(): if not value.mode == "dg_cell_dofs": continue if value.interpolation_scheme is not None: self._write_interpolation_scheme(fd, value.interpolation_scheme) interpolation_scheme_name = value.interpolation_scheme.name data = value.data n_el_nod = nm.shape(data)[1] fd.write("$ElementNodeData\n") fd.write("{}\n".format(1 if interpolation_scheme_name is None else 2)) fd.write('"{}"\n'.format(key)) # name if interpolation_scheme_name is not None: fd.write('"{}"\n'.format(interpolation_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 into msh v2.0 file, handles dg_cell_dofs data from DGField if provided in out. Parameters ---------- filename : string Path to file. mesh : sfepy.discrete.fem.mesh.Mesh Computational mesh to write. out : dictionary, optional Dictionary containing data to write, expected to be in format generated by DGField.create_output(), key is name of data, value is Struct containing: - mode : string, so far only `dg_cell_dofs`, representing modal data in cells is supported. - data : array, DOFs as defined in DG Field. - interpolation_scheme : Struct, interpolation scheme used in data, only one interpolation scheme is allowed. See :func:`Msh2MeshIO._write_interpolation_scheme()`. ts : sfepy.solvers.ts.TimeStepper instance, optional Provides data to write time step. """ fd = open(filename, 'w') fd.writelines(self.msh20header) self._write_mesh(fd, mesh) if out: self._write_elementnodedata(fd, out, ts) fd.close() 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) 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) - 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
[docs]def guess_format(filename, ext, formats, io_table): """ Guess the format of filename, candidates are in formats. """ ok = False for format in formats: output('guessing %s' % format) try: ok = io_table[format].guess(filename) except AttributeError: pass if ok: break else: raise NotImplementedError('cannot guess format of a *%s file!' % ext) return format
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): """ 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) ext = op.splitext(filename)[1].lower() try: format = supported_formats[ext] except KeyError: raise ValueError('unsupported mesh file suffix! (%s)' % ext) if isinstance(format, tuple): format = guess_format(filename, ext, format, io_table) if prefix_dir is not None: filename = op.normpath(op.join(prefix_dir, filename)) return io_table[format](filename) insert_static_method(MeshIO, any_from_filename) del any_from_filename def for_format(filename, format=None, writable=False, prefix_dir=None): """ Create a MeshIO instance for file `filename` with forced `format`. Parameters ---------- filename : str The name of the mesh file. format : str One of supported formats. If None, :func:`MeshIO.any_from_filename()` is called instead. writable : bool If True, verify that the mesh format is writable. prefix_dir : str The directory name to prepend to `filename`. Returns ------- io : MeshIO subclass instance The MeshIO subclass instance corresponding to the `format`. """ ext = op.splitext(filename)[1].lower() try: _format = supported_formats[ext] except KeyError: _format = None format = get_default(format, _format) if format is None: io = MeshIO.any_from_filename(filename, prefix_dir=prefix_dir) else: if not isinstance(format, basestr): raise ValueError('ambigous suffix! (%s -> %s)' % (ext, format)) if format not in io_table: raise ValueError('unknown output mesh format! (%s)' % format) if writable and ('w' not in supported_capabilities[format]): output('writable mesh formats:') output_mesh_formats('w') msg = 'write support not implemented for output mesh format "%s",' \ ' see above!' % format raise ValueError(msg) if prefix_dir is not None: filename = op.normpath(op.join(prefix_dir, filename)) io = io_table[format](filename) return io insert_static_method(MeshIO, for_format) del for_format