def read_results(filename, only_names=None):
"""
Read probing results from a file.
Parameters
----------
filename : str or file object
The probe results file name.
Returns
-------
header : Struct instance
The probe data header.
results : dict
The dictionary of probing results. Keys are data names, values are
the probed values.
"""
from sfepy.base.ioutils import read_array
only_names = get_default(only_names, [])
fd = open(filename, 'r') if isinstance(filename, basestr) else filename
header = read_header(fd)
results = {}
for name, nc in get_data_name(fd):
if name not in only_names: continue
result = read_array(fd, header.n_point, nc + 1, nm.float64)
results[name] = result
return header, results
def read_boundin_box(self, ret_fd=False, ret_dim=False):
fd = open(self.filename, "r")
while 1:
try:
line = fd.readline().split()
if line[0] == "POINTS":
nod = read_array(fd, 1, -1, nm.float64)
dim = nod.shape[1]
break
except:
output("reading " + fd.name + " failed!")
raise
bbox = [[nod[0][0]] * 2, [nod[0][1]] * 2, [nod[0][2]] * 2]
for inod in nod[1:]:
for idim in range(dim):
if inod[idim] < bbox[idim][0]:
bbox[idim][0] = inod[idim]
if inod[idim] > bbox[idim][1]:
bbox[idim][1] = inod[idim]
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
def read_results(filename, only_names=None):
"""
Read probing results from a file.
Parameters
----------
filename : str or file object
The probe results file name.
Returns
-------
header : Struct instance
The probe data header.
results : dict
The dictionary of probing results. Keys are data names, values are
the probed values.
"""
from sfepy.base.ioutils import read_array
only_names = get_default(only_names, [])
fd = open(filename, 'r') if isinstance(filename, basestr) else filename
header = read_header(fd)
results = {}
for name, nc in get_data_name(fd):
if name not in only_names: continue
result = read_array(fd, header.n_point, nc + 1, nm.float64)
results[name] = result
return header, results
def read_boundin_box(self, ret_fd=False, ret_dim=False):
fd = open(self.filename, "r")
while 1:
try:
line = fd.readline()
except:
output("reading " + fd.name + " failed!")
raise
if len(line) == 0:
break
if len(line) == 1:
continue
if line[0] == "#":
continue
aux = line.split()
if aux[0] == "Dimension":
if len(aux) == 2:
dim = int(aux[1])
else:
dim = int(fd.readline())
elif aux[0] == "Vertices":
num = int(read_token(fd))
nod = read_array(fd, num, dim + 1, nm.float64)
break
bbox = [[nod[0][0]] * 2, [nod[0][1]] * 2, [nod[0][2]] * 2]
for inod in nod[1:]:
for idim in range(dim):
if inod[idim] < bbox[idim][0]:
bbox[idim][0] = inod[idim]
if inod[idim] > bbox[idim][1]:
bbox[idim][1] = inod[idim]
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
def read_dimension(self, ret_fd=False):
fd = open(self.filename, "r")
while 1:
try:
line = fd.readline().split()
if not line:
continue
if line[0] == "CELL_TYPES":
cell_types = read_array(fd, 1, -1, nm.int32)
dim = vtk_dims[cell_types[0, 0]]
break
except:
output("reading " + fd.name + " failed!")
raise
if ret_fd:
return dim, fd
else:
fd.close()
return dim
def postprocess(filename_input, filename_results, options):
"""
Postprocess probe data files - replot, integrate data.
"""
from matplotlib import pyplot as plt
only_names = options.only_names
fd = open(filename_input, 'r')
header = read_header(fd)
output(header)
fig = plt.figure()
for name in get_data_name(fd):
if (only_names is not None) and (name not in only_names): continue
data = read_array(fd, header.n_point, 2, nm.float64)
pars, vals = data[:, 0], data[:, 1]
ii = nm.where(nm.isfinite(vals))[0]
# Nans only at the edges.
assert_(nm.diff(ii).sum() == (len(ii) - 1))
val = integrate_along_line(pars[ii], vals[ii], options.radial)
label = r'%s: $\int\ %s' % (name, name)
if options.radial:
label += ' (r)'
label += '$ = %.5e' % val
plt.plot(pars, vals, label=label, lw=0.2, marker='+', ms=1)
plt.ylabel('probed data')
plt.xlabel('probe coordinate')
output(label)
plt.legend()
fig.savefig(filename_results)
fd.close()
def postprocess(filename_input, filename_results, options):
"""
Postprocess probe data files - replot, integrate data.
"""
from matplotlib import pyplot as plt
only_names = options.only_names
fd = open(filename_input, 'r')
header = read_header(fd)
output(header)
fig = plt.figure()
for name in get_data_name(fd):
if (only_names is not None) and (name not in only_names): continue
data = read_array(fd, header.n_point, 2, nm.float64)
pars, vals = data[:,0], data[:,1]
ii = nm.where(nm.isfinite(vals))[0]
# Nans only at the edges.
assert_(nm.diff(ii).sum() == (len(ii)-1))
val = integrate_along_line(pars[ii], vals[ii], options.radial)
label = r'%s: $\int\ %s' % (name, name)
if options.radial:
label += ' (r)'
label += '$ = %.5e'% val
plt.plot(pars, vals, label=label, lw=0.2, marker='+', ms=1)
plt.ylabel('probed data')
plt.xlabel('probe coordinate')
output(label)
plt.legend()
fig.savefig(filename_results)
fd.close()
def read(self, mesh, **kwargs):
self.fd = fd = open(self.filename, "r")
mode = "header"
nod = conns = desc = None
while 1:
if mode == "header":
line = skip_read_line(fd)
n_tags = self._read_commented_int()
for ii in xrange(n_tags):
skip_read_line(fd)
n_types = self._read_commented_int()
for ii in xrange(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":
nod = 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 xrange(n_types):
t_name = skip_read_line(fd).split()[1]
n_ep = self._read_commented_int()
n_el = self._read_commented_int()
if dim == 2:
aux = read_array(fd, n_el, n_ep, nm.int32)
if t_name == "tri":
conns.append(aux)
descs.append("2_3")
is_conn = True
else:
is_conn = False
else:
raise NotImplementedError
# Skip parameters.
n_pv = self._read_commented_int()
n_par = self._read_commented_int()
for ii in xrange(n_par):
skip_read_line(fd)
n_domain = self._read_commented_int()
assert_(n_domain == n_el)
if is_conn:
mat_id = read_array(fd, n_domain, 1, nm.int32)
mat_ids.append(mat_id)
else:
for ii in xrange(n_domain):
skip_read_line(fd)
# Skip up/down pairs.
n_ud = self._read_commented_int()
for ii in xrange(n_ud):
skip_read_line(fd)
break
nod = nm.concatenate((nod, nm.zeros((n_nod, 1), dtype=nm.int32)), 1)
nod = nm.ascontiguousarray(nod)
dim = nod.shape[1] - 1
conns2 = []
for ii, conn in enumerate(conns):
conns2.append(nm.c_[conn, mat_ids[ii]])
conns_in, mat_ids = sort_by_mat_id(conns2)
conns, mat_ids, descs = split_by_mat_id(conns_in, mat_ids, descs)
mesh._set_data(nod, conns, mat_ids, descs)
# mesh.write( 'pokus.mesh', io = 'auto' )
self.fd = None
return mesh
def read(self, mesh, **kwargs):
fd = open(self.filename, "r")
mode = "header"
mode_status = 0
nod = conns = desc = mat_id = None
while 1:
try:
line = fd.readline()
if len(line) == 0:
break
elif len(line) == 1:
continue
if line[0] == "#":
continue
except EOFError:
break
except:
output("reading " + fd.name + " failed!")
raise
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])
nod = read_array(fd, n_nod, -1, 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 = "mat_id"
elif mode == "mat_id":
if mode_status == 0:
line = line.split()
if line[0] == "CELL_DATA":
assert_(int(line[1]) == n_el)
mode_status = 1
elif mode_status == 1:
if line.strip() == "SCALARS mat_id float 1":
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 = "finished"
elif mode == "finished":
break
fd.close()
if mat_id is None:
mat_id = [[0]] * n_el
dim = vtk_dims[cell_types[0, 0]]
if dim == 3:
nod = nm.concatenate((nod, nm.zeros((n_nod, 1), dtype=nm.int32)), 1)
else:
nod[:, 2] = 0.0
nod = nm.ascontiguousarray(nod)
dim = nod.shape[1] - 1
cell_types = cell_types.squeeze()
dconns = {}
for iel, row in enumerate(raw_conn):
ct = vtk_inverse_cell_types[(cell_types[iel], dim)]
dconns.setdefault(ct, []).append(row[1:] + mat_id[iel])
desc = []
conns = []
for key, conn in dconns.iteritems():
desc.append(key)
conns.append(nm.array(conn, dtype=nm.int32))
conns_in, mat_ids = sort_by_mat_id(conns)
conns, mat_ids, descs = split_by_mat_id(conns_in, mat_ids, desc)
mesh._set_data(nod, conns, mat_ids, descs)
return mesh
def read(self, mesh, **kwargs):
dim, fd = self.read_dimension(ret_fd=True)
conns_in = []
descs = []
while 1:
try:
line = fd.readline()
if len(line) == 0:
break
if len(line) == 1:
continue
except EOFError:
break
except:
output("reading " + fd.name + " failed!")
raise
ls = line.strip()
if ls == "Vertices":
num = int(read_token(fd))
nod = read_array(fd, num, dim + 1, nm.float64)
## print nod
elif ls == "Tetrahedra":
num = int(read_token(fd))
conns_in.append(read_array(fd, num, 5, nm.int32))
conns_in[-1][:, :-1] -= 1
descs.append("3_4")
elif ls == "Hexahedra":
num = int(read_token(fd))
conns_in.append(read_array(fd, num, 9, nm.int32))
conns_in[-1][:, :-1] -= 1
descs.append("3_8")
elif ls == "Triangles":
num = int(read_token(fd))
conns_in.append(read_array(fd, num, 4, nm.int32))
conns_in[-1][:, :-1] -= 1
descs.append("2_3")
elif ls == "Quadrilaterals":
num = int(read_token(fd))
conns_in.append(read_array(fd, num, 5, nm.int32))
conns_in[-1][:, :-1] -= 1
descs.append("2_4")
elif ls == "End":
break
elif line[0] == "#":
continue
else:
msg = "corrupted file (line '%s')!" % line
raise ValueError(msg)
fd.close()
conns_in, mat_ids = sort_by_mat_id(conns_in)
# 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, 8], nm.int32)
conn.append(la.rect(conn_in, iw, ar))
desc.append("3_6")
ip = nm.where(flag == 2)[0]
if len(ip) > 0:
ar = nm.array([0, 1, 2, 3, 4, 8], nm.int32)
conn.append(la.rect(conn_in, ip, ar))
desc.append("3_5")
## print "brick split:", ic, ":", ib, iw, ip, desc
conns_in[ic:ic] = conn
del (descs[ic])
descs[ic:ic] = desc
conns, mat_ids, descs = split_by_mat_id(conns_in, mat_ids, descs)
mesh._set_data(nod, conns, mat_ids, descs)
return mesh
