def write_silo_datfile(fname,mname,cycle=0, time=0, nodefields=[], edgefields=[]):
from pyvisfile.silo import SiloFile, IntVector, DB_ZONETYPE_BEAM,\
DB_NODECENT, DB_ZONECENT, DBOPT_CYCLE, DBOPT_DTIME, DBOPT_TIME, DB_CLOBBER
from pyvisfile.silo import DBObjectType as DBOBjectType
import numpy as np
silo = SiloFile(fname, mode=DB_CLOBBER)
silo.put_multimesh('foo', [(mname+":foo",DBOBjectType.DB_UCDMESH)])
def putvar(n,fo,LOC):
if len(f.shape)==1 or f.shape[1]==1:
silo.put_ucdvar1("node_"+n,"foo",
np.asarray(f.T,order="C",dtype=np.double),
LOC, {DBOPT_CYCLE:cycle,DBOPT_DTIME:float(time),DBOPT_TIME:float(time)})
elif f.shape[1]==2:
silo.put_ucdvar("node_"+n,"foo", [n+"x",n+"y"],
np.asarray(f.T,order="C",dtype=np.double),
LOC, {DBOPT_CYCLE:cycle,DBOPT_DTIME:float(time),DBOPT_TIME:float(time)})
else:
silo.put_ucdvar("node_"+n,"foo", [n+"x",n+"y",n+"z"],
np.asarray(f.T,order="C",dtype=np.double),
LOC, {DBOPT_CYCLE:cycle,DBOPT_DTIME:float(time),DBOPT_TIME:float(time)})
for n,f in nodefields:
putvar(n,f,DB_NODECENT)
for n,f in edgefields:
putvar(n,f,DB_ZONECENT)
silo.close()
def silo_write_meshfile(fname, X, elems):
try:
from pyvisfile.silo import SiloFile, IntVector, DB_ZONETYPE_BEAM, DB_ZONETYPE_HEX, \
DB_NODECENT, DB_ZONECENT, DBOPT_CYCLE, DBOPT_DTIME, DBOPT_TIME, DB_CLOBBER
except ImportError:
print("Need PyVisFile to write silo files. Use vtk for now.")
raise
import numpy as np
silo = SiloFile(fname, mode=DB_CLOBBER)
# TODO: Check to see if it should be connections or bricks
zonelist_name = "foo_zonelist"
nodelist = IntVector()
nodelist.extend(int(i) for i in elems[:, :].flat)
shapetypes = IntVector()
if elems.shape[1] == 2:
shapetypes.append(DB_ZONETYPE_BEAM)
elif elems.shape[1] == 8:
shapetypes.append(DB_ZONETYPE_HEX)
shapesizes = IntVector()
shapesizes.append(elems.shape[1])
shapecounts = IntVector()
shapecounts.append(len(elems))
silo.put_zonelist_2(zonelist_name, len(elems), 2, nodelist, 0, 0,
shapetypes, shapesizes, shapecounts)
silo.put_ucdmesh("foo", [], np.asarray(X.T, order="C"), len(elems),
zonelist_name, None)
silo.close()
print("Wrote file " + fname)
def main():
path = tempfile.mkdtemp()
try:
silo = SiloFile(os.path.join(path, 'file.silo'))
add_to_silo_file(silo, Mesh())
silo.close()
finally:
shutil.rmtree(path)
def silo_write_datafile(fname,
mname,
cycle=0,
time=0,
nodefields={},
cellfields={}):
try:
from pyvisfile.silo import SiloFile, IntVector, DB_ZONETYPE_BEAM,\
DB_NODECENT, DB_ZONECENT, DBOPT_CYCLE, DBOPT_DTIME, DBOPT_TIME, DB_CLOBBER
from pyvisfile.silo import DBObjectType as DBOBjectType
except ImportError:
print("Need PyVisFile to write silo files. Use vtk for now.")
raise
import numpy as np
silo = SiloFile(fname, mode=DB_CLOBBER)
silo.put_multimesh('foo', [(mname + ":foo", DBOBjectType.DB_UCDMESH)])
def putvar(n, fo, LOC):
if len(f.shape) == 1 or f.shape[1] == 1:
silo.put_ucdvar1(
"node_" + n, "foo", np.asarray(f.T, order="C",
dtype=np.double), LOC, {
DBOPT_CYCLE: cycle,
DBOPT_DTIME: float(time),
DBOPT_TIME: float(time)
})
elif f.shape[1] == 2:
silo.put_ucdvar(
"node_" + n, "foo", [n + "x", n + "y"],
np.asarray(f.T, order="C", dtype=np.double), LOC, {
DBOPT_CYCLE: cycle,
DBOPT_DTIME: float(time),
DBOPT_TIME: float(time)
})
else:
silo.put_ucdvar(
"node_" + n, "foo", [n + "x", n + "y", n + "z"],
np.asarray(f.T, order="C", dtype=np.double), LOC, {
DBOPT_CYCLE: cycle,
DBOPT_DTIME: float(time),
DBOPT_TIME: float(time)
})
for n, f in nodefields.iteritems():
putvar(n, f, DB_NODECENT)
for n, f in cellfields.iteritems():
putvar(n, f, DB_ZONECENT)
silo.close()
print("Wrote file " + fname)
def make_file(self, pathname):
"""This function returns either a :class:`pyvisfile.silo.SiloFile` or a
:class:`pyvisfile.silo.ParallelSiloFile`, depending on the ParallelContext
under which we are running
An extension of .silo is automatically appended to *pathname*.
"""
if not self.generated:
self._generate()
if self.pcontext is None or len(self.pcontext.ranks) == 1:
from pyvisfile.silo import SiloFile
return SiloFile(pathname + ".silo")
else:
from pyvisfile.silo import ParallelSiloFile
return ParallelSiloFile(pathname, self.pcontext.rank,
self.pcontext.ranks)
def write_silo(fname, H,X,cycle=0, time=0,nodefields=[], edgefields=[], PUTMESH=True, PUTCONN=True):
from pyvisfile.silo import SiloFile, IntVector, DB_ZONETYPE_BEAM, DB_NODECENT, DB_ZONECENT, DBOPT_CYCLE, DBOPT_DTIME, DBOPT_TIME, DB_CLOBBER
import numpy as np
silo = SiloFile(fname, mode=DB_CLOBBER)
pair_edges = H.view()[0]
zonelist_name = "foo_zonelist"
nodelist = IntVector()
nodelist.extend( int(i) for i in pair_edges[:,0:2].flat)
shapetypes = IntVector()
shapetypes.append(DB_ZONETYPE_BEAM)
shapesizes = IntVector()
shapesizes.append(2)
shapecounts = IntVector()
shapecounts.append(len(pair_edges))
#from IPython import embed
#embed()
if PUTCONN:
silo.put_zonelist_2(zonelist_name, len(pair_edges), 2, nodelist,
0,0, shapetypes, shapesizes, shapecounts)
if PUTMESH:
silo.put_ucdmesh("foo", [],
np.asarray(X.T,order="C"), len(pair_edges),
zonelist_name, None)
def putvar(n,fo,LOC):
if len(f.shape)==1 or f.shape[1]==1:
silo.put_ucdvar1("node_"+n,"foo",
np.asarray(f,order="C",dtype=np.double),
LOC, {DBOPT_CYCLE:cycle,DBOPT_DTIME:float(time),DBOPT_TIME:float(time)})
elif f.shape[1]==2:
silo.put_ucdvar("node_"+n,"foo", [n+"x",n+"y"],
np.asarray(f.T,order="C",dtype=np.double),
LOC, {DBOPT_CYCLE:cycle,DBOPT_DTIME:float(time),DBOPT_TIME:float(time)})
else:
silo.put_ucdvar("node_"+n,"foo", [n+"x",n+"y",n+"z"],
np.asarray(f.T,order="C",dtype=np.double),
LOC, {DBOPT_CYCLE:cycle,DBOPT_DTIME:float(time),DBOPT_TIME:float(time)})
for n,f in nodefields:
putvar(n,f,DB_NODECENT)
for n,f in edgefields:
putvar(n,f,DB_ZONECENT)
silo.close()
def write_silo_meshfile(fname, H,X):
from pyvisfile.silo import SiloFile, IntVector, DB_ZONETYPE_BEAM, DB_NODECENT, DB_ZONECENT, DBOPT_CYCLE, DBOPT_DTIME, DBOPT_TIME, DB_CLOBBER
import numpy as np
silo = SiloFile(fname, mode=DB_CLOBBER)
pair_edges = H.view()[0]
zonelist_name = "foo_zonelist"
nodelist = IntVector()
nodelist.extend( int(i) for i in pair_edges[:,0:2].flat)
shapetypes = IntVector()
shapetypes.append(DB_ZONETYPE_BEAM)
shapesizes = IntVector()
shapesizes.append(2)
shapecounts = IntVector()
shapecounts.append(len(pair_edges))
silo.put_zonelist_2(zonelist_name, len(pair_edges), 2, nodelist,
0,0, shapetypes, shapesizes, shapecounts)
silo.put_ucdmesh("foo", [],
np.asarray(X.T,order="C"), len(pair_edges),
zonelist_name, None)
silo.close()
def main():
from pyvisfile.silo import SiloFile
silo = SiloFile("out.silo")
add_to_silo_file(silo, Mesh())
silo.close()
hi_offset = [(1, 1), (0, 1), (1, 0), (0, 0)]
data_global[:20, :20] = 0.
data_global[20:, :20] = 1.
data_global[:20, 20:] = 2.
data_global[20:, 20:] = 3.
mesh_names = []
var_names = []
for i in range(4):
file_name = 'example_%05d.silo' % i
s = SiloFile(file_name,
mode=DB_CLOBBER,
filetype=DB_HDF5,
target=DB_LOCAL,
fileinfo='Example Silo %05d.' % i)
axes = (x[x_from[i]:x_to[i]], y[y_from[i]:y_to[i]])
# Copy necessary due to slicing!
data = data_global[y_from[i]:y_to[i], x_from[i]:x_to[i]].copy()
options = dict()
options[DBOPT_CYCLE] = 99
options[DBOPT_DTIME] = 0.99
options[DBOPT_XLABEL] = 'X'
options[DBOPT_YLABEL] = 'Y'
options[DBOPT_XUNITS] = 'a'
options[DBOPT_YUNITS] = 'b'
from __future__ import absolute_import
from __future__ import print_function
from pyvisfile.silo import SiloFile, DB_READ
db = SiloFile("qmesh.silo", create=False, mode=DB_READ)
print(db.get_toc().qmesh_names)
print(db.get_toc().qvar_names)
qmesh = db.get_quadmesh("meshxy")
print(qmesh.coords)
qvar = db.get_quadvar("value")
print(qvar.vals)
hi_offset = [(1, 1), (0, 1), (1, 0), (0, 0)]
data_global[:20, :20] = 0.
data_global[20:, :20] = 1.
data_global[:20, 20:] = 2.
data_global[20:, 20:] = 3.
mesh_names = []
var_names = []
for i in range(4):
file_name = "example_%05d.silo" % i
s = SiloFile(file_name,
mode=DB_CLOBBER,
filetype=DB_HDF5,
target=DB_LOCAL,
fileinfo=f"Example Silo {i:05d}.")
axes = (x[x_from[i]:x_to[i]], y[y_from[i]:y_to[i]])
# Copy necessary due to slicing!
data = data_global[y_from[i]:y_to[i], x_from[i]:x_to[i]].copy()
options = dict()
options[DBOPT_CYCLE] = 99
options[DBOPT_DTIME] = 0.99
options[DBOPT_XLABEL] = "X"
options[DBOPT_YLABEL] = "Y"
options[DBOPT_XUNITS] = "a"
options[DBOPT_YUNITS] = "b"
def test_silo_unstructured():
from pyvisfile.silo import SiloFile
silo = SiloFile("out.silo")
add_to_silo_file(silo, Mesh())
silo.close()