def test_hdf5_meshio(self):
import tempfile
import numpy as nm
import scipy.sparse as sps
from sfepy.discrete.fem.meshio import HDF5MeshIO
from sfepy.base.base import Struct
from sfepy.base.ioutils import Cached, Uncached, SoftLink, \
DataSoftLink
from sfepy.discrete.iga.domain import IGDomain
from sfepy.discrete.iga.domain_generators import gen_patch_block_domain
from sfepy.solvers.ts import TimeStepper
from sfepy.discrete.fem import Mesh
conf_dir = op.dirname(__file__)
mesh0 = Mesh.from_file(data_dir +
'/meshes/various_formats/small3d.mesh',
prefix_dir=conf_dir)
shape = [4, 4, 4]
dims = [5, 5, 5]
centre = [0, 0, 0]
degrees = [2, 2, 2]
nurbs, bmesh, regions = gen_patch_block_domain(dims, shape, centre,
degrees,
cp_mode='greville',
name='iga')
ig_domain = IGDomain('iga', nurbs, bmesh, regions=regions)
int_ar = nm.arange(4)
data = {
'list': range(4),
'mesh1': mesh0,
'mesh2': mesh0,
'mesh3': Uncached(mesh0),
'mesh4': SoftLink('/step0/__cdata/data/data/mesh2'),
'mesh5': DataSoftLink('Mesh','/step0/__cdata/data/data/mesh1/data'),
'mesh6': DataSoftLink('Mesh','/step0/__cdata/data/data/mesh2/data',
mesh0),
'mesh7': DataSoftLink('Mesh','/step0/__cdata/data/data/mesh1/data',
True),
'iga' : ig_domain,
'cached1': Cached(1),
'cached2': Cached(int_ar),
'cached3': Cached(int_ar),
'types': ( True, False, None ),
'tuple': ('first string', 'druhý UTF8 řetězec'),
'struct': Struct(
double=nm.arange(4, dtype=float),
int=nm.array([2,3,4,7]),
sparse=sps.csr_matrix(nm.array([1,0,0,5]).
reshape((2,2)))
)
}
with tempfile.NamedTemporaryFile(suffix='.h5') as fil:
io = HDF5MeshIO(fil.name)
ts = TimeStepper(0,1.,0.1, 10)
io.write(fil.name, mesh0, {
'cdata' : Struct(
mode='custom',
data=data,
unpack_markers=False
)
}, ts=ts)
ts.advance()
mesh = io.read()
data['problem_mesh'] = DataSoftLink('Mesh', '/mesh', mesh)
io.write(fil.name, mesh0, {
'cdata' : Struct(
mode='custom',
data=data,
unpack_markers=True
)
}, ts=ts)
cache = {'/mesh': mesh }
fout = io.read_data(0, cache=cache)
fout2 = io.read_data(1, cache=cache )
out = fout['cdata']
out2 = fout2['cdata']
assert_(out['mesh7'] is out2['mesh7'],
'These two meshes should be in fact the same object')
assert_(out['mesh6'] is out2['mesh6'],
'These two meshes should be in fact the same object')
assert_(out['mesh5'] is not out2['mesh5'],
'These two meshes shouldn''t be in fact the same object')
assert_(out['mesh1'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh1'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh4'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh5'] is not out['mesh2'],
'These two meshes shouldn''t be in fact the same object')
assert_(out['mesh6'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh7'] is not out['mesh2'],
'These two meshes shouldn''t be in fact the same object')
assert_(out['mesh3'] is not out['mesh2'],
'These two meshes should be different objects')
assert_(out['cached2'] is out['cached3'],
'These two array should be the same object')
assert_(out2['problem_mesh'] is mesh,
'These two meshes should be the same objects')
assert_(self._compare_meshes(out['mesh1'], mesh0),
'Failed to restore mesh')
assert_(self._compare_meshes(out['mesh3'], mesh0),
'Failed to restore mesh')
assert_((out['struct'].sparse == data['struct'].sparse).todense()
.all(), 'Sparse matrix restore failed')
ts.advance()
io.write(fil.name, mesh0, {
'cdata' : Struct(
mode='custom',
data=[
DataSoftLink('Mesh',
'/step0/__cdata/data/data/mesh1/data',
mesh0),
mesh0
]
)
}, ts=ts)
out3 = io.read_data(2)['cdata']
assert_(out3[0] is out3[1])
#this property is not restored
del data['iga'].nurbs.nurbs
#not supporting comparison
del data['iga']._bnf
del out2['iga']._bnf
#restoration of this property fails
del data['iga'].vertex_set_bcs
del out2['iga'].vertex_set_bcs
#these soflink has no information how to unpack, so it must be
#done manually
data['mesh4'] = mesh0
data['mesh5'] = mesh0
data['mesh7'] = mesh0
for key, val in six.iteritems(out2):
self.report('comparing:', key)
self.assert_equal(val, data[key])
return True
def test_hdf5_meshio(self):
try:
from igakit import igalib
except ImportError:
self.report('hdf5_meshio not-tested (missing igalib module)!')
return True
import tempfile
import numpy as nm
import scipy.sparse as sps
from sfepy.discrete.fem.meshio import HDF5MeshIO
from sfepy.base.base import Struct
from sfepy.base.ioutils import Cached, Uncached, SoftLink, \
DataSoftLink
from sfepy.discrete.iga.domain import IGDomain
from sfepy.discrete.iga.domain_generators import gen_patch_block_domain
from sfepy.solvers.ts import TimeStepper
from sfepy.discrete.fem import Mesh
conf_dir = op.dirname(__file__)
mesh0 = Mesh.from_file(data_dir +
'/meshes/various_formats/small3d.mesh',
prefix_dir=conf_dir)
shape = [4, 4, 4]
dims = [5, 5, 5]
centre = [0, 0, 0]
degrees = [2, 2, 2]
nurbs, bmesh, regions = gen_patch_block_domain(dims,
shape,
centre,
degrees,
cp_mode='greville',
name='iga')
ig_domain = IGDomain('iga', nurbs, bmesh, regions=regions)
int_ar = nm.arange(4)
data = {
'list':
range(4),
'mesh1':
mesh0,
'mesh2':
mesh0,
'mesh3':
Uncached(mesh0),
'mesh4':
SoftLink('/step0/__cdata/data/data/mesh2'),
'mesh5':
DataSoftLink('Mesh', '/step0/__cdata/data/data/mesh1/data'),
'mesh6':
DataSoftLink('Mesh', '/step0/__cdata/data/data/mesh2/data', mesh0),
'mesh7':
DataSoftLink('Mesh', '/step0/__cdata/data/data/mesh1/data', True),
'iga':
ig_domain,
'cached1':
Cached(1),
'cached2':
Cached(int_ar),
'cached3':
Cached(int_ar),
'types': (True, False, None),
'tuple': ('first string', 'druhý UTF8 řetězec'),
'struct':
Struct(double=nm.arange(4, dtype=float),
int=nm.array([2, 3, 4, 7]),
sparse=sps.csr_matrix(
nm.array([1, 0, 0, 5]).reshape((2, 2))))
}
with tempfile.NamedTemporaryFile(suffix='.h5', delete=False) as fil:
io = HDF5MeshIO(fil.name)
ts = TimeStepper(0, 1., 0.1, 10)
io.write(fil.name,
mesh0, {
'cdata':
Struct(mode='custom', data=data, unpack_markers=False)
},
ts=ts)
ts.advance()
mesh = io.read()
data['problem_mesh'] = DataSoftLink('Mesh', '/mesh', mesh)
io.write(fil.name,
mesh0, {
'cdata':
Struct(mode='custom', data=data, unpack_markers=True)
},
ts=ts)
cache = {'/mesh': mesh}
fout = io.read_data(0, cache=cache)
fout2 = io.read_data(1, cache=cache)
out = fout['cdata']
out2 = fout2['cdata']
assert_(out['mesh7'] is out2['mesh7'],
'These two meshes should be in fact the same object')
assert_(out['mesh6'] is out2['mesh6'],
'These two meshes should be in fact the same object')
assert_(out['mesh5'] is not out2['mesh5'],
'These two meshes shouldn'
't be in fact the same object')
assert_(out['mesh1'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh1'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh4'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh5'] is not out['mesh2'],
'These two meshes shouldn'
't be in fact the same object')
assert_(out['mesh6'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh7'] is not out['mesh2'],
'These two meshes shouldn'
't be in fact the same object')
assert_(out['mesh3'] is not out['mesh2'],
'These two meshes should be different objects')
assert_(out['cached2'] is out['cached3'],
'These two array should be the same object')
assert_(out2['problem_mesh'] is mesh,
'These two meshes should be the same objects')
assert_(self._compare_meshes(out['mesh1'], mesh0),
'Failed to restore mesh')
assert_(self._compare_meshes(out['mesh3'], mesh0),
'Failed to restore mesh')
assert_((
out['struct'].sparse == data['struct'].sparse).todense().all(),
'Sparse matrix restore failed')
ts.advance()
io.write(fil.name,
mesh0, {
'cdata':
Struct(mode='custom',
data=[
DataSoftLink(
'Mesh',
'/step0/__cdata/data/data/mesh1/data',
mesh0), mesh0
])
},
ts=ts)
out3 = io.read_data(2)['cdata']
assert_(out3[0] is out3[1])
os.remove(fil.name)
#this property is not restored
del data['iga'].nurbs.nurbs
#not supporting comparison
del data['iga']._bnf
del out2['iga']._bnf
#restoration of this property fails
del data['iga'].vertex_set_bcs
del out2['iga'].vertex_set_bcs
#these soflink has no information how to unpack, so it must be
#done manually
data['mesh4'] = mesh0
data['mesh5'] = mesh0
data['mesh7'] = mesh0
for key, val in six.iteritems(out2):
self.report('comparing:', key)
self.assert_equal(val, data[key])
return True
