def extract_refined_mesh_data1(mesh, refine=None):
ndim = mesh.Dimension()
sdim = mesh.SpaceDimension()
ivert0 = [
mesh.GetElement(i).GetVerticesArray() for i in range(mesh.GetNE())
]
idx2 = np.arange(mesh.GetNE())
iv2 = [np.arange(mesh.GetNV())]
table = np.arange(mesh.GetNV())
battrs = mesh.GetAttributeArray()
gt = mesh.GetElementTransformation
cells = {}
cell_data = {}
ptx = [mesh.GetVertexArray() for i in range(mesh.GetNV())]
base = 1
from petram.mesh.refined_mfem_geom import get_geom
if len(idx2) > 0:
attr2, ptx2, ivx2, ivxe2, attrx2 = get_geom(
idx2,
2,
base,
gt,
battrs,
sdim,
refine,
)
ptx.append(ptx2)
cells['line_x'] = ivx2
cell_data['line_x'] = {}
cell_data['line_x']['physical'] = attrx2
cell_data['X_refined_edge'] = ptx2
X = np.vstack(ptx)
from petram.mesh.mesh_utils import populate_plotdata
l_s_loop = populate_plotdata(mesh, table, cells, cell_data)
iedge2bb = None # is it used?
#print "X", X.shape
#for k in cells['vertex']:print X[k]
return X, cells, cell_data, l_s_loop, iedge2bb
def extract_refined_mesh_data2(mesh, refine=None):
ndim = mesh.Dimension()
sdim = mesh.SpaceDimension()
ivert0 = [
mesh.GetElement(i).GetVerticesArray() for i in range(mesh.GetNE())
]
attrs = mesh.GetAttributeArray()
nvert = np.array([len(x) for x in ivert0])
idx3 = np.where(nvert == 3)[0]
idx4 = np.where(nvert == 4)[0]
ivert = []
ivert3 = None
ivert4 = None
iv3 = []
iv4 = []
iv3p = np.array([], dtype=int)
iv4p = np.array([], dtype=int)
from petram.mesh.refined_mfem_geom import get_geom
ptx = []
ivx3 = None
ptx3 = []
if len(idx3) != 0:
base = mesh.GetElementBaseGeometry(idx3[0])
gt = mesh.GetElementTransformation
attr3, ptx3, ivx3, ivxe3, attrx3 = get_geom(idx3, 3, base, gt, attrs,
sdim, refine)
ptx.append(ptx3)
npt = len(ptx3) // len(idx3)
lref = len(ivx3) // len(idx3)
iv3 = [ivert0[k] for k in idx3]
seen = defaultdict(int)
for iiv in ivx3[:lref].flatten():
seen[iiv] += 1
xxx = np.sort([kk for kk in seen if seen[kk] == 1])
iv3p = np.hstack([xxx + j * npt for j, k in enumerate(idx3)])
ivert3 = np.vstack(iv3)
if len(idx4) != 0:
base = mesh.GetElementBaseGeometry(idx4[0])
gt = mesh.GetElementTransformation
attr4, ptx4, ivx4, ivxe4, attrx4 = get_geom(idx4, 4, base, gt, attrs,
sdim, refine)
ptx.append(ptx4)
npt = len(ptx4) // len(idx4)
lref = len(ivx4) // len(idx4)
iv4 = [ivert0[k] for k in idx4]
seen = defaultdict(int)
for iiv in ivx4[:lref].flatten():
seen[iiv] += 1
xxx = np.sort([kk for kk in seen if seen[kk] == 1])
iv4p = np.hstack([xxx + j * npt
for j, k in enumerate(idx4)]) + len(ptx3)
ivert4 = np.vstack(iv4)
if ivx3 is not None:
ivx4 = ivx4 + len(ptx3)
ivxe4 = ivxe4 + len(ptx3)
ptx_face = np.vstack(ptx)
# unique edges for node
tmp = np.hstack(iv3 + iv4)
tmp2 = np.hstack((iv3p, iv4p))
u, indices = np.unique(tmp, return_inverse=True)
ll3 = 3 * len(idx3)
indices3 = indices[:ll3]
indices4 = indices[ll3:]
table = np.zeros(np.max(u) + 1, dtype=int) - 1
for k, u0 in enumerate(u):
table[u0] = tmp2[np.where(tmp == u0)[0][0]]
X = ptx_face
#X = np.vstack([mesh.GetVertexArray(k) for k in u])
if X.shape[1] == 2:
X = np.hstack((X, np.zeros((X.shape[0], 1))))
elif X.shape[1] == 1:
X = np.hstack((X, np.zeros((X.shape[0], 2))))
kdom = mesh.attributes.ToList()
cells = {}
cell_data = {}
cell_data['X_refined_face'] = ptx_face
if ivert3 is not None:
cells['triangle'] = indices3.reshape(ivert3.shape)
cells['triangle_x'] = ivx3
cells['triangle_xe'] = ivxe3
cell_data['triangle'] = {}
cell_data['triangle']['physical'] = attr3
cell_data['triangle_x'] = {}
cell_data['triangle_x']['physical'] = attrx3
if ivert4 is not None:
cells['quad'] = indices4.reshape(ivert4.shape)
cells['quad_x'] = ivx4
cells['quad_xe'] = ivxe4
cell_data['quad'] = {}
cell_data['quad']['physical'] = attr4
cell_data['quad_x'] = {}
cell_data['quad_x']['physical'] = attrx4
### process refined edges
battrs = mesh.GetBdrAttributeArray()
base = 1
gt = mesh.GetBdrElementTransformation
idx2 = range(mesh.GetNBE())
if len(idx2) > 0:
attr2, ptx2, ivx2, ivxe2, attrx2 = get_geom(idx2, 2, base, gt, battrs,
sdim, refine)
cells['line_x'] = ivx2
cell_data['line_x'] = {}
cell_data['line_x']['physical'] = attrx2
cell_data['X_refined_edge'] = ptx2
from petram.mesh.mesh_utils import populate_plotdata
l_s_loop = populate_plotdata(mesh, table, cells, cell_data)
iedge2bb = None # is it used?
#print "X", X.shape
#for k in cells['vertex']:print X[k]
return X, cells, cell_data, l_s_loop, iedge2bb
def extract_mesh_data(mesh, refine=1):
if isinstance(mesh, ParMesh):
assert False, "mesh data must be processed in serial"
hasNodal = mesh.GetNodalFESpace() is not None
ndim = mesh.Dimension()
if hasNodal and refine != 1:
if ndim == 3:
from petram.mesh.read_mfemmesh3 import extract_refined_mesh_data3
return extract_refined_mesh_data3(mesh, refine)
elif ndim == 2:
from petram.mesh.read_mfemmesh2 import extract_refined_mesh_data2
return extract_refined_mesh_data2(mesh, refine)
else:
from petram.mesh.read_mfemmesh1 import extract_refined_mesh_data1
return extract_refined_mesh_data1(mesh, refine)
if ndim == 3:
ivert0 = [mesh.GetBdrElement(i).GetVerticesArray()
for i in range(mesh.GetNBE())]
attrs = mesh.GetBdrAttributeArray()
elif ndim == 2:
ivert0 = [mesh.GetElement(i).GetVerticesArray()
for i in range(mesh.GetNE())]
attrs = mesh.GetAttributeArray()
else:
return extract_mesh_data_1D(mesh)
nvert = np.array([len(x) for x in ivert0])
idx3 = np.where(nvert == 3)[0]
idx4 = np.where(nvert == 4)[0]
ivert = []; ivert3 = None; ivert4 = None
iv3 = []; iv4 = []
if len(idx3) != 0:
iv3 = [ivert0[k] for k in idx3]
ivert3 = np.vstack(iv3)
attrs3 = attrs[idx3]
if len(idx4) != 0:
iv4 = [ivert0[k] for k in idx4]
ivert4 = np.vstack(iv4)
attrs4 = attrs[idx4]
tmp = np.hstack(iv3+iv4)
u, indices = np.unique(tmp, return_inverse=True)
ll3 = 3*len(idx3)
indices3 = indices[:ll3]
indices4 = indices[ll3:]
# table u -> u's idx
table = np.zeros(np.max(u)+1, dtype=int)-1
for k, u0 in enumerate(u):
table[u0] = k
X = np.vstack([mesh.GetVertexArray(k) for k in u])
if X.shape[1] == 2:
X = np.hstack((X, np.zeros((X.shape[0],1))))
elif X.shape[1] == 1:
X = np.hstack((X, np.zeros((X.shape[0],2))))
kdom = mesh.attributes.ToList()
cells = {}
cell_data = {}
if ivert3 is not None:
cells['triangle'] = indices3.reshape(ivert3.shape)
cell_data['triangle'] = {}
cell_data['triangle']['physical'] = attrs3
if ivert4 is not None:
cells['quad'] = indices4.reshape(ivert4.shape)
cell_data['quad'] = {}
cell_data['quad']['physical'] = attrs4
from petram.mesh.mesh_utils import populate_plotdata
l_s_loop = populate_plotdata(mesh, table, cells, cell_data)
iedge2bb = None # is it used?
return X, cells, cell_data, l_s_loop, iedge2bb
'''