def exportVTK(pontos, celulas, info, arquivo):
# info deve ser algum dado em formato array(ex. pressão, densidade, etc) e
# nome_info string com seu rótulo (ex. "pressure")
conn = np.empty(len(celulas) * 4)
ctype = np.ones(len(celulas)) * VtkQuad.tid
conn = np.ravel(celulas)
offset = np.array([i * 4 for i in range(1, len(celulas) + 1)])
unstructuredGridToVTK(arquivo, np.ravel(pontos[:,0]), np.ravel(pontos[:,1]),np.ravel(pontos[:,2]), \
connectivity = conn, offsets = offset, cell_types = ctype, \
cellData = info, pointData = None)
def write_tris(fname, verts, tris, data=None):
x = verts[:, 0].copy() # deep copy required
y = verts[:, 1].copy()
z = verts[:, 2].copy()
ntris = tris.shape[0]
conn = np.empty(3 * ntris)
for i in range(ntris):
conn[3 * i] = tris[i, 0] - 1 # index from zero
conn[3 * i + 1] = tris[i, 1] - 1
conn[3 * i + 2] = tris[i, 2] - 1
offset = np.zeros(ntris, dtype=int)
for i in range(ntris):
offset[i] = 3 * (i + 1)
ctype = np.full(ntris, VtkTriangle.tid)
unstructuredGridToVTK(fname, x, y, z, \
connectivity=conn, offsets=offset, cell_types=ctype, \
cellData=data, pointData=None) # write out vtu file
return
def evtk_fileCreation(fileLoc,
xcrd,
ycrd,
zcrd,
conn,
offsets,
cell_types,
cellData=None,
cellKeys=None,
ptsData=None,
ptsKeys=None):
'''
Wrapper around the unstructuredGridToVTK function
Export unstructured grid and associated data.
Inputs:
fileLoc: name of the file without extension where data should be saved.
xcrd, ycrd, zcrd: 1D arrays with coordinates of the vertices of cells.
It is assumed that each element has diffent number of vertices.
conn: 1D array that defines the vertices associated to
each element. Together with offset define the connectivity
or topology of the grid. It is assumed that vertices in
an element are listed consecutively.
offsets: 1D array with the index of the last vertex of each element
in the connectivity array. It should have length nelem,
where nelem is the number of cells or elements in the grid.
cell_types: 1D array with an integer that defines the cell type
of each element in the grid. It should have size nelem.
This should be assigned from evtk.vtk.VtkXXXX.tid,
where XXXX represent the type of cell. Please check the
VTK file format specification for allowed cell types.
cellData: Dictionary with variables associated to each line.
Keys should be the names of the variable stored in each array.
All arrays must have the same number of elements.
pointData: Dictionary with variables associated to each vertex.
Keys should be the names of the variable stored in each array.
All arrays must have the same number of elements.
Output:
fOut: Full path to saved file.
'''
fOut = unstructuredGridToVTK(fileLoc,
xcrd,
ycrd,
zcrd,
conn,
offsets,
cell_types,
cellData=cellData,
cellKeys=cellKeys,
pointData=ptsData,
pointKeys=ptsKeys)
return fOut
def write_tets(fname, verts, tets, data=None):
x = verts[:, 0].copy() # deep copy required
y = verts[:, 1].copy()
z = verts[:, 2].copy()
ntets = tets.shape[0]
conn = np.empty(4 * ntets)
for i in range(ntets):
conn[4 * i] = tets[i, 0] - 1 # index from zero
conn[4 * i + 1] = tets[i, 1] - 1
conn[4 * i + 2] = tets[i, 2] - 1
conn[4 * i + 3] = tets[i, 3] - 1
offset = np.zeros(ntets, dtype=int)
for i in range(ntets):
offset[i] = 4 * (i + 1)
ctype = np.zeros(ntets)
for i in range(ntets):
ctype[i] = VtkTetra.tid
unstructuredGridToVTK(fname, x, y, z, \
connectivity=conn, offsets=offset, cell_types=ctype, \
cellData=data, pointData=None) # write out vtu file
return
def save_mesh(fname, pts, facets, facet_type=5, **kwargs):
x = pts[:, 0].astype('float')
y = pts[:, 1].astype('float')
if pts.shape[1] >= 3:
z = pts[:, 2].astype('float')
else:
z = np.array([0] * x.size).astype('float')
connectivity = facets.flatten()
ncells = facets.shape[0]
offsets = 3 + 3 * np.arange(ncells)
types = np.array([facet_type] * ncells)
return vtk.unstructuredGridToVTK(fname, x, y, z, connectivity, offsets,
types, **kwargs)
def __init__(self, path, mesh, submesh):
'''Prebuild and then only receive data'''
comm = mesh.mpi_comm()
rank = comm.rank
size = comm.size
dirname, basaname = os.path.dirname(path), os.path.basename(path)
if dirname:
not os.path.exists(dirname) and comm.rank == 0 and os.mkdir(
dirname)
local_has_piece = np.zeros(comm.size, dtype=bool)
if submesh.num_cells() == 0:
self.write_vtu_piece = lambda data, counter, path=path, rank=rank, size=size: (
"%s_p%d_of%d_%06d.vtu" % (path, rank, size, counter))
else:
local_has_piece[comm.rank] = True
x, y, z = map(np.array, submesh.coordinates().T)
cells = submesh.cells()
ncells, nvertices_cell = cells.shape
assert nvertices_cell == 3
connectivity = cells.flatten()
offsets = np.cumsum(np.repeat(3, ncells))
connectivity = connectivity.astype(offsets.dtype)
cell_types = VtkTriangle.tid * np.ones(ncells)
self.write_vtu_piece = lambda data, counter, path=path, rank=rank, size=size: (
unstructuredGridToVTK("%s_p%d_of%d_%06d" %
(path, rank, size, counter),
x,
y,
z,
connectivity,
offsets,
cell_types,
cellData=data))
# Root will write the group file
global_has_piece = sum(comm.allgather(local_has_piece),
np.zeros_like(local_has_piece))
self.has_piece, = np.where(global_has_piece)
# Only other piece to remember is for parallel writeing on root
self.counter = 0 # Of times write_vtu_piece was called
self.path = path
self.world_rank = comm.rank
self.world_size = comm.size
# Also group file goes into the directory
self.world_rank == 0 and setattr(self, 'group', VtkGroup(path))
def write_tris(fname, verts, tris, data=None):
nverts = verts.shape[0]
xyz = np.empty([3, nverts]) # because it needs re-ordering
for i in range(nverts):
for j in range(3):
xyz[j, i] = verts[i, j]
ntris = tris.shape[0]
conn = np.empty(3 * ntris)
for i in range(ntris):
conn[3 * i] = tris[i, 0] - 1 # index from zero
conn[3 * i + 1] = tris[i, 1] - 1
conn[3 * i + 2] = tris[i, 2] - 1
offset = np.zeros(ntris, dtype=int)
for i in range(ntris):
offset[i] = 3 * (i + 1)
ctype = np.zeros(ntris)
for i in range(ntris):
ctype[i] = VtkTriangle.tid
unstructuredGridToVTK(fname, \
xyz[0,:], xyz[1,:], xyz[2,:], \
connectivity=conn, offsets=offset, cell_types=ctype, \
cellData=data, pointData=None) # write out vtu file
return
# Define connectivity or vertices that belongs to each element
conn = np.zeros(10)
conn[0], conn[1], conn[2] = 0, 1, 3 # first triangle
conn[3], conn[4], conn[5] = 1, 4, 3 # second triangle
conn[6], conn[7], conn[8], conn[9] = 1, 2, 5, 4 # rectangle
# Define offset of last vertex of each element
offset = np.zeros(3)
offset[0] = 3
offset[1] = 6
offset[2] = 10
# Define cell types
ctype = np.zeros(3)
ctype[0], ctype[1] = VtkTriangle.tid, VtkTriangle.tid
ctype[2] = VtkQuad.tid
comments = ["comment 1", "comment 2"]
unstructuredGridToVTK("unstructured",
x,
y,
z,
connectivity=conn,
offsets=offset,
cell_types=ctype,
cellData=None,
pointData=None,
comments=comments)
def toVTK(self, dst, vals = None, text = None , default_z = None, verbose = False, comments = None):
from evtk.hl import pointsToVTK, polyLinesToVTK, unstructuredGridToVTK
from evtk.vtk import VtkPolygon
x, y, z, pointsPerShape = self.get_xyz_lists(default_z, verbose)
nshapes = len(self.shapes)
import numpy as np
x = np.array(x)
y = np.array(y)
z = np.array(z)
pointsPerShape = np.array(pointsPerShape)
# Export cell data
if vals:
cellData = {}
for k, v in vals.items():
cellData[k] = np.array(v)
else:
cellData = None
#for k, v in cellData.items():
#print(k, v)
if comments:
pass
else:
comments = []
if text:
comments.append("Text fields as lists with one element for each shape follows...")
for k, v in text.items():
cmt = "%s: "%k + "[" + ",".join(v) + "]"
#print(cmt)
comments.append(cmt)
else:
comments = None
if verbose:
print("type (%d): %s"%(self.shape_type, SHP_TYPES[type]) )
st = self.shape_type
if st == TS["POINT"] or st == TS["POINTZ"]: # POINT
pointsToVTK(dst, x, y, z, data = cellData, comments = comments)
elif st == TS["MULTIPOINT"]: # MULTIPOINT
pointsToVTK(dst, x, y, z, data = cellData, comments = comments)
elif st == TS["POLYLINE"] or st == TS["POLYLINEZ"]: # POLYLINE
polyLinesToVTK(dst, x, y, z, pointsPerLine = pointsPerShape, cellData = None, pointData = None)
elif st == TS["POLYGON"] or st == TS["POLYGONZ"]: # POLYGON
# Points should be counter clock-wise
# Add a small check LATER
conn = np.array([i for i in range(len(x))])
offsets = np.zeros(nshapes)
cell_types = np.ones(nshapes) * VtkPolygon.tid
o = 0
for s in range(nshapes):
o = o + pointsPerShape[s]
offsets[s] = o
unstructuredGridToVTK(dst, x, y, z, conn, offsets, cell_types, cellData = cellData, pointData = None, comments = comments)
else:
assert False, "Not implemented for type %d"%st